A Qualitative Evaluation of Advances in Emergency Department Opioid Use Disorder Care in Michigan

The United States opioid epidemic claims the lives of tens of thousands of Americans each year due to opioid overdose. Hospital emergency departments (EDs) have been essential in combatting the crisis by stabilizing patients who are experiencing an overdose and other symptoms of their opioid use disorders (OUD). Over time, EDs have also become more involved in providing other addiction treatment services, such as prescribing and administering medications for opioid use disorder (MOUD) and referring their patients to outpatient behavioral health care providers for follow-up treatment. Policymakers have been essential in driving EDs to expand the scope of their addiction medicine services and referrals by creating specialized programs that provide incentivizes to participating hospitals.The following report summarizes advances in opioid use disorder care within EDs in 19 hospitals across 8 health systems in Michigan. These hospitals participated in an initiative created by the Community Foundation for Southeast Michigan (CFSEM) in collaboration with the Michigan Opioid Partnership (MOP), a public-private collaborative with a mission to reduce opioid overdoses in Michigan by improving the access and quality of prevention, treatment, harm reduction, and recovery services. The initiative was supported by State Opioid Response grants from the Michigan Department of Health and Human Services. Vital Strategies, a global public health organization that helps governments strengthen public health, provided support, technical assistance, and resources to improve hospital coordination and designed the evaluation. Specifically, hospitals were provided funding by CFSEM to improve OUD care training, coordination, delivery, and quality in their EDs. Hospitals and health systems funded by CFSEM included the University of Michigan Health System (Michigan Medicine hospital), Trinity Health (Mercy Health Muskegon, Mercy Health St. Mary, St. Joseph Mercy - Ann Arbor, St. Joseph Mercy Chelsea, St. Joseph Mercy Livingston, St. Joseph Mercy Oakland), Henry Ford Health Systems (Henry Ford – Main, Henry Ford - Wynadotte/ Brownstown), Beaumont Health Systems (Beaumont - Royal Oak, Beaumont – Troy, Beaumont – Wayne), Ascension (Ascension St. John Hospital, Ascension Genesys Hospital), Munson Healthcare (Munson Medical Center - Traverse City, Sparrow Health System (Sparrow Hospital - Lansing), Spectrum Health (Spectrum Health Butterworth), War Memorial, and Hurley Medical Center. After receiving funding, hospitals created work plans related to improving opioid use disorder care in their EDs, including by increasing their number of employed X-waivered providers, integrating clinical tracking and support tools into electronic medical records, and connecting patients with behavioral health care providers in the community to establish treatment continuity (i.e., "warm handoffs"). Researchers with the Bloomberg Overdose Prevention Initiative at the Johns Hopkins Bloomberg School of Public Health evaluated hospital improvement in these areas using surveys and qualitative interviews with participants

Climate change, climatic variation and extreme biological responses

Extreme climatic events could be major drivers of biodiversity change, but it is unclear whether extreme biological changes are (i) individualistic (species- or group-specific), (ii) commonly associated with unusual climatic events and/or (iii) important determinants of long-term population trends. Using population time series for 238 widespread species (207 Lepidoptera and 31 birds) in England since 1968, we found that population 'crashes' (outliers in terms of species' year-to-year population changes) were 46% more frequent than population 'explosions'. (i) Every year, at least three species experienced extreme changes in population size, and in 41 of the 44 years considered, some species experienced population crashes while others simultaneously experienced population explosions. This suggests that, even within the same broad taxonomic groups, species are exhibiting individualistic dynamics, most probably driven by their responses to different, short-term events associated with climatic variability. (ii) Six out of 44 years showed a significant excess of species experiencing extreme population changes (5 years for Lepidoptera, 1 for birds). These 'consensus years' were associated with climatically extreme years, consistent with a link between extreme population responses and climatic variability, although not all climatically extreme years generated excess numbers of extreme population responses. (iii) Links between extreme population changes and long-term population trends were absent in Lepidoptera and modest (but significant) in birds. We conclude that extreme biological responses are individualistic, in the sense that the extreme population changes of most species are taking place in different years, and that long-term trends of widespread species have not, to date, been dominated by these extreme changes.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'

RobotPerf: An Open-Source, Vendor-Agnostic, Benchmarking Suite for Evaluating Robotics Computing System Performance

