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Abstract Geographic variation in the vocal behavior of manatees has been reported but is largely unexplored. Vocalizations of wild West Indian manatees (Trichechus manatus) were recorded with hydrophones in Florida from Florida manatees (Trichechus manatus latirostris), and in Belize and Panama from Antillean manatees (Trichechus manatus manatus) to determine if calls varied between subspecies and geographic regions. Calls were visually classified into five categories: squeaks, high squeaks, squeals, squeak-squeals, and chirps. From these five categories, only three call types (squeaks, high squeaks and squeals) were observed in all three populations. Six parameters from the temporal and frequency domains were measured from the fundamental frequency of 2878 manatee vocalizations. A repeated measures PERMANOVA found significant differences for squeaks and high squeaks between each geographic location and for squeals between Belize and Florida. Almost all measured frequency and temporal parameters of manatee vocalizations differed between and within subspecies. Variables that may have influenced the variation observed may be related to sex, body size, habitat and/or other factors. Our findings provide critical information of manatee calls for wildlife monitoring and highlight the need for further study of the vocal behavior of manatees throughout their range.

Abstract During the COVID-19 pandemic, the scientific community developed predictive models to evaluate potential governmental interventions. However, the analysis of the effects these interventions had is less advanced. Here, we propose a data-driven framework to assess these effects retrospectively. We use a regularized regression to find a parsimonious model that fits the data with the least changes in the $$R_t$$ R t parameter. Then, we postulate each jump in $$R_t$$ R t as the effect of an intervention. Following the do-operator prescriptions, we simulate the counterfactual case by forcing $$R_t$$ R t to stay at the pre-jump value. We then attribute a value to the intervention from the difference between true evolution and simulated counterfactual. We show that the recommendation to use facemasks for all activities would reduce the number of cases by 200,000 ( $$95\%$$ 95 % CI 190,000–210,000) in Connecticut, Massachusetts, and New York State. The framework presented here might be used in any case where cause and effects are sparse in time.

The problem of solving the equivalent resistance between two points for resistor networks has important significance in physics. This paper mainly changes and rewrites the formula for calculating the resistance between two points of an unconventional m × n cylindrical resistor network with a zero resistor axis and any two left and right boundaries. To enhance the efficiency of calculating the equivalent resistance between two points, Chebyshev polynomials and hyperbolic cosine functions are employed to represent the new formula. And in the inference process, the famous discrete cosine transform of the third kind (DCT-III) is used to process the matrix. We give the equivalent resistance formula for several special cases, and display them by a three-dimensional graph. Subsequently, the calculation efficiency of the original formula and the rewritten formula are compared. At the end of the paper, a heuristic algorithm suitable for robot path planning on cylindrical environment is proposed. [ABSTRACT FROM AUTHOR]

A geometrically symmetric gear with asymmetric surface wettability exhibits one-way spin on a vibrating water bed. On the side face of the gear, a parafilm was coated to create asymmetry in the surface energy. The gear shows fluctuations in both directions within a shorter timescale; however, for a longer timescale, the gear exhibits a one-way spin. This unique motion is generated by a stochastic process with a biased driving force produced by the interaction between the vibrating water surface and the side face of the gear. This new model resembles an active Brownian ratchet. Until now, most ratchet motors, which obtain regular motion from nonthermal fluctuations, utilize a geometrical ratchet structure. However, in this study, the surface energy forms a ratchet that rectifies the noisy motion. [ABSTRACT FROM AUTHOR]

Vertebrate color vision is predominantly mediated by the presence of multiple cone photoreceptor subtypes that are each maximally sensitive to different wavelengths of light. Thyroid hormone (TH) has been shown to be essential in the spatiotemporal patterning of cone subtypes in many species, including cone subtypes that express opsins that are encoded by tandemly replicated genes. TH has been shown to differentially regulate the tandemly replicated lws opsin genes in zebrafish, and exogenous treatments alter the expression levels of these genes in larvae and juveniles. In this study, we sought to determine whether gene expression in cone photoreceptors remains plastic to TH treatment in adults. We used a transgenic lws reporter line, multiplexed fluorescence hybridization chain reaction in situ hybridization, and qPCR to examine the extent to which cone gene expression can be altered by TH in adults. Our studies revealed that opsin gene expression, and the expression of other photoreceptor genes, remains plastic to TH treatment in adult zebrafish. In addition to retinal plasticity, exogenous TH treatment alters skin pigmentation patterns in adult zebrafish after 5 days. Taken together, our results show a remarkable level of TH-sensitive plasticity in the adult zebrafish. [ABSTRACT FROM AUTHOR]

Odor perception affects physiological and psychological states. Pupillary light reflex (PLR) parameters can be affected by olfactory stimulation and psychological states, although it remains unclear whether the olfactory stimulation-induced psychological changes can associate with PLR parameter changes. This study aimed to investigate effects of olfactory stimulation-induced psychological changes on PLR parameter changes with repeated measurements. We collected data on six mood subscales of the profile of mood states, and on five PLR parameter measurements from 28 healthy participants. Participants underwent a 10-min olfactory stimulation on different days with six odorants available with the T&T olfactometer. As obtained data were clustered, we used linear mixed-effects models for statistical analyses. The olfactory stimulation using the no-odor liquid did not affect mood states and the initial pupil size (INIT). The sweat odorant worsened all mood subscales including fatigue–inertia (Fatigue)/Vigor–Activity (Vigor), and decreased INIT compared to the no-odor liquid. When comparing INIT responses related to changes in mood subscales between the no-odor liquid and the sweat odorant, worsened states of Fatigue/Vigor were associated with decreased INIT in the sweat odorant. Fatigue/Vigor can be used as mental fatigue indicators. Thus, mental fatigue can be associated with decreased INIT in the olfactory stimulation. [ABSTRACT FROM AUTHOR]

