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Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver condition in the United States, encompassing a wide spectrum of liver pathologies including steatosis, steatohepatitis, fibrosis, and cirrhosis. Despite its high prevalence, there are no medications currently approved by the Food and Drug Administration for the treatment of NAFLD. Recent work has suggested that NAFLD has a strong genetic component and identifying causative genes will improve our understanding of the molecular mechanisms contributing to NAFLD and yield targets for future therapeutic investigations. Oxidative stress is known to play an important role in NAFLD pathogenesis, yet the underlying mechanisms accounting for disturbances in redox status are not entirely understood. To better understand the relationship between the glutathione redox system and signs of NAFLD in a genetically-diverse population, we measured liver weight, serum biomarkers aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and graded liver pathology in a large cohort of Diversity Outbred mice. We compared hepatic endpoints to those of the glutathione redox system previously measured in the livers and kidneys of the same mice, and we screened for statistical and genetic associations using the R/qtl2 software. We discovered several novel genetic loci associated with markers of liver health, including loci that were associated with both liver steatosis and glutathione redox status. Candidate genes within each locus point to possible new mechanisms underlying the complex relationship between NAFLD and the glutathione redox system, which could have translational implications for future studies targeting NAFLD pathology.

Although the impact of the SARS-CoV-2 pandemic on major metropolitan areas is broadly reported and readily available, regions with lower populations and more remote areas in the United States are understudied. The objective of this study is to determine the progression of SARS-CoV-2 sequence variants in a frontier and remote intermountain west state among university-associated communities. This study was conducted at two intermountain west universities from 2020 to 2022. Positive SARS-CoV-2 samples were confirmed by quantitative real-time reverse transcription-polymerase chain reaction and variants were identified by the next-generation sequencing of viral genomes. Positive results were obtained for 5355 samples, representing a positivity rate of 3.5% overall. The median age was 22 years. Viral genomic sequence data were analyzed for 1717 samples and phylogeny was presented. Associations between viral variants, age, sex, and reported symptoms among 1522 samples indicated a significant association between age and the Delta variant (B 1.167.2), consistent with the findings for other regions. An outbreak event of AY122 was detected August–October 2021. A 2-month delay was observed with respect to the timing of the first documented viral infection within this region compared to major metropolitan regions of the US.

Background: Though governed by the same underlying biology, the differential physiology of children causes the temporal evolution from health to a septic/diseased state to follow trajectories that are distinct from adult cases. As pediatric sepsis data sets are less readily available than for adult sepsis, we aim to leverage this shared underlying biology by normalizing pediatric physiological data such that it would be directly comparable to adult data, and then develop machine-learning (ML) based classifiers to predict the onset of sepsis in the pediatric population. We then externally validated the classifiers in an independent adult dataset. Methods: Vital signs and laboratory observables were obtained from the Pediatric Intensive Care (PIC) database. These data elements were normalized for age and placed on a continuous scale, termed the Continuous Age-Normalized SOFA (CAN-SOFA) score. The XGBoost algorithm was used to classify pediatric patients that are septic. We tested the trained model using adult data from the MIMIC-IV database. Results: On the pediatric population, the sepsis classifier has an accuracy of 0.84 and an F1-Score of 0.867. On the adult population, the sepsis classifier has an accuracy of 0.80 and an F1-score of 0.88; when tested on the adult population, the model showed similar performance degradation (“data drift”) as in the pediatric population. Conclusions: In this work, we demonstrate that, using a straightforward age-normalization method, EHR's can be generalizable compared (at least in the context of sepsis) between the pediatric and adult populations.

