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Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19 k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~ 900,000 to one million individuals) between approximately 60,000–90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60–90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~ 1700 km2. The decline in effective population size of 89–99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations. [ABSTRACT FROM AUTHOR]

Background: Wearable devices generate signals detecting activity, sleep, and heart rate, all of which could enable detailed and near-continuous characterization of recovery following critical illness. Methods: To determine the feasibility of using a wrist-worn personal fitness tracker among patients recovering from critical illness, we conducted a prospective observational study of a convenience sample of 50 stable ICU patients. We assessed device wearability, the extent of data capture, sensitivity and specificity for detecting heart rate excursions, and correlations with questionnaire-derived sleep quality measures. Results: Wearable devices were worn over a 24-h period, with excellent capture of data. While specificity for the detection of tachycardia was high (98.8%), sensitivity was low to moderate (69.5%). There was a moderate correlation between wearable-derived sleep duration and questionnaire-derived sleep quality (r = 0.33, P = 0.03). Devices were well-tolerated and demonstrated no degradation in quality of data acquisition over time. Conclusions: We found that wearable devices could be worn by patients recovering from critical illness and could generate useful data for the majority of patients with little adverse effect. Further development and study are needed to better define and enhance the role of wearables in the monitoring of post-ICU recovery. [ABSTRACT FROM AUTHOR]

Background: Mammalian aging is a highly complex process, a full mechanistic understanding of which is still lacking. One way to help understand the molecular changes underlying aging is through a comprehensive analysis of the transcriptome, the primary determinant of age-related phenotypic diversity. Previous studies have relied on microarray analysis to examine gene expression profiles in different tissues of aging organisms. However, studies have shown microarray-based transcriptional profiling is less accurate and not fully capable of capturing certain intricacies of the global transcriptome. Methods: Here, using directional whole transcriptome RNA-sequencing of aged mouse liver we have identified a comprehensive high-resolution profile of differentially expressed liver transcripts comprised of canonical protein-coding transcripts, transcript isoforms, and non-coding RNA transcripts, including pseudogenes, long non-coding RNAs and small RNA species. Results: Results show extensive age-related changes in every component of the mouse liver transcriptome and a pronounced increase in inter-individual variation. Functional annotation of the protein-coding mRNAs and isoforms indicated broad alterations in immune response, cell activation, metabolic processes, and RNA modification. Interestingly, multiple lncRNAs (Meg3, Rian, Mirg) from the Dlk-Dio3 microRNA locus were found up-regulated in aging liver, classifying this locus as a putative regulatory hotspot locus in aging liver. Moreover, integration of the altered non-coding RNAs and protein-coding transcripts into interaction networks of age-related change revealed inflammation, cellular proliferation, and metabolism as the dominant aging phenotypes in mouse liver. Conclusions: Our analyses provide the first comprehensive dissection of the transcriptional landscape in aging mouse liver. [ABSTRACT FROM AUTHOR]

Background: Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, directly from paired-end short read data. Results: ISMapper was validated using three types of short read data: (i) simulated reads from a variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences were available for comparison, and (iii) Illumina reads from 7 Acinetobacter baumannii isolates for which predicted IS locations were tested using PCR. A total of 20 genomes, including 13 species and 32 distinct IS, were used for validation. ISMapper correctly identified 97 % of known IS insertions in the analysis of simulated reads, and 98 % in real Illumina reads. Subsampling of real Illumina reads to lower depths indicated ISMapper was able to correctly detect insertions for average genome-wide read depths >20x, although read depths >50x were required to obtain confident calls that were highly-supported by evidence from reads. All ISAba1 insertions identified by ISMapper in the A. baumannii genomes were confirmed by PCR. In each A. baumannii genome, ISMapper successfully identified an IS insertion upstream of the ampC beta-lactamase that could explain phenotypic resistance to third-generation cephalosporins. The utility of ISMapper was further demonstrated by profiling genome-wide IS6110 insertions in 138 publicly available Mycobacterium tuberculosis genomes, revealing lineage-specific insertions and multiple insertion hotspots. Conclusions: ISMapper provides a rapid and robust method for identifying IS insertion sites directly from short read data, with a high degree of accuracy demonstrated across a wide range of bacteria. [ABSTRACT FROM AUTHOR]

