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Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

Elucidating cell regulation remains a challenging task due to the complexity of metabolism and the difficulty of experimental measurements. Here we present a method for prediction of cell regulation to maximize cell growth rate while maintaining the solvent capacity of the cell. Prediction is formulated as an optimization problem using a thermodynamic framework that can leverage experimental data. We develop a formulation and variable initialization procedure that allows for computing solutions of the optimization with an interior point method. The approach is applied to photoheterotrophic growth of Rhodospirilium rubrum using ethanol as a carbon source, which has applications to biosynthesis of ethylene production. Growth is captured as the rate of synthesis of amino acids into proteins, and synthesis of nucleotide triphoshaptes into RNA and DNA. The method predicts regulation that produces a high rate of protein and RNA synthesis while DNA synthesis is reduced close to zero in agreement with production of DNA being turned off for much of the cell cycle.

Many potential immune therapeutic targets are similarly affected in adult-onset neurodegenerative diseases, such as Alzheimer’s (AD) disease, Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD), as well as in a seemingly distinct Niemann–Pick type C disease with primarily juvenile onset. This strongly argues for an overlap in pathogenic mechanisms. The commonly researched immune targets include various immune cell subsets, such as microglia, peripheral macrophages, and regulatory T cells (Tregs); the complement system; and other soluble factors. In this review, we compare these neurodegenerative diseases from a clinical point of view and highlight common pathways and mechanisms of protein aggregation, neurodegeneration, and/or neuroinflammation that could potentially lead to shared treatment strategies for overlapping immune dysfunctions in these diseases. These approaches include but are not limited to immunisation, complement cascade blockade, microbiome regulation, inhibition of signal transduction, Treg boosting, and stem cell transplantation.

Abstract Shaping single-mode operation in high-power fibers requires a precise knowledge of the gain-medium optical properties. This requires precise measurements of the refractive index differences (Δn) between the core and the cladding of the fiber. We exploit a quantum optical method based on low-coherence Hong-Ou-Mandel interferometry to perform practical measurements of the refractive index difference using broadband energy-time entangled photons. The precision enhancement reached with this method is benchmarked with a classical method based on single photon interferometry. We show in classical regime an improvement by an order of magnitude of the precision compared to already reported classical methods. Strikingly, in the quantum regime, we demonstrate an extra factor of 4 on the precision enhancement, exhibiting a state-of-the-art Δn precision of 6 × 10−7. This work sets the quantum photonics metrology as a powerful characterization tool that should enable a faster and reliable design of materials dedicated to light amplification.

Abstract Background Inflammatory bowel disease (IBD) is established to drive pathological sequelae in organ systems outside the intestine, including the central nervous system (CNS). Many patients exhibit cognitive deficits, particularly during disease flare. The connection between colonic inflammation and neuroinflammation remains unclear and characterization of the neuroinflammatory phenotype in the brain during colitis is ill-defined. Methods Transgenic mice expressing a bioluminescent reporter of active caspase-1 were treated with 2% dextran sodium sulfate (DSS) for 7 days to induce acute colitis, and colonic, systemic and neuroinflammation were assessed. In some experiments, mice were prophylactically treated with paquinimod (ABR-215757) to inhibit S100A9 inflammatory signaling. As a positive control for peripheral-induced neuroinflammation, mice were injected with lipopolysaccharide (LPS). Colonic, systemic and brain inflammatory cytokines and chemokines were measured by cytokine bead array (CBA) and Proteome profiler mouse cytokine array. Bioluminescence was quantified in the brain and caspase activation was confirmed by immunoblot. Immune cell infiltration into the CNS was measured by flow cytometry, while light sheet microscopy was used to monitor changes in resident microglia localization in intact brains during DSS or LPS-induced neuroinflammation. RNA sequencing was performed to identify transcriptomic changes occurring in the CNS of DSS-treated mice. Expression of inflammatory biomarkers were quantified in the brain and serum by qRT-PCR, ELISA and WB. Results DSS-treated mice exhibited clinical hallmarks of colitis, including weight loss, colonic shortening and inflammation in the colon. We also detected a significant increase in inflammatory cytokines in the serum and brain, as well as caspase and microglia activation in the brain of mice with ongoing colitis. RNA sequencing of brains isolated from DSS-treated mice revealed differential expression of genes involved in the regulation of inflammatory responses. This inflammatory phenotype was similar to the signature detected in LPS-treated mice, albeit less robust and transient, as inflammatory gene expression returned to baseline following cessation of DSS. Pharmacological inhibition of S100A9, one of the transcripts identified by RNA sequencing, attenuated colitis severity and systemic and neuroinflammation. Conclusions Our findings suggest that local inflammation in the colon drives systemic inflammation and neuroinflammation, and this can be ameliorated by inhibition of the S100 alarmin, S100A9.

