Opening Session

Chancellor Motley Jessica Cicchino – Insurance Institute for Highway Safety, National crash trends Jeanne Hathaway – MA DPH Injury Prevention Epidemiologist, MA context Beth Dugan – UMass Boston, Fatal Accidents in MA involving drivers age 65+; Summit aim

LakeMetabolizer: An R package for estimating lake metabolism from free-water oxygen using diverse statistical models

Metabolism is a fundamental process in ecosystems that crosses multiple scales of organization from individual organisms to whole ecosystems. To improve sharing and reuse of published metabolism models, we developed LakeMetabolizer, an R package for estimating lake metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models). These tools have been organized into an R package that contains example data, example use-cases, and function documentation. The release package version is available on the Comprehensive R Archive Network (CRAN), and the full open-source GPL-licensed code is freely available for examination and extension online. With this unified, open-source, and freely available package, we hope to improve access and facilitate the application of metabolism in studies and management of lentic ecosystems

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

The human X and Y chromosomes evolved from an ordinary pair of autosomes, but millions of years ago genetic decay ravaged the Y chromosome, and only three per cent of its ancestral genes survived. We reconstructed the evolution of the Y chromosome across eight mammals to identify biases in gene content and the selective pressures that preserved the surviving ancestral genes. Our findings indicate that survival was nonrandom, and in two cases, convergent across placental and marsupial mammals. We conclude that the gene content of the Y chromosome became specialized through selection to maintain the ancestral dosage of homologous X-Y gene pairs that function as broadly expressed regulators of transcription, translation and protein stability. We propose that beyond its roles in testis determination and spermatogenesis, the Y chromosome is essential for male viability, and has unappreciated roles in Turner (tm) s syndrome and in phenotypic differences between the sexes in health and disease

Convergent evolution of the genomes of marine mammals

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and are therefore a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and de novo assembled the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome, and that a subset were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that while convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare

Brief psychosocial education, not core stabilization, reduced incidence of low back pain: results from the Prevention of Low Back Pain in the Military (POLM) cluster randomized trial

<p>Abstract</p> <p>Background</p> <p>Effective strategies for the primary prevention of low back pain (LBP) remain elusive with few large-scale clinical trials investigating exercise and education approaches. The purpose of this trial was to determine whether core stabilization alone or in combination with psychosocial education prevented incidence of low back pain in comparison to traditional lumbar exercise.</p> <p>Methods</p> <p>The Prevention of Low Back Pain in the Military study was a cluster randomized clinical study with four intervention arms and a two-year follow-up. Participants were recruited from a military training setting from 2007 to 2008. Soldiers in 20 consecutive companies were considered for eligibility (n = 7,616). Of those, 1,741 were ineligible and 1,550 were eligible but refused participation. For the 4,325 Soldiers enrolled with no previous history of LBP average age was 22.0 years (SD = 4.2) and there were 3,082 males (71.3%). Companies were randomly assigned to receive traditional lumbar exercise, traditional lumbar exercise with psychosocial education, core stabilization exercise, or core stabilization with psychosocial education, The psychosocial education session occurred during one session and the exercise programs were done daily for 5 minutes over 12 weeks. The primary outcome for this trial was incidence of low back pain resulting in the seeking of health care.</p> <p>Results</p> <p>There were no adverse events reported. Evaluable patient analysis (4,147/4,325 provided data) indicated no differences in low back incidence resulting in the seeking of health care between those receiving the traditional exercise and core stabilization exercise programs. However, brief psychosocial education prevented low back pain episodes regardless of the assigned exercise approach, resulting in a 3.3% (95% CI: 1.1 to 5.5%) decrease over two years (numbers needed to treat (NNT) = 30.3, 95% CI = 18.2 to 90.9).</p> <p>Conclusions</p> <p>Core stabilization has been advocated as preventative, but offered no such benefit when compared to traditional lumbar exercise in this trial. Instead, a brief psychosocial education program that reduced fear and threat of low back pain decreased incidence of low back pain resulting in the seeking of health care. Since this trial was conducted in a military setting, future studies are necessary to determine if these findings can be translated into civilian populations.</p> <p>Trial Registration</p> <p><a href="http://www.clinicaltrials.gov/ct2/show/NCT00373009">NCT00373009</a> at ClinicalTrials.gov - <url>http://clinicaltrials.gov/</url></p

Predictors of Occurrence and Severity of First Time Low Back Pain Episodes: Findings from a Military Inception Cohort

Primary prevention studies suggest that additional research on identifying risk factors predictive of low back pain (LBP) is necessary before additional interventions can be developed. In the current study we assembled a large military cohort that was initially free of LBP and followed over 2 years. The purposes of this study were to identify baseline variables from demographic, socioeconomic, general health, and psychological domains that were predictive of a) occurrence; b) time; and c) severity for first episode of self-reported LBP. Baseline and outcome measures were collected via web-based surveillance system or phone to capture monthly information over 2 years. The assembled cohort consisted of 1230 Soldiers who provided self-report data with 518 (42.1%) reporting at least one episode of LBP over 2 years. Multivariate logistic regression analysis indicated that gender, active duty status, mental and physical health scores were significant predictors of LBP. Cox regression revealed that the time to first episode of LBP was significantly shorter for Soldiers that were female, active duty, reported previous injury, and had increased BMI. Multivariate linear regression analysis investigated severity of the first episode by identifying baseline predictors of pain intensity, disability, and psychological distress. Education level and physical fitness were consistent predictors of pain intensity, while gender, smoking status, and previous injury status were predictors of disability. Gender, smoking status, physical health scores, and beliefs of back pain were consistent predictors of psychological distress. These results provide additional data to confirm the multi-factorial nature of LBP and suggest future preventative interventions focus on multi-modal approaches that target modifiable risk factors specific to the population of interest

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl