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Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention., Author summary In this paper we present PopART-IBM, an individual-based model used to simulate HIV transmission in communities in high prevalence settings. We show that PopART-IBM can simulate transmission over a span of decades in a large community in less than a minute. This computational efficiency allows us to calibrate the model within an inference framework, and we show an illustrative example of calibration using an adaptive population Monte Carlo Approximate Bayesian Computation algorithm for a community in Zambia that was part of the HPTN-071 (PopART) trial. We compare the detailed model output to real-world data collected during the trial from this community. Finally, we project how the HIV epidemic would have changed over time in this community if no intervention from the trial had occurred.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus poses serious threats to the global public health and leads to worldwide crisis. No effective drug or vaccine is readily available. The viral RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target. A hybrid drug screening procedure was proposed and applied to identify potential drug candidates targeting RdRp from 1906 approved drugs. Among the four selected market available drug candidates, Pralatrexate and Azithromycin were confirmed to effectively inhibit SARS-CoV-2 replication in vitro with EC50 values of 0.008μM and 9.453 μM, respectively. For the first time, our study discovered that Pralatrexate is able to potently inhibit SARS-CoV-2 replication with a stronger inhibitory activity than Remdesivir within the same experimental conditions. The paper demonstrates the feasibility of fast and accurate anti-viral drug screening for inhibitors of SARS-CoV-2 and provides potential therapeutic agents against COVID-19., Author summary Currently, a novel coronavirus called SARS-COV-2 is spreading across many parts of the world. Unfortunately, there is still a lack of effective drugs against the virus. Additionally, it usually takes much longer time to develop a new drug using traditional methods. Thus, it is now better to rely on some alternative methods to develop drugs that can treat such a disease effectively. In this paper, we have proposed a deep learning and molecular dynamics simulation based hybrid drug screening procedure for identifying potential drug candidates targeting RdRp from 1906 market available drugs. Our screening have successfully identified a FDA-approved drug called Pralatrexate that strongly inhibits the replication of 2019-nCoV in vitro with EC50 values of 0.008μM. This work demonstrated the feasibility of accurate virtual drug screening for inhibitors of SARS-CoV-2 and provides potential therapeutic agents against COVID-19.

This paper describes a data-driven simulation study that explores the relative impact of several low-cost and practical non-pharmaceutical interventions on the spread of COVID-19 in an outpatient hospital dialysis unit. The interventions considered include: (i) voluntary self-isolation of healthcare personnel (HCPs) with symptoms; (ii) a program of active syndromic surveillance and compulsory isolation of HCPs; (iii) the use of masks or respirators by patients and HCPs; (iv) improved social distancing among HCPs; (v) increased physical separation of dialysis stations; and (vi) patient isolation combined with preemptive isolation of exposed HCPs. Our simulations show that under conditions that existed prior to the COVID-19 outbreak, extremely high rates of COVID-19 infection can result in a dialysis unit. In simulations under worst-case modeling assumptions, a combination of relatively inexpensive interventions such as requiring surgical masks for everyone, encouraging social distancing between healthcare professionals (HCPs), slightly increasing the physical distance between dialysis stations, and—once the first symptomatic patient is detected—isolating that patient, replacing the HCP having had the most exposure to that patient, and relatively short-term use of N95 respirators by other HCPs can lead to a substantial reduction in both the attack rate and the likelihood of any spread beyond patient zero. For example, in a scenario with R0 = 3.0, 60% presymptomatic viral shedding, and a dialysis patient being the infection source, the attack rate falls from 87.8% at baseline to 34.6% with this intervention bundle. Furthermore, the likelihood of having no additional infections increases from 6.2% at baseline to 32.4% with this intervention bundle., Author summary As we write this, the COVID-19 pandemic has essentially taken over the world, with more than 20 million cases spread over 216 countries. A big concern for policy makers all across the world has been the impact of COVID-19 on healthcare systems and whether these systems can cope with the enormous strain placed on them by COVID-19. In this paper, we consider the spread of COVID-19 in a specific healthcare setting: the outpatient dialysis unit. Hemodialysis patients are extremely vulnerable to infections in large part due to multiple immune-system deficiencies associated with renal failure and hemodialysis. Hemodialysis facilities also increase the risk of COVID-19 transmission because each patient is in frequent, close contact with other patients and healthcare personnel. Thus, a dialysis unit can be seen as a microcosm for the worst-case impacts of COVID-19 in a healthcare setting. In this manuscript, we show via high-fidelity modeling and simulations that under pessimistic modeling assumptions, there is a combination of relatively simple, inexpensive, and practical non-pharmaceutical interventions that can substantially lower the impact of COVID-19 in the dialysis unit. Our simulations are based on fine-grained healthcare personnel movement data that we make available for other modelers to use.

Dengue, a mosquito-borne infectious disease caused by the dengue viruses, is present in many parts of the tropical and subtropical regions of the world. All four serotypes of dengue viruses are endemic in Singapore, an equatorial city-state. Frequent outbreaks occur, sometimes leading to national epidemics. However, few studies have attempted to characterize breakpoints which precede large rises in dengue case counts. In this paper, Bayesian regime switching (BRS) models were employed to infer epidemic and endemic regimes of dengue transmissions, each containing regime specific autoregressive processes which drive the growth and decline of dengue cases, estimated using a custom built multi-move Gibbs sampling algorithm. Posterior predictive checks indicate that BRS replicates temporal trends in Dengue transmissions well and nowcast accuracy assessed using a post-hoc classification scheme showed that BRS classification accuracy is robust even under limited data with the AUC-ROC at 0.935. LASSO-based regression and bootstrapping was used to account for plausibly high dimensions of climatic factors affecting Dengue transmissions, which was then estimated using cross-validation to conduct statistical inference on long-run climatic effects on the estimated regimes. BRS estimates epidemic and endemic regimes of dengue in Singapore which are characterized by persistence across time, lasting an average of 20 weeks and 66 weeks respectively, with a low probability of transitioning away from their regimes. Climate analysis with LASSO indicates that long-run climatic effects up to 20 weeks ago do not differentiate epidemic and endemic regimes. Lastly, by fitting BRS to simulated disease data generated from a stochastic Susceptible-Infected-Recovered model, mechanistic links between infectivity and regimes classified using BRS were provided. The model proposed could be applied to other localities and diseases under minimal data requirements where transmission counts over time are collected., Author summary Dengue, a mosquito-borne infectious disease caused by the dengue viruses, is present in many parts of the tropical and subtropical regions of the world. All four serotypes of dengue viruses are endemic in Singapore, an equatorial city-state. Frequent outbreaks occur, sometimes leading to national epidemics. However, few studies have attempted to characterize breakpoints which precede large rises in dengue case counts. In this paper, Bayesian regime switching (BRS) models were employed to infer epidemic and endemic regimes of dengue transmissions, each containing regime specific processes which drive the growth and decline of dengue cases, estimated using a custom built multi-move Gibbs sampling algorithm. Assessments against various baseline showed that BRS performs better in characterizing dengue transmissions. The dengue regimes estimated by BRS are characterized by their persistent nature. Next, climate analysis showed no short nor long term associations between classified regimes with climate. Lastly, fitting BRS to simulated disease data generated from a mechanistic model, we showed links between disease infectivity and regimes classified using BRS. The model proposed could be applied to other localities and diseases under minimal data requirements where transmission counts over time are collected.

The cerebral vasculature has a complex and hierarchical network, ranging from vessels of a few millimeters to superficial cortical vessels with diameters of a few hundred micrometers, and to the microvasculature (arteriole/venule) and capillary beds in the cortex. In standard imaging techniques, it is difficult to segment all vessels in the network, especially in the case of the human brain. This study proposes a hybrid modeling approach that determines these networks by explicitly segmenting the large vessels from medical images and employing a novel vascular generation algorithm. The framework enables vasculatures to be generated at coarse and fine scales for individual arteries and veins with vascular subregions, following the personalized anatomy of the brain and macroscale vasculatures. In this study, the vascular structures of superficial cortical (pial) vessels before they penetrate the cortex are modeled as a mesoscale vasculature. The validity of the present approach is demonstrated through comparisons with partially observed data from existing measurements of the vessel distributions on the brain surface, pathway fractal features, and vascular territories of the major cerebral arteries. Additionally, this validation provides some biological insights: (i) vascular pathways may form to ensure a reasonable supply of blood to the local surface area; (ii) fractal features of vascular pathways are not sensitive to overall and local brain geometries; and (iii) whole pathways connecting the upstream and downstream entire-scale cerebral circulation are highly dependent on the local curvature of the cerebral sulci., Author summary Cerebral autoregulation in the complex vascular networks of the brain is an amazing achievement. We believe that numerical analysis of the cerebral blood circulation using an anatomically precise vascular model provides a powerful tool for evaluating the direct relationships between local- and global-scale blood flows. However, there is a lack of information about the overall vascular pathways in the human brain, preventing a monolithic model of the human cerebrovasculature from being established. This paper presents a multiscale model of human cerebrovasculature based on a hybrid approach that uses image-based geometries and a newly developed mathematical algorithm. One important argument of this paper is the validity of the cerebrovasculature represented in the model, which reflects anatomical features of major cerebral vasculatures and brain shape, and has strong similarities with available data for human superficial cortical vessels. Investigations of the reconstructed model allow us to derive some biological insights and associated hypotheses for the cerebral vasculature. The authors believe the present cerebrovascular model can be applied to numerical simulations of the entire-scale cerebral blood flow.

Striatal oscillatory activity is associated with movement, reward, and decision-making, and observed in several interacting frequency bands. Local field potential recordings in rodent striatum show dopamine- and reward-dependent transitions between two states: a “spontaneous” state involving β (∼15-30 Hz) and low γ (∼40-60 Hz), and a state involving θ (∼4-8 Hz) and high γ (∼60-100 Hz) in response to dopaminergic agonism and reward. The mechanisms underlying these rhythmic dynamics, their interactions, and their functional consequences are not well understood. In this paper, we propose a biophysical model of striatal microcircuits that comprehensively describes the generation and interaction of these rhythms, as well as their modulation by dopamine. Building on previous modeling and experimental work suggesting that striatal projection neurons (SPNs) are capable of generating β oscillations, we show that networks of striatal fast-spiking interneurons (FSIs) are capable of generating δ/θ (ie, 2 to 6 Hz) and γ rhythms. Under simulated low dopaminergic tone our model FSI network produces low γ band oscillations, while under high dopaminergic tone the FSI network produces high γ band activity nested within a δ/θ oscillation. SPN networks produce β rhythms in both conditions, but under high dopaminergic tone, this β oscillation is interrupted by δ/θ-periodic bursts of γ-frequency FSI inhibition. Thus, in the high dopamine state, packets of FSI γ and SPN β alternate at a δ/θ timescale. In addition to a mechanistic explanation for previously observed rhythmic interactions and transitions, our model suggests a hypothesis as to how the relationship between dopamine and rhythmicity impacts motor function. We hypothesize that high dopamine-induced periodic FSI γ-rhythmic inhibition enables switching between β-rhythmic SPN cell assemblies representing the currently active motor program, and thus that dopamine facilitates movement in part by allowing for rapid, periodic shifts in motor program execution., Author summary Striatal oscillatory activity is associated with movement, reward, and decision-making, and observed in several interacting frequency bands. The mechanisms underlying these rhythmic dynamics, their interactions, and their functional consequences are not well understood. In this paper, we propose a biophysical model of striatal microcircuits that comprehensively describes the generation and interaction of striatal rhythms, as well as their modulation by dopamine. Our model suggests a hypothesis as to how the relationship between dopamine and rhythmicity impacts the function of the motor system, enabling rapid, periodic shifts in motor program execution.