Proteinopathy and neuroinflammation are two main hallmarks of neurodegenerative diseases. They also represent rare common events in an exceptionally broad landscape of genetic, environmental, neuropathologic, and clinical heterogeneity present in patients. Here, we aim to recount the emerging trends in amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD) spectrum disorder. Our review will predominantly focus on neuroinflammation and systemic immune imbalance in ALS and FTD, which have recently been highlighted as novel therapeutic targets. A common mechanism of most ALS and ~50% of FTD patients is dysregulation of TAR DNA-binding protein 43 (TDP-43), an RNA/DNA-binding protein, which becomes depleted from the nucleus and forms cytoplasmic aggregates in neurons and glia. This, in turn, via both gain and loss of function events, alters a variety of TDP-43-mediated cellular events. Experimental attempts to target TDP-43 aggregates or manipulate crosstalk in the context of inflammation will be discussed. Targeting inflammation, and the immune system in general, is of particular interest because of the high plasticity of immune cells compared to neurons.

Abstract Neuroendocrine tumors (NETs) of the small intestine undergo large chromosomal and methylation changes. The objective of this study was to identify methylation differences in NETs and consider how the differentially methylated genes may impact patient survival. Genome-wide methylation and chromosomal copy number variation (CNV) of NETs from the small intestine and appendix were measured. Tumors were divided into three molecular subtypes according to CNV results: chromosome 18 loss (18LOH), Multiple CNV, and No CNV. Comparison of 18LOH tumors with MultiCNV and NoCNV tumors identified 901 differentially methylated genes. Genes from the G-protein coupled receptor (GPCR) pathways are statistically overrepresented in the differentially methylated genes. One of the highlighted genes from the GPCR pathway is somatostatin (SST), a clinical target for NETs. Patient survival based on low versus high methylation in all samples identified four significant genes (p

Heart failure exacerbations impart significant morbidity and mortality, however, large- scale studies assessing outcomes in the setting of concurrent coronavirus disease-19 (COVID-19) are limited. We utilized National Inpatient Sample (NIS) database to compare clinical outcomes in patients admitted with acute congestive heart failure exacerbation (CHF) with and without COVID-19 infection. A total of 2,101,980 patients (Acute CHF without COVID-19 (n = 2,026,765 (96.4%) and acute CHF with COVID-19 (n = 75,215, 3.6%)) were identified. Multivariate logistic regression analysis was utilized to compared outcomes and were adjusted for age, sex, race, income level, insurance status, discharge quarter, Elixhauser co-morbidities, hospital location, teaching status and bed size. Patients with acute CHF and COVID-19 had higher in-hospital mortality compared to patients with acute CHF alone (25.78% vs. 5.47%, adjust OR (aOR) 6.3 (95% CI 6.05–6.62, p < 0.001)) and higher rates of vasopressor use (4.87% vs. 2.54%, aOR 2.06 (95% CI 1.86–2.27, p < 0.001), mechanical ventilation (31.26% vs. 17.14%, aOR 2.3 (95% CI 2.25–2.44, p < 0.001)), sudden cardiac arrest (5.73% vs. 2.88%, aOR 1.95 (95% CI 1.79–2.12, p < 0.001)), and acute kidney injury requiring hemodialysis (5.56% vs. 2.94%, aOR 1.92 (95% CI 1.77–2.09, p < 0.001)). Moreover, patients with heart failure with reduced ejection fraction had higher rates of in-hospital mortality (26.87% vs. 24.5%, adjusted OR 1.26 (95% CI 1.16–1.36, p < 0.001)) with increased incidence of vasopressor use, sudden cardiac arrest, and cardiogenic shock as compared to patients with heart failure with preserved ejection fraction. Furthermore, elderly patients and patients with African-American and Hispanic descents had higher in-hospital mortality. Acute CHF with COVID-19 is associated with higher in-hospital mortality, vasopressor use, mechanical ventilation, and end organ dysfunction such as kidney failure and cardiac arrest.

Neurological hazard assessment of industrial and pesticidal chemicals demands a substantial amount of time and resources. Caenorhabditis elegans is an established model organism in developmental biology and neuroscience. It presents an ideal test system with relatively fewer neurons (302 in hermaphrodites) versus higher-order species, a transparent body, short lifespan, making it easier to perform neurotoxic assessment in a time and cost-effective manner. Yet, no regulatory testing guidelines have been developed for C. elegans in the field of developmental and adult neurotoxicity. Here, we describe a set of morphological and behavioral assessment protocols to examine neurotoxicity in C. elegans with relevance to cholinergic and dopaminergic systems. We discuss the homology of human genes and associated proteins in these two signaling pathways and evaluate the morphological and behavioral endpoints of C. elegans in the context of published adverse outcome pathways of neurodegenerative diseases. We conclude that C. elegans neurotoxicity testing will not only be instrumental to eliminating mammalian testing in neurological hazard assessment but also lead to new knowledge and mechanistic validation in the adverse outcome pathway framework.