Background: Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have increased the amount of data generated by the technology and outpaced the development of data analysis approaches. While there are advanced tools available, including many R/BioConductor packages, these are only accessible programmatically and therefore out of reach for most experimentalists. GenePattern is a powerful genomic analysis platform with over 200 tools for analysis of gene expression, proteomics, and other data. A web-based interface provides easy access to these tools and allows the creation of automated analysis pipelines enabling reproducible research. Results: In order to bring advanced flow cytometry data analysis tools to experimentalists without programmatic skills, we developed the GenePattern Flow Cytometry Suite. It contains 34 open source GenePattern flow cytometry modules covering methods from basic processing of flow cytometry standard (i.e., FCS) files to advanced algorithms for automated identification of cell populations, normalization and quality assessment. Internally, these modules leverage from functionality developed in R/BioConductor. Using the GenePattern web-based interface, they can be connected to build analytical pipelines. Conclusions: GenePattern Flow Cytometry Suite brings advanced flow cytometry data analysis capabilities to users with minimal computer skills. Functionality previously available only to skilled bioinformaticians is now easily accessible from a web browser. [ABSTRACT FROM AUTHOR]

Background: Sphingosine-1-phosophate (S1P) is a biologically active sphingolipid metabolite that influences cellular events including differentiation, proliferation, and migration. S1P acts through five distinct cell surface receptors designated S1P1-5R, with S1P1R having the highest expression level in the developing heart. S1P1R is critical for vascular maturation, with its loss leading to embryonic death by E14.5; however, its function during early cardiac development is not well known. Our previous studies demonstrated that altered S1P levels adversely affects atrioventricular (AV) canal development in vitro, with reduced levels leading to cell death and elevated levels inhibiting cell migration and endothelial to mesenchymal cell transformation (EMT). Results: We determined, by real-time PCR analysis, that S1P1R was expressed at least 10-fold higher than other S1P receptors in the developing heart. Immunohistochemical analysis revealed S1P1R protein expression in both endothelial and myocardial cells in the developing atrium and ventricle. Using AV canal cultures, we observed that treatment with either FTY720 (an S1P1,3,4,5R agonist) or KRP203 (an S1P1R-specific agonist) caused similar effects on AV canal cultures as S1P treatment, including induction of cell rounding, inhibition of cell migration, and inhibition of EMT. In vivo, morphological analysis of embryonic hearts at E10.5 revealed that S1P1R-/- hearts were malformed with reduced myocardial tissue. In addition to reduced myocardial tissue, E12.5 S1P1R-/- hearts had disrupted morphology of the heart wall and trabeculae, with thickened and disorganized outer compact layer and reduced fibronectin (FN) deposition compared to S1P1R+/+ littermates. The reduced myocardium was accompanied by a decrease in cell proliferation but not an increase in apoptosis. Conclusions: These data indicate that S1P1R is the primary mediator of S1P action in AV canal cultures and that loss of S1P1R expression in vivo leads to malformed embryonic hearts, in part due to reduced fibronectin expression and reduced cell proliferation. [ABSTRACT FROM AUTHOR]

Introduction: Common causes of non-traumatic acute cerebral edema include malignant hypertension, hyponatremia, anoxia, and cerebral vascular accident. The computed tomographic images and data obtained during care of the patient described in this case report provide evidence that hypercarbia can cause increased intracranial pressure and coma without permanent brain injury. Partial pressure of carbon dioxide evaluation for coma is essential to provide faster diagnosis and therapeutic correction in certain common critical disease states. We present the case of a patient in a coma associated with cerebral edema during a typical asthma exacerbation with hypercapnic respiratory failure.Case Presentation: An obese 63-year-old African American woman with asthma presented to our hospital with facial swelling and shortness of breath. Immediately following intubation for hypercapnic respiratory failure, she was noted to have a dilated, unresponsive right pupil. An emergent computed tomographic head scan revealed that she had increased intracranial pressure. A neurosurgeon agreed with the computed tomography interpretation and recommended no surgical intervention. The patient's respiratory acidosis was corrected with ventilatory management over several hours in the intensive care unit. Nine and one-half hours later a follow-up head computed tomographic scan was read as normal without cerebral edema. At 12 hours, the patient's right pupil was 5 mm in diameter and reactive. By 24 hours, her pupils were symmetrically equal and reactive. Her symptoms had improved, and she was extubated. A brain magnetic resonance imaging scan revealed no abnormalities.Conclusion: Alteration of consciousness related to hypercapnia during respiratory failure is not generally thought to be related to cerebral edema. Respiratory acidosis resulting from hypercarbia is known to produce carbon dioxide narcosis and coma, but no current treatment algorithm suggests that rapid hypercapnia correction can be critical to neurologic outcome. To the best of our knowledge, our case is a unique example of the physiological changes that may occur in relation to arterial carbon dioxide concentration in the normal brain in the setting of typical hypercapnic respiratory failure. Correction of respiratory acidosis reversed the neurologic symptoms and physiology causing cerebral edema and coma in our patient. Rare similar cases have been sporadically reported in the medical literature, typically in children. Our case is also unusual in that rapid deterioration and clinical status were directly observed on simultaneous computed tomographic scans. Had this patient been found unresponsive, or had she had brief respiratory or cardiac arrest, the scan could have been interpreted as global anoxic injury leading to a different therapeutic course. [ABSTRACT FROM AUTHOR]