As antimicrobial resistance increases, it is crucial to develop new treatment strategies to counter the emerging threat. In this paper, we consider combination therapies involving conventional antibiotics and debridement, coupled with a novel anti-adhesion therapy, and their use in the treatment of antimicrobial resistant burn wound infections. Our models predict that anti-adhesion–antibiotic–debridement combination therapies can eliminate a bacterial infection in cases where each treatment in isolation would fail. Antibiotics are assumed to have a bactericidal mode of action, killing bacteria, while debridement involves physically cleaning a wound (e.g. with a cloth); removing free bacteria. Anti-adhesion therapy can take a number of forms. Here we consider adhesion inhibitors consisting of polystyrene microbeads chemically coupled to a protein known as multivalent adhesion molecule 7, an adhesin which mediates the initial stages of attachment of many bacterial species to host cells. Adhesion inhibitors competitively inhibit bacteria from binding to host cells, thus rendering them susceptible to removal through debridement. An ordinary differential equation model is developed and the antibiotic-related parameters are fitted against new in vitro data gathered for the present study. The model is used to predict treatment outcomes and to suggest optimal treatment strategies. Our model predicts that anti-adhesion and antibiotic therapies will combine synergistically, producing a combined effect which is often greater than the sum of their individual effects, and that anti-adhesion–antibiotic–debridement combination therapy will be more effective than any of the treatment strategies used in isolation. Further, the use of inhibitors significantly reduces the minimum dose of antibiotics required to eliminate an infection, reducing the chances that bacteria will develop increased resistance. Lastly, we use our model to suggest treatment regimens capable of eliminating bacterial infections within clinically relevant timescales., Author summary Since the development of the first antibiotics, bacteria have utilised and developed resistance mechanisms, helping them to avoid being eliminated and to survive within a host. Traditionally, the solution to this problem has been to treat with multiple antibiotics, switching to a new type when the one currently in use proves ineffective. However, the development of antibiotics has slowed significantly in the past two decades, while multi-drug resistant strains, otherwise known as ‘super bugs’, are on the rise. In answer to this challenge, alternative approaches, such as anti-adhesion therapy, are being developed as a complement or alternative to traditional antimicrobials. In this paper we formulate and analyse a mathematical model of a combination therapy, applied in the context of an infected burn wound, bringing together antibiotics, anti-adhesion therapy and debridement (the physical cleaning of a wound). We use our models to make sense of how these treatments interact to combat a bacterial infection, to predict treatment outcomes for a range of strategies and to suggest optimal treatment regimens. It is hoped that this study will guide future experimental and clinical research, helping biomedical researchers to identify the most promising approaches to treatment.

This paper uses mathematical modeling to study the mechanisms of surround suppression in the primate visual cortex. We present a large-scale neural circuit model consisting of three interconnected components: LGN and two input layers (Layer 4Ca and Layer 6) of the primary visual cortex V1, covering several hundred hypercolumns. Anatomical structures are incorporated and physiological parameters from realistic modeling work are used. The remaining parameters are chosen to produce model outputs that emulate experimentally observed size-tuning curves. Our two main results are: (i) we discovered the character of the long-range connections in Layer 6 responsible for surround effects in the input layers; and (ii) we showed that a net-inhibitory feedback, i.e., feedback that excites I-cells more than E-cells, from Layer 6 to Layer 4 is conducive to producing surround properties consistent with experimental data. These results are obtained through parameter selection and model analysis. The effects of nonlinear recurrent excitation and inhibition are also discussed. A feature that distinguishes our model from previous modeling work on surround suppression is that we have tried to reproduce realistic lengthscales that are crucial for quantitative comparison with data. Due to its size and the large number of unknown parameters, the model is computationally challenging. We demonstrate a strategy that involves first locating baseline values for relevant parameters using a linear model, followed by the introduction of nonlinearities where needed. We find such a methodology effective, and propose it as a possibility in the modeling of complex biological systems., Author summary The visual cortex is a part of the cortex that processes visual signal. The visual signal from the retina is relayed through the lateral geniculate nucleus (LGN), and enters the primary visual cortex directly. The primary visual cortex consists of many layers. A phenomenon called surround suppression, which means a reduction of neuronal activities in response to stimuli of increasing size, is well-observed in all layers of the primate primary visual cortex. In this paper, we built a large scale mathematical model consisting of the LGN input and tens of thousands of neuron groups in Layer 4 and Layer 6 of the primary visual cortex to study the mechanism of surround suppression. This model is constrained by both anatomical structures and realistic physiological parameters. Remaining unknown parameters are reverse-engineered from experimental data. We showed how the character of the surround suppression depends on the long-range connections in the feedback layer, as well as the feedback current from Layer 6 to Layer 4.

[EN] Myriad risk factors-including uncontrolled hypertension, aging, and diverse genetic mutations-contribute to the development and enlargement of thoracic aortic aneurysms. Detailed analyses of clinical data and longitudinal studies of murine models continue to provide insight into the natural history of these potentially lethal conditions. Yet, because of the co-existence of multiple risk factors in most cases, it has been difficult to isolate individual effects of the many different factors or to understand how they act in combination. In this paper, we use a data-informed computational model of the initiation and progression of thoracic aortic aneurysms to contrast key predisposing risk factors both in isolation and in combination; these factors include localized losses of elastic fiber integrity, aberrant collagen remodeling, reduced smooth muscle contractility, and dysfunctional mechanosensing or mechanoregulation of extracellular matrix along with superimposed hypertension and aortic aging. In most cases, mild-to-severe localized losses in cellular function or matrix integrity give rise to varying degrees of local dilatations of the thoracic aorta, with enlargement typically exacerbated in cases wherein predisposing risk factors co-exist. The simulations suggest, for the first time, that effects of compromised smooth muscle contractility are more important in terms of dysfunctional mechanosensing and mechanoregulation of matrix than in vessel-level control of diameter and, furthermore, that dysfunctional mechanobiological control can yield lesions comparable to those in cases of compromised elastic fiber integrity. Particularly concerning, therefore, is that loss of constituents such as fibrillin-1, as in Marfan syndrome, can compromise both elastic fiber integrity and mechanosensing. Author summary Aneurysms are local dilatations of the arterial wall that are responsible for significant disability and death. Detailed analyses of clinical data continue to provide insight into the natural history of these potentially lethal conditions, with myriad risk factors-including uncontrolled hypertension, aging, and diverse genetic mutations-contributing to their development and enlargement. Yet, because of the co-existence of these risk factors in most cases, it has been difficult to isolate individual effects or to understand how they act in combination. In this paper, we use a computational model of the initiation and progression of thoracic aortic aneurysms to contrast key predisposing factors both in isolation and in combination as well as with superimposed hypertension and aging. The present study recovers many findings from mouse models but with new and important observations that promise to guide in vivo and ex vivo studies as we seek to understand and eventually better treat these complex, multi-factorial lesions, with data-informed patient-specific computations eventually the way forward., This work was supported, in part, by grants from the US NIH (P01 HL134605, U01 HL142518, and R01 HL146723) to JDH. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Dengue is an arbovirus affecting global populations. Frequent outbreaks occur, especially in equatorial cities such as Singapore, where year-round tropical climate, large daily influx of travelers and population density provide the ideal conditions for dengue to transmit. Little work has, however, quantified the peaks of dengue outbreaks, when health systems are likely to be most stretched. Nor have methods been developed to infer differences in exogenous factors which lead to the rise and fall of dengue case counts across extreme and non-extreme periods. In this paper, we developed time varying extreme mixture (tvEM) methods to account for the temporal dependence of dengue case counts across extreme and non-extreme periods. This approach permits inference of differences in climatic forcing across non-extreme and extreme periods of dengue case counts, quantification of their temporal dependence as well as estimation of thresholds with associated uncertainties to determine dengue case count extremities. Using tvEM, we found no evidence that weather affects dengue case counts in the near term for non-extreme periods, but that it has non-linear and mixed signals in influencing dengue through tvEM parameters in the extreme periods. Using the most appropriate tvEM specification, we found that a threshold at the 70th (95% credible interval 41.1, 83.8) quantile is optimal, with extreme events of 526.6, 1052.2 and 1183.6 weekly case counts expected at return periods of 5, 50 and 75 years. Weather parameters at a 1% scaled increase was found to decrease the long-run expected case counts, but larger increases would lead to a drastic expected rise from the baseline correspondingly. The tvEM approach can provide valuable inference on the extremes of time series, which in the case of infectious disease notifications, allows public health officials to understand the likely scale of outbreaks in the long run., Author summary Dengue is an arbovirus affecting populations across much of the globe. Frequent outbreaks occur, especially in equatorial cities such as Singapore, where the year-round tropical climate, large daily influx of travelers and population density provide the ideal conditions for dengue transmission. Little work has however quantified the peaks of dengue outbreaks, when health systems are likely to be most stretched. Nor have methods been developed to infer differences in exogenous factors which lead to the rise and fall of dengue case counts across extreme and non extreme periods. In this paper, we developed time varying extreme mixture (tvEM) methods to account for the temporal dependence of dengue case counts across extreme and non-extreme periods. tvEM is able to infer differences in climatic forcing across non-extreme and extreme periods of dengue case counts, their temporal dependence as well as estimate suitable thresholds with associated uncertainties to determine dengue case count extremities. Using tvEM, we found no evidence that weather affects dengue case counts in the near term for non extreme periods, but has non-linear and mixed signals in influencing dengue through tvEM parameters in the extreme periods. Using the most appropriate tvEM specification, we found that a high percentile threshold is estimated, with dengue outbreak events far larger than currently observed to be expected in 5, 50 and 75 years. Weather parameters at a 1% scaled increase was found to decrease the long-run expected case counts, but larger increases would lead to a drastic expected rise from the baseline correspondingly. tvEM can provide valuable inference on the extremes of time series, which in the case of infectious disease data, allows public health officials to understand factors and the likely scale of infectious disease outbreaks in the long run.

The processing of a visual stimulus can be subdivided into a number of stages. Upon stimulus presentation there is an early phase of feedforward processing where the visual information is propagated from lower to higher visual areas for the extraction of basic and complex stimulus features. This is followed by a later phase where horizontal connections within areas and feedback connections from higher areas back to lower areas come into play. In this later phase, image elements that are behaviorally relevant are grouped by Gestalt grouping rules and are labeled in the cortex with enhanced neuronal activity (object-based attention in psychology). Recent neurophysiological studies revealed that reward-based learning influences these recurrent grouping processes, but it is not well understood how rewards train recurrent circuits for perceptual organization. This paper examines the mechanisms for reward-based learning of new grouping rules. We derive a learning rule that can explain how rewards influence the information flow through feedforward, horizontal and feedback connections. We illustrate the efficiency with two tasks that have been used to study the neuronal correlates of perceptual organization in early visual cortex. The first task is called contour-integration and demands the integration of collinear contour elements into an elongated curve. We show how reward-based learning causes an enhancement of the representation of the to-be-grouped elements at early levels of a recurrent neural network, just as is observed in the visual cortex of monkeys. The second task is curve-tracing where the aim is to determine the endpoint of an elongated curve composed of connected image elements. If trained with the new learning rule, neural networks learn to propagate enhanced activity over the curve, in accordance with neurophysiological data. We close the paper with a number of model predictions that can be tested in future neurophysiological and computational studies., Author Summary Our experience with the visual world allows us to group image elements that belong to the same perceptual object and to segregate them from other objects and the background. If subjects learn to group contour elements, this experience influences neuronal activity in early visual cortical areas, including the primary visual cortex (V1). Learning presumably depends on alterations in the pattern of connections within and between areas of the visual cortex. However, the processes that control changes in connectivity are not well understood. Here we present the first computational model that can train a neural network to integrate collinear contour elements into elongated curves and to trace a curve through the visual field. The new learning algorithm trains fully recurrent neural networks, provided the connectivity causes the networks to reach a stable state. The model reproduces the behavioral performance of monkeys trained in these tasks and explains the patterns of neuronal activity in the visual cortex that emerge during learning, which is remarkable because the only feedback for the model is a reward for successful trials. We discuss a number of the model predictions that can be tested in future neuroscientific work.

