alignparse: A Python package for parsing complex features from high-throughput long-read sequencing.

Advances in sequencing technology have made it possible to generate large numbers of long, high-accuracy sequencing reads. For instance, the new PacBio Sequel platform can generate hundreds of thousands of high-quality circular consensus sequences in a single run (Hebert et al., 2018; Rhoads & Au, 2015).

From dangerous branches to urban banyan: Facilitating aerial root growth of Ficus rubiginosa.

Large urban trees have many benefits. However, falling branches pose a serious hazard to both people and infrastructure. In several tree species, aerial roots grow down from branches to the ground.

Human health risks due to airborne polychlorinated biphenyls are highest in New Bedford Harbor communities living closest to the harbor.

In response to concerns raised by communities surrounding the New Bedford Harbor Superfund site, we completed a field and modeling study that concluded the harbor is the primary source of polychlorinated biphenyls (PCBs) in air around the harbor. The follow-up question from residents was whether the PCBs measured in air pose a risk to their health. The US Environmental Protection Agency focuses their site-specific, risk-based decisions for site clean-up on cancers.

Center Variation in Chest Tube Duration and Length of Stay After Congenital Heart Surgery.

Background: Nearly every child undergoing congenital heart surgery has chest tubes placed intraoperatively. Center variation in removal practices and impact on outcomes has not been well described. This study evaluated variation in chest tube management practices and outcomes across centers.

Tributyltin disrupts fin development in Fundulus heteroclitus from both PCB-sensitive and resistant populations: Investigations of potential interactions between AHR and PPARγ.

Tributyltin (TBT) and dioxin-like polychlorinated biphenyls (PCBs) are environmental contaminants that are highly toxic to fish and co-occur in New Bedford Harbor (NBH), an estuarine Superfund site located in Massachusetts, USA. Atlantic killifish (Fundulus heteroclitus) that reside in NBH (and other highly contaminated sites along the east coast of the United States) have developed resistance to activation of the aryl hydrocarbon receptor (AHR) pathway and the toxicity of dioxin-like chemicals, such as 3,3',4,4',5-pentachlorobiphenyl, PCB126. In many biological systems, TBT disregulates adipose and bone development via the PPARγ-RXR pathway; AHR activation also disrupts adipose and bone homeostasis, potentially through molecular crosstalk between AHR and PPARγ.

Youth Study Recruitment Using Paid Advertising on Instagram, Snapchat, and Facebook: Cross-Sectional Survey Study.

Background: The use of paid social media advertising for targeted study recruitment is an effective strategy in health research and evaluation, specifically to reach diverse youth participants. Although the literature adequately describes the utility of Facebook in recruitment, limited information exists for social media platforms that are more popular with youth, specifically Instagram and Snapchat.

Objective: This paper outlines a paid advertising approach using Instagram, Snapchat, and Facebook to evaluate a statewide youth marijuana prevention campaign.

The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data.

Exploring food preparation practices in families with and without school-aged childhood cancer survivors.

Objective: Survival rates for paediatric cancers have increased dramatically since the 1970s, but childhood cancer survivors (CCS) are at increased risk for several chronic diseases throughout life. Nutrition interventions promoting healthy family meals may support wellness for survivors, but little research has explored CCS family food preparation habits. The goal of the present study was to describe and compare food preparation practices of CCS and non-CCS families.

Healthy Timing and Spacing of Pregnancy: Reducing Mortality Among Women and Their Children.

Accessible, affordable, and high-quality postabortion care (PAC) can prevent maternal death and disability and provides an important opportunity to prevent future unintended pregnancies. This supplement offers learnings on PAC provision from the community of partners around the world, including service delivery and community engagement models, approaches to support facility-based providers, best practices in pre- and post-procedure counseling, and approaches to institutionalize PAC in public- and private-sector health systems.

Persistent free-floating pelvic trophoblastic cysts following an interstitial ectopic pregnancy.

Persistent trophoblast after ectopic pregnancy has been demonstrated at the surgical site or as peritoneal implants. A 37-year-old woman (G5P2) experienced persistently low levels of beta-human chorionic gonadotropin (hCG) after surgical treatment for an interstitial pregnancy. Evaluation for persistent trophoblast, gestational trophoblastic neoplasm and heterophilic antibodies was negative.

Rheumatologists' insight into medication adherence in patients with rheumatoid arthritis: A qualitative study.

Background: Medication non-adherence is prevalent among patients with rheumatoid arthritis (RA). Rheumatologists are specialists in medication prescribing and counselling for RA, but their insights regarding medication adherence have not been studied.

Objective: To explore rheumatologists' insights into medication adherence in patients with RA.

Meal planning values impacted by the cancer experience in families with school-aged survivors-a qualitative exploration and recommendations for intervention development.

Purpose: Increased cardiovascular disease and second cancer risks among childhood cancer survivors (CCS) makes them and their families important audiences for nutrition intervention. Family meals and home cooking practices have been associated with improved diet and health, but there is a gap in the literature on understanding these behaviors and their motivating values among CCS families. This study qualitatively explores family meal values and behaviors in a sample of CCS parent-child dyads.

Recovery After Mild Traumatic Brain Injury in Patients Presenting to US Level I Trauma Centers: A Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study.

Importance: Most traumatic brain injuries (TBIs) are classified as mild (mTBI) based on admission Glasgow Coma Scale (GCS) scores of 13 to 15. The prevalence of persistent functional limitations for these patients is unclear.