Venous thromboembolism, in particular, pulmonary embolism (PE), is a significant contributor to the morbidity and mortality associated with COVID-19. In this study, we utilized the National Inpatient Sample (NIS) database 2020 to evaluate and compare clinical outcomes in patients with COVID-19 with and without PE. Our sample includes 1,659,040 patients hospitalized with COVID-19 pneumonia between January 2020 and December 2020. We performed propensity-matched analysis for patient characteristics and in-hospital outcomes, including the patient’s age, race, sex, insurance status, median income, length of stay, mortality, hospitalization cost, comorbidities, mechanical ventilation, and vasopressor support. Patients with COVID-19 with PE had a higher need for mechanical ventilation (25.7% vs. 15.6%, adjusted odds ratio 1.4, 95% CI 1.4–1.5, p < 0.001), the vasopressor requirement (5.4% vs. 2.6%, adjusted OR 1.6, 95% CI 1.4–1.8, p < 0.001), longer hospital stays (10.8 vs. 7.9 days, p < 0.001), and overall higher in-hospital mortality (19.1 vs. 13.9%, adjusted OR of 1.3, 95% CI 1.1–1.5, p < 0.001). This study highlights the need for more aggressive management of PE in COVID-19-positive patients with the aim to improve early diagnosis and treatment to reduce morbidity, mortality, and healthcare costs seen in the synchronous COVID-19 and PE-positive patients.

Cyclic peptides are an attractive option as therapeutics due to their ability to disrupt crucial protein–protein interactions and their flexibility in display type screening strategies, but they come with their own bioanalytical challenges in metabolite identification. Initial amide hydrolysis of a cyclic peptide results in a ring opening event in which the sequence is linearized. Unfortunately, the mass of the singly hydrolyzed sequence is the same (M + 18.0106 Da) irrespective of the initial site of hydrolysis, or soft spot. Soft spot identification at this point typically requires time-consuming manual interpretation of the tandem mass spectra, resulting in a substantial bottleneck in the hit to lead process. To overcome this, derivatization using 2-pyridine carboxaldehyde, which shows high selectivity for the alpha amine on the N-terminus, was employed. This strategy results in moderate- to high-efficiency derivatization with a unique mass tag and diagnostic ions that serve to highlight the first amino acid in the newly linearized peptide. The derivatization method and analytical strategy are demonstrated on a whole cell lysate digest, and the soft spot identification strategy is shown with two commercially available cyclic peptides: JB1 and somatostatin. Effective utilization of the automated sample preparation and interpretation of the resulting spectra shown here will serve to reduce the hit-to-lead time for generating promising proteolytically stable peptide candidates.

Alcohol can potentiate disease in a mouse model of dextran sodium sulfate (DSS) colitis; however, the underlying mechanism remains to be established. In this study, we assessed whether the potentiated disease could be related to Enterobacteriaceae and Lactobacillus, as changes in their relative abundance can impact intestinal health. We also assessed whether the intestinal barrier is compromised after alcohol and DSS as it may increase bacterial translocation and liver inflammation. Mice were administered DSS followed by binge ethanol or water vehicle, generating four experimental groups: (Control+Vehicle, Control+Ethanol, DSS+Vehicle, DSS+Ethanol). DNA was isolated from colon and cecal contents followed by qPCR for levels of Enterobacteriaceae and Lactobacillus. Colon and liver sections were taken for histology. Intestinal epithelial cells were isolated from the colon for RNA expression. DSS+Ethanol cecal contents exhibited a 1 log increase in Enterobacteriaceae (p

This article describes a dataset of facial electromyography and subjective liking data from 70 New Zealand participants used in the study “An unfamiliar presence reduces facial disgust responses to food stimuli” by Nath, Cannon and Philipp [1]. Participants’ facial muscle activity from zygomaticus major, corrugator supercilii, and levator labii superioris was recorded as they viewed and rated food images, and tasted samples of chocolate. Half of the participants were seated alone, and the other half was seated in the presence of the researcher. The data allows for investigations into the effect of social context on hedonic ratings and facial responses to food, and an exploration into the individual factors contributing to differences in facial reactivity. The data includes raw EMG files generated by Acqknowledge 4.2, raw subjective liking files generated by PsychoPy, a table of participant information, the food images stimuli, the PsychoPy code used for stimuli presentation, and the R scripts used to filter, aggregate and analyse the data. Keywords: Facial electromyography, Food preference, Food liking, Social context, Implicit emotion