In Parkinson’s disease, an increase in beta oscillations within the basal ganglia nuclei has been shown to be associated with difficulty in movement initiation. An important role in the generation of these oscillations is thought to be played by the motor cortex and by a network composed of the subthalamic nucleus (STN) and the external segment of globus pallidus (GPe). Several alternative models have been proposed to describe the mechanisms for generation of the Parkinsonian beta oscillations. However, a recent experimental study of Tachibana and colleagues yielded results which are challenging for all published computational models of beta generation. That study investigated how the presence of beta oscillations in a primate model of Parkinson’s disease is affected by blocking different connections of the STN-GPe circuit. Due to a large number of experimental conditions, the study provides strong constraints that any mechanistic model of beta generation should satisfy. In this paper we present two models consistent with the data of Tachibana et al. The first model assumes that Parkinsonian beta oscillation are generated in the cortex and the STN-GPe circuits resonates at this frequency. The second model additionally assumes that the feedback from STN-GPe circuit to cortex is important for maintaining the oscillations in the network. Predictions are made about experimental evidence that is required to differentiate between the two models, both of which are able to reproduce firing rates, oscillation frequency and effects of lesions carried out by Tachibana and colleagues. Furthermore, an analysis of the models reveals how the amplitude and frequency of the generated oscillations depend on parameters., Author Summary The collective firing of neurons is an essential mechanism for communicating information in the brain. However, in Parkinson’s disease there is a disruption of healthy brain dynamics, which interrupts the processing of normal movement. In particular, the neurons become overly synchronized and produce abnormally large oscillations in their activity. The frequency band of the oscillations associated with the difficulty of movement initiation in primate Parkinson’s disease is in the range of 13–30Hz, which is called the beta band. Understanding the generation of beta oscillations is important to improve treatments for Parkinson’s disease. Competing theories exist for how these oscillations are generated in the affected brain circuits, which include the motor cortex and a set of subcortical nuclei called the basal ganglia. This paper suggests two hypotheses for the generation of beta oscillations. The first hypothesis is that beta oscillations are generated in the motor cortex, and the basal ganglia resonate to the cortical input. The second hypothesis additionally proposes that feedback from the basal ganglia to cortex is critically important for the presence of the oscillations. We show that the models can successfully account for a wide range of experimental data concerning the presence of beta oscillations in Parkinson’s disease.

In 2009, we published a paper in PLOS Computational Biology [1] that described using a new, wavelet-based metric of phase synchronization in human MEG data. Specifically, we showed that this metric of phase synchronization, that we called the phase lock index (PLI), demonstrated power law scaling across all frequency intervals or wavelet scales from the low frequency delta band (1–2 Hz) to the high frequency gamma band (35–70 Hz). Based on these experimental results, and additional confirmatory data obtained from PLI measurements on time series generated by computational models of critical systems, we offered the interpretation that power law scaling of phase synchronization in human MEG recordings was compatible with the prior theory that human brain dynamics demonstrate self-organized criticality. More recently, in collaboration with a group at the National Institutes of Health (NIH), we published a paper in the Journal of Neuroscience [2] that described using a similar phase synchronization metric to explore scaling behaviour in MEG data recorded from normal human subjects and, crucially, in MEG data recorded with no human subject present, so-called “empty room” data. In Figure 9 of [2], we showed data indicating that phase synchronization appeared to demonstrate power law scaling even in empty room data; as reproduced here in Fig 1. Fig 1 First two panels of Figure 9 from Shriki et al. [2]. We originally judged this issue to be of minor concern, because, as shown in Figure 1 of [2], NIH empty scanner amplitude variance is about 1–2 orders of magnitude less than equivalent brain scans. This is most likely an underestimation given that data are Z-normalized and absolute amplitudes of empty scanner data should be lower than brain scans. Thus, we reasoned the contribution from “empty scanner” effects to PLI scaling in brain recordings should be insignificant. Nonetheless, the issue was addressed in the Discussion of [2], where we stated: “because of the ambiguity of PLI for brain scans and empty scanner, additional steps such as amplitude comparisons need to be taken into account” (page 7089 of [2]).

Cox regression is commonly used to predict the outcome by the time to an event of interest and in addition, identify relevant features for survival analysis in cancer genomics. Due to the high-dimensionality of high-throughput genomic data, existing Cox models trained on any particular dataset usually generalize poorly to other independent datasets. In this paper, we propose a network-based Cox regression model called Net-Cox and applied Net-Cox for a large-scale survival analysis across multiple ovarian cancer datasets. Net-Cox integrates gene network information into the Cox's proportional hazard model to explore the co-expression or functional relation among high-dimensional gene expression features in the gene network. Net-Cox was applied to analyze three independent gene expression datasets including the TCGA ovarian cancer dataset and two other public ovarian cancer datasets. Net-Cox with the network information from gene co-expression or functional relations identified highly consistent signature genes across the three datasets, and because of the better generalization across the datasets, Net-Cox also consistently improved the accuracy of survival prediction over the Cox models regularized by or . This study focused on analyzing the death and recurrence outcomes in the treatment of ovarian carcinoma to identify signature genes that can more reliably predict the events. The signature genes comprise dense protein-protein interaction subnetworks, enriched by extracellular matrix receptors and modulators or by nuclear signaling components downstream of extracellular signal-regulated kinases. In the laboratory validation of the signature genes, a tumor array experiment by protein staining on an independent patient cohort from Mayo Clinic showed that the protein expression of the signature gene FBN1 is a biomarker significantly associated with the early recurrence after 12 months of the treatment in the ovarian cancer patients who are initially sensitive to chemotherapy. Net-Cox toolbox is available at http://compbio.cs.umn.edu/Net-Cox/., Author Summary Network-based computational models are attracting increasing attention in studying cancer genomics because molecular networks provide valuable information on the functional organizations of molecules in cells. Survival analysis mostly with the Cox proportional hazard model is widely used to predict or correlate gene expressions with time to an event of interest (outcome) in cancer genomics. Surprisingly, network-based survival analysis has not received enough attention. In this paper, we studied resistance to chemotherapy in ovarian cancer with a network-based Cox model, called Net-Cox. The experiments confirm that networks representing gene co-expression or functional relations can be used to improve the accuracy and the robustness of survival prediction of outcome in ovarian cancer treatment. The study also revealed subnetwork signatures that are enriched by extracellular matrix receptors and modulators and the downstream nuclear signaling components of extracellular signal-regulators, respectively. In particular, FBN1, which was detected as a signature gene of high confidence by Net-Cox with network information, was validated as a biomarker for predicting early recurrence in platinum-sensitive ovarian cancer patients in laboratory.

The processing characteristics of neurons in the central auditory system are directly shaped by and reflect the statistics of natural acoustic environments, but the principles that govern the relationship between natural sound ensembles and observed responses in neurophysiological studies remain unclear. In particular, accumulating evidence suggests the presence of a code based on sustained neural firing rates, where central auditory neurons exhibit strong, persistent responses to their preferred stimuli. Such a strategy can indicate the presence of ongoing sounds, is involved in parsing complex auditory scenes, and may play a role in matching neural dynamics to varying time scales in acoustic signals. In this paper, we describe a computational framework for exploring the influence of a code based on sustained firing rates on the shape of the spectro-temporal receptive field (STRF), a linear kernel that maps a spectro-temporal acoustic stimulus to the instantaneous firing rate of a central auditory neuron. We demonstrate the emergence of richly structured STRFs that capture the structure of natural sounds over a wide range of timescales, and show how the emergent ensembles resemble those commonly reported in physiological studies. Furthermore, we compare ensembles that optimize a sustained firing code with one that optimizes a sparse code, another widely considered coding strategy, and suggest how the resulting population responses are not mutually exclusive. Finally, we demonstrate how the emergent ensembles contour the high-energy spectro-temporal modulations of natural sounds, forming a discriminative representation that captures the full range of modulation statistics that characterize natural sound ensembles. These findings have direct implications for our understanding of how sensory systems encode the informative components of natural stimuli and potentially facilitate multi-sensory integration., Author Summary We explore a fundamental question with regard to the representation of sound in the auditory system, namely: what are the coding strategies that underlie observed neurophysiological responses in central auditory areas? There has been debate in recent years as to whether neural ensembles explicitly minimize their propensity to fire (the so-called sparse coding hypothesis) or whether neurons exhibit strong, sustained firing rates when processing their preferred stimuli. Using computational modeling, we directly confront issues raised in this debate, and our results suggest that not only does a sustained firing strategy yield a sparse representation of sound, but the principle yields emergent neural ensembles that capture the rich structural variations present in natural stimuli. In particular, spectro-temporal receptive fields (STRFs) have been widely used to characterize the processing mechanisms of central auditory neurons and have revealed much about the nature of sound processing in central auditory areas. In our paper, we demonstrate how neurons that maximize a sustained firing objective yield STRFs akin to those commonly measured in physiological studies, capturing a wide range of aspects of natural sounds over a variety of timescales, suggesting that such a coding strategy underlies observed neural responses.

An integrative cell migration model incorporating focal adhesion (FA) dynamics, cytoskeleton and nucleus remodeling, actin motor activity, and lamellipodia protrusion is developed for predicting cell spreading and migration behaviors. This work is motivated by two experimental works: (1) cell migration on 2-D substrates under various fibronectin concentrations and (2) cell spreading on 2-D micropatterned geometries. These works suggest (1) cell migration speed takes a maximum at a particular ligand density (∼1140 molecules/µm2) and (2) that strong traction forces at the corners of the patterns may exist due to combined effects exerted by actin stress fibers (SFs). The integrative model of this paper successfully reproduced these experimental results and indicates the mechanism of cell migration and spreading. In this paper, the mechanical structure of the cell is modeled as having two elastic membranes: an outer cell membrane and an inner nuclear membrane. The two elastic membranes are connected by SFs, which are extended from focal adhesions on the cortical surface to the nuclear membrane. In addition, the model also includes ventral SFs bridging two focal adhesions on the cell surface. The cell deforms and gains traction as transmembrane integrins distributed over the outer cell membrane bond to ligands on the ECM surface, activate SFs, and form focal adhesions. The relationship between the cell migration speed and fibronectin concentration agrees with existing experimental data for Chinese hamster ovary (CHO) cell migrations on fibronectin coated surfaces. In addition, the integrated model is validated by showing persistent high stress concentrations at sharp geometrically patterned edges. This model will be used as a predictive model to assist in design and data processing of upcoming microfluidic cell migration assays., Author Summary Cell migration is a complex, multifaceted process, triggered by chemotaxis and haptotatic responses from the extracellular matrix (ECM). It is triggered by a thin lamellipodium protrusion at the leading edge, followed by the assembly of a number of focal adhesions between the lamellipodium base and the ECM. Afterwards, actin stress fibers extend from nascent focal adhesions, some of which connect to the nucleus. In this work, we have developed a dynamic model of cell migration incorporating these four mechanisms of cell biology, such as remodeling of cell and nuclear membranes, focal adhesion dynamics, actin motor activity, and lamellipodia protrusion at the leading edge. We successfully compared our model with existing experimental works of cell migration on (1) substrates with various fibronectin coating concentrations, and (2) cell spreading on three patterned surfaces. Finally, our model demonstrates how actin stress fibers anchored at the trailing edge play a key role, leading to an increase in cell migration speed. Thereby, the model will not only provide new insights on better building such an experiment, but also further experiments will allow us to better validate the model.

As a person learns a new skill, distinct synapses, brain regions, and circuits are engaged and change over time. In this paper, we develop methods to examine patterns of correlated activity across a large set of brain regions. Our goal is to identify properties that enable robust learning of a motor skill. We measure brain activity during motor sequencing and characterize network properties based on coherent activity between brain regions. Using recently developed algorithms to detect time-evolving communities, we find that the complex reconfiguration patterns of the brain's putative functional modules that control learning can be described parsimoniously by the combined presence of a relatively stiff temporal core that is composed primarily of sensorimotor and visual regions whose connectivity changes little in time and a flexible temporal periphery that is composed primarily of multimodal association regions whose connectivity changes frequently. The separation between temporal core and periphery changes over the course of training and, importantly, is a good predictor of individual differences in learning success. The core of dynamically stiff regions exhibits dense connectivity, which is consistent with notions of core-periphery organization established previously in social networks. Our results demonstrate that core-periphery organization provides an insightful way to understand how putative functional modules are linked. This, in turn, enables the prediction of fundamental human capacities, including the production of complex goal-directed behavior., Author Summary When someone learns a new skill, his/her brain dynamically alters individual synapses, regional activity, and larger-scale circuits. In this paper, we capture some of these dynamics by measuring and characterizing patterns of coherent brain activity during the learning of a motor skill. We extract time-evolving communities from these patterns and find that a temporal core that is composed primarily of primary sensorimotor and visual regions reconfigures little over time, whereas a periphery that is composed primarily of multimodal association regions reconfigures frequently. The core consists of densely connected nodes, and the periphery consists of sparsely connected nodes. Individual participants with a larger separation between core and periphery learn better in subsequent training sessions than individuals with a smaller separation. Conceptually, core-periphery organization provides a framework in which to understand how putative functional modules are linked. This, in turn, enables the prediction of fundamental human capacities, including the production of complex goal-directed behavior.