Hydrological disasters, such as floods, can have dire consequences for human societies. Historical information plays a key role in detecting whether particular types of hydrological disasters have increased in frequency and/or magnitude and, if so, they are more likely attributable to natural or human-induced climatic and other environmental changes. The identification of regions with similar flood conditions is essential for the analysis of regional flooding regimes. To this end, we here present the longest existing flood reconstruction for the Eastern Liguria Area (ELA) in northwestern Italy, covering 1582 to 2022 CE, which offers a case study representative of the central Mediterranean region. An Annual Flood Intensification Index was developed to transform the historical data into a continuous annual hydrological time-series contained by a homogeneous data structure for the study-area. We found two change-points (trend breaks) in the reconstructed time-series, in 1787 and 1967, with only occasional heavy floods comparable to present-day disasters occurring before the first change-point, and an increasing intensification of floods after the second change-point up to the present day. The recent intensification of flooding in the ELA, associated with changes in land use and land cover, also appears to coincide with phases in which hydrological hazards have become more changeable and extreme in disaster-affected areas. This is evidenced by river basin responses to human-induced disturbances. [ABSTRACT FROM AUTHOR]

The song control nucleus HVC of songbirds has emerged as a widespread model system to study adult neurogenesis and the factors that modulate the incorporation of new neurons, including seasonal state, sex differences or sex steroid hormone concentrations. However, the specific function of these new neurons born in adulthood remains poorly understood. We implemented a new procedure based on focal X-ray irradiation to deplete neural progenitors in the ventricular zone adjacent to HVC and study the functional consequences. A 23 Gy dose depleted by more than 50 percent the incorporation of BrdU in neural progenitors, a depletion that was confirmed by a significant decrease in doublecortin positive neurons. This depletion of neurogenesis significantly increased the variability of testosterone-induced songs in females and decreased their bandwidth. Expression of the immediate early gene ZENK in secondary auditory areas of the telencephalon that respond to song was also inhibited. These data provide evidence that new neurons in HVC play a role in both song production and perception and that X-ray focal irradiation represents an excellent tool to advance our understanding of adult neurogenesis. [ABSTRACT FROM AUTHOR]

Neurons are connected by complex branching processes—axons and dendrites—that process information for organisms to respond to their environment. Classifying neurons according to differences in structure or function is a fundamental part of neuroscience. Here, by constructing biophysical theory and testing against empirical measures of branching structure, we develop a general model that establishes a correspondence between neuron structure and function as mediated by principles such as time or power minimization for information processing as well as spatial constraints for forming connections. We test our predictions for radius scale factors against those extracted from neuronal images, measured for species that range from insects to whales, including data from light and electron microscopy studies. Notably, our findings reveal that the branching of axons and peripheral nervous system neurons is mainly determined by time minimization, while dendritic branching is determined by power minimization. Our model also predicts a quarter-power scaling relationship between conduction time delay and body size. [ABSTRACT FROM AUTHOR]

Deciphering the relationship between molecules, olfactory receptors (ORs) and corresponding odors remains a challenging task. It requires a comprehensive identification of ORs responding to a given odorant. With the recent advances in artificial intelligence and the growing research in decoding the human olfactory perception from chemical features of odorant molecules, the applications of advanced machine learning have been revived. In this study, Convolutional Neural Network (CNN) and Graphical Convolutional Network (GCN) models have been developed on odorant molecules-odors and odorant molecules-olfactory receptors using a large set of 5955 molecules, 160 odors and 106 olfactory receptors. The performance of such models is promising with a Precision/Recall Area Under Curve of 0.66 for the odorant-odor and 0.91 for the odorant-olfactory receptor GCN models respectively. Furthermore, based on the correspondence of odors and ORs associated for a set of 389 compounds, an odor-olfactory receptor pairwise score was computed for each odor-OR combination allowing to suggest a combinatorial relationship between olfactory receptors and odors. Overall, this analysis demonstrate that artificial intelligence may pave the way in the identification of the smell perception and the full repertoire of receptors for a given odorant molecule. [ABSTRACT FROM AUTHOR]

Since the very beginning of the COVID-19 pandemic, control policies and restrictions have been the hope for containing the rapid spread of the virus. However, the psychological and economic toll they take on society entails the necessity to develop an optimal control strategy. Assessment of the effectiveness of these interventions aided with mathematical modelling remains a non-trivial issue in terms of numerical conditioning due to the high number of parameters to estimate from a highly noisy dataset and significant correlations between policy timings. We propose a solution to the problem of parameter non-estimability utilizing data from a set of European countries. Treating a subset of parameters as common for all countries and the rest as country-specific, we construct a set of individualized models incorporating 13 different pandemic control measures, and estimate their parameters without prior assumptions. We demonstrate high predictive abilities of these models on an independent validation set and rank the policies by their effectiveness in reducing transmission rates. We show that raising awareness through information campaigns, providing income support, closing schools and workplaces, cancelling public events, and maintaining an open testing policy have the highest potential to mitigate the pandemic. [ABSTRACT FROM AUTHOR]