Extensive convergent evidence collectively suggests that mitochondrial dysfunction is central to the pathogenesis of Parkinson's disease (PD). Recently, changes in the dynamic properties of mitochondria have been increasingly implicated as a key proximate mechanism underlying neurodegeneration. However, studies have been limited by the lack of a model in which mitochondria can be imaged directly and dynamically in dopaminergic neurons of the intact vertebrate CNS. We generated transgenic zebrafish in which mitochondria of dopaminergic neurons are labeled with a fluorescent reporter, and optimized methods allowing direct intravital imaging of CNS dopaminergic axons and measurement of mitochondrial transport in vivo. The proportion of mitochondria undergoing axonal transport in dopaminergic neurons decreased overall during development between 2 days post-fertilization (dpf) and 5 dpf, at which point the major period of growth and synaptogenesis of the relevant axonal projections is complete. Exposure to 0.5–1.0 mM MPP+ between 4 and 5 dpf did not compromise zebrafish viability or cause detectable changes in the number or morphology of dopaminergic neurons, motor function or monoaminergic neurochemistry. However, 0.5 mM MPP+ caused a 300% increase in retrograde mitochondrial transport and a 30% decrease in anterograde transport. In contrast, exposure to higher concentrations of MPP+ caused an overall reduction in mitochondrial transport. This is the first time mitochondrial transport has been observed directly in CNS dopaminergic neurons of a living vertebrate and quantified in a PD model in vivo. Our findings are compatible with a model in which damage at presynaptic dopaminergic terminals causes an early compensatory increase in retrograde transport of compromised mitochondria for degradation in the cell body. These data are important because manipulation of early pathogenic mechanisms might be a valid therapeutic approach to PD. The novel transgenic lines and methods we developed will be useful for future studies on mitochondrial dynamics in health and disease.

The motor features of Parkinson's disease (PD) primarily result from a lesion to the nigrostriatal dopamine system. Numerous non-motor symptoms occur in PD, many of which are postulated to stem from pathology outside of the nigrostriatal dopamine system. Perturbations to protein trafficking, disruption of mitochondrial integrity, and impaired autophagy have repeatedly been implicated in dopaminergic neuron cell death. Previously, we demonstrated that multiple markers of autophagy are disrupted in a rotenone model of PD, with alterations occurring prior to an overt lesion to the nigrostriatal dopamine system. Whether these events occur in extra-nigral nuclei in PD and when relative to a lesion in the nigrostriatal dopamine system are generally unknown. The primary goal of these studies was to determine whether autophagy disruptions, in non-dopaminergic neuronal populations occur in an environmental model of PD utilizing a mitochondrial toxin. Here, we utilized the rat rotenone PD model, with sampling time-points before and after an overt lesion to the nigrostriatal dopamine system. In analyzing autophagy changes, we focused on optineurin (OPTN) and the autophagy marker, LC3. OPTN is an autophagy cargo adapter protein genetically linked to amyotrophic lateral sclerosis and glaucoma. In the present study, we observed OPTN enrichment in all PD-relevant brain regions examined. Further, alterations in OPTN and LC3 expression and colocalized puncta suggest specific impairments to autophagy that will inform future mechanistic studies. Thus, our data suggest that autophagy disruptions may be critical to PD pathogenesis in non-dopaminergic neurons and the onset of non-motor symptoms.

Repeated seizures are often associated with development of refractory chronic epilepsy, the most common form of which is temporal lobe epilepsy. G-protein-coupled cannabinoid receptors (CB1 and CB2 receptors) regulate neuronal excitability and have been shown to mediate acute anticonvulsant effects of cannabinoids in animal models. However, the potential of cannabinoids to prevent chronic neuronal damage and development of epilepsy remains unexplored. We hypothesized that treatment with a CB receptor agonist after an episode of status epilepticus – but before development of spontaneous recurrent seizures – might prevent the development of functional changes that lead to chronic epilepsy. Using the rat pilocarpine model, a therapeutic approach was simulated by administering the CB agonist, WIN 55,212-2 after an episode of status epilepticus. Epileptic behavior was monitored during development of spontaneous recurrent seizures for up to 6 months. Histology, neurochemistry, redox status and NMDA receptor subunit expression were assessed at 6 months after pilocarpine-induced seizures. Sub-acute treatment with WIN 55,212-2 (for 15 days starting 24 h after PILO injection) dramatically attenuated the severity, duration and frequency of spontaneous recurrent seizures. Further, in contrast to vehicle-treated animals, hippocampi from WIN 55,212-2-treated animals showed: normal thiol redox state, normal NR2A and NR2B subunit expression, preservation of GABAergic neurons and prevention of abnormal proliferation of GABAergic progenitors. This study shows for the first time that, after a known inciting event, treatment with a compound targeting CB receptors has the potential to prevent the epileptogenic events that result in chronic epileptic damage.