The free-energy principle has recently been proposed as a unified Bayesian account of perception, learning and action. Despite the inextricable link between emotion and cognition, emotion has not yet been formulated under this framework. A core concept that permeates many perspectives on emotion is valence, which broadly refers to the positive and negative character of emotion or some of its aspects. In the present paper, we propose a definition of emotional valence in terms of the negative rate of change of free-energy over time. If the second time-derivative of free-energy is taken into account, the dynamics of basic forms of emotion such as happiness, unhappiness, hope, fear, disappointment and relief can be explained. In this formulation, an important function of emotional valence turns out to regulate the learning rate of the causes of sensory inputs. When sensations increasingly violate the agent's expectations, valence is negative and increases the learning rate. Conversely, when sensations increasingly fulfil the agent's expectations, valence is positive and decreases the learning rate. This dynamic interaction between emotional valence and learning rate highlights the crucial role played by emotions in biological agents' adaptation to unexpected changes in their world., Author Summary Emotion plays a crucial role in the adaptation of humans and other animals to changes in their world. Nevertheless, emotion has been neglected in Bayesian models of learning in non-stationary environments. The free-energy principle has recently been proposed as a unified account of learning, perception and action in biological agents. In this paper, we propose a formal definition of emotional valence (i.e., the positive and negative character of emotion) in terms of the rate of change of free-energy or, under some simplifying assumptions, of prediction error over time. This formalization leads to a straightforward and simple meta-learning scheme that accounts for the complex and reciprocal interaction between cognition and emotion. We instantiate this scheme with an emotional agent who is able to dynamically assign emotional valence to every new state of the world that is visited and to experience basic forms of emotion. Crucially, our hypothetical agent uses emotional valence to dynamically adapt to unexpected changes in the world. The proposed scheme is very general in the sense that it is not tied to any particular generative model of sensory inputs.

For many infectious disease processes such as emerging zoonoses and vaccine-preventable diseases, and infections occur as self-limited stuttering transmission chains. A mechanistic understanding of transmission is essential for characterizing the risk of emerging diseases and monitoring spatio-temporal dynamics. Thus methods for inferring and the degree of heterogeneity in transmission from stuttering chain data have important applications in disease surveillance and management. Previous researchers have used chain size distributions to infer , but estimation of the degree of individual-level variation in infectiousness (as quantified by the dispersion parameter, ) has typically required contact tracing data. Utilizing branching process theory along with a negative binomial offspring distribution, we demonstrate how maximum likelihood estimation can be applied to chain size data to infer both and the dispersion parameter that characterizes heterogeneity. While the maximum likelihood value for is a simple function of the average chain size, the associated confidence intervals are dependent on the inferred degree of transmission heterogeneity. As demonstrated for monkeypox data from the Democratic Republic of Congo, this impacts when a statistically significant change in is detectable. In addition, by allowing for superspreading events, inference of shifts the threshold above which a transmission chain should be considered anomalously large for a given value of (thus reducing the probability of false alarms about pathogen adaptation). Our analysis of monkeypox also clarifies the various ways that imperfect observation can impact inference of transmission parameters, and highlights the need to quantitatively evaluate whether observation is likely to significantly bias results., Author Summary This paper focuses on infectious diseases such as monkeypox, Nipah virus and avian influenza that transmit weakly from human to human. These pathogens cannot cause self-sustaining epidemics in the human population, but instead cause limited transmission chains that stutter to extinction. Such pathogens would go extinct if they were confined to humans, but they persist because of continual introduction from an external reservoir (such as animals, for the zoonotic diseases mentioned above). They are important to study because they pose a risk of emerging if they become more transmissible, or conversely to monitor the success of efforts to locally eliminate a pathogen by vaccination. A crucial challenge for these ‘stuttering’ pathogens is to quantify their transmissibility, in terms of the intensity and heterogeneity of disease transmission by infected individuals. In this paper, we use monkeypox as an example to show how these transmission properties can be estimated from commonly available data describing the size of observed stuttering chains. These results make it easier to monitor diseases that pose a risk of emerging (or re-emerging) as self-sustaining human pathogens, or to decide whether a seemingly large chain may signal a worrisome change in transmissibility.

Spike-timing-dependent plasticity (STDP) has been observed in many brain areas such as sensory cortices, where it is hypothesized to structure synaptic connections between neurons. Previous studies have demonstrated how STDP can capture spiking information at short timescales using specific input configurations, such as coincident spiking, spike patterns and oscillatory spike trains. However, the corresponding computation in the case of arbitrary input signals is still unclear. This paper provides an overarching picture of the algorithm inherent to STDP, tying together many previous results for commonly used models of pairwise STDP. For a single neuron with plastic excitatory synapses, we show how STDP performs a spectral analysis on the temporal cross-correlograms between its afferent spike trains. The postsynaptic responses and STDP learning window determine kernel functions that specify how the neuron “sees” the input correlations. We thus denote this unsupervised learning scheme as ‘kernel spectral component analysis’ (kSCA). In particular, the whole input correlation structure must be considered since all plastic synapses compete with each other. We find that kSCA is enhanced when weight-dependent STDP induces gradual synaptic competition. For a spiking neuron with a “linear” response and pairwise STDP alone, we find that kSCA resembles principal component analysis (PCA). However, plain STDP does not isolate correlation sources in general, e.g., when they are mixed among the input spike trains. In other words, it does not perform independent component analysis (ICA). Tuning the neuron to a single correlation source can be achieved when STDP is paired with a homeostatic mechanism that reinforces the competition between synaptic inputs. Our results suggest that neuronal networks equipped with STDP can process signals encoded in the transient spiking activity at the timescales of tens of milliseconds for usual STDP., Author Summary Tuning feature extraction of sensory stimuli is an important function for synaptic plasticity models. A widely studied example is the development of orientation preference in the primary visual cortex, which can emerge using moving bars in the visual field. A crucial point is the decomposition of stimuli into basic information tokens, e.g., selecting individual bars even though they are presented in overlapping pairs (vertical and horizontal). Among classical unsupervised learning models, independent component analysis (ICA) is capable of isolating basic tokens, whereas principal component analysis (PCA) cannot. This paper focuses on spike-timing-dependent plasticity (STDP), whose functional implications for neural information processing have been intensively studied both theoretically and experimentally in the last decade. Following recent studies demonstrating that STDP can perform ICA for specific cases, we show how STDP relates to PCA or ICA, and in particular explains the conditions under which it switches between them. Here information at the neuronal level is assumed to be encoded in temporal cross-correlograms of spike trains. We find that a linear spiking neuron equipped with pairwise STDP requires additional mechanisms, such as a homeostatic regulation of its output firing, in order to separate mixed correlation sources and thus perform ICA.

How should we define translational bioinformatics? I had to answer this question unambiguously in March 2008 when I was asked to deliver a review of ‘‘recent progress in translational bioinformatics’’ at the American Medical Informatics Association’s Summit on Translational Bioinformatics. The lecture required me to define papers in the field, and then highlight exciting progress that occurred over the previous ,12 months. I have repeated this for the last few years, and the most difficult part of the exercise is limiting my review only to those papers that are within the field. I have never worried much about definitions within informatics fields; they tend to overlap, merge and evolve. ‘‘Informatics’’ seems clear: the study of how to represent, store, search, retrieve and analyze information. The adjectives in front of ‘‘informatics’’ vary but also tend to make sense: medical informatics concerns medical information, bioinformatics concerns basic biological information, clinical informatics focuses on the clinical delivery part of medical informatics, biomedical informatics merges bioinformatics and medical informatics, imaging informatics focuses on...images, and so on. So what does this adjective ‘‘translational’’ denote? Translational medical research has emerged as an important theme in the last decade. Starting with top-down leadership from the National Institutes of Health and its former Director, Dr. Elias Zerhouni, and moving through academic medical centers, research institutes and industrial research and development efforts, there has been interest in more effectively moving the discoveries and innovations in the laboratory to the bedside, leading to improved diagnosis, prognosis, and treatment. Translational research encompasses many activities including the creation of medical devices, molecular diagnostics, small molecule therapeutics, biological therapeutics, vaccines, and others. One of the main targets of translation, however, is revolutionary explosion of knowledge in molecular biology, genetics, and genomics. Some believe that the tremendous progress in discovery over the last 50+ years since elucidation of the double helix structure has not translated (there’s that word!) into much practical health benefit. While the accuracy of this claim can be debated, there can be no debate that our ability to measure (1) DNA sequence (including entire genomes!), (2) RNA sequence and expression, (3) protein sequence, structure, expression and modification, and (4) small molecule metabolite structure, presence, and quantity has advanced rapidly and enables us to imagine fantastic new technologies in pursuit of human health. There are many barriers to translating our molecular understanding into technologies that impact patients. These include understanding health market size and forces, the regulatory milieu, how to harden the technology for routine use, and how to navigate an increasingly complex intellectual property landscape. But before those activities can begin, we must overcome an even more fundamental barrier: connecting the stuff of molecular biology to the clinical world. Molecular and cellular biology studies genes, DNA, RNA messengers, microRNAs, proteins, signaling molecules and their cascades, metabolites, cellular communication processes and cellular organization. These data are freely available in valuable resources such as Genbank (http://www. ncbi.nlm.nih.gov/genbank/), Gene Expression Omnibus (http://www.ncbi.nlm. nih.gov/geo/), Protein Data Bank (http:// www.wwpdb.org/), KEGG (http://www. genome.jp/kegg/), MetaCyc (http:// metacyc.org/), Reactome (http://www. reactome.org), and many other resources. The clinical world studies diseases, signs, symptoms, drugs, patients, clinical laboratory measurements, and clinical images. The emergence of clinical and health information technologies has begun to make these clinical data available for research through biobanks, electronic medical records, FDA resources about drug labels and adverse events, and claims data. Therefore, a major challenge for translational medicine is to connect the molecular/cellular world with the clinical world. The published literature, available in PubMED (http://www.ncbi.nlm.nih. gov/pubmed), does this, as does the Unified Medical Language System (UMLS) that provides a lingua franca (http://www.nlm.nih.gov/research/umls/ ). However, it falls to translational bioinformatics to engineer the tools that link molecular/cellular entities and clinical entities. Thus, I define ‘‘translational bioinformatics’’ research as the development and application of informatics methods that connect molecular entities to clinical entities. In this collection, Dr. Kann and colleagues have assembled a wonderful group of authors to introduce the key threads of translational bioinformatics to those new to the field. The collection first provides

Hepatitis C virus (HCV) p7 is a membrane-associated oligomeric protein harboring ion channel activity. It is essential for effective assembly and release of infectious HCV particles and an attractive target for antiviral intervention. Yet, the self-assembly and molecular mechanism of p7 ion channelling are currently only partially understood. Using molecular dynamics simulations (aggregate time 1.2 µs), we show that p7 can form stable oligomers of four to seven subunits, with a bias towards six or seven subunits, and suggest that p7 self-assembles in a sequential manner, with tetrameric and pentameric complexes forming as intermediate states leading to the final hexameric or heptameric assembly. We describe a model of a hexameric p7 complex, which forms a transiently-open channel capable of conducting ions in simulation. We investigate the ability of the hexameric model to flexibly rearrange to adapt to the local lipid environment, and demonstrate how this model can be reconciled with low-resolution electron microscopy data. In the light of these results, a view of p7 oligomerization is proposed, wherein hexameric and heptameric complexes may coexist, forming minimalist, yet robust functional ion channels. In the absence of a high-resolution p7 structure, the models presented in this paper can prove valuable as a substitute structure in future studies of p7 function, or in the search for p7-inhibiting drugs., Author Summary Hepatitis C remains a serious global health problem affecting more than 2% of the world's population, and current therapies are effective in only a subset of patients, necessitating an ongoing search for new treatments. The p7 viroporin is considered to be an attractive possible drug target, but rational drug design is hampered by the absence of a high-resolution p7 structure. In this paper, we explore possible structures of oligomeric p7 channels, and discuss the strengths and shortcomings of these models with respect to experimentally determined properties, such as pore-lining residues, ion conductance, and compatibility with low-resolution electron microscopy images. Our results present an image of p7 as a rudimentary, minimalistic ion channel, capable of existing in multiple oligomeric states but exhibiting a bias towards hexamers and heptamers. We believe that the work presented here will be valuable for future research by providing plausible 3-dimensional atomic-resolution models for the visualization of the p7 viroporin and serve as a basis for future computational studies.