IntroductionB-cells are essential components of the immune system that neutralize infectious agents through the generation of antigen-specific antibodies and through the phagocytic functions of naïve and memory B-cells. However, the B-cell response can become compromised by a variety of conditions that alter the overall inflammatory milieu, be that due to substantial, acute insults as seen in sepsis, or due to those that produce low-level, smoldering background inflammation such as diabetes, obesity, or advanced age. This B-cell dysfunction, mediated by the inflammatory cytokines Interleukin-6 (IL-6) and Tumor Necrosis Factor-alpha (TNF-α), increases the susceptibility of late-stage sepsis patients to nosocomial infections and increases the incidence or severity of recurrent infections, such as SARS-CoV-2, in those with chronic conditions. We propose that modeling B-cell dynamics can aid the investigation of their responses to different levels and patterns of systemic inflammation.MethodsThe B-cell Immunity Agent-based Model (BCIABM) was developed by integrating knowledge regarding naïve B-cells, short-lived plasma cells, long-lived plasma cells, memory B-cells, and regulatory B-cells, along with their various differentiation pathways and cytokines/mediators. The BCIABM was calibrated to reflect physiologic behaviors in response to: 1) mild antigen stimuli expected to result in immune sensitization through the generation of effective immune memory, and 2) severe antigen challenges representing the acute substantial inflammation seen during sepsis, previously documented in studies on B-cell behavior in septic patients. Once calibrated, the BCIABM was used to simulate the B-cell response to repeat antigen stimuli during states of low, chronic background inflammation, implemented as low background levels of IL-6 and TNF-α often seen in patients with conditions such as diabetes, obesity, or advanced age. The levels of immune responsiveness were evaluated and validated by comparing to a Veteran's Administration (VA) patient cohort with COVID-19 infection known to have a higher incidence of such comorbidities.ResultsThe BCIABM was successfully able to reproduce the expected appropriate development of immune memory to mild antigen exposure, as well as the immunoparalysis seen in septic patients. Simulation experiments then revealed significantly decreased B-cell responsiveness as levels of background chronic inflammation increased, reproducing the different COVID-19 infection data seen in a VA population.ConclusionThe BCIABM proved useful in dynamically representing known mechanisms of B-cell function and reproduced immune memory responses across a range of different antigen exposures and inflammatory statuses. These results elucidate previous studies demonstrating a similar negative correlation between the B-cell response and background inflammation by positing an established and conserved mechanism that explains B-cell dysfunction across a wide range of phenotypic presentations.

Societal Impact Statement Climate resilient crops will become increasingly important, especially in regions where smallholder farmers are vulnerable to climate extremes. Enset, a multipurpose perennial staple crop consumed by over 20 million people in Ethiopia, purportedly provides food security during periods of drought. Here, we find evidence that frequent severe drought events led to an increase in enset production area. This is consistent with a broader pattern whereby farmers preferentially cultivate perennial and storable crops after long‐term drought events, providing an example of adaptation to fluctuations in climate through crop choice in indigenous agrisystems. Summary Smallholder farms in the semiarid and subhumid tropics are particularly vulnerable to increased climate variability. Indigenous agrisystems that have co‐evolved with climate variability may have developed resilience strategies. In the Southwest Ethiopian Highlands, agrisystems are dominated by the multipurpose perennial staple enset (Ensete ventricosum), characterised by flexible harvest timing, high yield, long storage, and putative drought tolerance, earning it the name ‘the tree against hunger’. We tested three hypotheses using crop production area and climate data. First, that enset production area is greatest in the most drought‐prone locations. Second, that farmers respond to drought events by increasing enset production area. And third, that drought encourages shifts in agrisystem composition more widely towards perennial or storable crops. We found that regions with a higher severe drought frequency are associated with significantly higher proportion of enset production. Similarly, the Standardised Precipitation Evapotranspiration Index of the previous 3 years is significantly negatively correlated with enset production area time series, suggesting that prior drier conditions led farmers to increase the land under enset production. Regarding other crops, storage crops roots and tubers were also preferentially selected after long‐term drought over annual crops, indicating their capacity for longer‐term resilience. Promoting the production of crops such as perennials, which have more extensive and established root systems, may be a strategy to ensure food security during drought or climate variability. These results indicate the potential of farmer's resilience strategies to improve food security in a changing climate.