The rewarding sensation of touch in affiliative interactions is hypothesized to be underpinned by a specialized system of nerve fibers called C-Tactile afferents (CTs), which respond optimally to slowly moving, gentle touch, typical of a caress. However, empirical evidence to support the theory that CTs encode socially relevant, rewarding tactile information in humans is currently limited. While in healthy participants, touch applied at CT optimal velocities (1-10cm/sec) is reliably rated as subjectively pleasant, neuronopathy patients lacking large myelinated afferents, but with intact C-fibres, report that the conscious sensation elicited by stimulation of CTs is rather vague. Given this weak perceptual impact the value of self-report measures for assessing the specific affective value of CT activating touch appears limited. Therefore, we combined subjective ratings of touch pleasantness with implicit measures of affective state (facial electromyography) and autonomic arousal (heart rate) to determine whether CT activation carries a positive affective value. We recorded the activity of two key emotion-relevant facial muscle sites (zygomaticus major-smile muscle, positive affect & corrugator supercilii-frown muscle, negative affect) while participants evaluated the pleasantness of experimenter administered stroking touch, delivered using a soft brush, at two velocities (CT optimal 3cm/sec & CT non-optimal 30cm/sec), on two skin sites (CT innervated forearm & non-CT innervated palm). On both sites, 3cm/sec stroking touch was rated as more pleasant and produced greater heart rate deceleration than 30cm/sec stimulation. However, neither self-report ratings nor heart rate responses discriminated stimulation on the CT innervated arm from stroking of the non-CT innervated palm. In contrast, significantly greater activation of the zygomaticus major (smiling muscle) was seen specifically to CT optimal, 3cm/sec, stroking on the forearm in comparison to all other stimuli. These results offer the first empirical evidence in humans that tactile stimulation that optimally activates CTs carries a positive affective valence that can be measured implicitly.

Interactions between genetic factors and environmental exposures are thought to be major contributors to the etiology of Parkinson's disease. While such interactions are poorly defined and incompletely understood, recent epidemiological studies have identified specific interactions of potential importance to human PD. In this review, the most current data on gene–environment interactions in PD from human studies are critically discussed. Animal models have also highlighted the importance of genetic susceptibility to toxicant exposure and data of potential relevance to human PD are discussed. Goals and needs for the future of the field are proposed.

Gastrointestinal disorders, particularly severe constipation and delayed gastric emptying, are core symptoms of Parkinson's disease that affect most patients. However, the neuropathological substrate and physiological basis for this dysfunction are poorly defined. To begin to explore these phenomena in laboratory models of PD, rats were treated with either vehicle or rotenone (2.0 mg/kg, i.p.; 5 days/week) for 6-weeks. Myenteric plexus α-synuclein aggregate pathology and neuron loss were assessed 3-days and 6-months after the last rotenone injection. Gastrointestinal motility was assessed at 3-days, 1-month and 6-months after the last rotenone injection. Rotenone treatment caused an acute reduction in α-synuclein-immunoreactivity, but this was followed 6 months later by a robust increase in aggregate pathology and cytoplasmic inclusions that were similar in appearance to enteric Lewy-bodies in idiopathic PD. Rotenone-treated rats also had a moderate but permanent loss of small intestine myenteric neurons and an associated modest slowing of gastrointestinal motility 6-months after treatment. Our results suggest that a circumscribed exposure to an environmental toxicant can cause the delayed appearance of parkinsonian α-synuclein pathology in the enteric nervous system and an associated functional deficit in gastrointestinal motility. The rotenone model may therefore, provide a means to investigate pathogenic mechanisms and to test new therapeutic interventions into gastrointestinal dysfunction in PD.

The systemic rotenone model of Parkinson's disease (PD) accurately replicates many aspects of the pathology of human PD and has provided insights into the pathogenesis of PD. The major limitation of the rotenone model has been its variability, both in terms of the percentage of animals that develop a clear-cut nigrostriatal lesion and the extent of that lesion. The goal here was to develop an improved and highly reproducible rotenone model of PD. In these studies, male Lewis rats in three age groups (3, 7 or 12–14 months) were administered rotenone (2.75 or 3.0 mg/kg/day) in a specialized vehicle by daily intraperitoneal injection. All rotenone-treated animals developed bradykinesia, postural instability, and/or rigidity, which were reversed by apomorphine, consistent with a lesion of the nigrostriatal dopamine system. Animals were sacrificed when the PD phenotype became debilitating. Rotenone treatment caused a 45% loss of tyrosine hydroxylase-positive substantia nigra neurons and a commensurate loss of striatal dopamine. Additionally, in rotenone-treated animals, α-synuclein and poly-ubiquitin positive aggregates were observed in dopamine neurons of the substantia nigra. In summary, this version of the rotenone model is highly reproducible and may provide an excellent tool to test new neuroprotective strategies.

