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Abstract Background Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations. Results We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. Conclusions In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract

Background: Although the current combination of surgery, radiation, and chemotherapy is used in the breast-cancer setting, the administration of the anticancer drugs doxorubicin and trastuzumab is associated with an increased risk of developing heart failure. The aim of this study is to determine whether dietary flaxseed is comparable and/or synergistic with the angiotensin-converting enzyme inhibitor perindopril in the treatment of doxorubicin- and trastuzumab-mediated cardiotoxicity. Methods: In a chronic in vivo murine model (n = 110), doxorubicin and trastuzumab (8 mg/kg and 3 mg/kg, respectively) were administered weekly for 3 weeks. Following this period, the mice were randomized to daily consumption of a 10% flaxseed supplemented diet, administration of perindopril (3 mg/kg) via oral gavage, or a combination of both flaxseed and perindopril for an additional 3 weeks. Results: In mice treated with doxorubicin and trastuzumab, the left ventricular ejection fraction decreased from 74% ± 4% at baseline to 30% ± 2% at week 6. Treatment with either flaxseed or perindopril, or with flaxseed and perindopril improved left ventricular ejection fraction to 52% ± 4%, 54% ± 4%, and 55% ± 3%, respectively (P < 0.05). Although histologic analyses confirmed significant loss of sarcomere integrity and vacuolization in the doxorubicin- and trastuzumab-treated mice, treatment with flaxseed or perindopril, or with flaxseed and perindopril improved myocyte integrity. Finally, the level of Bcl-2 interacting protein 3, high-mobility group box 1 protein expression, and the levels of select oxylipins, were significantly elevated in mice receiving doxorubicin and trastuzumab; these markers were attenuated by treatment with either flaxseed or perindopril, or with flaxseed and perindopril. Conclusions: Flaxseed was equivalent to perindopril at improving cardiovascular remodelling by reducing biomarkers of inflammation, mitochondrial damage, and cell death. Résumé: Contexte: Si l’association actuelle de la chirurgie, de la radiothérapie et de la chimiothérapie est utilisée pour le traitement du cancer du sein, on observe néanmoins que l’administration de la doxorubicine et du trastuzumab, deux anticancéreux, augmente les risques d’insuffisance cardiaque. Cette étude vise à déterminer si les graines de lin alimentaires ont un effet comparable et/ou synergique à celui du périndopril, un inhibiteur de l’enzyme de conversion de l’angiotensine, dans le traitement de la cardiotoxicité liée à la doxorubicine et au trastuzumab. Méthodologie: Dans un modèle murin chronique in vivo (n = 110), la doxorubicine et le trastuzumab (8 mg/kg et 3 mg/kg, respectivement) ont été administrés une fois par semaine pendant trois semaines. Après cette période, les souris ont été réparties de façon aléatoire dans trois groupes : l’un recevant tous les jours un régime alimentaire contenant 10 % de graines de lin, un autre recevant du périndopril (3 mg/kg) par gavage oral et un troisième recevant à la fois des graines de lin et du périndopril pendant trois semaines supplémentaires. Résultats: Chez les souris recevant la doxorubicine et le trastuzumab, la fraction d’éjection ventriculaire gauche est passée de 74 % ± 4 % au départ à 30 % ± 2 % à la semaine 6. Avec le traitement par les graines de lin seules, le périndopril seul ou les graines de lin et le périndopril en association, la fraction d’éjection ventriculaire gauche est passée à 52 % ± 4 %, à 54 % ± 4 % et à 55 % ± 3 %, respectivement (p < 0,05). Bien que les analyses histologiques aient permis de confirmer une perte significative de l’intégrité des sarcomères et une vacuolisation chez les souris recevant la doxorubicine et le trastuzumab, le traitement par les graines de lin seules, le périndopril seul ou les graines de lin et le périndopril en association a amélioré l’intégrité des myocytes. Enfin, les taux de protéine 3 interagissant avec BCL-2, l’expression de la protéine HMGB1 (high-mobility group box 1) et les taux de certaines oxylipines étaient significativement élevés chez les souris recevant la doxorubicine et le trastuzumab. Ces marqueurs ont été atténués par les graines de lin, le périndopril ou l’association des deux. Conclusions: En diminuant les biomarqueurs de l’inflammation, les dommages aux mitochondries et la mort cellulaire, les graines de lin ont un effet équivalant à celui du périndopril quant à l’amélioration du remodelage cardiovasculaire.

AbstractObjective The onset of the COVID-19 pandemic engendered a host of different behavioral responses in key areas such as resource purchasing and compliance with COVID regulations. This study explores why participation in these behaviors may have varied by examining the role of perseverative cognition (i.e., worry, rumination).Method A representative sample of U.S. adults (N = 230, Mage = 45.4, 50% female) was recruited online early in the COVID-19 pandemic (June 2020), approximately three months into safety-related school and business shutdowns. Participants completed a series of questionnaires on COVID-19-related worry, non-specific rumination, and a range of behaviors observed during the early stages of the pandemic (e.g., excessive shopping, purchasing guns, following isolation guidelines). Exploratory principal axis factoring and reliability studies of the newly created COVID-19 worry and behavior scales were performed, followed by an examination of the associations between worrying, ruminating and COVID-19-related early behaviors.Results COVID-related worry and reflective rumination were positively associated with purchasing behavior (i.e., purchasing household items, items for security, and items for entertainment). COVID-related worry was also positively associated with compliance behavior (i.e., watching the news, following government directives strictly, and staying home but contacting family and friends remotely). Brooding rumination was not significantly associated with either type of behavior.Conclusions Perseverative cognition can help explain patterns in COVID-related behaviors, what motivated differences in these behaviors and, thereby, help explain how people coped during this trying time.

Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory network function. Here, we introduce a five-step computational pipeline, called iModulonMiner, to compile, process, curate, analyze, and characterize the totality of RNA-seq data for a given organism or cell type. This workflow is centered around the data-driven computation of co-regulated gene sets using Independent Component Analysis, called iModulons, which have been shown to have broad applications. As a demonstration, we applied this workflow to generate the iModulon structure of Bacillus subtilis using all high-quality, publicly-available RNA-seq data. Using this structure, we predicted regulatory interactions for multiple transcription factors, identified groups of co-expressed genes that are putatively regulated by undiscovered transcription factors, and predicted properties of a recently discovered single-subunit phage RNA polymerase. We also present a Python package, PyModulon, with functions to characterize, visualize, and explore computed iModulons. The pipeline, available at https://github.com/SBRG/iModulonMiner, can be readily applied to diverse organisms to gain a rapid understanding of their transcriptional regulatory network structure and condition-specific activity.

ABSTRACT Microorganisms with simplified genomes represent interesting cell chassis for systems and synthetic biology. However, genome reduction can lead to undesired traits, such as decreased growth rate and metabolic imbalances. To investigate the impact of genome reduction on Escherichia coli strain DGF-298, a strain in which ~ 36% of the genome has been removed, we reconstructed a strain-specific metabolic model (iAC1061), investigated the regulation of gene expression using iModulon-based transcriptome analysis, and performed adaptive laboratory evolution to let the strain correct potential imbalances that arose during its simplification. The model notably predicted that the removal of all three key pathways for glycolaldehyde disposal in this microorganism would lead to a metabolic bottleneck through folate starvation. Glycolaldehyde is also known to cause self-generation of reactive oxygen species, as evidenced by the increased expression of oxidative stress resistance genes in the SoxS iModulon. The reintroduction of the aldA gene, responsible for one native glycolaldehyde disposal route, alleviated the constitutive oxidative stress response. Our results suggest that systems-level approaches and adaptive laboratory evolution have additive benefits when trying to repair and optimize genome-engineered strains.IMPORTANCEGenomic streamlining can be employed in model organisms to reduce complexity and enhance strain predictability. One of the most striking examples is the bacterial strain Escherichia coli DGF-298, notable for having over one-third of its genome deleted. However, such extensive genome modifications raise the question of how similar this simplified cell remains when compared with its parent, and what are the possible unintended consequences of this simplification. In this study, we used metabolic modeling along with iModulon-based transcriptomic analysis in different growth conditions to assess the impact of genome reduction on metabolism and gene regulation. We observed little impact of genomic reduction on the regulatory network of E. coli DGF-298 and identified a potential metabolic bottleneck leading to the constitutive activity of the SoxS iModulon. We then leveraged the model's predictions to successfully restore SoxS activity to the basal level.