BackgroundAchieving functional repair after peripheral nerve injury (PNI) remains problematic despite considerable advances in surgical technique. Therein, questions lie regarding the variable capacity of peripheral nerves to regenerate based on environmental influence. In-depth analyses of multiple therapeutic strategies have ensued to overcome these natural obstacles. Of these candidate therapies, electrical stimulation has emerged a frontrunner. Extensive animal studies have reported the ability of brief intraoperative electrical stimulation (BES) to enhance functional regeneration after PNI. Despite these reports, the exact mechanisms by which BES enhances regeneration and its effects on long nerve lesions are largely unknown. Indeed, clinical translation of this seemingly simple therapeutic has not been so simple, but a few studies performed in humans have yielded highly encouraging results.ObjectiveWe aimed to help bridge this translational gap by presenting the latest clinical trials on electrical stimulation for PNIs in combination with relevant etiologies, treatments and nonclinical findings.MethodsTo do so, a systematic search was performed on PubMed, IEEE, and Web of Science databases up to February 2020 using keywords significant to our study. References of each manuscript were screened for additional manuscripts of relevance to our study.ResultsWe found multiple BES clinical studies reporting enhanced functional recovery or increased nerve regeneration. Although improved outcomes were reported, high variability after BES is seen between and within species likely due to injury severity, location and timeline along with other factors.ConclusionFurther clinical studies and introduction of novel delivery platforms are vital to uncover the true regenerative potential of electrical stimulationtherapy.

A method for true random number generation by directly sampling a high frequency chaotic jerk circuit is explored. A method for determination of the maximum Lyapunov exponent, and thus the maximum bit rate for true random number generation, of the jerk system of interest is shown. The system is tested over a wide range of sampling parameters in order to simulate possible hardware configurations. The system is then implemented in high speed electronics on a small printed circuit board to verify its performance over the chosen parameters. The resulting circuit is well suited for random number generation due to its high dynamic complexity, long term aperiodicity, and extreme sensitivity to initial conditions. This system passes the Dieharder RNG test suite at 3.125 Mbps.

BackgroundAs trachoma is eliminated, skilled field graders become less adept at correctly identifying active disease (trachomatous inflammation—follicular [TF]). Deciding if trachoma has been eliminated from a district or if treatment strategies need to be continued or reinstated is of critical public health importance. Telemedicine solutions require both connectivity, which can be poor in the resource-limited regions of the world in which trachoma occurs, and accurate grading of the images. ObjectiveOur purpose was to develop and validate a cloud-based “virtual reading center” (VRC) model using crowdsourcing for image interpretation. MethodsThe Amazon Mechanical Turk (AMT) platform was used to recruit lay graders to interpret 2299 gradable images from a prior field trial of a smartphone-based camera system. Each image received 7 grades for US $0.05 per grade in this VRC. The resultant data set was divided into training and test sets to internally validate the VRC. In the training set, crowdsourcing scores were summed, and the optimal raw score cutoff was chosen to optimize kappa agreement and the resulting prevalence of TF. The best method was then applied to the test set, and the sensitivity, specificity, kappa, and TF prevalence were calculated. ResultsIn this trial, over 16,000 grades were rendered in just over 60 minutes for US $1098 including AMT fees. After choosing an AMT raw score cut point to optimize kappa near the World Health Organization (WHO)–endorsed level of 0.7 (with a simulated 40% prevalence TF), crowdsourcing was 95% sensitive and 87% specific for TF in the training set with a kappa of 0.797. All 196 crowdsourced-positive images received a skilled overread to mimic a tiered reading center and specificity improved to 99%, while sensitivity remained above 78%. Kappa for the entire sample improved from 0.162 to 0.685 with overreads, and the skilled grader burden was reduced by over 80%. This tiered VRC model was then applied to the test set and produced a sensitivity of 99% and a specificity of 76% with a kappa of 0.775 in the entire set. The prevalence estimated by the VRC was 2.70% (95% CI 1.84%-3.80%) compared to the ground truth prevalence of 2.87% (95% CI 1.98%-4.01%). ConclusionsA VRC model using crowdsourcing as a first pass with skilled grading of positive images was able to identify TF rapidly and accurately in a low prevalence setting. The findings from this study support further validation of a VRC and crowdsourcing for image grading and estimation of trachoma prevalence from field-acquired images, although further prospective field testing is required to determine if diagnostic characteristics are acceptable in real-world surveys with a low prevalence of the disease.