Background: Flow cytometry is a widely used analytical technique for examining microscopic particles, such as cells. The Flow Cytometry Standard (FCS) was developed in 1984 for storing flow data and it is supported by all instrument and third party software vendors. However, FCS does not capture the full scope of flow cytometry (FCM)-related data and metadata, and data standards have recently been developed to address this shortcoming. Findings: The Data Standards Task Force (DSTF) of the International Society for the Advancement of Cytometry (ISAC) has developed several data standards to complement the raw data encoded in FCS files. Efforts started with the Minimum Information about a Flow Cytometry Experiment, a minimal data reporting standard of details necessary to include when publishing FCM experiments to facilitate third party understanding. MIFlowCyt is now being recommended to authors by publishers as part of manuscript submission, and manuscripts are being checked by reviewers and editors for compliance. Gating-ML was then introduced to capture gating descriptions - an essential part of FCM data analysis describing the selection of cell populations of interest. The Classification Results File Format was developed to accommodate results of the gating process, mostly within the context of automated clustering. Additionally, the Archival Cytometry Standard bundles data with all the other components describing experiments. Here, we introduce these recent standards and provide the very first example of how they can be used to report FCM data including analysis and results in a standardized, computationally exchangeable form. Conclusions: Reporting standards and open file formats are essential for scientific collaboration and independent validation. The recently developed FCM data standards are now being incorporated into third party software tools and data repositories, which will ultimately facilitate understanding and data reuse. [ABSTRACT FROM AUTHOR]

Background: Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval. Results: The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI. Conclusion: We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components. Availability: OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl [ABSTRACT FROM AUTHOR]

Background: Our understanding of the mechanisms that protect the developing embryo from intrauterine stress is limited. Recently, adenosine has been demonstrated to play a critical role in protecting the embryo against hypoxia via adenosine A1 receptors (A1ARs), which are expressed in the heart, nervous system, and other sites during development. However, the sites of A1AR action that mediate embryo protection are not known. To determine if the heart is a key site of adenosine-mediated embryo protection, A1ARs were selectively deleted in the embryonic heart using a Cre-LoxP system in which the alpha-myosin heavy chain promoter drives Cre-recombinase expression and excision of the A1AR gene from cardiomyocytes. Results: With increasing exposure of maternal hypoxia (10% O2) from 48-96 hours beginning at embryonic day (E) 8.5, embryo viability decreased in the cardiac-A1AR deleted embryos. 48 hours of hypoxia reduced embryonic viability by 49% in embryos exposed from E10.5-12.5 but no effect on viability was observed in younger embryos exposed to hypoxia from E8.5-10.5. After 72 hours of hypoxia, 57.8% of the cardiac-A1AR deleted embryos were either dead or reabsorbed compared to 13.7% of control littermates and after 96 hours 81.6% of cardiac-A1AR deleted embryos were dead or re-absorbed. After 72 hours of hypoxia, cardiac size was reduced significantly more in the cardiac-A1AR deleted hearts compared to controls. Gene expression analysis revealed clusters of genes that are regulated by both hypoxia and A1AR expression. Conclusions: These data identify the embryonic heart as the critical site where adenosine acts to protect the embryo against hypoxia. As such these studies identify a previously unrecognized mechanism of embryo protection. [ABSTRACT FROM AUTHOR]

