Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement.

The Data Coordinating Center (DCC) of the Human Tumor Atlas Network (HTAN) has played a crucial role in enabling the broad sharing and effective utilization of HTAN data within the scientific community. Data from the first phase of HTAN are now available publicly. We describe the diverse datasets and modalities shared, multiple access routes to HTAN assay data and metadata, data standards, technical infrastructure and governance approaches, as well as our approach to sustained community engagement.

The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI.

The exploration of genotypic variants impacting phenotypes is a cornerstone in genetics research. The emergence of vast collections containing deeply genotyped and phenotyped families has made it possible to pursue the search for variants associated with complex diseases. However, managing these large-scale datasets requires specialized computational tools tailored to organize and analyze the extensive data.

Text Captioning Buffers Against the Effects of Background Noise and Hearing Loss on Memory for Speech.

Objective: Everyday speech understanding frequently occurs in perceptually demanding environments, for example, due to background noise and normal age-related hearing loss. The resulting degraded speech signals increase listening effort, which gives rise to negative downstream effects on subsequent memory and comprehension, even when speech is intelligible. In two experiments, we explored whether the presentation of realistic assistive text captioned speech offsets the negative effects of background noise and hearing impairment on multiple measures of speech memory.

Getting comfortable with disability: The short- and long-term effects of a clinical encounter.

Background: Physicians report discomfort when interacting with patients with disabilities, which can negatively impact the quality of healthcare they provide.

Objective/hypothesis: An intervention structured around a formative clinical encounter was assessed for its effectiveness in changing comfort towards treating patients with disabilities. It was predicted that this encounter would have a positive short- and long-term impact on medical students.

Family Involvement in Traumatic Brain Injury Inpatient Rehabilitation: A Propensity Score Analysis of Effects on Outcomes During the First Year After Discharge.

Objective: To evaluate the effect of family attendance at inpatient rehabilitation therapy sessions on traumatic brain injury (TBI) patient outcomes at discharge and up to 9 months postdischarge.

Design: Propensity score methods are applied to the TBI Practice-Based Evidence database, a database consisting of multisite, prospective, longitudinal, and observational data.

Setting: Nine inpatient rehabilitation centers in the United States.

Contextualized Treatment in Traumatic Brain Injury Inpatient Rehabilitation: Effects on Outcomes During the First Year After Discharge.

Objective: To evaluate the effect of providing a greater percentage of therapy as contextualized treatment on acute traumatic brain injury (TBI) rehabilitation outcomes.

Design: Propensity score methods are applied to the TBI Practice-Based Evidence (TBI-PBE) database, a database consisting of multi-site, prospective, longitudinal observational data.

Setting: Acute inpatient rehabilitation.

Advanced Therapy in Traumatic Brain Injury Inpatient Rehabilitation: Effects on Outcomes During the First Year After Discharge.

Objective: To use causal inference methods to determine if receipt of a greater proportion of inpatient rehabilitation treatment focused on higher level functions, for example, executive functions, ambulating over uneven surfaces (advanced therapy [AdvTx]), results in better rehabilitation outcomes.

Design: A cohort study using propensity score methods applied to the traumatic brain injury practice-based evidence (TBI-PBE) database, a database consisting of multisite, prospective, longitudinal observational data.

Setting: Acute inpatient rehabilitation facilities.

Simplifying research access to genomics and health data with Library Cards.

The volume of genomics and health data is growing rapidly, driven by sequencing for both research and clinical use. However, under current practices, the data is fragmented into many distinct datasets, and researchers must go through a separate application process for each dataset. This is time-consuming both for the researchers and the data stewards, and it reduces the velocity of research and new discoveries that could improve human health.

Damaging de novo mutations diminish motor skills in children on the autism spectrum.

In individuals with autism spectrum disorder (ASD), de novo mutations have previously been shown to be significantly correlated with lower IQ but not with the core characteristics of ASD: deficits in social communication and interaction and restricted interests and repetitive patterns of behavior. We extend these findings by demonstrating in the Simons Simplex Collection that damaging de novo mutations in ASD individuals are also significantly and convincingly correlated with measures of impaired motor skills. This correlation is not explained by a correlation between IQ and motor skills.

Coaching the Coach: A Program for Development of Faculty Portfolio Coaches.

Problem: Faculty coaching is recognized as an essential element for effective use of portfolios in undergraduate medical education, yet best practices for training these coaches are uncertain.

Intervention: New portfolio coaches participated in a multifaceted training program that included orienting modules, a 7.5-hr training workshop featuring analysis of reflective writing, an Observed Structured Teaching Exercise (OSTE), and subsequent longitudinal coaches' meetings for timely task training.

Cavitation and spallation in liquid metal droplets produced by subpicosecond pulsed laser radiation.

The deformation and fragmentation of liquid metal microdroplets by intense subpicosecond Ti:sapphire laser pulses is experimentally studied with stroboscopic shadow photography. The experiments are performed at a peak intensity of 10^{14}W/cm^{2} at the target's surface, which produces shock waves with pressures in the Mbar range. As a result of such a strong impact, the droplet is transformed into a complex-shaped hollow structure that undergoes asymmetrical expansion and eventually fragments.

Effort Not Speed Characterizes Comprehension of Spoken Sentences by Older Adults with Mild Hearing Impairment.

In spite of the rapidity of everyday speech, older adults tend to keep up relatively well in day-to-day listening. In laboratory settings older adults do not respond as quickly as younger adults in off-line tests of sentence comprehension, but the question is whether comprehension itself is actually slower. Two unique features of the human eye were used to address this question.