Histopathological classification of human tumors relies in part on the degree of differentiation of the tumor sample. To date, there is no objective systematic method to categorize tumor subtypes by maturation. In this paper, we introduce a novel computational algorithm to rank tumor subtypes according to the dissimilarity of their gene expression from that of stem cells and fully differentiated tissue, and thereby construct a phylogenetic tree of cancer. We validate our methodology with expression data of leukemia, breast cancer and liposarcoma subtypes and then apply it to a broader group of sarcomas. This ranking of tumor subtypes resulting from the application of our methodology allows the identification of genes correlated with differentiation and may help to identify novel therapeutic targets. Our algorithm represents the first phylogeny-based tool to analyze the differentiation status of human tumors., Author Summary Gene expression profiling of malignancies is often held to demonstrate genes that are “up-regulated” or “down-regulated”, but the appropriate frame of reference against which observations should be compared has not been determined. Fully differentiated somatic cells arise from stem cells, with changes in gene expression that can be experimentally determined. If cancers arise as the result of an abruption of the differentiation process, then poorly differentiated cancers would have a gene expression more similar to stem cells than to normal differentiated tissue, and well differentiated cancers would have a gene expression more similar to fully differentiated cells than to stem cells. In this paper, we describe a novel computational algorithm that allows orientation of cancer gene expression between the poles of the gene expression of stem cells and of fully differentiated tissue. Our methodology allows the construction of a multi-branched phylogeny of human malignancies and can be used to identify genes related to differentiation as well as novel therapeutic targets.

The chemotaxis system in the bacterium Escherichia coli is remarkably sensitive to small relative changes in the concentrations of multiple chemical signals over a broad range of ambient concentrations. Interactions among receptors are crucial to this sensitivity as is precise adaptation, the return of chemoreceptor activity to prestimulus levels in a constant chemoeffector environment. Precise adaptation relies on methylation and demethylation of chemoreceptors by the enzymes CheR and CheB, respectively. Experiments indicate that when transiently bound to one receptor, these enzymes act on small assistance neighborhoods (AN) of five to seven receptor homodimers. In this paper, we model a strongly coupled complex of receptors including dynamic CheR and CheB acting on ANs. The model yields sensitive response and precise adaptation over several orders of magnitude of attractant concentrations and accounts for different responses to aspartate and serine. Within the model, we explore how the precision of adaptation is limited by small AN size as well as by CheR and CheB kinetics (including dwell times, saturation, and kinetic differences among modification sites) and how these kinetics contribute to noise in complex activity. The robustness of our dynamic model for precise adaptation is demonstrated by randomly varying biochemical parameters., Author Summary Bacteria swim in relatively straight lines and change directions through tumbling. In the process of chemotaxis, a network of receptors and other proteins controls the tumbling frequency to direct an otherwise random walk toward nutrients and away from repellents. Receptor clustering and adaptation to persistent stimuli through covalent modification allow chemotaxis to be sensitive over a large range of ambient concentrations. The individual components of the chemotaxis network are well characterized, and signaling measurements by fluorescence microscopy quantify the network's response, making the system well suited for modeling and analysis. In this paper, we expand upon a previous model based on experiments indicating that the covalent modifications required for adaptation occur through the action of enzymes on groups of neighboring receptors, referred to as assistance neighborhoods. Simulations show that our proposed molecular model of a strongly coupled complex of receptors produces accurate responses to different stimuli and is robust to parameter variation. Within this model, the correct adaptation response is limited by small assistance-neighborhood size as well as enzyme kinetics. We also explore how these kinetics contribute to noise in the chemotactic response.

Neuronal microcircuits generate oscillatory activity, which has been linked to basic functions such as sleep, learning and sensorimotor gating. Although synaptic release processes are well known for their ability to shape the interaction between neurons in microcircuits, most computational models do not simulate the synaptic transmission process directly and hence cannot explain how changes in synaptic parameters alter neuronal network activity. In this paper, we present a novel neuronal network model that incorporates presynaptic release mechanisms, such as vesicle pool dynamics and calcium-dependent release probability, to model the spontaneous activity of neuronal networks. The model, which is based on modified leaky integrate-and-fire neurons, generates spontaneous network activity patterns, which are similar to experimental data and robust under changes in the model's primary gain parameters such as excitatory postsynaptic potential and connectivity ratio. Furthermore, it reliably recreates experimental findings and provides mechanistic explanations for data obtained from microelectrode array recordings, such as network burst termination and the effects of pharmacological and genetic manipulations. The model demonstrates how elevated asynchronous release, but not spontaneous release, synchronizes neuronal network activity and reveals that asynchronous release enhances utilization of the recycling vesicle pool to induce the network effect. The model further predicts a positive correlation between vesicle priming at the single-neuron level and burst frequency at the network level; this prediction is supported by experimental findings. Thus, the model is utilized to reveal how synaptic release processes at the neuronal level govern activity patterns and synchronization at the network level., Author Summary The activity of neuronal networks underlies basic neural functions such as sleep, learning and sensorimotor gating. Computational models of neuronal networks have been developed to capture the complexity of the network activity and predict how neuronal networks generate spontaneous activity. However, most computational models do not simulate the intricate synaptic release process that governs the interaction between neurons and has been shown to significantly impact neuronal network activity and animal behavior, learning and memory. Our paper demonstrates the importance of simulating the elaborate synaptic release process to understand how neuronal networks generate spontaneous activity and respond to manipulations of the release process. The model provides mechanistic explanations and predictions for experimental pharmacological and genetic manipulations. Thus, the model presents a novel computational platform to understand how mechanistic changes in the synaptic release process modulate network oscillatory activity that might impact basic neural functions.

An important goal in molecular biology is to understand functional changes upon single-point mutations in proteins. Doing so through a detailed characterization of structure spaces and underlying energy landscapes is desirable but continues to challenge methods based on Molecular Dynamics. In this paper we propose a novel algorithm, SIfTER, which is based instead on stochastic optimization to circumvent the computational challenge of exploring the breadth of a protein’s structure space. SIfTER is a data-driven evolutionary algorithm, leveraging experimentally-available structures of wildtype and variant sequences of a protein to define a reduced search space from where to efficiently draw samples corresponding to novel structures not directly observed in the wet laboratory. The main advantage of SIfTER is its ability to rapidly generate conformational ensembles, thus allowing mapping and juxtaposing landscapes of variant sequences and relating observed differences to functional changes. We apply SIfTER to variant sequences of the H-Ras catalytic domain, due to the prominent role of the Ras protein in signaling pathways that control cell proliferation, its well-studied conformational switching, and abundance of documented mutations in several human tumors. Many Ras mutations are oncogenic, but detailed energy landscapes have not been reported until now. Analysis of SIfTER-computed energy landscapes for the wildtype and two oncogenic variants, G12V and Q61L, suggests that these mutations cause constitutive activation through two different mechanisms. G12V directly affects binding specificity while leaving the energy landscape largely unchanged, whereas Q61L has pronounced, starker effects on the landscape. An implementation of SIfTER is made available at http://www.cs.gmu.edu/~ashehu/?q=OurTools. We believe SIfTER is useful to the community to answer the question of how sequence mutations affect the function of a protein, when there is an abundance of experimental structures that can be exploited to reconstruct an energy landscape that would be computationally impractical to do via Molecular Dynamics., Author Summary Important human diseases are linked to mutations in proteins. One such protein, Ras, undergoes mutations in over 25% of human cancers. Its biological activity involves switching between two distinct states, and several oncogenic mutations affect this switching. Despite significant investigation in silico via methods based on Molecular Dynamics, details are missing on how mutations affect the ability of Ras to access the states it needs to perform its biological activity. In this paper we present an algorithm that is capable of providing such details by exploring the breadth of the structure space of a given protein. The algorithm leverages information gathered in the wet laboratory on long-lived structures of the healthy/wildtype and mutated versions of a protein to effectively explore its structure space and reconstruct the underlying energy landscape. We apply this algorithm to the wildtype H-Ras and two known oncogenic variants, G12V and Q61L. Comparison of the energy landscapes elucidates the detailed mechanism by which the oncogenic mutations affect biological activity. We provide the algorithm for the research community to allow further investigation of the open question on how mutations to the sequence of a protein affect biological activity.

I wish to comment on a paper recently published in the Journal of Neuroscience [1] and relate this paper to one previously published in PLOS Computational Biology [2]. In [1] and [2] among other results, a power law relationship was discovered in a measure of magnetoencephalography (MEG) intra-areal synchronization: the distribution of phase-locking intervals (PLI). However, in [1] the authors also show that the same PLI power law measure cannot distinguish between human MEG and empty MEG scanner data, suggesting that the measure is vulnerable to artefact. This is important because the first description of the PLI power law methodology, as well as its application to MEG and functional magnetic resonance imaging (fMRI) data, was published in PLOS Computational Biology [2]. The senior author of [2] is also an author of [1]. The results obtained with the PLI methodology published in [2] were presented as evidence for broadband criticality of human brain network synchronization because the PLI method (which applies a threshold to MEG/fMRI data and returns a power law) will also return a power law distribution for PLIs when applied to a model system of Kuramoto oscillators tuned to a critical phase transition. However, it should be noted in this regard that a recent modelling study indicates that power laws also emerge when PLI is applied to noncritical Kuramoto oscillators, and caution is needed when interpreting power laws derived from time series data passed through a threshold [3]. The paper published in PLOS Computational Biology [2] has received multiple citations, and the PLI methodology has been further applied to human neurophysiological data in other studies. From its use, claims have been made about changes in broadband criticality during disease states, e.g., epilepsy [4]. I am concerned that the results presented in [1] indicate that the methodology described in [2] may be unsound and therefore should not be used for inferring criticality of human brain network synchronisation. The presentation of the empty MEG scanner results in [1] is not sufficiently explicit in this sense, and it should have been made much clearer that the influential PLI power law methodology presented in [2] might be problematic. Science of course moves forward through a process of exploration and correction, and the initial idea presented in PLOS Computational Biology [2] was exciting and innovative; however, the authors should reconsider the interpretation of their findings in light of the empty MEG scanner data. I feel it is therefore important to bring these papers and their conflicting results to the attention of the readers of PLOS Computational Biology and I would ask that the authors of [1,2] clarify the discrepancy in between their data sets and publish an erratum in PLOS Computational Biology if a conflict exists.