Background: Tissue plasminogen activator (tPA) is known to have functions beyond fibrinolysis in acute ischemic stroke, such as blood brain barrier disruption. To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke. Results: tPA differentially expressed 929 genes in the blood of rats (p ≤ 0.05, fold change ≥ ∣1.2∣). Genes identified had functions related to modulation of immune cells. tPA gene expression was found to be dependent on the reperfusion status of cerebral vasculature. The majority of genes regulated by tPA were different from genes regulated by ischemic stroke. Conclusions: tPA modulates gene expression in the blood of rats involving immune cells in a manner that is dependent on the status of vascular reperfusion. These non-fibrinolytic activities of tPA in the blood serve to better understand tPA-related complications. [ABSTRACT FROM AUTHOR]

Background: Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms. Findings: OntoFox http://ontofox.hegroup.org/ is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated. Conclusions: OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies. [ABSTRACT FROM AUTHOR]

Background: Recent biological discoveries have shown that clustering large datasets is essential for better understanding biology in many areas. Spectral clustering in particular has proven to be a powerful tool amenable for many applications. However, it cannot be directly applied to large datasets due to time and memory limitations. To address this issue, we have modified spectral clustering by adding an information preserving sampling procedure and applying a post-processing stage. We call this entire algorithm SamSPECTRAL. Results: We tested our algorithm on flow cytometry data as an example of large, multidimensional data containing potentially hundreds of thousands of data points (i.e., "events" in flow cytometry, typically corresponding to cells). Compared to two state of the art model-based flow cytometry clustering methods, SamSPECTRAL demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. Conclusions: This work is the first successful attempt to apply spectral methodology on flow cytometry data. An implementation of our algorithm as an R package is freely available through BioConductor. [ABSTRACT FROM AUTHOR]

Background: Microsatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti. Results: From 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority (51%) of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus (mean = 8.75). Allelic polymorphic information content varied from 0.171 to 0.867 (mean = 0.545). Most loci met Hardy-Weinberg expectations across populations and pairwise FST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed. Conclusion: Despite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient screening of genome supercontig assemblies. These loci are suitable for genetic and population studies using multiplex-PCR. [ABSTRACT FROM AUTHOR]

Background: Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the presence of multiple covariates. Results: We developed a set of flexible open source computational tools in the R package flowCore to facilitate the analysis of these complex data. A key component of which is having suitable data structures that support the application of similar operations to a collection of samples or a clinical cohort. In addition, our software constitutes a shared and extensible research platform that enables collaboration between bioinformaticians, computer scientists, statisticians, biologists and clinicians. This platform will foster the development of novel analytic methods for flow cytometry. Conclusion: The software has been applied in the analysis of various data sets and its data structures have proven to be highly efficient in capturing and organizing the analytic work flow. Finally, a number of additional Bioconductor packages successfully build on the infrastructure provided by flowCore, open new avenues for flow data analysis. [ABSTRACT FROM AUTHOR]

Background: Human breast cancer is a heterogeneous disease, histopathologically, molecularly and phenotypically. The molecular basis of this heterogeneity is not well understood. We have used a mouse model of DCIS that consists of unique lines of mammary intraepithelial neoplasia (MIN) outgrowths, the premalignant lesion in the mouse that progress to invasive carcinoma, to understand the molecular changes that are characteristic to certain phenotypes. Each MIN-O line has distinguishable morphologies, metastatic potentials and estrogen dependencies. Methods: We utilized oligonucleotide expression arrays and high resolution array comparative genomic hybridization (aCGH) to investigate whole genome expression patterns and whole genome aberrations in both the MIN-O and tumor from four different MIN-O lines that each have different phenotypes. From the whole genome analysis at 35 kb resolution, we found that chromosome 1, 2, 10, and 11 were frequently associated with whole chromosome gains in the MIN-Os. In particular, two MINO lines had the majority of the chromosome gains. Although we did not find any whole chromosome loss, we identified 3 recurring chromosome losses (2F1-2, 3E4, 17E2) and two chromosome copy number gains on chromosome 11. These interstitial deletions and duplications were verified with a custom made array designed to interrogate the specific regions at approximately 550 bp resolution. Results: We demonstrated that expression and genomic changes are present in the early premalignant lesions and that these molecular profiles can be correlated to phenotype (metastasis and estrogen responsiveness). We also identified expression changes associated with genomic instability. Progression to invasive carcinoma was associated with few additional changes in gene expression and genomic organization. Therefore, in the MIN-O mice, early premalignant lesions have the major molecular and genetic changes required and these changes have important phenotypic significance. In contrast, the changes that occur in the transition to invasive carcinoma are subtle, with few consistent changes and no association with phenotype. Conclusion: We propose that the early lesions carry the important genetic changes that reflect the major phenotypic information, while additional genetic changes that accumulate in the invasive carcinoma are less associated with the overall phenotype. [ABSTRACT FROM AUTHOR]