Background: Periprosthetic femur fractures (PPFFs) following total hip arthroplasty (THA) have increased in the past decade as the demand for primary surgery continues to grow. Although there is now more evidence to describe the treatment of Vancouver B fractures, there is still limited knowledge regarding factors that cause surgeons to perform either an open reduction and internal fixation (ORIF) or revision THA (rTHA). The purpose of this study was to determine what type of surgeons treat Vancouver B PPFFs at 11 major academic institutions and if there are trends in treatment decision-making regarding the use of ORIF or rTHA based on surgical training or patient factors. Methods: This multicenter retrospective study evaluated patients surgically treated for Vancouver B PPFF after THA between 2014 and 2019. Patients from 11 academic centers located in the United States were included in this study. Surgical outcomes and patient demographics were evaluated based on surgeon training, surgical treatment type, and institution. Results: Presence of Vancouver B2 (odds ratio [OR]: 0.02, P < .001) or B3 (OR: 0.04, P < .001) fractures were independent risk factors for treatment with rTHA. Treatment by a trauma (OR: 12.49, P < .001) or other-specified surgeon (OR: 13.63, P < .001) were independent risk factors for ORIF repair of Vancouver B fractures. There were no differences in outcomes based on surgeon subspecialty training. Conclusions: This study showed the trends in surgeons who surgically manage Vancouver B fractures at 11 major academic institutions and highlighted that regardless of surgical training or surgical treatment type, postoperative outcomes following management of PPFF were similar.

Abstract Human infections with the Japanese encephalitis virus (JEV) are a leading cause of viral encephalitis. An unprecedented outbreak of JEV genotype 4 was recently reported in Australia, with an isolate (JEVNSW/22) obtained from a stillborn piglet brain. Herein we conduct a thorough characterization of JEVNSW/22 in three different mouse strains and in human cortical brain organoids (hBOs), and determined the ability of JEVNSW/22 to be neutralized by sera from humans vaccinated with IMOJEV. JEVNSW/22 was less virulent than JEVFU (genotype 2) and JEVNakayama (genotype 3) in C57BL/6J mice and in interferon regulatory factor 7 deficient (Irf7 −/− ) mice, with infection of wild-type and knockout murine embryonic fibroblasts indicating JEVNSW/22 is more sensitive to type I interferon responses. Irf7 −/− mice provide a new model for JEVNSW/22, showing higher viremia levels compared to C57BL/6J mice, and allowing for lethal neuroinvasive infection. All JEV strains were universally lethal in Ifnar −/− mice by day 3, with histological signs of brain hemorrhage, but no other lesions. There were no indications of brain infection in Ifnar −/− mice, with viral protein detected in blood vessels, but not neurons. All JEV isolates showed robust cytopathic infection of human cortical brain organoids, albeit lower for JEVNSW/22. IMOJEV vaccination in humans induced antibodies capable of neutralizing JEVNSW/22, although, for all JEV strains, cross-neutralization titers declined with increasing divergence from IMOJEV in the envelope amino acid sequences. Overall, our study establishes JEVNSW/22 mouse and hBO models of infection, allowing for possible lethal neuroinvasive infection in mice that was rarer than for other JEV genotypes. JEV vaccination regimens may afford protection against this newly emerged JEV genotype 4 strain, although neutralizing antibody responses are sub-optimal.

Abstract Background Human genetic contribution to HIV progression remains inadequately explained. The type 1 interferon (IFN) pathway is important for host control of HIV and variation in type 1 IFN genes may contribute to disease progression. This study assessed the impact of variations at the gene and pathway level of type 1 IFN on HIV-1 viral load (VL). Methods Two cohorts of antiretroviral (ART) naïve participants living with HIV (PLWH) with either early (START) or advanced infection (FIRST) were analysed separately. Type 1 IFN genes (n = 17) and receptor subunits (IFNAR1, IFNAR2) were examined for both cumulated type 1 IFN pathway analysis and individual gene analysis. SKAT-O was applied to detect associations between the genotype and HIV-1 study entry viral load (log10 transformed) as a proxy for set point VL; P-values were corrected using Bonferroni (P G) was associated with study entry VL (p = 0.0020, beta = 0.32; G associated with higher study entry VL than A) in single SNP association analyses. The findings were not reproduced in FIRST participants. Conclusion Across 19 type 1 IFN genes, only IFNW1 was associated with HIV-1 study entry VL in a cohort of ART-naïve individuals in early stages of their infection, however, this was no longer significant in sensitivity analyses that controlled for population structures using LME.

Introduction The Road to Recovery (R2R) Initiative is an innovative model of substance use care that seeks to increase treatment capacity by creating approximately 100 new addiction treatment beds to provide on-demand addiction care in Vancouver, British Columbia, for patients with substance use disorders. The new model also coordinates the region’s existing clinical substance use services to support patients across a care continuum that includes traditional office-based addiction treatment and harm reduction services, early withdrawal management and more intensive abstinence-based treatment programming. To understand the impact of offering on-demand and coordinated substance use care, an observational cohort of individuals who access any R2R clinical service will be created to examine health and social outcomes over time.Methods and analysis This prospective mixed-methods study will invite individuals from Vancouver, Canada, who access substance use treatment through the R2R model of care to (1) complete a baseline and 12-month follow-up quantitative questionnaire that solicits sociodemographic, substance use and previous addiction treatment data and (2) provide consent to the use of participants’ personal identifiers to access health records for chart review and for annual linkage to select health and administrative databases to allow for ongoing (virtual) community follow-up over 5 years. Additionally, a purposive sample of cohort participants will be invited to participate in baseline and 12-month follow-up qualitative interviews to share their experiences accessing R2R and identify challenges and opportunities associated with the implementation of R2R.Ethics and dissemination The study was approved by the University of British Columbia Providence Health Care Research Ethics Board in September 2023. Results from the proposed study will be published in peer-reviewed journals, presented at national and international scientific conferences and disseminated through regular meetings with policymakers, individuals with lived and living experience, and other high-level stakeholders, academic presentations and lay media.

IntroductionThe severity of Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often dictated by a range of comorbidities. A considerable literature suggests iron deficiency and iron overload may contribute to increased infection, inflammation and disease severity, although direct causal relationships have been difficult to establish.MethodsHere we generate iron deficient and iron loaded C57BL/6 J mice by feeding standard low and high iron diets, with mice on a normal iron diet representing controls. All mice were infected with a primary SARS-CoV-2 omicron XBB isolate and lung inflammatory responses were analyzed by histology, immunohistochemistry and RNA-Seq.ResultsCompared with controls, iron deficient mice showed no significant changes in lung viral loads or histopathology, whereas, iron loaded mice showed slightly, but significantly, reduced lung viral loads and histopathology. Transcriptional changes were modest, but illustrated widespread dysregulation of inflammation signatures for both iron deficient vs. controls, and iron loaded vs. controls. Some of these changes could be associated with detrimental outcomes, whereas others would be viewed as beneficial.DiscussionDiet-associated iron deficiency or overload thus induced modest modulations of inflammatory signatures, but no significant histopathologically detectable disease exacerbations.