We draw current efforts towards proposing a wing-type micro UAV with characteristics of being a basic operation risk self handled (Micro-Brosh) platform. Its micro-sized wingspan and weight, which are less than 0.30 m and 0.150 kg, respectively, guarantee the low risk to the operator and installations in case of crashing. It can be launched manually without using an appropriate runway, besides using a soft grass field for landing is recommended. Its associated costs for construction and maintenance are very low (below US$ 500) if compared to traditional aircraft. The main contribution here is the architectural design, besides we provide detailed documentation including techniques for determining lift, thrust, drag, minimum flight velocity, maximum time of flight and distance (autonomy), and other issues that we have solved related to the aircraft development. We validate our prototype with experiments including several tests done with the UAV with results that have proven its flight ability. To the end, we understand that this work provides a nice starting document to researchers that intend to develop a UAV or enter this field. [ABSTRACT FROM AUTHOR]

Binding interactions of the spike proteins of the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) to a peptide fragment derived from the human angiotensin converting enzyme 2 (hACE2) receptor are investigated. The peptide is employed as capture moiety in enzyme linked immunosorbent assays (ELISA) and quantitative binding interaction measurements that are based on fluorescence proximity sensing (switchSENSE). In both techniques, the peptide is presented on an oligovalent DNA nanostructure, in order to assess the impact of mono- versus trivalent binding modes. As the analyte, the spike protein and several of its subunits are tested as well as inactivated SARS-CoV-2 and pseudo viruses. While binding of the peptide to the full-length spike protein can be observed, the subunits RBD and S1 do not exhibit binding in the employed concentrations. Variations of the amino acid sequence of the recombinant full-length spike proteins furthermore influence binding behavior. The peptide was coupled to DNA nanostructures that form a geometric complement to the trimeric structure of the spike protein binding sites. An increase in binding strength for trimeric peptide presentation compared to single peptide presentation could be generally observed in ELISA and was quantified in switchSENSE measurements. Binding to inactivated wild type viruses could be shown as well as qualitatively different binding behavior of the Alpha and Beta variants compared to the wild type virus strain in pseudo virus models. [ABSTRACT FROM AUTHOR]

Podocytes are highly specialized cells playing a key role in the filtration function of the kidney. A damaged podocyte ultrastructure is associated with a reorganization of the actin cytoskeleton and accompanied with a loss of adhesion to the glomerular basement membrane leading to proteinuria in many forms of glomerular diseases, e.g. nephrotic syndrome. If the first-line therapy with glucocorticoids fails, alternative immunosuppressive agents are used, which are known to have the potential to stabilize the actin cytoskeleton. A new option for preventing relapses in steroid dependent nephrotic syndrome is the monoclonal antibody rituximab, which, in addition to its B-cell depleting effect, is assumed to have direct effects on podocytes. We here provide data on the non-immunological off-target effects of the immunosuppressant rituximab on podocyte structure and dynamics in an in vitro puromycin aminonucleoside model of podocyte injury. A conditionally immortalized human podocyte cell line was used. Differentiated podocytes were treated with puromycin aminonucleoside and rituximab. Our studies focussed on analyzing the structure of the actin cytoskeleton, cellular adhesion and apoptosis using immunofluorescence staining and protein biochemistry methods. Treatment with rituximab resulted in a stabilization of podocyte actin stress fibers in the puromycin aminonucleoside model, leading to an improvement in cell adhesion. A lower apoptosis rate was observed after parallel treatment with puromycin aminonucleoside and rituximab visualized by reduced nuclear fragmentation. Consistent with this data, Western-blot analyses demonstrated that rituximab directly affects the caspase pathways by inhibiting the activation of Caspases-8, -9 and -3, suggesting that rituximab may inhibit apoptosis. In conclusion, our results indicate an important role of the immunosuppressant rituximab in terms of stability and morphogenesis of podocytes, involving apoptosis pathways. This could help to improve therapeutical concepts for patients with proteinuria mediated by diseased podocytes. [ABSTRACT FROM AUTHOR]

Optimizing passengers routes is crucial to design efficient transportation networks. Recent results show that optimal transport provides an efficient alternative to standard optimization methods. However, it is not yet clear if this formalism has empirical validity on engineering networks. We address this issue by considering different response functions—quantities determining the interaction between passengers—in the dynamics implementing the optimal transport formulation. Particularly, we couple passengers' fluxes by taking their sum or the sum of their squares. The first choice naturally reflects edges occupancy in transportation networks, however the second guarantees convergence to an optimal configuration of flows. Both modeling choices are applied to the Paris metro. We measure the extent of traffic bottlenecks and infrastructure resilience to node removal, showing that the two settings are equivalent in the congested transport regime, but different in the branched one. In the latter, the two formulations differ on how fluxes are distributed, with one function favoring routes consolidation, thus potentially being prone to generate traffic overload. Additionally, we compare our method to Dijkstra's algorithm to show its capacity to efficiently recover shortest-path-like graphs. Finally, we observe that optimal transport networks lie in the Pareto front drawn by the energy dissipated by passengers, and the cost to build the infrastructure. [ABSTRACT FROM AUTHOR]

Diminished sense of smell impairs the quality of life but olfactorily disabled people are hardly considered in measures of disability inclusion. We aimed to stratify perceptual characteristics and odors according to the extent to which they are perceived differently with reduced sense of smell, as a possible basis for creating olfactory experiences that are enjoyed in a similar way by subjects with normal or impaired olfactory function. In 146 subjects with normal or reduced olfactory function, perceptual characteristics (edibility, intensity, irritation, temperature, familiarity, hedonics, painfulness) were tested for four sets of 10 different odors each. Data were analyzed with (i) a projection based on principal component analysis and (ii) the training of a machine-learning algorithm in a 1000-fold cross-validated setting to distinguish between olfactory diagnosis based on odor property ratings. Both analytical approaches identified perceived intensity and familiarity with the odor as discriminating characteristics between olfactory diagnoses, while evoked pain sensation and perceived temperature were not discriminating, followed by edibility. Two disjoint sets of odors were identified, i.e., d = 4 "discriminating odors" with respect to olfactory diagnosis, including cis-3-hexenol, methyl salicylate, 1-butanol and cineole, and d = 7 "non-discriminating odors", including benzyl acetate, heptanal, 4-ethyl-octanoic acid, methional, isobutyric acid, 4-decanolide and p-cresol. Different weightings of the perceptual properties of odors with normal or reduced sense of smell indicate possibilities to create sensory experiences such as food, meals or scents that by emphasizing trigeminal perceptions can be enjoyed by both normosmic and hyposmic individuals. [ABSTRACT FROM AUTHOR]