The ongoing SARS-Cov-2 pandemic had many drastic effects upon society beyond the illness and death it caused. Pandemic mitigation measures disrupted and altered behaviors related to social mobility, significantly increasing the time spent at home compared to the pre-pandemic period. Further, it was well documented that social anxiety and stress increased at a population level. Early in the pandemic there was speculation in the popular media that reporting of paranormal phenomena (e.g., UFOs, ghosts, etc.) increased due to factors associated with the pandemic. Past research on UFO/UAP reporting has theorized that increases are triggered by social factors, and so the pandemic provided a natural experiment to test these claims. To measure UFO reports we utilized two public databases of UFO reports for sightings in the United States, provided by the National UFO Reporting Center and the Mutual UFO Network. To estimate the impact of the pandemic we utilized two measures, one for social mobility and one for pandemic/disease severity. Google Community Mobility Reports provided a metric of social mobility for people who use Google Maps on their cellular telephone (i.e., amount of time spent at work compared to home), which we aggregated to a state level to estimate time spent at home. Second, we used new weekly SARS-CoV-2 cases and deaths, both absolute counts and per capita, which can be considered to be an indirect measure of anxiety and stress. We find that UFO reports did increase in 2020 compared to 2019 (p

BackgroundThough significant progress in disease elimination has been made over the past decades, trachoma is the leading infectious cause of blindness globally. Further efforts in trachoma elimination are paradoxically being limited by the relative rarity of the disease, which makes clinical training for monitoring surveys difficult. In this work, we evaluate the plausibility of an Artificial Intelligence model to augment or replace human image graders in the evaluation/diagnosis of trachomatous inflammation-follicular (TF).MethodsWe utilized a dataset consisting of 2300 images with a 5% positivity rate for TF. We developed classifiers by implementing two state-of-the-art Convolutional Neural Network architectures, ResNet101 and VGG16, and applying a suite of data augmentation/oversampling techniques to the positive images. We then augmented our data set with additional images from independent research groups and evaluated performance.ResultsModels performed well in minimizing the number of false negatives, given the constraint of the low numbers of images in which TF was present. The best performing models achieved a sensitivity of 95% and positive predictive value of 50-70% while reducing the number images requiring skilled grading by 66-75%. Basic oversampling and data augmentation techniques were most successful at improving model performance, while techniques that are grounded in clinical experience, such as highlighting follicles, were less successful.DiscussionThe developed models perform well and significantly reduce the burden on graders by minimizing the number of false negative identifications. Further improvements in model skill will benefit from data sets with more TF as well as a range in image quality and image capture techniques used. While these models approach/meet the community-accepted standard for skilled field graders (i.e., Cohen's Kappa >0.7), they are insufficient to be deployed independently/clinically at this time; rather, they can be utilized to significantly reduce the burden on skilled image graders.