Background: Veterans are at elevated risk for suicide compared to non-Veteran U.S. adults. Data sources and analyses to inform prevention efforts, especially for those who do not use Department of Veterans Affairs (VA) healthcare services, are needed. This study aimed to link VA and CDC's National Violent Death Reporting System (NVDRS) data to create a novel data source to characterize the circumstances precipitating and preceding suicide among Veterans, including among those who did not use VA healthcare., Methods: Multi-variable, multi-stage, deterministic linkage of VA-Department of Defense (DoD) Mortality Data Repository (MDR) and NVDRS-Restricted Access Database suicide and undetermined intent mortality records within 189 state-year strata (42 states, 2012-2018). Three linkage stages: (1) exact (matched on: age, sex, death date, underlying cause of death, day of month of birth, first initial of last name); (2) probable (all but one variable matched); (3) possible (all but 2 variables matched). Linkage success and accuracy of NVDRS-documented military history were assessed., Results: Across all state-years, 22,019 matches (89.20% of 24,685 MDR Veteran records) were identified (65.47% exact). When high missingness (2 + matching variables in > 10% of records; n = 23) or incomplete reporting (n = 12) state-years were excluded, match rate increased to 94.29% (77.15% exact). NVDRS-documented military history (ever served) was accurate for 87.79% of matched records, with an overall sensitivity of 84.62%. Sensitivity was lower for female (61.01%) and younger (17-39 years; 77.51%) Veterans., Conclusions: Accurate linkage of VA-DoD and NVDRS data is feasible and offers potential to improve understanding of circumstances surrounding suicide among Veterans., Competing Interests: Declarations. Consent for publication: Not applicable. Competing interests: All authors were employed by the VA (CAH, ALS, LAG, JAK, RH, LLM) or CDC (JL) while conducting this research and/or writing this manuscript. However, the views expressed are those of the authors and do not necessarily represent the views or policy of the VA, CDC, or the U.S. Government. Authors have received grant funding from the VA Office of Mental Health and Suicide Prevention (CAH, ALS, LAG, JAK, RH, LLM), VA Health Services Research and Development (CAH, ALS, RH, LLM), VA Office of Health Equity (RH, LLM), VA National Center for Patient Safety (LLM), the National Institutes of Health (CAH, RH), and the Department of Defense (CAH, RH, LLM). Ethics approval: This study was approved by the Colorado Multiple Institution Review Board (COMIRB; #19–0833) and designated as exempt. A waiver of documentation of consent was granted., (© 2025. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Background: Rates of suicide remain elevated among U.S. Veterans and have increased disproportionately among Asian American and Pacific Islander (AAPI) Veterans. Knowledge is limited regarding suicide prevention considerations for clinicians working with AAPI Veterans, yet culturally responsive strategies tend to be most effective. To address this gap, we sought to elucidate subject matter experts' perspectives regarding suicide prevention considerations for AAPI Veterans., Methods: Qualitative interviews were conducted with 14 key informants (e.g., clinicians, researchers) in 2023 to understand their experiences with, and recommendations for, preventing suicide among AAPI Veterans in the Continental U.S. Interview transcripts were analyzed through thematic analysis, with an inductive approach., Results: Key informants discussed the heterogeneity of the AAPI population and emphasized the need to balance cultural sensitivity and cultural humility in suicide prevention with AAPI Veterans. Fear of bringing shame and dishonor upon one's family was described as a factor which may prevent AAPI Veterans from disclosing mental health concerns and suicide risk and which may prevent them from accessing healthcare services for mental health and suicidality. Suicide risk among AAPI Veterans was viewed as being shaped by shame and the centrality of the family-collective, with family conferring both protection against and risk for suicide. Cultural norms and beliefs regarding suicide were considered pertinent to suicide among AAPI Veterans and included beliefs about perseverance in coping with distress to permittance of suicide in specific circumstances. Somatic idioms were described as a means by which AAPI Veterans may communicate distress and suicidality, with key informants discussing how this may impact treatment and outreach., Conclusion: Key informant interviews provided crucial insights into cultural factors salient to conceptualizing and addressing AAPI Veterans' risk for suicide. These findings can be utilized to inform tailored suicide prevention for this population, with emphasis on addressing mental health stigma, considering somatic idioms of distress, and considering the role of family in suicide risk and prevention., Competing Interests: Declarations. Ethics approval and consent to participate: The Colorado Multiple Institutional Review Board approved this study (21-4023). Informed consent was obtained prior to initiating study procedures, with verbal communication of consent. Consent for publication: Not applicable. Competing interests: All authors report grant funding from the VA. ERP, CMR, RH and LLM also report funding from the Department of Defense. RH reports funding from the state of Colorado. LLM reports funding from the Face-the-Fight Initiative., (© 2025. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