Summary: Background: Genetic variants in COL4A1 and COL4A2 (encoding collagen IV alpha chain 1/2) occur in genetic and sporadic forms of cerebral small vessel disease (CSVD), a leading cause of stroke, dementia and intracerebral haemorrhage (ICH). However, the molecular mechanisms of CSVD with ICH and COL4A1/COL4A2 variants remain obscure. Methods: Vascular function and molecular investigations in mice with a Col4a1 missense mutation and heterozygous Col4a2 knock-out mice were combined with analysis of human brain endothelial cells harboring COL4A1/COL4A2 mutations, and brain tissue of patients with sporadic CSVD with ICH. Findings: Col4a1 missense mutations cause early-onset CSVD independent of hypertension, with enhanced vasodilation of small arteries due to endothelial dysfunction, vascular wall thickening and reduced stiffness. Mechanistically, the early-onset dysregulated endothelium-dependent hyperpolarization (EDH) is due to reduced collagen IV levels with elevated activity and levels of endothelial Ca2+-sensitive K+ channels. This results in vasodilation via the Na/K pump in vascular smooth muscle cells. Our data support this endothelial dysfunction preceding development of CSVD-associated ICH is due to increased cytoplasmic Ca2+ levels in endothelial cells. Moreover, cerebral blood vessels of patients with sporadic CSVD show genotype-dependent mechanisms with wall thickening and lower collagen IV levels in those harboring common non-coding COL4A1/COL4A2 risk alleles. Interpretation: COL4A1/COL4A2 variants act in genetic and sporadic CSVD with ICH via dysregulated EDH, and altered vascular wall thickness and biomechanics due to lower collagen IV levels and/or mutant collagen IV secretion. These data highlight EDH and collagen IV levels as potential treatment targets. Funding: MRC, Wellcome Trust, BHF.

ABSTRACT Multidrug-resistant Staphylococcus aureus is one of the most clinically important pathogens in the world, with infections leading to high rates of morbidity and mortality in both humans and animals. The ability of S. aureus to form biofilms protects cells from antibiotics and promotes the transfer of antibiotic resistance genes; therefore, new strategies aimed at inhibiting biofilm growth are urgently needed. Probiotic species, including Bacillus subtilis, are gaining interest as potential therapies against S. aureus for their ability to reduce S. aureus colonization and virulence. Here, we search for strains and microbially derived compounds with strong antibiofilm activity against multidrug-resistant S. aureus by isolating and screening Bacillus strains from a variety of agricultural environments. From a total of 1,123 environmental isolates, we identify a single strain B. subtilis 6D1, with a potent ability to inhibit biofilm growth, disassemble mature biofilm, and improve antibiotic sensitivity of S. aureus biofilms through an Agr quorum sensing interference mechanism. Biochemical and molecular networking analysis of an active organic fraction revealed multiple surfactin isoforms, and an uncharacterized peptide was driving this antibiofilm activity. Compared with commercial high-performance liquid chromatography grade surfactin obtained from B. subtilis, we show these B. subtilis 6D1 peptides are significantly better at inhibiting biofilm formation in all four S. aureus Agr backgrounds and preventing S. aureus-induced cytotoxicity when applied to HT29 human intestinal cells. Our study illustrates the potential of exploring microbial strain diversity to discover novel antibiofilm agents that may help combat multidrug-resistant S. aureus infections and enhance antibiotic efficacy in clinical and veterinary settings.IMPORTANCEThe formation of biofilms by multidrug-resistant bacterial pathogens, such as Staphylococcus aureus, increases these microorganisms’ virulence and decreases the efficacy of common antibiotic regimens. Probiotics possess a variety of strain-specific strategies to reduce biofilm formation in competing organisms; however, the mechanisms and compounds responsible for these phenomena often go uncharacterized. In this study, we identified a mixture of small probiotic-derived peptides capable of Agr quorum sensing interference as one of the mechanisms driving antibiofilm activity against S. aureus. This collection of peptides also improved antibiotic killing and protected human gut epithelial cells from S. aureus-induced toxicity by stimulating an adaptive cytokine response. We conclude that purposeful strain screening and selection efforts can be used to identify unique probiotic strains that possess specially desired mechanisms of action. This information can be used to further improve our understanding of the ways in which probiotic and probiotic-derived compounds can be applied to prevent bacterial infections or improve bacterial sensitivity to antibiotics in clinical and agricultural settings.

Study objective: African Americans (AAs) show early signs of vascular dysfunction paired with elevated blood pressure (BP) and total peripheral resistance (TPR), which is thought to underlie their increased rates of cardiovascular health complications relative to European Americans (EAs). AAs paradoxically have higher cardiac vagal tone, indexed by heart rate variability (HRV), which is cardio-protective. This paradox has been termed the Cardiovascular Conundrum. The physiological mechanism underlying this phenomenon is not well understood. We examined race differences in baroreflex function, which might be an important mechanism underlying the Cardiovascular Conundrum. Design: Participants completed a 5-minute baseline period where resting cardiac metrics were assessed. Setting: Laboratory. Participants: 130 college-aged individuals (54 women, 57 AAs). Main outcome measures: Baroreflex function was indexed as baroreflex sensitivity (BRS; the magnitude of changes in cardiovascular activity in accordance with BP changes) and effectiveness (BEI; the ratio of BP changes that elicit changes in cardiovascular activity) in the cardiac, vascular, and myocardial limbs. Results and conclusions: Results showed AAs to have higher HRV and cardiac BRS in comparison to EAs, suggesting the baroreflex is more sensitive to correcting the heart period for changes in BP among AAs compared to EAs. However, AAs showed lower vascular BEI relative to EAs, suggesting less effective control of TPR. In sum, lower BEI in the vascular branch might be an important mechanism underlying the Cardiovascular Conundrum (i.e., higher HRV and BP) and by extension, health disparities in cardiovascular diseases between AAs and EAs.

Abstract Myeloid derived suppressor cells (MDSCs) are key regulators of immune responses and correlate with poor outcomes in hematologic malignancies. Here, we identify that MDSC mitochondrial fitness controls the efficacy of doxorubicin chemotherapy in a preclinical lymphoma model. Mechanistically, we show that triggering STAT3 signaling via β2-adrenergic receptor (β2-AR) activation leads to improved MDSC function through metabolic reprograming, marked by sustained mitochondrial respiration and higher ATP generation which reduces AMPK signaling, altering energy metabolism. Furthermore, induced STAT3 signaling in MDSCs enhances glutamine consumption via the TCA cycle. Metabolized glutamine generates itaconate which downregulates mitochondrial reactive oxygen species via regulation of Nrf2 and the oxidative stress response, enhancing MDSC survival. Using β2-AR blockade, we target the STAT3 pathway and ATP and itaconate metabolism, disrupting ATP generation by the electron transport chain and decreasing itaconate generation causing diminished MDSC mitochondrial fitness. This disruption increases the response to doxorubicin and could be tested clinically.

Understanding the mechanisms that drive HIV expression and latency is a key goal for achieving an HIV cure. Here we investigate the role of the SETD2 histone methyltransferase, which deposits H3K36 trimethylation (H3K36me3), in HIV infection. We show that prevention of H3K36me3 by a potent and selective inhibitor of SETD2 (EPZ-719) leads to reduced post-integration viral gene expression and accelerated emergence of latently infected cells. CRISPR/Cas9-mediated knockout of SETD2 in primary CD4 T cells confirmed the role of SETD2 in HIV expression. Transcriptomic profiling of EPZ-719-exposed HIV-infected cells identified numerous pathways impacted by EPZ-719. Notably, depletion of H3K36me3 prior to infection did not prevent HIV integration but resulted in a shift of integration sites from highly transcribed genes to quiescent chromatin regions and to polycomb repressed regions. We also observed that SETD2 inhibition did not apparently affect HIV RNA levels, indicating a post-transcriptional mechanism affecting HIV expression. Viral RNA splicing was modestly reduced in the presence of EPZ-719. Intriguingly, EPZ-719 exposure enhanced responsiveness of latent HIV to the HDAC inhibitor vorinostat, suggesting that H3K36me3 can contribute to a repressive chromatin state at the HIV locus. These results identify SETD2 and H3K36me3 as novel regulators of HIV integration, expression and latency.