ABSTRACT Individuals co-infected with HIV and Mycobacterium tuberculosis (Mtb) are more likely to develop severe tuberculosis (TB) disease than HIV-naive individuals. To understand how a chronic pre-existing Simian immunodeficiency virus (SIV) infection impairs the early immune response to Mtb, we used the Mauritian cynomolgus macaque (MCM) model of SIV/Mtb co-infection. We examined the relationship between peripheral viral control and Mtb burden, Mtb dissemination, and T cell function between SIV+ spontaneous controllers, SIV+ non-controllers, and SIV-naive MCM who were challenged with a barcoded Mtb Erdman strain 6 months post-SIV infection and necropsied 6 weeks post-Mtb infection. Mycobacterial burden was highest in the SIV+ non-controllers in all assessed tissues. In lung granulomas, the frequency of TNF-α-producing CD4+ T cells was reduced in all SIV+ MCM, but IFNγ-producing CD4+ T cells were only lower in the SIV+ non-controllers. Further, while all SIV+ MCM had more PD1+ and TIGIT+ T cells in the lung granulomas relative to SIV-naive MCM, SIV+ controllers exhibited the highest frequency of cells expressing these markers. To measure the effect of SIV infection on within-host bacterial dissemination, we sequenced the molecular barcodes of Mtb present in each tissue and characterized the Mtb population complexity. While Mtb population complexity was not associated with SIV infection group, lymph nodes had increased complexity when compared with lung granulomas across all groups. These results provide evidence that SIV+ animals, independent of viral control, exhibit a dysregulated T cell immune response and enhanced dissemination of Mtb, likely contributing to the poor TB disease course across all SIV/Mtb co-infected animals. IMPORTANCE HIV and TB remain significant global health issues, despite the availability of treatments. Individuals with HIV, including those who are virally suppressed, are at an increased risk to develop and succumb to severe TB disease when compared with HIV-naive individuals. Our study aims to understand the relationship between the extent of SIV replication, mycobacterial growth, and T cell function in the tissues of co-infected Mauritian cynomolgus macaques during the first 6 weeks of Mtb infection. Here we demonstrate that increased viral replication is associated with increased bacterial burden in the tissues and impaired T cell responses, and that the immunological damage attributed to virus infection is not fully eliminated when animals spontaneously control virus replication.

Chemotherapy has been used to inhibit cancer growth for decades, but emerging evidence shows it can affect the tumor stroma, unintentionally promoting cancer malignancy. After treatment of primary tumors, remaining drugs drain via lymphatics. Though all drugs interact with the lymphatics, we know little of their impact on them. Here, we show a previously unknown effect of platinums, a widely used class of chemotherapeutics, to directly induce systemic lymphangiogenesis and activation. These changes are dose-dependent, long-lasting, and occur in healthy and cancerous tissue in multiple mouse models of breast cancer. We found similar effects in human ovarian and breast cancer patients whose treatment regimens included platinums. Carboplatin treatment of healthy mice prior to mammary tumor inoculation increased cancer metastasis as compared to no pre-treatment. These platinum-induced phenomena could be blocked by VEGFR3 inhibition. These findings have implications for cancer patients receiving platinums and may support the inclusion of anti-VEGFR3 therapy into treatment regimens or differential design of treatment regimens to alter these potential effects.

Abdominal adhesions are a common cause of bowel obstruction, but knowledge regarding adhesion biology and anti-adhesion therapies remains limited. Here the authors report a systematic analysis of mouse and human adhesion tissues demonstrating that visceral fibroblast JUN and associated PDGFRA expression promote adhesions, and JUN suppression can prevent adhesion formation.

ABSTRACT Macrophages are a protective replicative niche for Mycobacterium tuberculosis (Mtb) but can kill the infecting bacterium when appropriately activated. To identify mechanisms of clearance, we compared levels of bacterial restriction by human macrophages after treatment with 26 compounds, including some currently in clinical trials for tuberculosis. All-trans-retinoic acid (ATRA), an active metabolite of vitamin A, drove the greatest increase in Mtb control. Bacterial clearance was transcriptionally and functionally associated with changes in macrophage cholesterol trafficking and lipid metabolism. To determine how these macrophage changes affected bacterial control, we performed the first Mtb CRISPR interference screen in an infection model, identifying Mtb genes specifically required to survive in ATRA-activated macrophages. These data showed that ATRA treatment starves Mtb of cholesterol and the downstream metabolite propionyl coenzyme A (propionyl-CoA). Supplementation with sources of propionyl-CoA, including cholesterol, abrogated the restrictive effect of ATRA. This work demonstrates that targeting the coupled metabolism of Mtb and the macrophage improves control of infection and that it is possible to genetically map the mode of bacterial death using CRISPR interference. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a leading cause of death due to infectious disease. Improving the immune response to tuberculosis holds promise for fighting the disease but is limited by our lack of knowledge as to how the immune system kills M. tuberculosis. Our research identifies a potent way to make relevant immune cells more effective at fighting M. tuberculosis and then uses paired human and bacterial genomic methods to determine the mechanism of that improved bacterial clearance.