The purpose of this study was to determine if there were correlations between the length of time from hospital admission to surgical intervention and the frequency of complications in patients with odontogenic infections. While odontogenic infection is well studied in terms of interventions and outcomes, less is known about hospital utilization and resource burden of odontogenic infection with respect to timeliness to intervention. A retrospective cohort analysis was used to examine correlations between time from admission to surgical intervention and clinical outcomes. Patients included in this study were divided into three categories of length of time to the operating room: 0-12 h, 12.1-24 h, and greater than 24 h. Time of admission, time of surgical intervention, patient demographics, admission lab values, and space involvement were measured and compared to the primary outcome variables including complications of intubation attempts and type, ICU admission, length of hospitalization, number of changes in antibiotic therapy, and frequency of return to the operating room. We found that the length of time to the OR had a statistically significant association with length of hospital stay (p = 0.003) and number of changes in antibiotic therapy (p = 0.033). While overall length of hospital stay is inherently dependent on length of time to the OR, this relationship highlights the importance of timeliness to definitive intervention in order to reduce hospital burden. This study provides evidence on how to prioritize odontogenic infections in a hospital setting. We recommend treating odontogenic infection in less than 24 h from the time of admission in order to reduce costs and improve outcomes for patients., Competing Interests: Declarations. Ethics approval and consent to participate: All experiments were performed in accordance with relevant guidelines and regulations. The need for consent to participate was waived by an Institutional Review Board (IRB). This work was approved by the Augusta University IRB, protocol 1323780-3, and a waiver was granted for this retrospective chart review. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Background: Cancer is a complex set of diseases, and many have decades-long lag times between possible exposure and diagnosis. Environmental exposures, such as per- and poly-fluoroalkyl substances (PFAS) and area-level risk factors (e.g., socioeconomic variables), vary for people over time and space. Evidence suggests PFAS exposure is associated with several cancers; however, studies to date have various limitations. Few studies have used rigorous spatiotemporal approaches, and, to our knowledge, none have assessed cumulative exposures given residential histories or incorporated chemical mixture modeling. Thus, spatiotemporal analysis using advanced statistical approaches, accounting for spatially structured and unstructured heterogeneity in risk, can be a highly informative strategy for addressing the potential health effects of PFAS exposure., Methods: Using population-based incident cancer cases and cancer-free controls in a 12-county area of southeastern Pennsylvania, we will apply Bayesian spatiotemporal analysis methods using historically reconstructed PFAS-contaminated water exposure given residential histories, and other potential cancer determinants over time. Bayesian group index models enable assessment of various mixtures of highly correlated PFAS chemical exposures incorporating mobility/residential history, and contextual factors to determine the association of PFAS-related exposures and cancer incidence., Discussion: The purpose of this paper is to describe the Enhanced PFAS Spatial Analysis study rationale, study design, and methods., Competing Interests: Declarations. Ethics approval and consent to participate: This project was reviewed and approved by the Temple University Institutional Review Board (#265091), which includes a waiver of consent (per 45 CFR 46.116 [d]) and a HIPAA waiver of authorization (per 45 CFR 164.512(i)(1)(ii)). Consent for publication: Not applicable. Competing interests: The authors declare no competing interests. Disclaimer: The protocol and information in this manuscript are those of the authors., (© 2025. The Author(s).)