In the present paper, we quantify, with a rigorous approach, the nature of motor activity in response to Deep Brain Stimulation (DBS), in the mouse. DBS is currently being used in the treatment of a broad range of diseases, but its underlying principles are still unclear. Because mouse movement involves rapidly repeated starting and stopping, one must statistically verify that the movement at a given stimulation time was not just coincidental, endogenously-driven movement. Moreover, the amount of activity changes significantly over the circadian rhythm, and hence the means, variances and autocorrelations are all time varying. A new methodology is presented. For example, to discern what is and what is not impacted by stimulation, velocity is classified (in a time-evolving manner) as being zero-, one- and two-dimensional movement. The most important conclusions of the paper are: (1) (DBS) stimulation is proven to be truly effective; (2) it is two-dimensional (2-D) movement that strongly differs between light and dark and responds to stimulation; and, (3) stimulation in the light initiates a manner of movement, 2-D movement, that is more commonly seen in the (non-stimulated) dark. Based upon these conclusions, it is conjectured that the above patterns of 2-D movement could be a straightforward, easy to calculate correlate of arousal. The above conclusions will aid in the systematic evaluation and understanding of how DBS in CNS arousal pathways leads to the activation of behavior., Author Summary Brainstem and thalamic regulation of arousal has been studied experimentally since the mid 20-th century. Today, Deep Brain Stimulation (DBS) is used in the treatment of movement disorders, chronic pain, clinical depression, amongst others. At present, the proper choice of DBS parameters (frequency and strength of the electric stimulation), and how those parameters should be modified as conditions change, are not well understood. In this work, using motor activity as the observed response, a statistical framework is developed for such study, and a quantitative relationship between parameter values and response is established. Within this framework, a possible correlate of arousal, the rapid onset of spatial (two-dimensional) movement, is uncovered and also studied. One long-term hope for techniques such as DBS are that they could assist in the treatment of disorders of consciousness, by supplementing or replacing (e.g., in Traumatic Brain Injury) what should ordinarily be the appropriate endogenous stimulation.

The study of synchronization in biological systems is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. In this paper, by using simple dynamical systems theory, we present a novel mechanism, named transient resetting, for the synchronization of uncoupled biological oscillators with stimuli. This mechanism not only can unify and extend many existing results on (deterministic and stochastic) stimulus-induced synchrony, but also may actually play an important role in biological rhythms. We argue that transient resetting is a possible mechanism for the synchronization in many biological organisms, which might also be further used in the medical therapy of rhythmic disorders. Examples of the synchronization of neural and circadian oscillators as well as a chaotic neuron model are presented to verify our hypothesis., Synopsis Synchronization of dynamical systems is a process whereby two or more systems adjust a given property of their motions to a common behavior due to coupling or forcing. Synchronization has attracted much attention from physicists, biologists, applied mathematicians, and engineers for many years and is a ubiquitous phenomenon. In this paper, Li et al. present a very simple, but general mechanism, called transient resetting, that explains stimulus-induced synchronization in dynamic systems. The mechanism pertains not only to periodic oscillators but also to chaotic ones, and not only to continuous time systems but also to discrete time systems. Biological systems are dynamic, and their synchronization is essential, for example, in the genesis of rhythmic phenomena and information processing. In this paper, the authors study several possible instances of their novel mechanism in a biological context. They also suggest that transient resetting might be used therapeutically in rhythmic disorders. The beneficial role of noise in biological systems has been studied extensively in recent years. Li and colleagues' mechanism provides an explanation for this role in the synchronization in biological systems, even when the stimulus or input to the system is not random or noisy.

Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Stress release experiments show that nonuniform anisotropic elastic stresses can be distributed throughout. The elastic stresses are maintained by structural proteins and adhesive molecules, and can be actively relaxed by a variety of biophysical processes. In this paper, we present a new continuum model to investigate how the growth-induced elastic stresses and active stress relaxation, in conjunction with cell size control feedback machinery, regulate the cell density and stress distributions within growing tumors as well as the tumor sizes in the presence of external physical confinement and gradients of growth-promoting chemical fields. We introduce an adaptive reference map that relates the current position with the reference position but adapts to the current position in the Eulerian frame (lab coordinates) via relaxation. This type of stress relaxation is similar to but simpler than the classical Maxwell model of viscoelasticity in its formulation. By fitting the model to experimental data from two independent studies of tumor spheroid growth and their cell density distributions, treating the tumors as incompressible, neo-Hookean elastic materials, we find that the rates of stress relaxation of tumor tissues can be comparable to volumetric growth rates. Our study provides insight on how the biophysical properties of the tumor and host microenvironment, mechanical feedback control and diffusion-limited differential growth act in concert to regulate spatial patterns of stress and growth. When the tumor is stiffer than the host, our model predicts tumors are more able to change their size and mechanical state autonomously, which may help to explain why increased tumor stiffness is an established hallmark of malignant tumors., Author summary The mechanical state of cells can modulate their growth and division dynamics via mechanotransduction, which affects both the cell size distribution and the tissue size as a whole. Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Besides external confinement and compression on the tumor border, a heterogeneous stress field can be generated inside the tumor by nutrient-driven differential growth. Such growth-induced mechanical stresses can be relaxed by tissue rearrangement, which happens during cell neighbor exchanges, cell divisions, and extracellular matrix renewal. In this study, we have developed a continuum model that describes the above mechanical interactions and the dynamics of tissue rearrangement explicitly. Motivated by published experimental data, we consider mechanotransduction where the local compressive stress slows down cell growth and cell size reduction limits cell division. We have analyzed how external mechanical stimuli and internal processes influence the outcome of cell-and-tissue sizes and spatial patterns of cell density and mechanical stress in growing tumors.

The sleep onset process (SOP) is a dynamic process correlated with a multitude of behavioral and physiological markers. A principled analysis of the SOP can serve as a foundation for answering questions of fundamental importance in basic neuroscience and sleep medicine. Unfortunately, current methods for analyzing the SOP fail to account for the overwhelming evidence that the wake/sleep transition is governed by continuous, dynamic physiological processes. Instead, current practices coarsely discretize sleep both in terms of state, where it is viewed as a binary (wake or sleep) process, and in time, where it is viewed as a single time point derived from subjectively scored stages in 30-second epochs, effectively eliminating SOP dynamics from the analysis. These methods also fail to integrate information from both behavioral and physiological data. It is thus imperative to resolve the mismatch between the physiological evidence and analysis methodologies. In this paper, we develop a statistically and physiologically principled dynamic framework and empirical SOP model, combining simultaneously-recorded physiological measurements with behavioral data from a novel breathing task requiring no arousing external sensory stimuli. We fit the model using data from healthy subjects, and estimate the instantaneous probability that a subject is awake during the SOP. The model successfully tracked physiological and behavioral dynamics for individual nights, and significantly outperformed the instantaneous transition models implicit in clinical definitions of sleep onset. Our framework also provides a principled means for cross-subject data alignment as a function of wake probability, allowing us to characterize and compare SOP dynamics across different populations. This analysis enabled us to quantitatively compare the EEG of subjects showing reduced alpha power with the remaining subjects at identical response probabilities. Thus, by incorporating both physiological and behavioral dynamics into our model framework, the dynamics of our analyses can finally match those observed during the SOP., Author Summary How can we tell when someone has fallen asleep? Understanding the way we fall asleep is an important problem in sleep medicine, since sleep disorders can disrupt the process of falling asleep. In the case of insomnia, subjects may fall asleep too slowly, whereas during sleep deprivation or narcolepsy, subjects fall asleep too quickly. Current methods for tracking the wake/sleep transition are time-consuming, subjective, and simplify the sleep onset process in a way that severely limits the accuracy, power, and scope of any resulting clinical metrics. In this paper, we describe a new physiologically principled method that dynamically combines information from brainwaves, muscle activity, and a novel minimally-disruptive behavioral task, to automatically create a continuous dynamic characterization of a person's state of wakefulness. We apply this method to a cohort of healthy subjects, successfully tracking the changes in wakefulness as the subjects fall asleep. This analysis reveals and statistically quantifies a subset of subjects who still respond to behavioral stimuli even though their brain would appear to be asleep by clinical measures. By developing an automated tool to precisely track the wake/sleep transition, we can better characterize and diagnose sleep disorders, and more precisely measure the effect of sleep medications.

Advances in high-throughput, single cell gene expression are allowing interrogation of cell heterogeneity. However, there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level. We assess the effect of cell cycle phase on gene expression in single cells by measuring 333 genes in 930 cells across three phases and three cell lines. We determine each cell's phase non-invasively without chemical arrest and use it as a covariate in tests of differential expression. We observe bi-modal gene expression, a previously-described phenomenon, wherein the expression of otherwise abundant genes is either strongly positive, or undetectable within individual cells. This bi-modality is likely both biologically and technically driven. Irrespective of its source, we show that it should be modeled to draw accurate inferences from single cell expression experiments. To this end, we propose a semi-continuous modeling framework based on the generalized linear model, and use it to characterize genes with consistent cell cycle effects across three cell lines. Our new computational framework improves the detection of previously characterized cell-cycle genes compared to approaches that do not account for the bi-modality of single-cell data. We use our semi-continuous modelling framework to estimate single cell gene co-expression networks. These networks suggest that in addition to having phase-dependent shifts in expression (when averaged over many cells), some, but not all, canonical cell cycle genes tend to be co-expressed in groups in single cells. We estimate the amount of single cell expression variability attributable to the cell cycle. We find that the cell cycle explains only 5%–17% of expression variability, suggesting that the cell cycle will not tend to be a large nuisance factor in analysis of the single cell transcriptome., Author Summary Recent technological advances have enabled the measurement of gene expression in individual cells, revealing that there is substantial variability in expression, even within a homogeneous cell population. In this paper, we develop new analytical methods that account for the intrinsic, stochastic nature of single cell expression in order to characterize the effect of cell cycle on gene expression at the single-cell level. Applying these methods to populations of asynchronously cycling cells, we are able to identify large numbers of genes with cell cycle-associated expression patterns. By measuring and adjusting for cellular-level factors, we are able to derive estimates of co-expressing gene networks that more closely reflect cellular-level processes as opposed to sample-level processes. We find that cell cycle phase only accounts for a modest amount of the overall variability of gene expression within an individual cell. The analytical methods demonstrated in this paper are universally applicable to single cell expression data and represent a promising tool to the scientific community.

How the brain stores information about a sensory stimulus in working memory is not completely known. Clues about the mechanisms responsible for working memory can be gleaned by recording from neurons during the performance of a delayed response task. I focus on the data recorded during such an experiment, a classic tactile discrimination task. I describe how the observed variability in the firing rate during a trial suggests that the type of attractor that is responsible for holding the stimulus information is not a fixed-point type attractor. I propose an alternate mechanism to a line attractor that allows the network to hold the value of an analog stimulus variable for the duration of the delay period, but rather than maintain a constant level of activity, the cells' firing rate varies throughout the delay period. I describe how my proposed mechanism offers a substantial advantage over a line attractor: The tuning requirements of cell to cell connections are greatly eased from that of a line attractor. To accommodate a change in the length of the delay period, I show that the network can be altered by changing a single parameter - the timing of an executive signal that originates outside of the network. To demonstrate the mechanism, as well as the tuning benefits, I use a well known model of propagation in neuronal networks., Author Summary The ability to retain stimulus information after the stimulus has ceased is important for survival. The term “working memory” refers to storage of stimulus information for a short period of time, so that this information can be recalled for a decision making process. A common way to probe for the cellular basis of working memory is recording of neurons during a delayed response task. This study focuses on one of these studies - the now classic experiments of Romo et al.. This experiment demonstrates that the frequency of a tactile vibration is held in memory using a type of encoding where the cellular output depends monotonically on the stimulus variable (frequency). In this paper, I develop a model that accounts for a number of features found in the data. Using the model, I am able to account for a diversity of cellular responses, as well as variability during a trial. This paper builds on previous modeling studies of this data set. The advance is an executive input that controls the behavior of the network, and reduces the burden of tuning compared to previous models.