Endometriosis presents a diagnostic conundrum due to its diverse clinical manifestations, ranging from asymptomatic to acute obstructive uropathy. This is a case of a 30-year-old woman with a history of endometriosis and rapidly progressing left flank pain culminating in rupture of the renal pelvis in her left kidney. Initial investigations revealed left-sided hydronephrosis without evidence of nephrolithiasis. Subsequent imaging showed active extravasation indicative of urinary obstruction attributable to endometriosis. Placement of a left nephrostomy tube alleviated her symptoms, and follow-up imaging revealed a distal ureteral stricture. A stent was subsequently placed, which resolved the obstruction and obviated the need for extensive surgical intervention. In this case, the patient's history of endometriosis prompted consideration of its role in urinary obstruction, despite the absence of typical symptoms, and underscores the importance of considering endometriosis as a potential cause of acute urinary obstruction, particularly in patients with a history of the disease. Physicians in the emergency department should maintain a high index of suspicion for endometriosis-related complications to facilitate timely intervention and prevent adverse outcomes. Awareness of the variable presentations of endometriosis is paramount for ensuring comprehensive patient care and optimal outcomes.

IntroductionGlobal microplastic (MP) pollution is now well recognized, with humans and animals consuming and inhaling MPs on a daily basis, with a growing body of concern surrounding the potential impacts on human health.MethodsUsing a mouse model of mild COVID-19, we describe herein the effects of azide-free 1 μm polystyrene MP beads, co-delivered into lungs with a SARS-CoV-2 omicron BA.5 inoculum. The effect of MPs on the host response to SARS-CoV-2 infection was analysed using histopathology and RNA-Seq at 2 and 6 days post-infection (dpi).ResultsAlthough infection reduced clearance of MPs from the lung, virus titres and viral RNA levels were not significantly affected by MPs, and overt MP-associated clinical or histopathological changes were not observed. However, RNA-Seq of infected lungs revealed that MP exposure suppressed innate immune responses at 2 dpi and increased pro-inflammatory signatures at 6 dpi. The cytokine profile at 6 dpi showed a significant correlation with the ‘cytokine release syndrome’ signature observed in some COVID-19 patients.DiscussionThe findings are consistent with the recent finding that MPs can inhibit phagocytosis of apoptotic cells via binding of Tim4. They also add to a growing body of literature suggesting that MPs can dysregulate inflammatory processes in specific disease settings.

A unique acoustic call type was identified and attributed to Bryde’s whales in the central North Pacific in 2015, but little is known about the distribution, calling behavior, or swimming behavior of Bryde’s whales in the region. Acoustic detections attributed to Bryde’s whales were used to localize and track individual whales on the U.S. Pacific Missile Range Facility (PMRF) in Kaua‘i, Hawai‘i. This study included 150 acoustically derived tracks from recordings spanning the years 2011–2022 with recording effort in nearly every month. Bryde’s whale movement was examined relative to calendar year, day of year, hour of day, wind speed, and acoustic calling rate. Hidden Markov models were used to identify two kinematic states (slower, less directional movement and faster, more directional movement). The findings indicate that Bryde’s whales were more likely to travel in a faster and more directional state during the daytime than at night and between May and August when compared to other times of year. The along-track acoustic cue rate was examined for 118 tracks, and the findings indicate a possible lengthening of the median inter-call interval over the duration of the study period. These results are an important first step in understanding more about behavior in Bryde’s whales, a relatively under-studied species.

Summary: Background: Although immunomodulators have established benefit against the new coronavirus disease (COVID-19) in general, it is uncertain whether such agents improve outcomes without increasing the risk of secondary infections in the specific subgroup of previously immunocompromised patients. We assessed the effect of immunomodulators on outcomes of immunocompromised patients hospitalized for COVID-19. Methods: The protocol was prospectively registered with PROSPERO (CRD42022335397). MEDLINE, Cochrane Central Register of Controlled Trials and references of relevant articles were searched up to 01-06-2022. Authors of potentially eligible randomized controlled trials were contacted to provide data on immunocompromised patients randomized to immunomodulators vs control (i.e., placebo or standard-of-care). Findings: Eleven randomized controlled trials involving 397 immunocompromised patients hospitalized for COVID-19 were included. Ten trials had low risk of bias. There was no difference between immunocompromised patients randomized to immunomodulators vs control regarding mortality [30/182 (16.5%) vs 41/215 (19.1%); RR 0.93, 95% CI 0.61–1.41; p = 0.74], secondary infections (RR 1.00, 95% CI 0.64–1.58; p = 0.99) and change in World Health Organization ordinal scale from baseline to day 15 (weighed mean difference 0.27, 95% CI -0.09–0.63; p = 0.15). In subgroup analyses including only patients with hematologic malignancy, only trials with low risk of bias, only trials administering IL-6 inhibitors, or only trials administering immunosuppressants, there was no difference between comparators regarding mortality. Interpretation: Immunomodulators, compared to control, were not associated with harmful or beneficial outcomes, including mortality, secondary infections, and change in ordinal scale, when administered to immunocompromised patients hospitalized for COVID-19. Funding: Hellenic Foundation for Research and Innovation.

ABSTRACTDisturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticcacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticcacaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95–7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity–disturbance relationships observed in microbial systems.IMPORTANCEA generalizable diversity–disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community’s response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.

Clinical grade magnetic bead implants have important applications in interfacing with the human body, providing contactless mechanical attachment or wireless communication through human tissue. We recently developed a new strategy, magnetomicrometry, that uses magnetic bead implants as passive communication devices to wirelessly sense muscle tissue lengths. We manufactured clinical-grade magnetic bead implants and verified their biocompatibility via intramuscular implantation, cytotoxicity, sensitization, and intracutaneous irritation testing. In this work, we test the pyrogenicity of the magnetic bead implants via a lagomorph model, and we test the biocompatibility of the magnetic bead implants via a full chemical characterization and toxicological risk assessment. Further, we test the cleaning, sterilization, and dry time of the devices that are used to deploy these magnetic bead implants. We find that the magnetic bead implants are non-pyrogenic and biocompatible, with the insertion device determined to be safe to clean, sterilize, and dry in a healthcare setting. These results provide confidence for the safe use of these magnetic bead implants in humans.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which can result in severe disease, often characterised by a 'cytokine storm' and the associated acute respiratory distress syndrome. However, many infections with SARS-CoV-2 are mild or asymptomatic throughout the course of infection. Although blood biomarkers of severe disease are well studied, less well understood are the inflammatory signatures in lung tissues associated with mild disease or silent infections, wherein infection and inflammation are rapidly resolved leading to sequelae-free recovery. Herein we described RNA-Seq and histological analyses of lungs over time in an omicron BA.1/K18-hACE2 mouse infection model, which displays these latter features. Although robust infection was evident at 2 days post infection (dpi), viral RNA was largely cleared by 10 dpi. Acute inflammatory signatures showed a slightly different pattern of cytokine signatures compared with severe infection models, and where much diminished 30 dpi and absent by 66 dpi. Cellular deconvolution identified significantly increased abundance scores for a number of anti-inflammatory pro-resolution cell types at 5/10 dpi. These included type II innate lymphoid cells, T regulatory cells, and interstitial macrophages. Genes whose expression trended downwards over 2-66 dpi included biomarkers of severe disease and were associated with 'cytokine storm' pathways. Genes whose expression trended upward during this period were associated with recovery of ciliated cells, AT2 to AT1 transition, reticular fibroblasts and innate lymphoid cells, indicating a return to homeostasis. Very few differentially expressed host genes were identified at 66 dpi, suggesting near complete recovery. The parallels between mild or subclinical infections in humans and those observed in this BA.1/K18-hACE2 mouse model are discussed with reference to the concept of "protective inflammation".