Phase II Study of a Non-Platinum-Containing Doublet of Paclitaxel and Pemetrexed with Bevacizumab as Initial Therapy for Patients with Advanced Lung Adenocarcinomas.

Introduction: Many patients with lung cancers cannot receive platinum-containing regimens owing to comorbid medical conditions. We designed the PPB (paclitaxel, pemetrexed, and bevacizumab) regimen to maintain or improve outcomes while averting the unique toxicities of platinum-based chemotherapies.

Methods: We enrolled patients with untreated, advanced lung adenocarcinomas with measurable disease and no contraindications to bevacizumab.

Robust classification of protein variation using structural modelling and large-scale data integration.

Existing methods for interpreting protein variation focus on annotating mutation pathogenicity rather than detailed interpretation of variant deleteriousness and frequently use only sequence-based or structure-based information. We present VIPUR, a computational framework that seamlessly integrates sequence analysis and structural modelling (using the Rosetta protein modelling suite) to identify and interpret deleterious protein variants. To train VIPUR, we collected 9477 protein variants with known effects on protein function from multiple organisms and curated structural models for each variant from crystal structures and homology models.

Cognitive aging and hearing acuity: modeling spoken language comprehension.

The comprehension of spoken language has been characterized by a number of "local" theories that have focused on specific aspects of the task: models of word recognition, models of selective attention, accounts of thematic role assignment at the sentence level, and so forth. The ease of language understanding (ELU) model (Rönnberg et al., 2013) stands as one of the few attempts to offer a fully encompassing framework for language understanding.

A Bruner-Potter effect in audition? Spoken word recognition in adult aging.

Bruner and Potter (1964) demonstrated the surprising finding that incrementally increasing the clarity of images until they were correctly recognized (ascending presentation) was less effective for recognition than presenting images in a single presentation at that same clarity level. This has been attributed to interference from incorrect perceptual hypotheses formed on the initial presentations under ascending conditions. We demonstrate an analogous effect for spoken word recognition in older adults, with the size of the effect predicted by working memory span.

Development of a database for translational spinal cord injury research.

Efforts to understand spinal cord injury (SCI) and other complex neurotrauma disorders at the pre-clinical level have shown progress in recent years. However, successful translation of basic research into clinical practice has been slow, partly because of the large, heterogeneous data sets involved. In this sense, translational neurological research represents a "big data" problem.

Cultural Validation of the Turkish Version of the Infertility Self-Efficacy Scale-Short Form (TISE-SF).

Purpose: To translate and test the psychometric properties of the Turkish version of the Infertility Self-Efficacy Scale-Short Form (TISE-SF).

Methods: The convenience sample consisted of 120 infertile women. A psychometric research design was used with content and construct validity and reliability.

Harnessing technology to improve clinical trials: study of real-time informatics to collect data, toxicities, image response assessments, and patient-reported outcomes in a phase II clinical trial.

Purpose: In clinical trials, traditional monitoring methods, paper documentation, and outdated collection systems lead to inaccuracies of study information and inefficiencies in the process. Integrated electronic systems offer an opportunity to collect data in real time.

Patients And Methods: We created a computer software system to collect 13 patient-reported symptomatic adverse events and patient-reported Karnofsky performance status, semi-automated RECIST measurements, and laboratory data, and we made this information available to investigators in real time at the point of care during a phase II lung cancer trial.

Expectation and entropy in spoken word recognition: effects of age and hearing acuity.

Unlabelled: BACKGROUND/STUDY CONTEXT: Older adults, especially those with reduced hearing acuity, can make good use of linguistic context in word recognition. Less is known about the effects of the weighted distribution of probable target and nontarget words that fit the sentence context (response entropy). The present study examined the effects of age, hearing acuity, linguistic context, and response entropy on spoken word recognition.

The PPAR alpha agonist gemfibrozil is an ineffective treatment for spinal cord injured mice.

Peroxisome Proliferator Activated Receptor (PPAR)-α is a key regulator of lipid metabolism and recent studies reveal it also regulates inflammation in several different disease models. Gemfibrozil, an agonist of PPAR-α, is a FDA approved drug for hyperlipidemia and has been shown to inhibit clinical signs in a rodent model of multiple sclerosis. Since many studies have shown improved outcome from spinal cord injury (SCI) by anti-inflammatory and neuroprotective agents, we tested the efficacy of oral gemfibrozil given before or after SCI for promoting tissue preservation and behavioral recovery after spinal contusion injury in mice.

Germline mutations in BAP1 predispose to melanocytic tumors.

Common acquired melanocytic nevi are benign neoplasms that are composed of small, uniform melanocytes and are typically present as flat or slightly elevated pigmented lesions on the skin. We describe two families with a new autosomal dominant syndrome characterized by multiple, skin-colored, elevated melanocytic tumors. In contrast to common acquired nevi, the melanocytic neoplasms in affected family members ranged histopathologically from epithelioid nevi to atypical melanocytic proliferations that showed overlapping features with melanoma.

Trends in hypothesis testing and related variables in nursing research: a retrospective exploratory study.

Aim: To compare the inclusion and the influences of selected variables on hypothesis testing during the 1980s and 1990s.

Background: In spite of the emphasis on conducting inquiry consistent with the tenets of logical positivism, there have been no studies investigating the frequency and patterns of hypothesis testing in nursing research

Data Sources: The sample was obtained from the journal Nursing Research which was the research journal with the highest circulation during the study period under study. All quantitative studies published during the two decades including briefs and historical studies were included in the analyses

Review Methods: A retrospective design was used to select the sample.