Rapid diagnostic tests are tools of paramount impact both for improving patient care and in antimicrobial management programs. Particularly in the case of respiratory infections, it is of great importance to quickly confirm/exclude the involvement of pathogens, be they bacteria or viruses, while obtaining information about the presence/absence of a genetic target of resistance to modulate antibiotic therapy. In this paper, we present our experiences with the use of the Biofire® FilmArray® Pneumonia Panel Plus (FAPP; bioMérieux; Marcy l'Etoile, France) to assess coinfection in COVID-19 patients. A total of 152 respiratory samples from consecutive patients were examined, and 93 (61%) were found to be FAPP positive, with the detection of bacteria and/or viruses. The patients were 93 males and 59 females with an average age of 65 years who were admitted to our hospital due to moderate/severe acute respiratory symptoms. Among the positive samples were 52 from sputum (SPU) and 41 from bronchoalveolar lavage (BAL). The most representative species was S. aureus (most isolates were mecA positive; 30/44, 62%), followed by gram-negative pathogens such as P. aeruginosa, K. pneumoniae, and A. baumannii. Evidence of a virus was rare. Cultures performed from BAL and SPU samples gave poor results. Most of the discrepant negative cultures were those in which FAPP detected pathogens with a microbial count ≤ 105 CFU/mL. H. influenzae was one of the most common pathogens lost by the conventional method. Despite the potential limitations of FAPP, which detects a defined number of pathogens, its advantages of rapid detection combined with predictive information regarding the antimicrobial resistance of pathogens through the detection of some relevant markers of resistance could be very useful for establishing empirical targeted therapy for the treatment of patients with respiratory failure. In the COVID era, we understand the importance of using antibiotics wisely to curb the phenomenon of antibiotic resistance. [ABSTRACT FROM AUTHOR]

Several dynamical systems in nature can be maintained out-of-equilibrium, either through mutual interaction of particles or by external fields. The particle's transport and the transient dynamics are landmarking of such systems. While single ratchet systems are genuine candidates to describe unbiased transport, we demonstrate here that coupled ratchets exhibit collective transient ratchet transport. Extensive numerical simulations for up to N = 1024 elastically interacting ratchets establish the generation of large transient ratchet currents (RCs). The lifetimes of the transient RCs increase with N and decrease with the coupling strength between the ratchets. We demonstrate one peculiar case having a coupling-induced transient RC through the asymmetric destruction of attractors. Results suggest that physical devices built with coupled ratchet systems should present large collective transient transport of particles, whose technological applications are undoubtedly appealing and feasible. [ABSTRACT FROM AUTHOR]

Advances in technological capabilities, operational simplicity and cost efficiency have promoted the rapid integration of unmanned aerial vehicles (UAVs) into ecological research, providing access to study taxa that are otherwise difficult to survey, such as bats. Many bat species are currently at risk, but accurately surveying populations is challenging for species that do not roost in large aggregations. Acoustic recorders attached to UAVs provide an opportunity to survey bats in challenging habitats. However, UAVs may alter bat behaviour, leading to avoidance of the UAV, reduced detection rates and inaccurate surveys. We evaluated the number of bat passes detected with and without the presence of a small, commercial UAV in open habitats. Only 22% of bat passes were recorded in the presence of the UAV (0.23 ± 0.09 passes/min) compared to control periods without the UAV (1.03 ± 0.17 passes/min), but the effect was smaller on the big brown bat/silver-haired bat (Eptesicus fuscus/Lasionycteris noctivagans) acoustic complex. Noise interference from the UAV also reduced on-board bat detection rates. We conclude that acoustic records attached to UAVs may inaccurately survey bat populations due to low and variable detection rates by such recorders. [ABSTRACT FROM AUTHOR]

Vocal behavior can be dramatically changed by both neural circuit development and postnatal maturation of the body. During song learning in songbirds, both the song system and syringeal muscles are functionally changing, but it is unknown if maturation of sound generators within the syrinx contributes to vocal development. Here we densely sample the respiratory pressure control space of the zebra finch syrinx in vitro. We show that the syrinx produces sound very efficiently and that key acoustic parameters, minimal fundamental frequency, entropy and source level, do not change over development in both sexes. Thus, our data suggest that the observed acoustic changes in vocal development must be attributed to changes in the motor control pathway, from song system circuitry to muscle force, and not by material property changes in the avian analog of the vocal folds. We propose that in songbirds, muscle use and training driven by the sexually dimorphic song system are the crucial drivers that lead to sexual dimorphism of the syringeal skeleton and musculature. The size and properties of the instrument are thus not changing, while its player is. [ABSTRACT FROM AUTHOR]