The authors study the problem $u_t=u_{xx}-au$, $00$; $u(x,0)=0$, and $-u_x(0,t)=u_x(1,t)=phi(t)$, where $a=a(x,t,u)$, and $phi(t)=1$ for $t_{2k} < t

Sepsis remains one of the leading causes of death in burn patients who survive the initial insult of injury. Disruption of the intestinal epithelial barrier has been shown after burn injury; this can lead to the translocation of bacteria or their products (e.g., endotoxin) from the intestinal lumen to the circulation, thereby increasing the risk for sepsis in immunocompromised individuals. Since the maintenance of the epithelial barrier is largely dependent on the intestinal microbiota, we examined the diversity of the intestinal microbiome of severely burned patients and a controlled mouse model of burn injury. We show that burn injury induces a dramatic dysbiosis of the intestinal microbiome of both humans and mice and allows for similar overgrowths of Gram-negative aerobic bacteria. Furthermore, we show that the bacteria increasing in abundance have the potential to translocate to extra-intestinal sites. This study provides an insight into how the diversity of the intestinal microbiome changes after burn injury and some of the consequences these gut bacteria can have in the host.

The modeling of the chemical reactions involved in metabolism is a daunting task. Ideally, the modeling of metabolism would use kinetic simulations, but these simulations require knowledge of the thousands of rate constants involved in the reactions. The measurement of rate constants is very labor intensive, and hence rate constants for most enzymatic reactions are not available. Consequently, flux-based approaches have been the methods of choice because they do not require the use of the rate constants of the law of mass action. However, this convenience also limits the predictive power of flux-based approaches in that the law of mass action is not used directly, making it very difficult to predict metabolite levels or energy requirements of pathways.An alternative to both of these approaches is to model metabolism using simulations of states rather than simulations of reactions, in which the state is defined as the set of all metabolite counts or concentrations. While kinetic simulations model reactions based on the likelihood of the reaction derived from the law of mass action, states are modeled based on likelihood ratios of mass action. Both approaches provide information on the energy requirements of metabolic reactions and pathways. However, modeling states rather than reactions has the advantage that the parameters needed to model states (chemical potentials) are much easier to determine than the parameters needed to model reactions (rate constants). Herein we discuss recent results, assumptions and issues in using simulations of state to model metabolism.

We construct and analyze a nonlocal global pandemic model that comprises a system of two nonlocal integrodifferential equations (functional differential equations) and an ordinary differential equation. This model was constructed by considering a spherical coordinate transformation of a previously established epidemiology model that can be applied to insect-borne diseases, like yellow fever. This transformation amounts to a nonlocal boundary value problem on the unit sphere and therefore can be interpreted as a global pandemic model for insect-borne diseases. We ultimately show that a weak solution to the weak formulation of this model exists using a fixed point argument, which calls upon the construction of a weak formulation and the existence and uniqueness of an auxiliary problem.

New methods are needed for large scale modeling of metabolism that predict metabolite levels and characterize the thermodynamics of individual reactions and pathways. Current approaches use either kinetic simulations, which are difficult to extend to large networks of reactions because of the need for rate constants, or flux-based methods, which have a large number of feasible solutions because they are unconstrained by the law of mass action. This report presents an alternative modeling approach based on statistical thermodynamics. The principles of this approach are demonstrated using a simple set of coupled reactions, and then the system is characterized with respect to the changes in energy, entropy, free energy, and entropy production. Finally, the physical and biochemical insights that this approach can provide for metabolism are demonstrated by application to the tricarboxylic acid (TCA) cycle of Escherichia coli. The reaction and pathway thermodynamics are evaluated and predictions are made regarding changes in concentration of TCA cycle intermediates due to 10- and 100-fold changes in the ratio of NAD+:NADH concentrations. Finally, the assumptions and caveats regarding the use of statistical thermodynamics to model non-equilibrium reactions are discussed.

Purpose: We reviewed all tumours of the sternum referred to The London Bone and Soft Tissue Tumour Service between 1956 and 1997 inclusive.