Motor vehicle accidents are the leading cause of death for young adults 18-29 years old worldwide, resulting in nearly 1 million years of life lost annually in the United States. Despite improvements in vehicle safety technologies, young women are at higher risk of dying in car crashes compared with men in matched scenarios. Vehicle crash testing primarily revolves around test dummies representative of the 50th percentile adult male, potentially resulting in these differences in fatality risk for female occupants compared to males. Vehicle occupants involved in fatal car crashes were matched using seating location, vehicle type, airbag deployment, seatbelt usage, and age. The relative risk for fatality (R) between males and females was calculated using a Double Pair Comparison. Young women (20s-40s) are at approximately 20% higher risk of dying in car crashes compared with men of the same age in matched scenarios. In passenger cars, 25-year-old female occupants in passenger car crashes from 1975-2020 exhibit R = 1.201 (95% CI 1.160-1.250) compared to 25-year-old males, and R-1.117 (95% CI 1.040-1.207) for passenger car crashes from 2010-2020. This trend persists across vehicle type, airbag deployment, seatbelt use, and number of vehicles involved in a crash. Known sex-based differences do not explain this large risk differential, suggesting a need for expanded test methodologies and research strategies to address as-yet unexplored sex differences in crash fatalities. These differences should be further investigated to ensure equitable crash protection.

The transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions between regulators and DNA sequences. Regulons are typically determined either from resource-intensive experimental measurement of functional binding sites, or inferred from analysis of high-throughput gene expression datasets. Recently, independent component analysis (ICA) of RNA-seq compendia has shown to be a powerful method for inferring bacterial regulons. However, it remains unclear to what extent regulons predicted by ICA structure have a biochemical basis in promoter sequences. Here, we address this question by developing machine learning models that predict inferred regulon structures in E. coli based on promoter sequence features. Models were constructed successfully (cross-validation AUROC > = 0.8) for 85% (40/47) of ICA-inferred E. coli regulons. We found that: 1) The presence of a high scoring regulator motif in the promoter region was sufficient to specify regulatory activity in 40% (19/47) of the regulons, 2) Additional features, such as DNA shape and extended motifs that can account for regulator multimeric binding, helped to specify regulon structure for the remaining 60% of regulons (28/47); 3) investigating regulons where initial machine learning models failed revealed new regulator-specific sequence features that improved model accuracy. Finally, we found that strong regulatory binding sequences underlie both the genes shared between ICA-inferred and experimental regulons as well as genes in the E. coli core pan-regulon of Fur. This work demonstrates that the structure of ICA-inferred regulons largely can be understood through the strength of regulator binding sites in promoter regions, reinforcing the utility of top-down inference for regulon discovery.

Case Presentation: We describe a case of a man who developed severe caustic injury of his upper gastrointestinal tract after ingestion of a commercially available 9.5% hydrochloric acidic cleaning solution. He rapidly deteriorated and required endotracheal intubation. He underwent several imaging modalities demonstrating his injuries and ultimately succumbed to his injuries. Discussion: Acidic caustic ingestions may range in severity and uncommonly result in death. Diagnosis is most often achieved by esophagogastroduodenoscopy, although computed tomography may increasingly play a role in defining the extent of injury. Esophagogastroduodenoscopy findings are often assigned a Zargar grade, which guides management. Medical management of acidic caustic ingestion may include bowel rest, steroids, antibiotics, and proton pump inhibitors depending on the extent of injury, although surgery may be required if esophageal perforation occurs.

Abstract Although major advancements have been made in the therapeutics for people with cystic fibrosis (PwCF), many still require the use of multiple medications to manage acute exacerbations of disease and maintain health. Iterative trial and error processes of pharmacotherapeutic management can be optimized by assessing and incorporating pharmacogenetics. For 82 PwCF, we reviewed 2 years of medication use and response history and interrogated metabolizer status for common pharmacogenes, revealing 3336 medication exposure events (MEEs) to 286 unique medications. As expected, the more frequent MEEs were those commonly used to treat cystic fibrosis (CF), such as antibiotics and respiratory medications. Antibiotics also comprised 56.7% of the undesirable drug responses. The impact of gene variants on drug responses was assessed using Pharmacogenomics Knowledgebase (PharmGKB) and Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. Thirty‐three (11.5%) medications have strong evidence of genetic influence on response as evidenced by gene‐based dosing guidelines. 110 (38.5%) unique medications had at least one association with a very important pharmacogene, whereas 143 (50%) were associated with at least one clinical or variant annotation. Over 97% of participants had at least one actionable genotype. Eleven (13.4%) patients with an actionable genotype, taking the impacted medication, had an undesirable drug response described in the CPIC guidelines that could potentially have been mitigated with a priori knowledge of the genotype. PwCF take many medications for disease management, with frequent dose changes to elicit a desired clinical effect. As CF care evolves, implementing pharmacogenetics testing can improve efficiency and safety of prescribing practices using precision selection and dosing at medication initiation.

Type 2 diabetes mellitus (T2DM) can be multifactorial where both genetics and environmental factors play a role. We aimed to investigate the use of polygenic risk scores (PRS) in the prediction of pre-transplant T2DM and post-transplant diabetes mellitus (PTDM) among solid organ transplant (SOT) patients. Using non-genetic risk scores alone; and the combination with PRS, separate logistic regression models were built and compared using receiver operator curves. Patients were assessed pre-transplant and in three post-transplant periods: 0–45, 46–365 and >365 days. A higher PRS was significantly associated with increased odds of pre-transplant T2DM. However, no improvement was observed for pre-transplant T2DM prediction when comparing PRS combined with non-genetic risk scores to using non-genetic risk scores alone. This was also true for predictions of PTDM in all three post-transplant periods. This study demonstrated that polygenic risk was only associated with the risk of T2DM among SOT recipients prior to transplant and not for PTDM. Combining PRS with a clinical model of non-genetic risk scores did not significantly improve the predictive ability, indicating its limited clinical utility in identifying patients at high risk for T2DM before transplantation, suggesting that non-genetic or different genetic factors may contribute to PTDM.

The reduced pathogenicity of the omicron BA.1 sub-lineage compared to earlier variants is well described, although whether such attenuation is retained for later variants like BA.5 and XBB remains controversial. We show that BA.5 and XBB isolates were significantly more pathogenic in K18-hACE2 mice than a BA.1 isolate, showing increased neurotropic potential, resulting in fulminant brain infection and mortality, similar to that seen for original ancestral isolates. BA.5 also infected human cortical brain organoids to a greater extent than the BA.1 and original ancestral isolates. In the brains of mice, neurons were the main target of infection, and in human organoids neuronal progenitor cells and immature neurons were infected. The results herein suggest that evolving omicron variants may have increasing neurotropic potential.

Background. Hepatitis C virus (HCV) nucleic acid amplification test (NAAT)–positive donors have increased the organ pool. Direct-acting antivirals (DAAs) have led to high rates of treatment success and sustained virologic response (SVR) in recipients with donor-derived HCV infection without significant adverse effects, although variability remains in the timing and duration of antivirals. Methods. This retrospective study analyzed all adult HCV-NAAT–negative transplant recipients who received an organ from HCV-NAAT–positive donors from November 24, 2018, to March 31, 2022, at Duke University Medical Center with protocolized delay of DAA initiation until after hospital discharge, with at least 180-d follow-up on all patients. Transplant and HCV-related outcomes were analyzed. Results. Two hundred eleven transplants (111 kidneys, 41 livers, 34 hearts, and 25 lungs) were performed from HCV-NAAT–positive donors to HCV-NAAT–negative recipients. Ninety percent of recipients became viremic within 7 d posttransplant. Ninety-nine percent of recipients were initiated on pangenotypic DAAs in the outpatient setting a median of 52 d posttransplant, most commonly with 12-wk courses of sofosbuvir–velpatasvir (lungs) and glecaprevir–pibrentasvir (heart, kidney, and liver). Ninety-seven percent of recipients had SVR after a first-line DAA; all ultimately achieved SVR at 12 wk after subsequent treatment courses. The median peak HCV RNA for all organ systems was 2 436 512 IU/mL; the median time from antiviral to undetectable RNA was 48 d, although differences were noted between organ groups. No patient deaths or graft losses were directly attributable to HCV infection. Conclusions. One hundred percent of transplant recipients of HCV-NAAT–positive organs ultimately developed SVR without significant adverse effects when HCV antivirals were initiated in the outpatient setting after transplant hospitalization, suggesting that this real-world treatment pathway is a viable option.