Stay-at-home orders and shutdowns of non-essential businesses are powerful, but socially costly, tools to control the pandemic spread of SARS-CoV-2. Mass testing strategies, which rely on widely administered frequent and rapid diagnostics to identify and isolate infected individuals, could be a potentially less disruptive management strategy, particularly where vaccine access is limited. In this paper, we assess the extent to which mass testing and isolation strategies can reduce reliance on socially costly non-pharmaceutical interventions, such as distancing and shutdowns. We develop a multi-compartmental model of SARS-CoV-2 transmission incorporating both preventative non-pharmaceutical interventions (NPIs) and testing and isolation to evaluate their combined effect on public health outcomes. Our model is designed to be a policy-guiding tool that captures important realities of the testing system, including constraints on test administration and non-random testing allocation. We show how strategic changes in the characteristics of the testing system, including test administration, test delays, and test sensitivity, can reduce reliance on preventative NPIs without compromising public health outcomes in the future. The lowest NPI levels are possible only when many tests are administered and test delays are short, given limited immunity in the population. Reducing reliance on NPIs is highly dependent on the ability of a testing program to identify and isolate unreported, asymptomatic infections. Changes in NPIs, including the intensity of lockdowns and stay at home orders, should be coordinated with increases in testing to ensure epidemic control; otherwise small additional lifting of these NPIs can lead to dramatic increases in infections, hospitalizations and deaths. Importantly, our results can be used to guide ramp-up of testing capacity in outbreak settings, allow for the flexible design of combined interventions based on social context, and inform future cost-benefit analyses to identify efficient pandemic management strategies., Author summary The global spread of SARS-CoV-2 and the strategies used to manage it have come at significant societal costs. We analyze how mixed control strategies, which utilize interventions that prevent new infections from occurring (e.g., distancing or shut-downs) and others that actively search for and isolate existing infections (here, mass testing), can achieve improved public health outcomes while avoiding severe socio-economic burdens. Our results suggest that increasing testing capacity, including the number of tests available and the speed at which test results are provided, can reduce reliance on costly preventative interventions. Such reduction is possible with more isolation of active infections, including those without reported symptoms. However, failing to maintain preventative interventions without sufficient testing capacity can lead to large increases in infection burdens. By defining the combined effect of these interventions through mathematical models, this study provides insight into relaxation of distancing measures, and lays the groundwork for future public health economics analyses on the cost-effectiveness of combined management strategies.

Although chemotherapy is a standard treatment for cancer, it comes with significant side effects. In particular, certain agents can induce severe muscle loss, known as cachexia, worsening patient quality of life and treatment outcomes. 5-fluorouracil, an anti-cancer agent used to treat several cancers, has been shown to cause muscle loss. Experimental data indicates a non-linear dose-dependence for muscle loss in mice treated with daily or week-day schedules. We present a mathematical model of chemotherapy-induced muscle wasting that captures this non-linear dose-dependence. Area-under-the-curve metrics are proposed to quantify the treatment’s effects on lean mass and tumour control. Model simulations are used to explore alternate dosing schedules, aging effects, and morphine use in chemotherapy treatment with the aim of better protecting lean mass while actively targeting the tumour, ultimately leading to improved personalization of treatment planning and improved patient quality of life.Author SummaryIn this paper we present a novel mathematical model for muscle loss due to cancer chemotherapy treatment. Loss of muscle mass relates to increased drug toxicity and side-effects, and to decreased patient quality of life and survival rates. With our model, we examine the therapeutic efficacy of various dosing schedules with the aim of controlling a growing tumour while also preserving lean mass. Preservation of body composition, in addition to consideration of inflammation and immune interactions, the gut microbiome, and other systemic health measures, may lead to improved patient-specific treatment plans that improve patient quality of life.

Animals rely on sensory feedback to generate accurate, reliable movements. In many flying insects, strain-sensitive neurons on the wings provide rapid feedback that is critical for stable flight control. While the impacts of wing structure on aerodynamic performance have been widely studied, the impacts of wing structure on sensing are largely unexplored. In this paper, we show how the structural properties of the wing and encoding by mechanosensory neurons interact to jointly determine optimal sensing strategies and performance. Specifically, we examine how neural sensors can be placed effectively on a flapping wing to detect body rotation about different axes, using a computational wing model with varying flexural stiffness. A small set of mechanosensors, conveying strain information at key locations with a single action potential per wingbeat, enable accurate detection of body rotation. Optimal sensor locations are concentrated at either the wing base or the wing tip, and they transition sharply as a function of both wing stiffness and neural threshold. Moreover, the sensing strategy and performance is robust to both external disturbances and sensor loss. Typically, only five sensors are needed to achieve near-peak accuracy, with a single sensor often providing accuracy well above chance. Our results show that small-amplitude, dynamic signals can be extracted efficiently with spatially and temporally sparse sensors in the context of flight. The demonstrated interaction of wing structure and neural encoding properties points to the importance of understanding each in the context of their joint evolution., Author summary In addition to generating forces for flight, insect wings also serve an important role as sensory structures, providing rapid feedback about wing bending that is used to stabilize flight. While much is known about how wing structure affects aerodynamic performance, the effects of wing structure on sensing remain unexplored. Using a computational model of a flapping wing, we examine how sensing strategies depend on wing stiffness and sensor properties. We show that body rotations can be accurately detected with a small number of sensors on the wing across a wide range of conditions. Optimal sensor locations are clustered at either the wing base or wing tip, depending on a combination of wing stiffness and sensor properties. Moreover, sensing performance is robust to multiple kinds of perturbations. Our work provides a basis for understanding how wing structure impacts incoming sensory information during flight.

Ethanol is one of the most widely used recreational substances in the world and due to its ubiquitous use, ethanol abuse has been the cause of over 3.3 million deaths each year. In addition to its effects, ethanol’s primary metabolite, acetaldehyde, is a carcinogen that can cause symptoms of facial flushing, headaches, and nausea. How strongly ethanol or acetaldehyde affects an individual depends highly on the genetic polymorphisms of certain genes. In particular, the genetic polymorphisms of mitochondrial aldehyde dehydrogenase, ALDH2, play a large role in the metabolism of acetaldehyde. Thus, it is important to characterize how genetic variations can lead to different exposures and responses to ethanol and acetaldehyde. While the pharmacokinetics of ethanol metabolism through alcohol dehydrogenase have been thoroughly explored in previous studies, in this paper, we combined a base physiologically-based pharmacokinetic (PBPK) model with a whole-body genome-scale model (WBM) to gain further insight into the effect of other less explored processes and genetic variations on ethanol metabolism. This combined model was fit to clinical data and used to show the effect of alcohol concentrations, organ damage, ALDH2 enzyme polymorphisms, and ALDH2-inhibiting drug disulfiram on ethanol and acetaldehyde exposure. Through estimating the reaction rates of auxiliary processes with dynamic Flux Balance Analysis, The PBPK-WBM was able to navigate around a lack of kinetic constants traditionally associated with PK modelling and demonstrate the compensatory effects of the body in response to decreased liver enzyme expression. Additionally, the model demonstrated that acetaldehyde exposure increased with higher dosages of disulfiram and decreased ALDH2 efficiency, and that moderate consumption rates of ethanol could lead to unexpected accumulations in acetaldehyde. This modelling framework combines the comprehensive steady-state analyses from genome-scale models with the dynamics of traditional PK models to create a highly personalized form of PBPK modelling that can push the boundaries of precision medicine., Author summary Alcohol is a widely used recreational drug in many parts of the world and it is often abused or misused, leading to the deaths of millions of people each year from driving under the influence and overdose. Additionally, the body breaks down alcohol into acetaldehyde, a carcinogen that has its own effects ranging from headaches and nausea to liver damage. The effects of ethanol and acetaldehyde vary due to genetic variations that create different forms of the enzymes responsible for breaking them down. Due to these differences, it is important to characterize how these changes affect the metabolism of alcohol and acetaldehyde. To capture these differences, we have created a new model that integrates the traditional pharmacokinetic model with a whole-body genome-scale model that can characterize different genetic variations. In addition, traditional models often require experimentally measured data, yet with this new framework we avoid this tedious process by mathematically solving the genome-scale model with the dynamic Flux Balance Analysis technique, allowing for gap filling. Through this model, we show that the whole-body genome-scale model demonstrates flexibility and robustness that has not been seen before in pharmacokinetic models. Our model combines advantages from both pharmacokinetic and genome-scale modelling and can be personalized to characterize individual reactions to other drugs and further precision medicine.

Binocular rivalry and cross-orientation suppression are well-studied forms of competition in visual cortex, but models of these two types of competition are in tension with one another. Binocular rivalry occurs during the presentation of dichoptic grating stimuli, where two orthogonal gratings presented separately to the two eyes evoke strong alternations in perceptual dominance. Cross-orientation suppression occurs during the presentation of plaid stimuli, where the responses to a component grating presented to both eyes is weakened by the presence of a superimposed orthogonal grating. Conventional models of rivalry that rely on strong competition between orientation-selective neurons incorrectly predict rivalry between the components of plaids. Lowering the inhibitory weights in such models reduces rivalry for plaids, but also reduces it for dichoptic gratings. Using an exhaustive grid search, we show that this problem cannot be solved simply by adjusting the parameters of the model. Instead, we propose a robust class of models that rely on ocular opponency neurons, previously proposed as a mechanism for efficient stereo coding, to yield rivalry only for dichoptic gratings, not for plaids. This class of models reconciles models of binocular rivalry with the divisive normalization framework that has been used to explain cross-orientation. Our model makes novel predictions that we confirmed with psychophysical tests., Author Summary Binocular rivalry is a visual illusion that occurs when the two eyes are presented with incompatible images. Instead of perceiving a mixture of the two images, most people tend to experiences alternations in which they only see one image at a time. Binocular rivalry is more than just an interesting illusion: it reflects actual competition between neurons in the brain, and therefore provides a rare window into neural dynamics. To help us understand these mechanisms, researchers have developed several computational models of binocular rivalry. Yet surprisingly, as we show in this paper, previous computational models of rivalry make an incorrect prediction. They predict that certain types of images (similar to checkerboards) will cause strong perceptual alternations even when viewed normally. Since this prediction doesn't hold up, the existing models must not be telling the whole story. In this paper, we develop a new model of binocular rivalry that doesn't make this prediction. The model also makes novel predictions – not made by conventional models – that stand up to experimental test. Our model thus provides a better account of how neurons in the visual system interact with one another.

Why are sensory signals and motor command signals combined in the neurons of origin of the spinocerebellar pathways and why are the granule cells that receive this input thresholded with respect to their spike output? In this paper, we synthesize a number of findings into a new hypothesis for how the spinocerebellar systems and the cerebellar cortex can interact to support coordination of our multi-segmented limbs and bodies. A central idea is that recombination of the signals available to the spinocerebellar neurons can be used to approximate a wide array of functions including the spatial and temporal dependencies between limb segments, i.e. information that is necessary in order to achieve coordination. We find that random recombination of sensory and motor signals is not a good strategy since, surprisingly, the number of granule cells severely limits the number of recombinations that can be represented within the cerebellum. Instead, we propose that the spinal circuitry provides useful recombinations, which can be described as linear projections through aspects of the multi-dimensional sensorimotor input space. Granule cells, potentially with the aid of differentiated thresholding from Golgi cells, enhance the utility of these projections by allowing the Purkinje cell to establish piecewise-linear approximations of non-linear functions. Our hypothesis provides a novel view on the function of the spinal circuitry and cerebellar granule layer, illustrating how the coordinating functions of the cerebellum can be crucially supported by the recombinations performed by the neurons of the spinocerebellar systems., Author Summary The movement control of the brain excels in the seamless coordination of our multi-segmented limbs and bodies and in this respect the brain widely outperforms the most advanced technical systems. So far, however, there is little knowledge about the neuronal circuitry mechanisms by which this coordination could be achieved. The present paper makes a synthesis of some recent findings of cerebellar neuronal circuitry functions and spinocerebellar systems to introduce a novel hypothesis of how the cerebellar and spinal cord neuronal networks together establish signals that form a basis for coordination control in the mammalian central nervous system. The hypothesis takes into account some recent, surprising findings about cerebellar granule cell function and explains some long-standing enigmas concerning the structure of and information mediated by the spinocerebellar pathways. It describes some interesting parallels between the spinocerebellar network and Artificial Neural Networks (ANNs), and capitalizes on some of the major conclusions from ANN studies to explain the biological observations.