Neuronal activity in auditory cortex is often highly synchronous between neighboring neurons. Such coordinated activity is thought to be crucial for information processing. We determined the functional properties of coordinated neuronal ensembles (cNEs) within primary auditory cortical (AI) columns relative to the contributing neurons. Nearly half of AI cNEs showed robust spectro-temporal receptive fields whereas the remaining cNEs showed little or no acoustic feature selectivity. cNEs can therefore capture either specific, time-locked information of spectro-temporal stimulus features or reflect stimulus-unspecific, less-time specific processing aspects. By contrast, we show that individual neurons can represent both of those aspects through membership in multiple cNEs with either high or absent feature selectivity. These associations produce functionally heterogeneous spikes identifiable by instantaneous association with different cNEs. This demonstrates that single neuron spike trains can sequentially convey multiple aspects that contribute to cortical processing, including stimulus-specific and unspecific information. [ABSTRACT FROM AUTHOR]

The acellular slime mold Physarum polycephalum provides an excellent model to study network formation, as its network is remodelled constantly in response to mass gain/loss and environmental conditions. How slime molds networks are built and fuse to allow for efficient exploration and adaptation to environmental conditions is still not fully understood. Here, we characterize the network organization of slime molds exploring homogeneous neutral, nutritive and adverse environments. We developed a fully automated image analysis method to extract the network topology and followed the slime molds before and after fusion. Our results show that: (1) slime molds build sparse networks with thin veins in a neutral environment and more compact networks with thicker veins in a nutritive or adverse environment; (2) slime molds construct long, efficient and resilient networks in neutral and adverse environments, whereas in nutritive environments, they build shorter and more centralized networks; and (3) slime molds fuse rapidly and establish multiple connections with their clone-mates in a neutral environment, whereas they display a late fusion with fewer connections in an adverse environment. Our study demonstrates that slime mold networks evolve continuously via pruning and reinforcement, adapting to different environmental conditions. [ABSTRACT FROM AUTHOR]

The inner ear, or cochlea, is a fluid-filled organ housing the mechanosensitive hair cells. Sound stimulation is relayed to the hair cells through waves that propagate on the elastic basilar membrane. Sensorineural hearing loss occurs from damage to the hair cells and cannot currently be cured. Although drugs have been proposed to prevent damage or restore functionality to hair cells, a difficulty with such treatments is ensuring adequate drug delivery to the cells. Because the cochlea is encased in the temporal bone, it can only be accessed from its basal end. However, the hair cells that are responsible for detecting speech-frequency sounds reside at the opposite, apical end. In this paper we show that steady streaming can be used to transport drugs along the cochlea. Steady streaming is a nonlinear process that accompanies many fluctuating fluid motions, including the sound-evoked waves in the inner ear. We combine an analytical approximation for the waves in the cochlea with computational fluid dynamic simulations to demonstrate that the combined steady streaming effects of several different frequencies can transport drugs from the base of the cochlea further towards the apex. Our results therefore show that multi-frequency sound stimulation can serve as a non-invasive method to transport drugs efficiently along the cochlea. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network is used to characterize the typical search time as a function of network connectivity. We find that global structural properties — the total edge length and number of loops — are sufficient to largely determine network exploration times for a variety of both synthetic planar networks and organelle morphologies extracted from living cells. For synthetic networks on a lattice, we predict the search time dependence on these global structural parameters by connecting with percolation theory, providing a bridge from irregular real-world networks to a simpler physical model. The dependence of search time on global network structural properties suggests that network architecture can be designed for efficient search without controlling the precise arrangement of connections. Specifically, increasing the number of loops substantially decreases search times, pointing to a potential physical mechanism for regulating reaction rates within organelle network structures. [ABSTRACT FROM AUTHOR]

Identifying trustworthy partners is an important adaptive challenge for establishing mutually cooperative relationships. Previous studies have demonstrated a marked relationship between a person's attractiveness and his apparent trustworthiness (beauty premium). Kin selection theory, however, suggests that cues to kinship enhance trustworthiness. Here we directly tested predictions of the beauty premium and kin selection theory by using body odours as cues to trustworthiness. Body odours reportedly portray information about an individuals' genotype at the human leucocyte antigen system (HLA) and thus olfactory cues in body odours serve as a promising means for kin recognition. Ninety men played trust games in which they divided uneven sums of monetary units between two male trustees represented by their body odour and rated each body odour for pleasantness. Half of the odours came from HLA-similar men (suggesting closer kin) and half from HLA dissimilar men (suggesting non-kin). We found that the amount of money the players transferred was not related to HLA-similarity, but to the pleasantness of the trustee's body odour. By showing that people with more pleasant body odours are trusted more than people with unpleasant body odour we provide evidence for a "beauty-premium" that overrides any putative effect of kin. [ABSTRACT FROM AUTHOR]

Podocytes are specialized cells with a limited capacity for cell division that do not regenerate in response to injury and loss. Insults that compromise the integrity of podocytes promote proteinuria and progressive renal disease. The aim of this study was to evaluate the potential renoprotective and regenerative effects of mesenchymal stromal cells (mSC) in a severe form of the podocyte injury model induced by intraperitoneal administration of puromycin, aggravated by unilateral nephrectomy. Bone derived mSC were isolated and characterized according to flow cytometry analyses and to their capacity to differentiate into mesenchymal lineages. Wistar rats were divided into three groups: Control, PAN, and PAN+ mSC, consisting of PAN rats treated with 2 × 105 mSC. PAN rats developed heavy proteinuria, hypertension, glomerulosclerosis and significant effacement of the foot process. After 60 days, PAN rats treated with mSC presented a significant amelioration of all these abnormalities. In addition, mSC treatment recovered WT1 expression, improved nephrin, podocin, synaptopodin, podocalyxin, and VEGF expression, and downregulated proinflammatory Th1 cytokines in the kidney with a shift towards regulatory Th2 cytokines. In conclusion, mSC administration induced protection of podocytes in this experimental PAN model, providing new perspectives for the treatment of renal diseases associated with podocyte damage. [ABSTRACT FROM AUTHOR]