ABSTRACT The transcriptional regulatory network (TRN) of the phytopathogen Pseudomonas syringae pv. tomato DC3000 regulates its response to environmental stimuli, including interactions with hosts and neighboring bacteria. Despite the importance of transcriptional regulation during these agriculturally significant interactions, a comprehensive understanding of the TRN of P. syringae is yet to be achieved. Here, we collected and decomposed a compendium of public RNA-seq data from P. syringae to obtain 45 independently modulated gene sets (iModulons) that quantitatively describe the TRN and its activity state across diverse conditions. Through iModulon analysis, we (i) untangle the complex interspecies interactions between P. syringae and other terrestrial bacteria in cocultures, (ii) expand the current understanding of the Arabidopsis thaliana-P. syringae interaction, and (iii) elucidate the AlgU-dependent regulation of flagellar gene expression. The modularized TRN yields a unique understanding of interaction-specific transcriptional regulation in P. syringae. IMPORTANCE Pseudomonas syringae pv. tomato DC3000 is a model plant pathogen that infects tomatoes and Arabidopsis thaliana. The current understanding of global transcriptional regulation in the pathogen is limited. Here, we applied iModulon analysis to a compendium of RNA-seq data to unravel its transcriptional regulatory network. We characterize each co-regulated gene set, revealing the activity of major regulators across diverse conditions. We provide new insights on the transcriptional dynamics in interactions with the plant immune system and with other bacterial species, such as AlgU-dependent regulation of flagellar genes during plant infection and downregulation of siderophore production in the presence of a siderophore cheater. This study demonstrates the novel application of iModulons in studying temporal dynamics during host-pathogen and microbe-microbe interactions, and reveals specific insights of interest.

Defect engineering and doping of semiconductors by ion irradiation are essential in large-scale integration of electronic devices. Here, intense ion pulses from a laser-accelerator, with flux levels up to 1022 ions cm-2 s-1, are used to induce and optimize silicon color centers and photon emitters in the telecom band.

The Odonata are not typically regarded as informative taxa for stream bioassessment in North America compared to other insects, particularly when monitoring the ecological impacts of organic pollution. However, we hypothesized that stream-dwelling odonates are useful bioindicators of riparian conditions because vegetation associated with streams is used for oviposition and establishing breeding territories and is likely a cue for a suitable nymphal habitat. We sampled odonates from multiple microhabitats and all macroinvertebrates from riffle habitat in 12 Ozark Highlands (USA) spring streams along a gradient of riparian conditions. We also measured a standard suite of physical and chemical variables in each stream. We compared various aspects of the odonate and riffle macroinvertebrate assemblages among sites to evaluate sensitivity to variables associated with riparian structure compared to the other physical and chemical variables measured. The odonates were strongly associated with riparian-specific variables, while riffle macroinvertebrates were associated with riparian variables to a lesser degree. The additional environmental variables explained minimal variation in either assemblage. Overall, our results suggest that Odonata alone could be useful for biomonitoring associated with riparian structure around Ozark spring streams. The sensitivity of odonates to riparian conditions in other Nearctic regions should be further studied to identify regional and species-specific differences.

Abstract Water vapor's contribution to Earth's radiative forcing is most sensitive to changes in its lower stratosphere concentration. One recognized pathway for rapid increases in stratospheric water vapor is tropopause‐overshooting convection. Since this pathway has been rarely sampled, the NASA Dynamics and Chemistry of the Summer Stratosphere (DCOTSS) field project focused on obtaining in situ observations of stratospheric air recently affected by convection over the United States. This study reports on the extreme altitudes to which convective hydration was observed. The data show that the overworld stratosphere is routinely hydrated by convection and that past documented records of stratospheric heights of convective hydration were exceeded during several DCOTSS flights. The most extreme event sampled is highlighted, for which stratospheric water vapor was increased by up to 26% at an altitude of 19.25 km, a potential temperature of 463 K, and an ozone mixing ratio >1500 ppbv.

Literature reports the chemical constituent yields of electronic nicotine delivery systems (ENDS) aerosol collected using a range of aerosol collection strategies. The number of puffs to deplete an ENDS product varies widely, but collections often consist of data from the first 50–100 puffs. However, it is not clear whether these discrete puff blocks are representative of constituent yields over the life of a pod. We aimed to assess the effect of differing aerosol collection strategies on reported yields for select chemical constituents in the aerosol of closed pod-based ENDS products. Constituents analyzed were chosen to reflect important classes of compounds from the Final Premarket Tobacco Product Application Guidance. Yields were normalized to total device mass loss (DML). Collection strategies that consisted of partial pod collection were valid for determining yields of constituents whose DML normalized yields were consistent for the duration of pod life. These included primary aerosol constituents, such as propylene glycol, glycerol, and nicotine, and whole pod yields could be determined from initial puff blocks. However, changes were observed in the yields of some metals, some carbonyl compounds, and glycidol over pod life in a chemical constituent and product dependent manner. These results suggest that collection strategies consisting of initial puff block collections require validation per chemical constituent/product and are not appropriate for chemical constituents with variable yields over pod life. Whole pod collection increased sensitivity and accuracy in determining metal, carbonyl, and glycidol yields compared to puff block-based collection methodologies for all products tested.

An accelerated observer moving through empty space sees particles appearing and disappearing, while an observer with a constant velocity does not register any particles. This phenomenon, generally known as the Unruh effect, relies on an initial vacuum state, thereby unifying the experience of all inertial observers. We propose an experiment to probe this observer-dependent detector response, using a laser beam in circular motion as a local detector of superfluid helium-4 surface modes or third sound waves. To assess experimental feasibility, we develop a theoretical framework to include a non-zero temperature initial state. We find that an acceleration-dependent signal persists, independent of the initial temperature. By introducing a signal-to-noise measure we show that observing this signal is within experimental reach.

ABSTRACT Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. An underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt to each unique host environment. Consequently, an in-depth understanding of the comprehensive dynamics of the S. pyogenes TRN could inform new therapeutic strategies. Here, we compiled 116 existing high-quality RNA sequencing data sets of invasive S. pyogenes serotype M1 and estimated the TRN structure in a top-down fashion by performing independent component analysis (ICA). The algorithm computed 42 independently modulated sets of genes (iModulons). Four iModulons contained the nga-ifs-slo virulence-related operon, which allowed us to identify carbon sources that control its expression. In particular, dextrin utilization upregulated the nga-ifs-slo operon by activation of two-component regulatory system CovRS-related iModulons, altering bacterial hemolytic activity compared to glucose or maltose utilization. Finally, we show that the iModulon-based TRN structure can be used to simplify the interpretation of noisy bacterial transcriptome data at the infection site. IMPORTANCE S. pyogenes is a pre-eminent human bacterial pathogen that causes a wide variety of acute infections throughout the body of its host. Understanding the comprehensive dynamics of its TRN could inform new therapeutic strategies. Since at least 43 S. pyogenes transcriptional regulators are known, it is often difficult to interpret transcriptomic data from regulon annotations. This study shows the novel ICA-based framework to elucidate the underlying regulatory structure of S. pyogenes allows us to interpret the transcriptome profile using data-driven regulons (iModulons). Additionally, the observations of the iModulon architecture lead us to identify the multiple regulatory inputs governing the expression of a virulence-related operon. The iModulons identified in this study serve as a powerful guidepost to further our understanding of S. pyogenes TRN structure and dynamics.