Chondrosarcoma is the second most common primary malignant bone tumour. Distinguishing between grades is not necessarily straightforward and may alter the disease management. We evaluated the correlation between histological grading of the preoperative image-guided needle biopsy and the resection specimen of 78 consecutive cases of chondrosarcoma of the femur, humerus, and tibia. In 11 instances, there was a discrepancy in histological grade between the biopsy and surgical specimen. Therefore, there was an 85.9% (67/78) accuracy rate for pre-operative histological grading of chondrosarcoma, based on needle biopsy. However, the accuracy of the diagnostic biopsy to distinguish low-grade from high-grade chondrosarcoma was 93.6% (73/78). We conclude that accurate image-guided biopsy is a very useful adjunct in determining histological grade of chondrosarcoma and the subsequent treatment plan. At present, a multidisciplinary approach, comprising experienced orthopaedic surgeons, radiologists, and pathologists, offers the most reliable means of accurately diagnosing and grading of chondrosarcoma of long bones.

Limited literature is available on the reconstruction of the distal radius using prosthetic replacement following resection of a bone tumour. We present the first reported case, in the English literature, of the use of an entirely metal endoprosthesis for the reconstruction of the distal radius. This case involves a 66-year-old male who was treated for giant cell tumour of the distal radius with surgical excision of the lesion and replacement of the defect using a predominantly titanium endoprosthesis. He was followed-up for 56 months following surgery and had a good functional outcome with no associated pain or complications. We propose that the use of a primarily titanium endoprosthesis for the reconstruction of a bone defect of the distal radius is a suitable alternative, providing good function of the forearm with satisfactory range of movement at the wrist and adequate pain relief.

Myolipoma is a rare, benign, lipomatous tumour which most commonly occurs in the retroperitoneum, pelvis, and abdomen. A 4-year-old boy presented with a painless enlarging mass in the left paraspinal region. Magnetic Resonance Imaging (MRI) revealed a soft tissue lesion with high fat content and areas of calcification. Excision and histopathological analysis revealed a tumour composed of lobules of mature adipose tissue and broad septa of well-differentiated smooth muscle tissue. The smooth muscle nature of the nonfatty component was demonstrated by a diffuse and strong immunoreactivity for smooth muscle actin and desmin. The mass was reported as a myolipoma. The patient made an unremarkable recovery from surgery and remains healthy with no signs of recurrence at seven years. This paper represents the youngest patient diagnosed with this rare soft tissue tumour which is normally confined to the adult population. A newly reported site of the tumour is also highlighted.

Purpose. We report a series of 58 patients with metastatic bone disease treated with resection and endoprosthetic reconstruction over a five-year period at our institution. Introduction. The recent advances in adjuvant and neoadjuvant therapy in cancer treatment have resulted in improved prognosis of patients with bone metastases. Most patients who have either an actual or impending pathological fracture should have operative stabilisation or reconstruction. Endoprosthetic reconstructions are indicated in patients with extensive bone loss, failed conventional reconstructions, and selected isolated metastases. Methods and Results. We identified all patients who were diagnosed with metastatic disease to bone between 1999 and 2003. One hundred and seventy-one patients were diagnosed with bone metastases. Metastatic breast and renal cancer accounted for 84 lesions (49%). Fifty-eight patients with isolated bone metastasis to the appendicular skeleton had an endoprosthetic reconstruction. There were 28 males and 30 females. Twelve patients had an endoprosthesis in the upper extremity and 46 patients had an endoprosthesis in the lower extremity. The mean age at presentation was 62 years (24 to 88). At the time of writing, 19 patients are still alive, 34 patients have died, and 5 have been lost to follow up. Patients were followed up and evaluated using the musculoskeletal society tumour score (MSTS) and the Toronto extremity salvage score (TESS). The mean MSTS was 73% (57% to 90%) and TESS was 71% (46% to 95%). Mean follow-up was 48.2 months (range 27 to 82 months) and patients died of disease at a mean of 22 months (2 to 51 months) from surgery. Complications included 5 superficial wound infections, 1 aseptic loosening, 4 dislocations, 1 subluxation, and 1 case, where the tibial component of a prosthesis rotated requiring open repositioning. Conclusions. We conclude that endoprosthetic replacement for the treatment of isolated bone metastases is a reliable method of limb reconstruction in selected cases. It is associated with low complication and failure rates in our series, and achieves the aims of restoring function, allowing early weight bearing and alleviating pain.