Introduction: Disease states are being characterized at finer and finer levels of resolution via biomarker or gene expression profiles, while at the same time. Machine learning (ML) is increasingly used to analyze and potentially classify or predict the behavior of biological systems based on such characterization. As ML applications are extremely data-intensive, given the relative sparsity of biomedical data sets ML training of artificial neural networks (ANNs) often require the use of synthetic training data. Agent-based models (ABMs) that incorporate known biological mechanisms and their associated stochastic properties are a potential means of generating synthetic data. Herein we present an example of ML used to train an artificial neural network (ANN) as a surrogate system used to predict the time evolution of an ABM focusing on the clinical condition of sepsis.Methods: The disease trajectories for clinical sepsis, in terms of temporal cytokine and phenotypic dynamics, can be interpreted as a random dynamical system. The Innate Immune Response Agent-based Model (IIRABM) is a well-established model that utilizes known cellular and molecular rules to simulate disease trajectories corresponding to clinical sepsis. We have utilized two distinct neural network architectures, Long Short-Term Memory and Multi-Layer Perceptron, to take a time sequence of five measurements of eleven IIRABM simulated serum cytokine concentrations as input and to return both the future cytokine trajectories as well as an aggregate metric representing the patient’s state of health.Results: The ANNs predicted model trajectories with the expected amount of error, due to stochasticity in the simulation, and recognizing that the mapping from a specific cytokine profile to a state-of-health is not unique. The Multi-Layer Perceptron neural network, generated predictions with a more accurate forecasted trajectory cone.Discussion: This work serves as a proof-of-concept for the use of ANNs to predict disease progression in sepsis as represented by an ABM. The findings demonstrate that multicellular systems with intrinsic stochasticity can be approximated with an ANN, but that forecasting a specific trajectory of the system requires sequential updating of the system state to provide a rolling forecast horizon.

Zinc oxide is an environmentally friendly and readily synthesized semiconductor with many industrial applications. ZnO powders were prepared by alkali precipitation using different [Zn(acetate)2(amine)x] compounds to alter the particle size and aspect ratio. Slow precipitations from 95 °C solutions produced micron-scale particles with morphologies of hexagonal plates, rods, and needles, depending on the precursor used. Powders prepared at 65 °C with rapid precipitation yielded particles with minimal morphology differences, but particle size was dependent on the precursor used. The smallest particles were produced using precursors that yielded crystals with low aspect ratios during high-temperature synthesis. Particles produced during rapid synthesis had sizes ranging from 21–45 nm. The materials were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, thermogravimetric analysis, BET, and diffuse reflectance. The materials prepared using precursors with less-volatile amines were found to retain more organic material than ZnO produced using precursors with more volatile amines. The amount of organic material associated with the nanoparticles influenced the photocatalytic activity of the ZnO, with powders containing less organic material producing faster rate constants for the decolorizing of malachite green solutions under ultraviolet illumination, independent of particle size. [Zn(acetate)2(hydrazine)2] produced ZnO with the fastest rate constant and was recycled five times for dye degradation studies that revealed minimal to no reduction in catalytic efficiency.

Bacillus cereus, a ubiquitous environmental microorganism known to cause foodborne illness, was isolated from samples taken from imported baby wipes from two different countries. These strains were characterized using a comprehensive molecular approach involving endpoint PCR, whole genome sequencing (WGS), comparative genomics, and biochemical analyses. A multiplex endpoint PCR assay was used to identify the enterotoxins: hemolysin BL, nonhemolytic enterotoxin, cytotoxin K, and enterotoxin FM toxin genes. Phylogenetically, the strains clustered into two major groups according to sequence type (ST) and singleton. We used the Center for Food Safety and Applied Nutrition (CFSAN) GalaxyTrakr BTyper computational tool to characterize the strains further. As an additional means of characterization, we investigated the possible role of carbohydrate transport systems and their role in nutrient uptake by performing a BLAST analysis of the 40 B. cereus genomes recovered from baby wipes. This study outlines a multifaceted workflow that uses the analysis of enterotoxigenic potential, bioinformatics, genomic diversity, genotype, phenotype, and carbohydrate utilization as a comprehensive strategy to characterize these B. cereus strains isolated from baby wipes and further our understanding of the phylogenetic relatedness of strains associated with baby wipe production facilities that could potentially pose an infection risk to a vulnerable infant population.

Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.

Moyamoya is a rare, steno-occlusive cerebrovascular disorder that often presents as ischemic or hemorrhagic intracerebral events. This review provides an overview of various surgical revascularization techniques used in treating Moyamoya disease including direct, indirect, and combined revascularization, as well as the benefits, drawbacks, and indications of each technique. The future role of novel perioperative preventative methods in the treatment of Moyamoya disease is also discussed.

Cronobacter species are opportunistic pathogens capable of causing life-threatening infections in humans, with serious complications arising in neonates, infants, immuno-compromised individuals, and elderly adults. The genus is comprised of seven species: Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite a multiplicity of genomic data for the genus, little is known about likely transmission vectors. Using DNA microarray analysis, in parallel with whole genome sequencing, and targeted PCR analyses, the total gene content of two C. malonaticus, three C. turicensis, and 14 C. sakazaki isolated from various filth flies was assessed. Phylogenetic relatedness among these and other strains obtained during surveillance and outbreak investigations were comparatively assessed. Specifically, microarray analysis (MA) demonstrated its utility to cluster strains according to species-specific and sequence type (ST) phylogenetic relatedness, and that the fly strains clustered among strains obtained from clinical, food and environmental sources from United States, Europe, and Southeast Asia. This combinatorial approach was useful in data mining for virulence factor genes, and phage genes and gene clusters. In addition, results of plasmidotyping were in agreement with the species identity for each strain as determined by species-specific PCR assays, MA, and whole genome sequencing. Microarray and BLAST analyses of Cronobacter fly sequence datasets were corroborative and showed that the presence and absence of virulence factors followed species and ST evolutionary lines even though such genes were orthologous. Additionally, zebrafish infectivity studies showed that these pathotypes were as virulent to zebrafish embryos as other clinical strains. In summary, these findings support a striking phylogeny amongst fly, clinical, and surveillance strains isolated during 2010–2015, suggesting that flies are capable vectors for transmission of virulent Cronobacter spp.; they continue to circulate among United States and European populations, environments, and that this “pattern of circulation” has continued over decades.

Abstract Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazakii, which were obtained from dried spices from the USA, the Middle East, China, and the Republic of Korea. The average genome size of the C. sakazakii genomes was 4393 kb, with an average of 4055 protein coding genes, and an average genome G + C content of 56.9%. The genomes contained genes related to carbohydrate transport and metabolism, amino acid transport and metabolism, and cell wall/membrane biogenesis. In addition, we identified genes encoding proteins involved in osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as virulence-related and heat shock-related proteins. Interestingly, a metabolic island comprised of a variably-sized xylose utilization operon was found within the spice-associated C. sakazakii genomes, which supports the hypothesis that plants may serve as transmission vectors or alternative hosts for Cronobacter species. The presence of the genes identified in this study can support the remarkable phenotypic traits of C. sakazakii such as the organism’s capabilities of adaptation and survival in response to adverse growth environmental conditions (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses provided insights into many aspects of physiology and evolutionary history of this important foodborne pathogen.