ABSTRACT Moraxella catarrhalis is found almost exclusively within the human respiratory tract. This pathobiont is associated with ear infections and the development of respiratory illnesses, including allergies and asthma. Given the limited ecological distribution of M. catarrhalis, we hypothesized that we could leverage the nasal microbiomes of healthy children without M. catarrhalis to identify bacteria that may represent potential sources of therapeutics. Rothia was more abundant in the noses of healthy children compared to children with cold symptoms and M. catarrhalis. We cultured Rothia from nasal samples and determined that most isolates of Rothia dentocariosa and “Rothia similmucilaginosa” were able to fully inhibit the growth of M. catarrhalis in vitro, whereas isolates of Rothia aeria varied in their ability to inhibit M. catarrhalis. Using comparative genomics and proteomics, we identified a putative peptidoglycan hydrolase called secreted antigen A (SagA). This protein was present at higher relative abundance in the secreted proteomes of R. dentocariosa and R. similmucilaginosa than in those from non-inhibitory R. aeria, suggesting that it may be involved in M. catarrhalis inhibition. We produced SagA from R. similmucilaginosa in Escherichia coli and confirmed its ability to degrade M. catarrhalis peptidoglycan and inhibit its growth. We then demonstrated that R. aeria and R. similmucilaginosa reduced M. catarrhalis levels in an air-liquid interface culture model of the respiratory epithelium. Together, our results suggest that Rothia restricts M. catarrhalis colonization of the human respiratory tract in vivo. IMPORTANCE Moraxella catarrhalis is a pathobiont of the respiratory tract, responsible for ear infections in children and wheezing illnesses in children and adults with chronic respiratory diseases. Detection of M. catarrhalis during wheezing episodes in early life is associated with the development of persistent asthma. There are currently no effective vaccines for M. catarrhalis, and most clinical isolates are resistant to the commonly prescribed antibiotics amoxicillin and penicillin. Given the limited niche of M. catarrhalis, we hypothesized that other nasal bacteria have evolved mechanisms to compete against M. catarrhalis. We found that Rothia are associated with the nasal microbiomes of healthy children without Moraxella. Next, we demonstrated that Rothia inhibit M. catarrhalis in vitro and on airway cells. We identified an enzyme produced by Rothia called SagA that degrades M. catarrhalis peptidoglycan and inhibits its growth. We suggest that Rothia or SagA could be developed as highly specific therapeutics against M. catarrhalis.

Behavioral responses to sonar have been observed in a number of baleen whales, including minke whales (Balaenoptera acutorostrata). Previous studies used acoustic minke whale boing detections to localize and track individual whales on the U.S. Pacific Missile Range Facility (PMRF) in Kaua ‘i, Hawai‘i before, during, and after Navy training activities. These analyses showed significant changes in central North Pacific minke whale distribution and swimming behavior during Navy sonar events. For the purposes of contextualizing changes in animal movement relative to Navy sonar, we expanded on this research to examine the natural variation in minke whale movement when Navy sonar was not present. This study included 2,245 acoustically derived minke whale tracks spanning the years 2012–2017 over all months that minke whales were detected (October–May). Minke whale movement was examined relative to calling season, day of the year, hour of day, wind speed, calling state (nominal or rapid), and distance to the nearest calling conspecific. Hidden Markov models were used to identify two kinematic states (slower, less directional movement and faster, more directional movement). The findings indicate that minke whales were more likely to travel in a faster and more directional state when they were calling rapidly, when other vocalizing minke whales were nearby, during certain times of the day and calling seasons, and in windier conditions, but these changes in movement were less intense than the changes observed during exposure to Navy sonar, when swim speeds were the fastest. These results start to put behavioral responses to Navy sonar into an environmental context to understand the severity of responses relative to natural changes in behavior.

Abstract Background Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. Results We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. Conclusions We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.

Background: Two anti-cancer agents, doxorubicin (DOX) and trastuzumab (TRZ), are commonly used in the management of breast cancer in women. Despite their efficacy in reducing the morbidity and mortality of individuals with breast cancer, the use of these agents is limited by adverse cardiotoxic side effects. Both the nutraceutical agent flaxseed (FLX) and the pharmaceutical drug perindopril (PER) have been studied individually in the prevention of chemotherapy-mediated cardiac dysfunction. The objective of this study was to determine whether the prophylactic administration of FLX is comparable and/or synergistic with PER in preventing DOX + TRZ-induced cardiotoxicity. Methods: Over a six-week period, 81 wild-type C57Bl/6 female mice (8–12 weeks old) were randomized to receive regular chow (RC) or 10% FLX-supplemented diets with or without PER (3 mg/kg/week; oral gavage). Starting at week 4, mice were randomized to receive a weekly injection of saline or DOX (8 mg/kg) + TRZ (3 mg/kg). Serial echocardiography was conducted weekly and histological and biochemical analyses were performed at the end of the study. Results: In mice treated with RC + DOX + TRZ, left ventricular ejection (LVEF) decreased from 75 ± 2% at baseline to 37 ± 3% at week 6. However, prophylactic treatment with either FLX, PER, or FLX + PER partially preserved left ventricular systolic function with LVEF values of 61 ± 2%, 62 ± 2%, and 64 ± 2%, respectively. The administration of FLX, PER, or FLX + PER was also partially cardioprotective in preserving cardiomyocyte integrity and attenuating the expression of the inflammatory biomarker NF-κB due to DOX + TRZ administration. Conclusion: FLX was equivalent to PER at preventing DOX + TRZ-induced cardiotoxicity in a chronic in vivo murine model.

Deep learning has enabled advances in understanding biology. In this review, the authors outline advances, and limitations of deep learning in five broad areas and the future challenges for the biosciences.

Background: Reverse total shoulder arthroplasty (RTSA) is a procedure growing in prevalence among younger populations. Consequently, its use in revision arthroplasty is growing in this demographic. However, studies examining the functional outcomes of revision RTSA in younger populations compared with older populations are lacking. The primary purpose of this study is to evaluate the functional outcomes of revision RTSA in patients 65 years old and younger compared with older patients who underwent revision RTSA. We hypothesized that younger patients would have similar outcomes to older patients and both groups would demonstrate improvement in outcomes. Methods: A retrospective review was conducted on a prospectively collected research database at a single tertiary referral center of all patients who underwent RTSA between 2007 and 2018. Patients 65 years old or younger who underwent a revision RTSA and had minimum 2-year follow-up were evaluated. A control group of patients ≥70 years old who underwent revision RTSA were also evaluated. Demographics, surgical factors, active range of motion (ROM), and patient-reported outcomes (PROMs) were compared. The ROM parameters measured were forward elevation, abduction, external rotation, and level of internal rotation. The PROMs collected included American Shoulder and Elbow Surgeons score, Simple Shoulder Test score, University of California–Los Angeles score, Constant score, normalized Constant, and Shoulder Pain and Disability Index 130. The differences in outcomes were compared against the minimal clinically important difference and substantial clinical benefit reported for primary reverse shoulder arthroplasty. Results: A total of 81 patients undergoing revision RTSA were evaluated at a mean follow-up of 4.5 years with 42 patients in the study group and 39 patients in the control group. Both groups demonstrated similar demographics and rates of prior surgeries. Preoperative outcome scores were lower in the study group (≤65 years old) than those in the older control group with American Shoulder and Elbow Surgeons score, Simple Shoulder Test score, and Shoulder Pain and Disability Index 130 remaining worse postoperatively. Both groups experienced statistically significant improvements in ROM from before operation to after operation, with slightly higher improvements in overhead motion in the younger cohort. Both the study group and the control group demonstrated statistically significant improvements in all PROMs with improvement above the substantial clinical benefit for the Constant and Simple Shoulder Test scores. Despite lower functional outcomes reported in the study group postoperatively, the improvement from before operation to after operation in all PROMs was similar between groups. Conclusion: Revision RTSA is a viable option for patients ≤65 years old with a poorly functioning shoulder arthroplasty. ROM and outcome improvements are similar compared with older patients undergoing revision RTSA, but the preoperative and postoperative functional outcomes are worse in the younger patients.