Burn severity is fundamental to post‐fire impact assessment and emergency response. Vegetation Burn Severity (VBS) can be derived from satellite observations. However, Soil Burn Severity (SBS) assessment—critical for mitigating hydrologic and geologic hazards—requires costly and laborious field recalibration of VBS maps. Here, we develop a physics‐informed Machine Learning model capable of accurately estimating SBS while revealing the intricate relationships between soil and vegetation burn severities. Our SBS classification model uses VBS, as well as climatological, meteorological, ecological, geological, and topographical wildfire covariates. This model demonstrated an overall accuracy of 89% for out‐of‐sample test data. The model exhibited scalability with additional data, and was able to extract universal functional relationships between vegetation and soil burn severities across the western US. VBS had the largest control on SBS, followed by weather (e.g., wind, fire danger, temperature), climate (e.g., annual precipitation), topography (e.g., elevation), and soil characteristics (e.g., soil organic carbon content). The relative control of processes on SBS changes across regions. Our model revealed nuanced relationships between VBS and SBS; for example, a similar VBS with lower wind speeds—that is, higher fire residence time—translates to a higher SBS. This transferrable model develops reliable and timely SBS maps using satellite and publicly accessible data, providing science‐based insights for managers and diverse stakeholders. Plain Language Summary: Post‐fire impact assessment and hazard mitigation heavily relies on burn severity metrics. Vegetation burn severity (VBS)—most relevant for ecological impacts—can be remotely sensed, but soil burn severity (SBS)—most relevant for hydrological impacts—requires laborious field recalibration of VBS maps. Lack of near real‐time SBS information is currently a data gap. Climate change‐driven weather whiplash can narrow the time interval between large wildfires and the ensuing precipitation events, requiring tools for rapid and accurate assessment of SBS without the need for laborious field recalibration of satellite‐derived metrics. Here we developed a physic‐informed Machine Learning model that can accurately develop SBS maps using readily available data without the need for resource and time intensive field assessments of burn severity. Additionally, SBS maps are developed for only a small fraction (less than 0.1%) of all wildfires in the US. Our model can develop SBS maps for all satellite‐observed wildfires in the western US, and has the potential to accomplish this task globally with further training. Finally, our model exhibited scalability with additional data, and was able to extract universal functional relationships between vegetation and soil burn severities across the western US. Key Points: Soil burn severity (SBS) assessment is key for hydrological hazard mitigationVegetation burn severity (VBS) can be remotely sensed, SBS is measured in the fieldPhysics‐informed Machine Learning models to translate VBS to SBS are developed [ABSTRACT FROM AUTHOR]

In a warming climate, an intensifying fire regime and higher likelihood of extreme rain are expected to increase watershed sediment yield in many regions. Understanding regional variability in landscape response to fire and post‐fire rainfall is essential for managing water resources and infrastructure. We measured sediment yield resulting from sequential wildfire and extreme rain and flooding in the upper Carmel River watershed (116 km2), on the central California coast, USA, using changes in sediment volume mapped in a reservoir. We determined that the sediment yield after fire and post‐fire flooding was 854–1,100 t/km2/yr, a factor of 3.5–4.6 greater than the long‐term yield from this watershed and more than an order of magnitude greater than during severe drought conditions. In this first large‐scale field validation test of the WEPPcloud/wepppy framework for the Water Erosion Prediction Project (WEPP) model on a burned landscape, WEPP predicted 81%–106% of the measured sediment yield. These findings will facilitate assessing and predicting future fire effects in steep watersheds with a Mediterranean climate and indicate that the increasingly widespread use of WEPP is appropriate for evaluating post‐fire hillslope erosion even across 100‐km2 scales under conditions without debris flows. Plain Language Summary: In a warming climate, more wildfire and more extreme rain will cause more erosion, producing more sediment that will be carried downstream by rivers. Understanding how much sediment a landscape produces after fire and extreme rain is essential for managing water resources and infrastructure, because sediment fills up storage space in reservoirs and can interfere with proper functioning of water systems and roads. We measured how much sediment was produced in a watershed due to wildfire followed by extreme rain and flooding, studying the Carmel River on the central California coast, USA. We evaluated how much sediment this watershed produced by measuring the volume of sediment deposited within a reservoir that the watershed drains into. We determined that the rate of sediment exported from the study watershed due to a large fire and post‐fire floods was much greater than the long‐term rate there. Having compared our results with the amount of sediment predicted by a model called the Water Erosion Prediction Project model, we found that the model performed well and realistically predicted the amount of sediment that this landscape would shed. These findings will facilitate assessing and predicting future fire effects in steep watersheds with a Mediterranean‐type climate. Key Points: A 116‐km2 central California watershed produced sediment yield of 854–1,100 t/km2/yr in the first year after a fire and extreme rainPost‐fire sediment yield in an extremely wet year without debris flows was 3.5–4.6 times greater than the long‐term rateThe Water Erosion Prediction Project model predicted 81%–106% of the measured post‐fire sediment eroded from hillslopes [ABSTRACT FROM AUTHOR]