Several experiments indicate that there exists substantial synaptic-depression at the synapses between olfactory receptor neurons (ORNs) and neurons within the drosophila antenna lobe (AL). This synaptic-depression may be partly caused by vesicle-depletion, and partly caused by presynaptic-inhibition due to the activity of inhibitory local neurons within the AL. While it has been proposed that this synaptic-depression contributes to the nonlinear relationship between ORN and projection neuron (PN) firing-rates, the precise functional role of synaptic-depression at the ORN synapses is not yet fully understood. In this paper we propose two hypotheses linking the information-coding properties of the fly AL with the network mechanisms responsible for ORNAL synaptic-depression. Our first hypothesis is related to variance coding of ORN firing-rate information — once stimulation to the ORNs is sufficiently high to saturate glomerular responses, further stimulation of the ORNs increases the regularity of PN spiking activity while maintaining PN firing-rates. The second hypothesis proposes a tradeoff between spike-time reliability and coding-capacity governed by the relative contribution of vesicle-depletion and presynaptic-inhibition to ORNAL synaptic-depression. Synaptic-depression caused primarily by vesicle-depletion will give rise to a very reliable system, whereas an equivalent amount of synaptic-depression caused primarily by presynaptic-inhibition will give rise to a less reliable system that is more sensitive to small shifts in odor stimulation. These two hypotheses are substantiated by several small analyzable toy models of the fly AL, as well as a more physiologically realistic large-scale computational model of the fly AL involving glomerular channels., Author Summary Understanding the intricacies of sensory processing is a major scientific challenge. In this paper we examine the early stages of the olfactory system of the fruit-fly. Many experiments have revealed a great deal regarding the architecture of this system, including the types of neurons within it, as well as the connections those neurons make amongst one another. In this paper we examine the potential dynamics produced by this neuronal network. Specifically, we construct a computational model of this early olfactory system and study the effects of synaptic-depression within this system. We find that the dynamics and coding properties of this system depend strongly on the strength, and sources of, synaptic-depression. This work has ramifications for understanding the coding properties of other insect olfactory systems, and perhaps even other sensory modalities in other animals.

Drug-drug interactions (DDIs) are a common cause of adverse drug events. In this paper, we combined a literature discovery approach with analysis of a large electronic medical record database method to predict and evaluate novel DDIs. We predicted an initial set of 13197 potential DDIs based on substrates and inhibitors of cytochrome P450 (CYP) metabolism enzymes identified from published in vitro pharmacology experiments. Using a clinical repository of over 800,000 patients, we narrowed this theoretical set of DDIs to 3670 drug pairs actually taken by patients. Finally, we sought to identify novel combinations that synergistically increased the risk of myopathy. Five pairs were identified with their p-values less than 1E-06: loratadine and simvastatin (relative risk or RR = 1.69); loratadine and alprazolam (RR = 1.86); loratadine and duloxetine (RR = 1.94); loratadine and ropinirole (RR = 3.21); and promethazine and tegaserod (RR = 3.00). When taken together, each drug pair showed a significantly increased risk of myopathy when compared to the expected additive myopathy risk from taking either of the drugs alone. Based on additional literature data on in vitro drug metabolism and inhibition potency, loratadine and simvastatin and tegaserod and promethazine were predicted to have a strong DDI through the CYP3A4 and CYP2D6 enzymes, respectively. This new translational biomedical informatics approach supports not only detection of new clinically significant DDI signals, but also evaluation of their potential molecular mechanisms., Author Summary Drug-drug interactions are a common cause of adverse drug events. In this paper, we developed an automated search algorithm which can predict new drug interactions based on published literature. Using a large electronic medical record database, we then analyzed the correlation between concurrent use of these potentially interacting drugs and the incidence of myopathy as an adverse drug event. Myopathy comprises a range of musculoskeletal conditions including muscle pain, weakness, and tissue breakdown (rhabdomyolysis). Our statistical analysis identified 5 drug interaction pairs: (loratadine, simvastatin), (loratadine, alprazolam), (loratadine, duloxetine), (loratadine, ropinirole), and (promethazine, tegaserod). When taken together, each drug pair showed a significantly increased risk of myopathy when compared to the expected additive myopathy risk from taking either of the drugs alone. Further investigation suggests that two major drug metabolism proteins, CYP2D6 and CYP3A4, are involved with these five drug pairs' interactions. Overall, our method is robust in that it can incorporate all published literature, all FDA approved drugs, and very large clinical datasets to generate predictions of clinically significant interactions. The interactions can then be further validated in future cell-based experiments and/or clinical studies.

Relay cells are prevalent throughout sensory systems and receive two types of inputs: driving and modulating. The driving input contains receptive field properties that must be transmitted while the modulating input alters the specifics of transmission. For example, the visual thalamus contains relay neurons that receive driving inputs from the retina that encode a visual image, and modulating inputs from reticular activating system and layer 6 of visual cortex that control what aspects of the image will be relayed back to visual cortex for perception. What gets relayed depends on several factors such as attentional demands and a subject's goals. In this paper, we analyze a biophysical based model of a relay cell and use systems theoretic tools to construct analytic bounds on how well the cell transmits a driving input as a function of the neuron's electrophysiological properties, the modulating input, and the driving signal parameters. We assume that the modulating input belongs to a class of sinusoidal signals and that the driving input is an irregular train of pulses with inter-pulse intervals obeying an exponential distribution. Our analysis applies to any order model as long as the neuron does not spike without a driving input pulse and exhibits a refractory period. Our bounds on relay reliability contain performance obtained through simulation of a second and third order model, and suggest, for instance, that if the frequency of the modulating input increases or the DC offset decreases, then relay increases. Our analysis also shows, for the first time, how the biophysical properties of the neuron (e.g. ion channel dynamics) define the oscillatory patterns needed in the modulating input for appropriately timed relay of sensory information. In our discussion, we describe how our bounds predict experimentally observed neural activity in the basal ganglia in (i) health, (ii) in Parkinson's disease (PD), and (iii) in PD during therapeutic deep brain stimulation. Our bounds also predict different rhythms that emerge in the lateral geniculate nucleus in the thalamus during different attentional states., Author Summary In cellular biology, it is important to characterize the electrophysiological dynamics of a cell as a function of the cell type and its inputs. Typically, these dynamics are modeled as a set of parametric nonlinear ordinary differential equations which are not always easy to analyze. Previous studies performed phase-plane analysis and/or simulations to understand how constant inputs impact a cell's output for a given cell type. In this paper, we use systems theoretic tools to compute analytic bounds of how well a single neuron's output relays a driving input signal as a function of the neuron type, modulating input signal, and driving signal parameters. The methods used here are generally applicable to understanding cell behavior under various conditions and enables rigorous analysis of electrophysiological changes that occur in health and in disease.

The tumor suppressor protein p53 can lose its function upon single-point missense mutations in the core DNA-binding domain (“cancer mutants”). Activity can be restored by second-site suppressor mutations (“rescue mutants”). This paper relates the functional activity of p53 cancer and rescue mutants to their overall molecular dynamics (MD), without focusing on local structural details. A novel global measure of protein flexibility for the p53 core DNA-binding domain, the number of clusters at a certain RMSD cutoff, was computed by clustering over 0.7 µs of explicitly solvated all-atom MD simulations. For wild-type p53 and a sample of p53 cancer or rescue mutants, the number of clusters was a good predictor of in vivo p53 functional activity in cell-based assays. This number-of-clusters (NOC) metric was strongly correlated (r2 = 0.77) with reported values of experimentally measured ΔΔG protein thermodynamic stability. Interpreting the number of clusters as a measure of protein flexibility: (i) p53 cancer mutants were more flexible than wild-type protein, (ii) second-site rescue mutations decreased the flexibility of cancer mutants, and (iii) negative controls of non-rescue second-site mutants did not. This new method reflects the overall stability of the p53 core domain and can discriminate which second-site mutations restore activity to p53 cancer mutants., Author Summary p53 is a tumor suppressor protein that controls a central apoptotic pathway (programmed cell death). Thus, it is the most-mutated gene in human cancers. Due to the marginal stability of p53, a single mutation can abolish p53 function (“cancer mutants”), while a second mutation (or several) can restore it (“rescue mutants”). Restoring p53 function is a promising therapeutic goal that has been strongly supported by recent experimental results on mice. Understanding of the effects of p53 cancer and rescue mutations would be helpful for designing drugs that are able to achieve the same goal. The challenge is that cancer and rescue mutations are distributed widely in the protein, and experimental testing of all possible combinations of mutations is not feasible. This paper describes a simple computational metric that reflects the overall stability of the p53 core domain and can discriminate which second-site mutations restore activity to p53 cancer mutants.

Because local field potentials (LFPs) arise from multiple sources in different spatial locations, they do not easily reveal coordinated activity across neural populations on a trial-to-trial basis. As we show here, however, once disparate source signals are decoupled, their trial-to-trial fluctuations become more accessible, and cross-population correlations become more apparent. To decouple sources we introduce a general framework for estimation of current source densities (CSDs). In this framework, the set of LFPs result from noise being added to the transform of the CSD by a biophysical forward model, while the CSD is considered to be the sum of a zero-mean, stationary, spatiotemporal Gaussian process, having fast and slow components, and a mean function, which is the sum of multiple time-varying functions distributed across space, each varying across trials. We derived biophysical forward models relevant to the data we analyzed. In simulation studies this approach improved identification of source signals compared to existing CSD estimation methods. Using data recorded from primate auditory cortex, we analyzed trial-to-trial fluctuations in both steady-state and task-evoked signals. We found cortical layer-specific phase coupling between two probes and showed that the same analysis applied directly to LFPs did not recover these patterns. We also found task-evoked CSDs to be correlated across probes, at specific cortical depths. Using data from Neuropixels probes in mouse visual areas, we again found evidence for depth-specific phase coupling of primary visual cortex and lateromedial area based on the CSDs., Author summary To better understand information processing in the brain, it is important to identify situations in which neural activity is coordinated across populations of neurons, including those in distinct layers of the cortex. Bulk population activity results in voltage changes across extracellular electrodes, but in raw form such voltage recordings can be hard to analyze and interpret. In this paper, we develop a novel framework for locating the sources of currents that produce the measured voltages, and decomposing those currents into interpretable components. We use this flexible framework to develop statistical methods of analysis, and we show that our methodology can be more effective than existing techniques for current source localization. We apply the method to extracellular recordings in two contexts: primate auditory cortex in response to tone stimuli, and mouse visual cortex in response to visual stimuli. In both cases, we get results that are useful for understanding cross-population activity while being difficult or impossible to obtain using the raw voltage signals. We thereby demonstrate the broad utility of our approach for identifying coordinated neural activity based on extracellular voltage recordings.

There are two distinct classes of cells in the primary visual cortex (V1): simple cells and complex cells. One defining feature of complex cells is their spatial phase invariance; they respond strongly to oriented grating stimuli with a preferred orientation but with a wide range of spatial phases. A classical model of complete spatial phase invariance in complex cells is the energy model, in which the responses are the sum of the squared outputs of two linear spatially phase-shifted filters. However, recent experimental studies have shown that complex cells have a diverse range of spatial phase invariance and only a subset can be characterized by the energy model. While several models have been proposed to explain how complex cells could learn to be selective to orientation but invariant to spatial phase, most existing models overlook many biologically important details. We propose a biologically plausible model for complex cells that learns to pool inputs from simple cells based on the presentation of natural scene stimuli. The model is a three-layer network with rate-based neurons that describes the activities of LGN cells (layer 1), V1 simple cells (layer 2), and V1 complex cells (layer 3). The first two layers implement a recently proposed simple cell model that is biologically plausible and accounts for many experimental phenomena. The neural dynamics of the complex cells is modeled as the integration of simple cells inputs along with response normalization. Connections between LGN and simple cells are learned using Hebbian and anti-Hebbian plasticity. Connections between simple and complex cells are learned using a modified version of the Bienenstock, Cooper, and Munro (BCM) rule. Our results demonstrate that the learning rule can describe a diversity of complex cells, similar to those observed experimentally., Author summary Many cortical functions originate from the learning ability of the brain. How the properties of cortical cells are learned is vital for understanding how the brain works. There are many models that explain how V1 simple cells can be learned. However, how V1 complex cells are learned still remains unclear. In this paper, we propose a model of learning in complex cells based on the Bienenstock, Cooper, and Munro (BCM) rule. We demonstrate that properties of receptive fields of complex cells can be learned using this biologically plausible learning rule. Quantitative comparisons between the model and experimental data are performed. Results show that model complex cells can account for the diversity of complex cells found in experimental studies. In summary, this study provides a plausible explanation for how complex cells can be learned using biologically plausible plasticity mechanisms. Our findings help us to better understand biological vision processing and provide us with insights into the general signal processing principles that the visual cortex employs to process visual information.