Background: Since 2015, the Complex Reviews Synthesis Unit (CRSU) has developed a suite of web-based applications (apps) that conduct complex evidence synthesis meta-analyses through point-and-click interfaces. This has been achieved in the R programming language by combining existing R packages that conduct meta-analysis with the shiny web-application package. The CRSU apps have evolved from two short-term student projects into a suite of eight apps that are used for more than 3,000 h per month., Aim: Here, we present our experience of developing production grade web-apps from the point-of-view of individuals trained primarily as statisticians rather than software developers in the hopes of encouraging and inspiring other groups to develop valuable open-source statistical software whilst also learning from our experiences., Key Challenges: We discuss how we have addressed challenges to research software development such as responding to feedback from our real-world users to improve the CRSU apps, the implementation of software engineering principles into our app development process and gaining recognition for non-traditional research work within the academic environment., Future Developments: The CRSU continues to seek funding opportunities both to maintain and further develop our shiny apps. We aim to increase our user base by implementing new features within the apps and building links with other groups developing complementary evidence synthesis tools., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Rotator cuff repairs may fail because of compromised blood supply, suture anchor pullout, or poor fixation to bone. To augment the repairs and promote healing of the tears, orthobiologics, such a platelet-rich plasma (PRP), and biologic scaffolds have been applied with mixed results. Adipose allograft matrix (AAM), which recruits native cells to damaged tissues, may also be a potential treatment for rotator cuff tears., Methods: To assess the potential use of AAM on rotator cuff tears, humeral head cartilage and subscapularis tendon were collected from patients undergoing reverse shoulder arthroplasty (RSA). Punch biopsies of the tissues were used to create explants for tissue culture, and the remaining tissue was digested to isolate the chondrocytes and tenocytes for cell culture. Explants and cells were then cultured in media containing AAM. After 48 h, the tissues and cells were measured for cell viability, cell proliferation, extracellular matrix (ECM) and metalloproteinase (MMP) gene expression and for MMP, inflammatory cytokine, and growth factor concentrations., Results: Cell viability was increased in humeral head chondrocytes and rotator cuff tenocytes cultured with AAM. Gene expression of the matrix proteoglycan, aggrecan, and of the proteolytic enzyme MMP-13 were downregulated in humeral head chondrocytes. MMP-13 concentrations were increased in subscapularis tenocytes and in humeral head chondrocyte/subscapularis tenocyte co-cultures. The anti-inflammatory cytokine, IL-1ra was increased in cartilage/tendon explant co-cultures. TGF-β1 concentrations were increased in chondrocytes, but decreased in tenocytes., Conclusions: Overall, AAM had no significant negative effects on the cells or explants. The results of these experiments provide the basis for the future use of AAM as a scaffolding for tissue engineering, preclinical animal models of rotator cuff tear and glenohumeral osteoarthritis, and clinical models., Clinical Trial Number: Not applicable., Competing Interests: Declarations. Ethical approval: This study was approved by the Biomedical Institutional Review Board of The Ohio State University (#2022HO233). Written informed consent was obtained from all participants. All study procedures adhered to the Declaration of Helsinki. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets have enabled an increased understanding of senescent cell heterogeneity., Methods: Here we present SenPred, a machine-learning pipeline which identifies fibroblast senescence based on single-cell transcriptomics from fibroblasts grown in 2D and 3D., Results: Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental fibroblast senescence to a high degree of accuracy (> 99% true positives). Applying SenPred to in vivo whole skin scRNA-seq datasets reveals that cells grown in 2D cannot accurately detect fibroblast senescence in vivo. Importantly, utilising scRNA-seq from 3D deeply senescent fibroblasts refines our ML model leading to improved detection of senescent cells in vivo. This is context specific, with the SenPred pipeline proving effective when detecting senescent human dermal fibroblasts in vivo, but not the senescence of lung fibroblasts or whole skin., Conclusions: We position this as a proof-of-concept study based on currently available scRNA-seq datasets, with the intention to build a holistic model to detect multiple senescent triggers using future emerging datasets. The development of SenPred has allowed for the detection of an in vivo senescent fibroblast burden in human skin, which could have broader implications for the treatment of age-related morbidities. All code for the SenPred pipeline is available at the following URL: https://github.com/bethk-h/SenPred_HDF ., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: Authors AD, LJW and DAG are Unilever employees. The remaining authors declare that they have no competing interests., (© 2025. The Author(s).)