DNA topoisomerases control the topology of DNA. Type II topoisomerases exhibit topology simplification, whereby products of their reactions are simplified beyond that expected based on thermodynamic equilibrium. The molecular basis for this process is unknown, although DNA bending has been implicated. To investigate the role of bending in topology simplification, the DNA bend angles of four enzymes of different types (IIA and IIB) were measured using atomic force microscopy (AFM). The enzymes tested were Escherichia coli topo IV and yeast topo II (type IIA enzymes that exhibit topology simplification), and Methanosarcina mazei topo VI and Sulfolobus shibatae topo VI (type IIB enzymes, which do not). Bend angles were measured using the manual tangent method from topographical AFM images taken with a novel amplitude-modulated imaging mode: small amplitude small set-point (SASS), which optimises resolution for a given AFM tip size and minimises tip convolution with the sample. This gave improved accuracy and reliability and revealed that all 4 topoisomerases bend DNA by a similar amount:~120° between the DNA entering and exiting the enzyme complex. These data indicate that DNA bending alone is insufficient to explain topology simplification and that the 'exit gate' may be an important determinant of this process. [ABSTRACT FROM AUTHOR]

Transfer entropy is a recently introduced information-theoretic measure quantifying directed statistical coherence between spatiotemporal processes, and is widely used in diverse fields ranging from finance to neuroscience. However, its relationships to fundamental limits of computation, such as Landauer's limit, remain unknown. Here we show that in order to increase transfer entropy (predictability) by one bit, heat flow must match or exceed Landauer's limit. Importantly, we generalise Landauer's limit to bi-directional information dynamics for non-equilibrium processes, revealing that the limit applies to prediction, in addition to retrodiction (information erasure). Furthermore, the results are related to negentropy, and to Bremermann's limit and the Bekenstein bound, producing, perhaps surprisingly, lower bounds on the computational deceleration and information loss incurred during an increase in predictability about the process. The identified relationships set new computational limits in terms of fundamental physical quantities, and establish transfer entropy as a central measure connecting information theory, thermodynamics and theory of computation. [ABSTRACT FROM AUTHOR]

Shortest paths are not always simple. In planar networks, they can be very different from those with the smallest number of turns - the simplest paths. The statistical comparison of the lengths of the shortest and simplest paths provides a non trivial and non local information about the spatial organization of these graphs. We define the simplicity index as the average ratio of these lengths and the simplicity profile characterizes the simplicity at different scales. We measure these metrics on artificial (roads, highways, railways) and natural networks (leaves, slime mould, insect wings) and show that there are fundamental differences in the organization of urban and biological systems, related to their function, navigation or distribution: straight lines are organized hierarchically in biological cases, and have random lengths and locations in urban systems. In the case of time evolving networks, the simplicity is able to reveal important structural changes during their evolution. [ABSTRACT FROM AUTHOR]

Routing optimization is a relevant problem in many contexts. Solving directly this type of optimization problem is often computationally intractable. Recent studies suggest that one can instead turn this problem into one of solving a dynamical system of equations, which can instead be solved efficiently using numerical methods. This results in enabling the acquisition of optimal network topologies from a variety of routing problems. However, the actual extraction of the solution in terms of a final network topology relies on numerical details which can prevent an accurate investigation of their topological properties. In fact, in this context, theoretical results are fully accessible only to an expert audience and ready-to-use implementations for non-experts are rarely available or insufficiently documented. In particular, in this framework, final graph acquisition is a challenging problem in-and-of-itself. Here we introduce a method to extract network topologies from dynamical equations related to routing optimization under various parameters' settings. Our method is made of three steps: first, it extracts an optimal trajectory by solving a dynamical system, then it pre-extracts a network, and finally, it filters out potential redundancies. Remarkably, we propose a principled model to address the filtering in the last step, and give a quantitative interpretation in terms of a transport-related cost function. This principled filtering can be applied to more general problems such as network extraction from images, thus going beyond the scenarios envisioned in the first step. Overall, this novel algorithm allows practitioners to easily extract optimal network topologies by combining basic tools from numerical methods, optimization and network theory. Thus, we provide an alternative to manual graph extraction which allows a grounded extraction from a large variety of optimal topologies. The analysis of these may open up the possibility to gain new insights into the structure and function of optimal networks. We provide an open source implementation of the code online. [ABSTRACT FROM AUTHOR]

Machine learning and data analytics are being increasingly used for quantitative structure property relation (QSPR) applications in the chemical domain where the traditional Edisonian approach towards knowledge-discovery have not been fruitful. The perception of odorant stimuli is one such application as olfaction is the least understood among all the other senses. In this study, we employ machine learning based algorithms and data analytics to address the efficacy of using a data-driven approach to predict the perceptual attributes of an odorant namely the odorant characters (OC) of "sweet" and "musky". We first analyze a psychophysical dataset containing perceptual ratings of 55 subjects to reveal patterns in the ratings given by subjects. We then use the data to train several machine learning algorithms such as random forest, gradient boosting and support vector machine for prediction of the odor characters and report the structural features correlating well with the odor characters based on the optimal model. Furthermore, we analyze the impact of the data quality on the performance of the models by comparing the semantic descriptors generally associated with a given odorant to its perception by majority of the subjects. The study presents a methodology for developing models for odor perception and provides insights on the perception of odorants by untrained human subjects and the effect of the inherent bias in the perception data on the model performance. The models and methodology developed here could be used for predicting odor characters of new odorants. [ABSTRACT FROM AUTHOR]