We introduce RobotPerf, a vendor-agnostic benchmarking suite designed to evaluate robotics computing performance across a diverse range of hardware platforms using ROS 2 as its common baseline. The suite encompasses ROS 2 packages covering the full robotics pipeline and integrates two distinct benchmarking approaches: black-box testing, which measures performance by eliminating upper layers and replacing them with a test application, and grey-box testing, an application-specific measure that observes internal system states with minimal interference. Our benchmarking framework provides ready-to-use tools and is easily adaptable for the assessment of custom ROS 2 computational graphs. Drawing from the knowledge of leading robot architects and system architecture experts, RobotPerf establishes a standardized approach to robotics benchmarking. As an open-source initiative, RobotPerf remains committed to evolving with community input to advance the future of hardware-accelerated robotics

Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set

BACKGROUND: While clinical outcomes following immunotherapy have shown an association with tumor mutation load using whole exome sequencing (WES), its clinical applicability is currently limited by cost and bioinformatics requirements. METHODS: We developed a method to accurately derive the predicted total mutation load (PTML) within individual tumors from a small set of genes that can be used in clinical next generation sequencing (NGS) panels. PTML was derived from the actual total mutation load (ATML) of 575 distinct melanoma and lung cancer samples and validated using independent melanoma (n = 312) and lung cancer (n = 217) cohorts. The correlation of PTML status with clinical outcome, following distinct immunotherapies, was assessed using the Kaplan–Meier method. RESULTS: PTML (derived from 170 genes) was highly correlated with ATML in cutaneous melanoma and lung adenocarcinoma validation cohorts (R(2) = 0.73 and R(2) = 0.82, respectively). PTML was strongly associated with clinical outcome to ipilimumab (anti-CTLA-4, three cohorts) and adoptive T-cell therapy (1 cohort) clinical outcome in melanoma. Clinical benefit from pembrolizumab (anti-PD-1) in lung cancer was also shown to significantly correlate with PTML status (log rank P value < 0.05 in all cohorts). CONCLUSIONS: The approach of using small NGS gene panels, already applied to guide employment of targeted therapies, may have utility in the personalized use of immunotherapy in cancer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12916-016-0705-4) contains supplementary material, which is available to authorized users

MLSys: The New Frontier of Machine Learning Systems

Machine learning (ML) techniques are enjoying rapidly increasing adoption. However, designing and implementing the systems that support ML models in real-world deployments remains a significant obstacle, in large part due to the radically different development and deployment profile of modern ML methods, and the range of practical concerns that come with broader adoption. We propose to foster a new systems machine learning research community at the intersection of the traditional systems and ML communities, focused on topics such as hardware systems for ML, software systems for ML, and ML optimized for metrics beyond predictive accuracy. To do this, we describe a new conference, MLSys, that explicitly targets research at the intersection of systems and machine learning with a program committee split evenly between experts in systems and ML, and an explicit focus on topics at the intersection of the two

Identification of a Gene Regulatory Network Necessary for the Initiation of Oligodendrocyte Differentiation

Differentiation of oligodendrocyte progenitor cells (OPCs) into mature oligodendrocytes requires extensive changes in gene expression, which are partly mediated by post-translational modifications of nucleosomal histones. An essential modification for oligodendrocyte differentiation is the removal of acetyl groups from lysine residues which is catalyzed by histone deacetylases (HDACs). The transcriptional targets of HDAC activity within OPCs however, have remained elusive and have been identified in this study by interrogating the oligodendrocyte transcriptome. Using a novel algorithm that allows clustering of gene transcripts according to expression kinetics and expression levels, we defined major waves of co-regulated genes. The initial overall decrease in gene expression was followed by the up-regulation of genes involved in lipid metabolism and myelination. Functional annotation of the down-regulated gene clusters identified transcripts involved in cell cycle regulation, transcription, and RNA processing. To define whether these genes were the targets of HDAC activity, we cultured rat OPCs in the presence of trichostatin A (TSA), an HDAC inhibitor previously shown to inhibit oligodendrocyte differentiation. By overlaying the defined oligodendrocyte transcriptome with the list of ‘TSA sensitive’ genes, we determined that a high percentage of ‘TSA sensitive’ genes are part of a normal program of oligodendrocyte differentiation. TSA treatment increased the expression of genes whose down-regulation occurs very early after induction of OPC differentiation, but did not affect the expression of genes with a slower kinetic. Among the increased ‘TSA sensitive’ genes we detected several transcription factors including Id2, Egr1, and Sox11, whose down-regulation is critical for OPC differentiation. Thus, HDAC target genes include clusters of co-regulated genes involved in transcriptional repression. These results support a de-repression model of oligodendrocyte lineage progression that relies on the concurrent down-regulation of several inhibitors of differentiation

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Background The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. Results The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. Conclusions By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available