Abstract Background Malonate utilization, an important differential trait, well recognized as being possessed by six of the seven Cronobacter species is thought to be largely absent in Cronobacter sakazakii (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other C. sakazakii strains. Results In this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 C. sakazakii strains tested could utilize malonate. Zebrafish embryo infection studies showed that C. sakazakii ST64 strains are as virulent as other Cronobacter species. Parallel whole genome sequencing (WGS) and MA showed that the strains phylogenetically grouped as a separate clade among the Csak species cluster. Additionally, these strains possessed the Csak O:2 serotype. The nine-gene, ~ 7.7 kbp malonate utilization operon was located in these strains between two conserved flanking genes, gyrB and katG. Plasmidotyping results showed that these strains possessed the virulence plasmid pESA3, but in contrast to the USA ST64 Csak strains, ST64 Csak strains isolated from sources in Europe and the Middle East, did not possess the type six secretion system effector vgrG gene. Conclusions Until this investigation, the presence of malonate-positive Csak strains, which are associated with foods and clinical cases, was under appreciated. If this trait was used solely to identify Cronobacter strains, many strains would likely be misidentified. Parallel WGS and MA were useful in characterizing the total genome content of these Csak O:2, ST64, malonate-positive strains and further provides an understanding of their phylogenetic relatedness among other virulent C. sakazakii strains.

Peripheral nerve injury results in loss of motor and sensory function distal to the nerve injury and is often permanent in nerve gaps longer than 5 cm. Autologous nerve grafts (nerve autografts) utilize patients' own nerve tissue from another part of their body to repair the defect and are the gold standard in care. However, there is a limited autologous tissue supply, size mismatch between donor nerve and injured nerve, and morbidity at the site of nerve donation. Decellularized cadaveric nerve tissue alleviates some of these limitations and has demonstrated success clinically. We previously developed an alternative apoptosis-assisted decellularization process for nerve tissue. This new process may result in an ideal scaffold for peripheral nerve regeneration by gently removing cells and antigens while preserving delicate topographical cues. In addition, the apoptosis-assisted process requires less active processing time and is inexpensive. This study examines the utility of apoptosis-decellularized peripheral nerve scaffolds compared to detergent-decellularized peripheral nerve scaffolds and isograft controls in a rat nerve gap model. Results indicate that, at 8 weeks post-injury, apoptosis-decellularized peripheral nerve scaffolds perform similarly to detergent-decellularized and isograft controls in both functional (muscle weight recovery, gait analysis) and histological measures (neurofilament staining, macrophage infiltration). These new apoptosis-decellularized scaffolds hold great promise to provide a less expensive scaffold for nerve injury repair, with the potential to improve nerve regeneration and functional outcomes compared to current detergent-decellularized scaffolds. [ABSTRACT FROM AUTHOR]

Abstract Background The perspectives of people who use drugs are critical in understanding why people choose to reduce harm in relation to drug use, what practices are considered or preferred in conceptualizations of harm reduction, and which environmental factors interfere with or support the use of harm reduction strategies. This study explores how people who inject drugs (PWID) think about harm reduction and considers the critical imperative of equity in health and social services delivery for this community. Methods This community-based participatory research study was conducted in a Canadian urban centre. Using a peer-based recruitment and interviewing strategy, semi-structured qualitative interviews were conducted by and with PWID. The Vidaview Life Story Board, an innovative tool where interviewers and participant co-construct a visual “life-scape” using a board, markers, and customized picture magnets, was used to facilitate the interviews. The topics explored included injection drug use and harm reduction histories, facilitators and barriers to using harm reduction strategies, and suggestions for improving services and supports. Results Twenty-three interviews with PWID (14 men and 9 women) were analysed, with a median age of 50. Results highlighted an expanded conceptualization of harm reduction from the perspectives of PWID, including motivations for adopting harm reduction strategies and a description of harm reduction practices that went beyond conventional health-focused concerns. The most common personal practices that PWID used included working toward moderation, employing various cognitive strategies, and engaging in community activities. The importance of social or peer support and improving self-efficacy was also evident. Further, there was a call for less rigid eligibility criteria and procedures in health and social services, and the need to more adequately address the stigmatization of drug users. Conclusions These findings demonstrated that PWID incorporate many personal harm reduction practices in their daily lives to improve their well-being, and these practices highlight the importance of agency, self-care, and community building. Health and social services are needed to better support these practices because the many socio-structural barriers this community faces often interfere with harm reduction efforts. Finally, “one size does not fit all” when it comes to harm reduction, and more personalized or de-medicalized conceptualizations are recommended.

[This corrects the article DOI: 10.1371/journal.ppat.1006939.].