Objectives: To characterize the natural history of recovery of daily function following mTBI vs peripheral orthopedic traumatic injury in the first 12 months postinjury using data from the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) study, and, using clinical computed tomographic (CT) scans, examine whether the presence (CT+) or absence (CT-) of acute intracranial findings in the mTBI group was associated with outcomes.

When and where plant-soil feedback may promote plant coexistence: a meta-analysis.

Plant-soil feedback (PSF) theory provides a powerful framework for understanding plant dynamics by integrating growth assays into predictions of whether soil communities stabilise plant-plant interactions. However, we lack a comprehensive view of the likelihood of feedback-driven coexistence, partly because of a failure to analyse pairwise PSF, the metric directly linked to plant species coexistence. Here, we determine the relative importance of plant evolutionary history, traits, and environmental factors for coexistence through PSF using a meta-analysis of 1038 pairwise PSF measures.

Assessment of Explicitly Stated Interval Change on Noncontrast Head CT Radiology Reports.

Background And Purpose: Consistent and standardized reporting of interval change for certain diagnoses may improve the clinical utility of radiology reports. The purpose of this study was to assess explicitly stated interval change of various findings in noncontrast head CT reports.

Materials And Methods: A retrospective review was performed on successive noncontrast head CT radiology reports from the first 2 weeks of January 2014.

Multimodal Sensing with a Three-Dimensional Piezoresistive Structure.

Sensors that reproduce the complex characteristics of cutaneous receptors in the skin have important potential in the context of artificial systems for controlled interactions with the physical environment. Multimodal responses with high sensitivity and wide dynamic range are essential for many such applications. This report introduces a simple, three-dimensional type of microelectromechanical sensor that incorporates monocrystalline silicon nanomembranes as piezoresistive elements in a configuration that enables separate, simultaneous measurements of multiple mechanical stimuli, such as normal force, shear force, and bending, along with temperature.

Improving medication adherence in adult kidney transplantation (IMAKT): A pilot randomised controlled trial.

Resources to support long-term medication adherence in kidney transplantation are limited. This study aimed to determine the efficacy of an intervention designed for kidney transplant recipients to enhance medication adherence. A single-blind, multi-site, 12-month pilot randomised controlled trial was conducted at all five public hospitals providing adult kidney transplantation in Victoria, Australia.

A randomized trial to reduce smoking among American Indians in South Dakota: The walking forward study.

Background: Lung cancer is an important public health issue, particularly among American Indians (AIs). The reported decline in tobacco use for most racial/ethnic groups is not observed among AIs. This project was designed to address the research question, "Why don't more Northern Plains American Indians alter tobacco use behaviors known to increase the risk of cancer?"

Methods: Guided by the Theory of Planned Behavior, a multi-component intervention study was implemented.

Medication adherence and cost-related medication non-adherence in patients with rheumatoid arthritis: A cross-sectional study.

Aim: First, to assess the clinical characteristics and medication adherence to oral rheumatoid arthritis (RA) medications in patients with RA. Second, to examine adherence determinants with a focus on the effect of medication out-of-pocket (OOP) costs on medication adherence to oral RA medications. Lastly, to examine cost-related medication non-adherence (CRN) in patients with RA.

Advanced approaches for quantitative characterization of thermal transport properties in soft materials using thin, conformable resistive sensors.

Noninvasive methods for precise characterization of the thermal properties of soft biological tissues such as the skin can yield vital details about physiological health status including at critical intervals during recovery following skin injury. Here, we introduce quantitative measurement and characterization methods that allow rapid, accurate determination of the thermal conductivity of soft materials using thin, skin-like resistive sensor platforms. Systematic evaluations of skin at eight different locations and of six different synthetic skin-mimicking materials across sensor sizes, measurement times, and surface geometries (planar, highly curvilinear) validate simple scaling laws for data interpretation and parameter extraction.

Visual Attention Cut Points for Driver Fitness in Parkinson's Disease.

This study determined whether the Useful Field of View™ Risk Index (UFOV RI) adds value as a predictor of on-road outcomes in drivers with Parkinson's disease (PD) and compared with community-dwelling older drivers (Controls). A total of 101 PD drivers and 138 Controls underwent a comprehensive driving evaluation, including an on-road assessment. Logistic regression analyses determined the associations of age, gender, visual attention, and disease severity to on-road outcomes.

Polycyclic aromatic hydrocarbon contamination and source profiling in watersheds serving three small Wisconsin, USA cities.

Polycyclic aromatic hydrocarbons (PAHs) continue to be common environmental contaminants. The anthropogenic sources of these compounds are broadly classed as petrogenic and pyrogenic, but more importantly specific sources including activities such as coal burning, oil spills, and application of coal tar sealants can be identified based on several types of data analysis. Several studies have focused on PAHs in sediments of lakes, streams, and stormwater ponds in larger urban areas, finding contamination arising from a number of different sources and correlating well to land use in the nearby watershed.

Transitioning adolescents to adult nephrology care: a systematic review of the experiences of adolescents, parents, and health professionals.

A challenging phase for adolescents with chronic kidney disease (CKD) is the transition from a pediatric to an adult health service. Failure to adequately prepare adolescents for transfer to adult care can lead to a decline in attendance to the adult clinic and an increase in the rate of non-adherence to medical treatment. The aim of this systematic review was to analyze studies exploring the experiences of adolescents, parents, and health professionals regarding the transition process of adolescents with CKD.