Background: Current guidelines recommend empiric antibiotic therapy for patients who require hospitalization for community-acquired pneumonia (CAP). We sought to determine whether clinical, imaging or laboratory features in patients hospitalized for CAP in whom PCR is positive for a respiratory virus enable exclusion of bacterial coinfection so that antibiotics can be withheld., Methods: For this prospective study, we selected patients in whom an etiologic diagnosis was likely to be reached, namely those who provided a high-quality sputum sample at or shortly after admission, and in whom PCR was done to test for a respiratory virus. We performed quantitative bacteriologic studies on sputum to determine the presence of bacterial infection or coinfection and reviewed all clinical, imaging and laboratory studies., Results: Of 122 CAP patients studied, 77 (63.1%) had bacterial infection, 16 (13.1%) viral infection, and 29 (23.8%) bacterial/viral coinfection. Underlying pulmonary disease and a history of smoking were more common in bacterial pneumonia. Upper respiratory symptoms were more common, and mean white blood cell (WBC) counts were lower viral pneumonia. Nevertheless, no clinical, laboratory or imaging findings allowed exclusion of bacterial coinfection in patients who tested positive for a respiratory virus. In fact, patients with bacterial/viral coinfection were sicker than those with bacterial or viral pneumonia; 30% were admitted required transfer to the ICU during their hospital course, compared to 17% and 19% of patients with bacterial or viral infection, respectively (p < .05). In this study, 64.4% of patients who tested positive for a respiratory virus had a bacterial coinfection., Conclusions: If a test for a respiratory virus test is positive in a patient hospitalized for CAP, no sufficiently differentiating features exclude bacterial coinfection, thereby supporting the recommendation that empiric antibiotics be administered to all patients who are sufficiently ill to require hospitalization for CAP., Competing Interests: Declarations. Ethics approval and consent to participate: This protocol was approved by the Institutional Review Board, Baylor College of Medicine, protocol H-29468. Consent for publication: None required. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Evolutionary tradeoffs between life-history strategies are important in animal evolution. Because microbes can influence multiple aspects of host physiology, including growth rate and susceptibility to disease or stress, changes in animal-microbial symbioses have the potential to mediate life-history tradeoffs. Scleractinian corals provide a biodiverse, data-rich, and ecologically-relevant host system to explore this idea., Results: Using a comparative approach, we tested if coral microbiomes correlate with disease susceptibility across 425 million years of coral evolution by conducting a cross-species coral microbiome survey (the "Global Coral Microbiome Project") and combining the results with long-term global disease prevalence and coral trait data. Interpreting these data in their phylogenetic context, we show that microbial dominance predicts disease susceptibility, and traced this dominance-disease association to a single putatively beneficial symbiont genus, Endozoicomonas. Endozoicomonas relative abundance in coral tissue explained 30% of variation in disease susceptibility and 60% of variation in microbiome dominance across 40 coral genera, while also correlating strongly with high growth rates., Conclusions: These results demonstrate that the evolution of Endozoicomonas symbiosis in corals correlates with both disease prevalence and growth rate, and suggest a mediating role. Exploration of the mechanistic basis for these findings will be important for our understanding of how microbial symbioses influence animal life-history tradeoffs., Competing Interests: Declarations. Ethics approval and consent to participate: Ethical approval is not applicable to research on corals. Consent for publication: Not applicable. Competing interests: Rob Knight is a scientific advisory board member, and consultant for BiomeSense, Inc., has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant for DayTwo, and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma, and has equity and is a scientific advisory board member. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies., (© 2024. The Author(s).)

Metastasis remains a leading cause of cancer-related mortality, irrespective of the primary tumour origin. However, the core gene regulatory program governing distinct stages of metastasis across cancers remains poorly understood. We investigate this through single-cell transcriptome analysis encompassing over two hundred patients with metastatic and non-metastatic tumours across six cancer types. Our analysis revealed a prognostic core gene signature that provides insights into the intricate cellular dynamics and gene regulatory networks driving metastasis progression at the pan-cancer and single-cell level. Notably, the dissection of transcription factor networks active across different stages of metastasis, combined with functional perturbation, identified SP1 and KLF5 as key regulators, acting as drivers and suppressors of metastasis, respectively, at critical steps of this transition across multiple cancer types. Through in vivo and in vitro loss of function of SP1 in cancer cells, we revealed its role in driving cancer cell survival, invasive growth, and metastatic colonisation. Furthermore, tumour cells and the microenvironment increasingly engage in communication through WNT signalling as metastasis progresses, driven by SP1. Further validating these observations, a drug repurposing analysis identified distinct FDA-approved drugs with anti-metastasis properties, including inhibitors of WNT signalling across various cancers., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)