We scrutinize the length dependency of the binding affinity of bacterial repressor TrpR protein to trpO (specific site) on DNA. A footprinting experiment shows that the longer the DNA length, the larger the affinity of TrpR to the specific site on DNA. This effect termed "antenna effect" might be interpreted as follows: longer DNA provides higher probability for TrpR to access to the specific site aided by one-dimensional diffusion along the nonspecific sites of DNA. We show that, however, the antenna effect cannot be explained while detailed balance holds among three kinetic states, that is, free protein/DNA, nonspecific complexes, and specific complex. We propose a working hypothesis that slow degree(s) of freedom in the system switch(es) different potentials of mean force causing transitions among the three states. This results in a deviation from detailed balance on the switching timescale. We then derive a simple reaction diffusion/binding model that describes the antenna effect on TrpR binding to its target operator. Possible scenarios for such slow degree(s) of freedom in TrpR–DNA complex are addressed. [ABSTRACT FROM AUTHOR]

Obesity is accompanied by dysfunction of many organs, but effects on the skin have received little attention. We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin of 10 obese (BMI 35–50) and 10 normal weight (BMI 18.5–26.9) postmenopausal women paired by age and ethnicity. Epidermal thickness did not differ with obesity but the expression of genes encoding proteins associated with skin blood supply and wound healing were altered. In the obese, many gene expression pathways were broadly downregulated and subdermal fat showed pronounced inflammation. There were no changes in skin microbiota or metabolites. African American subjects differed from European Americans with a trend to increased epidermal thickening. In obese African Americans, compared to obese European Americans, we observed altered gene expression that may explain known differences in water content and stress response. African Americans showed markedly lower expression of the gene encoding the cystic fibrosis transmembrane regulator characteristic of the disease cystic fibrosis. The results from this preliminary study may explain the functional changes found in the skin of obese subjects and African Americans. [ABSTRACT FROM AUTHOR]

Hair cells of the auditory and vestibular systems are capable of detecting sounds that induce sub-nanometer vibrations of the hair bundle, below the stochastic noise levels of the surrounding fluid. Furthermore, the auditory system exhibits a highly rapid response time, in the sub-millisecond regime. We propose that chaotic dynamics enhance the sensitivity and temporal resolution of the hair bundle response, and we provide experimental and theoretical evidence for this effect. We use the Kolmogorov entropy to measure the degree of chaos in the system and the transfer entropy to quantify the amount of stimulus information captured by the detector. By varying the viscosity and ionic composition of the surrounding fluid, we are able to experimentally modulate the degree of chaos observed in the hair bundle dynamics in vitro. We consistently find that the hair bundle is most sensitive to a stimulus of small amplitude when it is poised in the weakly chaotic regime. Further, we show that the response time to a force step decreases with increasing levels of chaos. These results agree well with our numerical simulations of a chaotic Hopf oscillator and suggest that chaos may be responsible for the high sensitivity and rapid temporal response of hair cells. [ABSTRACT FROM AUTHOR]

Activity cascades are found in many complex systems. In the cortex, they arise in the form of neuronal avalanches that capture ongoing and evoked neuronal activities at many spatial and temporal scales. The scale-invariant nature of avalanches suggests that the brain is in a critical state, yet predictions from critical theory on the temporal unfolding of avalanches have yet to be confirmed in vivo. Here we show in awake nonhuman primates that the temporal profile of avalanches follows a symmetrical, inverted parabola spanning up to hundreds of milliseconds. This parabola constrains how avalanches initiate locally, extend spatially and shrink as they evolve in time. Importantly, parabolas of different durations can be collapsed with a scaling exponent close to 2 supporting critical generational models of neuronal avalanches. Spontaneously emerging, transient γ–oscillations coexist with and modulate these avalanche parabolas thereby providing a temporal segmentation to inherently scale-invariant, critical dynamics. Our results identify avalanches and oscillations as dual principles in the temporal organization of brain activity. [ABSTRACT FROM AUTHOR]

The tumor immune microenvironment (TIME) consists of multiple cell types that contribute to the heterogeneity and complexity of prostate cancer (PCa). In this study, we sought to understand the gene-expression signature of patients with primary prostate tumors by investigating the co-expression profiles of patient samples and their corresponding clinical outcomes, in particular "disease-free months" and "disease reoccurrence". We tested the hypothesis that the CXCL13-CXCR5 axis is co-expressed with factors supporting TIME and PCa progression. Gene expression counts, with clinical attributes from PCa patients, were acquired from TCGA. Profiles of PCa patients were used to identify key drivers that influence or regulate CXCL13-CXCR5 signaling. Weighted gene co-expression network analysis (WGCNA) was applied to identify co-expression patterns among CXCL13-CXCR5, associated genes, and key genetic drivers within the CXCL13-CXCR5 signaling pathway. The processing of downloaded data files began with quality checks using NOISeq, followed by WGCNA. Our results confirmed the quality of the TCGA transcriptome data, identified 12 co-expression networks, and demonstrated that CXCL13, CXCR5 and associated genes are members of signaling networks (modules) associated with G protein coupled receptor (GPCR) responsiveness, invasion/migration, immune checkpoint, and innate immunity. We also identified top canonical pathways and upstream regulators associated with CXCL13-CXCR5 expression and function. [ABSTRACT FROM AUTHOR]