Summary: Abundant donor cytotoxic T cells that attack normal host organs remain a major problem for patients receiving allogeneic hematopoietic cell transplantation (allo-HCT). Despite an increase in our knowledge of the pathobiology of acute graft versus host disease (aGvHD), the mechanisms regulating the proliferation and function of donor T cells remain unclear. Here, we show that activated donor T cells express galectin-3 (Gal-3) after allo-HCT. In both major and minor histocompatibility-mismatched models of murine aGvHD, expression of Gal-3 is associated with decreased T cell activation and suppression of the secretion of effector cytokines, including IFN-γ and GM-CSF. Mechanistically, Gal-3 results in activation of NFAT signaling, which can induce T cell exhaustion. Gal-3 overexpression in human T cells prevents severe disease by suppressing cytotoxic T cells in xenogeneic aGvHD models. Together, these data identify the Gal-3-dependent regulatory pathway in donor T cells as a critical component of inflammation in aGvHD.

Abstract This study provides a method for assessing the need for spay and neuter services in Massachusetts by creating a composite index that accounts for spatial accessibility and social vulnerability. An accessibility index (AI) of existing low-cost spay/neuter (S/N) facilities was created using the two-step floating catchment area (2SFCA) method which was then combined with the social vulnerability index (SVI) from the Centers for Disease Control and Prevention to create a need index (NI). Two methods for selecting the final target areas from the NI results were examined and used to make recommendations for S/N funding allocation. The construction of the NI (i.e. factors included or weights applied to factors) had a significant impact on the results. The NI displayed statistically significant spatial autocorrelation, and hot spot analysis revealed statistically significant clusters of comparatively high- and low-need regions in the state. The target areas identified were strongly influenced by high levels of social vulnerability in urban areas and low spatial accessibility of low-cost S/N facilities in more rural western Massachusetts. The results of this project demonstrate the utility of geographic information systems (GIS)-based analysis in veterinary and shelter medicine, as well as the potential for the use of non-veterinary specific data, such as the CDC SVI, when planning the equitable distribution of limited resources. One Health impact statement Providing spay and neuter (S/N) services to owned and free-roaming cats, dogs and other companion animal species is integral to the health and well-being of the animals themselves. Their human companions also reap the physical and mental health benefits of the human–animal bond, in addition to the environmental and public health impact of limiting free-roaming dog and cat populations. By recognizing the relationships between human and animal populations, existing gaps in need can be addressed through the use of human data to inform decisions on animal health when relevant animal health service data are lacking. A composite index of factors accounting for the social vulnerability was combined with the spatial accessibility of existing S/N resources to create a final index of need for S/N resources. This transdisciplinary approach takes methodologies from public health, acknowledges the impact of the vulnerability of human populations on surrounding companion animal populations, and applies a practical method of identifying the need for specific veterinary medical services.

Large-bodied temnospondyl amphibians were the dominant predators in non-marine aquatic ecosystems from the Carboniferous to the Middle Triassic. In the Permian-aged lower Beaufort Group of the main Karoo Basin, South Africa, temnospondyls are represented exclusively by the family Rhinesuchidae and are well represented by body fossils, whereas trace fossils are scarce. Accordingly, most interpretations of the behaviour of this family are based on skeletal morphology and histological data. Here we document the sedimentology and palaeontology of a late Permian palaeosurface situated immediately below the palaeoshoreline of the Ecca Sea (transition from the Ecca Group to the Beaufort Group) near the town of Estcourt in KwaZulu-Natal Province. The surface preserves numerous ichnofossils, including tetrapod footprints and fish swim-trails, but most striking are seven body impressions and associated swim trails that we attribute to a medium-sized (~1.9 m long) rhinesuchid temnospondyl. These provide valuable insight into the behaviour of these animals. The sinuous shape of some of the traces suggest that the tracemaker swam with continuous sub-undulatory propulsion of the tail.

Rhinovirus causes many types of respiratory illnesses, ranging from minor colds to exacerbations of asthma. Moraxella catarrhalis is an opportunistic pathogen that is increased in abundance during rhinovirus illnesses and asthma exacerbations and is associated with increased severity of illness through mechanisms that are ill-defined. We used a co-infection model of human airway epithelium differentiated at the air-liquid interface to test the hypothesis that rhinovirus infection promotes M. catarrhalis adhesion and survival on the respiratory epithelium. Initial experiments showed that infection with M. catarrhalis alone did not damage the epithelium or induce cytokine production, but increased trans-epithelial electrical resistance, indicative of increased barrier function. In a co-infection model, infection with the more virulent rhinovirus-A and rhinovirus-C, but not the less virulent rhinovirus-B types, increased cell-associated M. catarrhalis. Immunofluorescent staining demonstrated that M. catarrhalis adhered to rhinovirus-infected ciliated epithelial cells and infected cells being extruded from the epithelium. Rhinovirus induced pronounced changes in gene expression and secretion of inflammatory cytokines. In contrast, M. catarrhalis caused minimal effects and did not enhance RV-induced responses. Our results indicate that rhinovirus-A or C infection increases M. catarrhalis survival and cell association while M. catarrhalis infection alone does not cause cytopathology or epithelial inflammation. Our findings suggest that rhinovirus and M. catarrhalis co-infection could promote epithelial damage and more severe illness by amplifying leukocyte inflammatory responses at the epithelial surface.

Abstract Background Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. Methods We computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension. Results We found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. Conclusions OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.

While developments in cancer therapeutics have greatly reduced morbidity and mortality in females with breast cancer, it comes at a cost of an increased risk of cardiovascular complications. In particular, anthracyclines, like doxorubicin, which are a mainstay of current chemotherapy regimens, are associated with dose-dependent cardiotoxicity. Exercise has been widely accepted as an effective intervention in reducing cardiovascular risk in a variety of different clinical conditions. However, the benefits of exercise in anthracycline-mediated cardiotoxicity are not clearly understood. First, this review discusses the pre-clinical studies which have elucidated the cardioprotective mechanisms of aerobic and resistance exercise in improving cardiovascular function in the setting of anthracycline treatment. Next, it aims to summarize the results of aerobic and resistance exercise clinical trials conducted in females with breast cancer who received anthracycline-based chemotherapy. The review further discusses the current exercise guidelines for women undergoing chemotherapy and contraindications for exercise. Finally, the review addresses gaps in research, specifically the need for further clinical trials to establish a recommended exercise prescription within this patient population.

IntroductionAn adult wild-type C57BL/6J mouse model of chikungunya virus (CHIKV) infection and disease has been extensively used to study the alphaviral arthritic immunopathology and to evaluate new interventions. How well mouse models recapitulate the gene expression profiles seen in humans remains controversial.MethodsHerein we perform a comparative transcriptomics analysis using RNA-Seq datasets from the C57BL/6J CHIKV mouse model with datasets obtained from adults and children acutely infected with CHIKV.ResultsDespite sampling quite different tissues, peripheral blood from humans and feet from mice, gene expression profiles were quite similar, with an overlap of up to ≈50% for up-regulated single copy orthologue differentially expressed genes. Furthermore, high levels of significant concordance between mouse and human were seen for immune pathways and signatures, which were dominated by interferons, T cells and monocyte/macrophages. Importantly, predicted responses to a series of anti-inflammatory drug and biologic treatments also showed cogent similarities between species.DiscussionComparative transcriptomics and subsequent pathway analysis provides a detailed picture of how a given model recapitulates human gene expression. Using this method, we show that the C57BL/6J CHIKV mouse model provides a reliable and representative system in which to study CHIKV immunopathology and evaluate new treatments.