Glioblastoma multiforme alters healthy tissue vasculature by inducing angiogenesis and vascular remodeling. To fully comprehend the structural and functional properties of the resulting vascular network, it needs to be studied collectively by considering both geometric and topological properties. Utilizing Single Plane Illumination Microscopy (SPIM), the detailed capillary structure in entire healthy and tumor-bearing mouse brains could be resolved in three dimensions. At the scale of the smallest capillaries, the entire vascular systems of bulk U87- and GL261-glioblastoma xenografts, their respective cores, and healthy brain hemispheres were modeled as complex networks and quantified with fundamental topological measures. All individual vessel segments were further quantified geometrically and modular clusters were uncovered and characterized as meta-networks, facilitating an analysis of large-scale connectivity. An inclusive comparison of large tissue sections revealed that geometric properties of individual vessels were altered in glioblastoma in a relatively subtle way, with high intra- and inter-tumor heterogeneity, compared to the impact on the vessel connectivity. A network topology analysis revealed a clear decomposition of large modular structures and hierarchical network organization, while preserving most fundamental topological classifications, in both tumor models with distinct growth patterns. These results augment our understanding of cerebrovascular networks and offer a topological assessment of glioma-induced vascular remodeling. The findings may help understand the emergence of hypoxia and necrosis, and prove valuable for therapeutic interventions such as radiation or antiangiogenic therapy. [ABSTRACT FROM AUTHOR]

Systemic inflammation and uremic toxins (UT) determine the increased cardiovascular mortality observed in chronic hemodialysis (HD) patients. Among UT, the adipokine Chemerin induces vascular dysfunction by targeting both endothelial and vascular smooth muscular cells (EC and VSMC). As Citrate anion modulates oxidative metabolism, systemic inflammation and vascular function, we evaluated whether citrate-buffered dialysis improves HD efficiency, inflammatory parameters and chemerin-mediated microvascular injury. 45 patients were treated in sequence with acetate, citrate and, again, acetate-buffered dialysis solution (3 months per interval). At study admission and after each treatment switch, we evaluated dialysis efficacy and circulating levels of chemerin and different inflammatory biomarkers. In vitro, we stimulated EC and VSMC with patients' plasma and we investigated the role of chemerin as UT. Citrate dialysis increased HD efficacy and reduced plasma levels of CRP, fibrinogen, IL6 and chemerin. In vitro, patients' plasma induced EC and VSMC dysfunction. These effects were reduced by citrate-buffered solutions and paralleled by the decrease of chemerin levels. Consistently, chemerin receptor knockdown reduced EC and VSMC dysfunction. In conclusion, Switching from acetate to citrate improved dialysis efficacy and inflammatory parameters; in vitro, chemerin-induced EC and VSMC injury were decreased by using citrate as dialysis buffer. [ABSTRACT FROM AUTHOR]

We live in a cluttered visual world that is overflowing with information, the continuous processing of which would be a truly daunting task. Nevertheless, our brains have evolved to select which part of a visual scene is to be prioritized and analysed in detail, and which parts can be discarded or analysed at a later stage. This selection is in part determined by the visual stimuli themselves, and is known as "selective attention", which, in turn, determines how we explore and interact with our environment, including the distinct human artefacts produced in different socio-cultural contexts. Here we hypothesize that visual responses and material objects should therefore co-evolve to reflect changes in social complexity and culture throughout history. Using eye-tracking, we analysed the eye scan paths in response to prehistoric pottery ranging from the Neolithic through to the Iron Age (ca 6000-2000 BP), finding that each ceramic style caused a particular pattern of visual exploration. Horizontal movements become dominant in earlier periods, while vertical movements are more frequent in later periods that were marked by greater social complexity. [ABSTRACT FROM AUTHOR]

Choosing food is not a trivial decision that people need to make daily, which is often subject to social influences. Here, we studied a human homolog of social transmission of food preference (STFP) as observed in rodents and other animals via chemosignals of body secretions. Human social chemosignals (sweat) produced during a disgust or neutral state among a group of donors were presented to participants undergoing a 2-alternative-forced-choice food healthiness judgment task during functional magnetic resonance imaging (fMRI). Response speed and two key signal detection indices—d’ (discrimination sensitivity) and β (response bias)—converged to indicate that social chemosignals of disgust facilitated food healthiness decisions, in contrast to primary disgust elicitors (disgust odors) that impaired the judgment. fMRI analyses (disgust vs. neutral sweat) revealed that the fusiform face area (FFA), amygdala, and orbitofrontal cortex (OFC) were engaged in processing social chemosignals of disgust during food judgment. Importantly, a double contrast of social signaling across modalities (olfactory vs. visual—facial expressions) indicated that the FFA and OFC exhibited preferential response to social chemosignals of disgust. Together, our findings provide initial evidence for human STFP, where social chemosignals are incorporated into food decisions by engaging social and emotional areas of the brain. [ABSTRACT FROM AUTHOR]

This research studies a lower down transition temperature composite polymer, modulated by multi microchannel fluidic flows to advance a thermally controllable material. Through modulating volumetric flow rates to manipulate fluid-material interface for heat transport within a microfluidic platform. Determining this optimization at any given flow rate will advance fluidics acting as a filter for invisible irradiation, near IR (NIR) range of the electromagnetic spectrum. In principle, filtering out this part of the solar irradiation spectrum can be achieved by selective fluidic absorption. By switchable control of conductance states to make the material switch on for high conductance or switch off for low conductance as a heat seeking targeting material. The challenges in material science is our ability to evaluate heat flow and monitor temperature with time. This research will determine the use of microfluidics based flows to direct the structural assembly of a polymer into a thermal switch. The research is inspired by nature’s vasculature leaf formations to modulate irradiance absorption by laminar fluidic flow. This bio-inspired engineering approach advances the structural assembly of polymers. By finely tuning flows to manipulate thermal gains in microchannel network architecture through flow rate switching to define composite function in differing conductance states. The research determines control of the thermodynamic state of a composite is directed by planar extensional flow in a microfluidic platform for high cooling surfaces. [ABSTRACT FROM AUTHOR]