Study design and the sampling of deleterious rare variants in biobank-scale datasets.

One key component of study design in population genetics is the "geographic breadth" of a sample (i.e., how broad a region across which individuals are sampled).

Nightingale: web components for protein feature visualization.

Motivation: The visualization of biological data is a fundamental technique that enables researchers to understand and explain biology. Some of these visualizations have become iconic, for instance: tree views for taxonomy, cartoon rendering of 3D protein structures or tracks to represent features in a gene or protein, for instance in a genome browser. Nightingale provides visualizations in the context of proteins and protein features.

Tyroviruses are a new group of temperate phages that infect Bacillus species in soil environments worldwide.

Background: Bacteriophages are widely considered to be highly abundant and genetically diverse, with their role in the evolution and virulence of many pathogens becoming increasingly clear. Less attention has been paid on phages preying on Bacillus, despite the potential for some of its members, such as Bacillus anthracis, to cause serious human disease.

Results: We have isolated five phages infecting the causative agent of anthrax, Bacillus anthracis.

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility.

Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls.

Polygenic score accuracy in ancient samples: Quantifying the effects of allelic turnover.

Polygenic scores link the genotypes of ancient individuals to their phenotypes, which are often unobservable, offering a tantalizing opportunity to reconstruct complex trait evolution. In practice, however, interpretation of ancient polygenic scores is subject to numerous assumptions. For one, the genome-wide association (GWA) studies from which polygenic scores are derived, can only estimate effect sizes for loci segregating in contemporary populations.

Implications of intensive care unit admissions among medicare beneficiaries following resection of pancreatic cancer.

Background: Intensive care unit (ICU) use has increased among patients with cancer. We sought to define factors associated with ICU admissions among patients with pancreatic cancer and characterize trends in mortality among hospital survivors.

Methods: The Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database was used to identify patients with pancreatic cancer who underwent resection.

Isolation and Characterisation of the Genus and Phylogenetic Investigation of the Bacteriophages.

is a highly diverse genus containing over 200 species that can be problematic in both industrial and medical settings. This is mainly attributed to sp. being intrinsically resistant to an array of antimicrobial compounds, hence alternative treatment options are needed.

End-of-Life Hospice Use and Medicare Expenditures Among Patients Dying of Hepatocellular Carcinoma.

Background: The increasing incidence of hepatocellular carcinoma (HCC) coupled with rising health care costs contributes to high end-of-life expenditures. The current study aimed to characterize health care expenditures and hospice use among patients with HCC using a large, national database.

Methods: The Surveillance, Epidemiology, and End Results (SEER)-Medicare-linked database was used to identify patients with HCC.

A variant-centric perspective on geographic patterns of human allele frequency variation.

A key challenge in human genetics is to understand the geographic distribution of human genetic variation. Often genetic variation is described by showing relationships among populations or individuals, drawing inferences over many variants. Here, we introduce an alternative representation of genetic variation that reveals the relative abundance of different allele frequency patterns.

A Rapid Method for the Detection of Diarrhetic Shellfish Toxins and Azaspiracid Shellfish Toxins in Washington State Shellfish by Liquid Chromatography Tandem Mass Spectrometry.

Background: Diarrhetic shellfish toxins (DSTs) in domestic shellfish and azaspiracids (AZAs) in imported products are emerging seafood safety issues in the United States. In addition to causing gastrointestinal illnesses, some of these toxins are also carcinogenic and genotoxic. Efficient analytical strategies are needed for their monitoring in U.

The community compositions of three nitrogen removal wastewater treatment plants of different configurations in Victoria, Australia, over a 12-month operational period.

Amplicon sequence fingerprinting of communities in activated sludge systems have provided data revealing the true level of their microbial biodiversity and led to suggestions of which intrinsic and extrinsic parameters might affect the dynamics of community assemblage. Most studies have been performed in China and Denmark, and comparatively little information is available for plants in other countries. This study looked at how the communities of three plants in Victoria, Australia, treating domestic sewage changed with season.

The religious/spiritual beliefs and needs of cancer survivors who underwent cancer-directed surgery.

Objective: We sought to characterize patients' preferences for the role of religious and spiritual (R&S) beliefs and practices during cancer treatment and describe the R&S resources desired by patients during the perioperative period.

Method: A cross-sectional survey was administered to individuals who underwent cancer-directed surgery. Data on demographics and R&S beliefs/preferences were collected and analyzed.

Inside the courtroom: An analysis of malpractice litigation in gallbladder surgery.

Background: Cholecystectomy is one of the most commonly performed operations in the United States, yet it still carries up to a 6% risk of major morbidity. Lawsuits are a major source of emotional, financial, and personal stress for surgeons. We sought to characterize malpractice claims associated with gallbladder surgery as well as define contributing factors and costs with these claims.

Do Religious/Spiritual Preferences and Needs of Cancer Patients Vary Based on Clinical- and Treatment-Level Factors?

Background: The objective of this study is to characterize the religion and spiritual (R&S) needs of patients who undergo cancer-directed surgery. In addition, we seek to examine how R&S needs vary based on R&S identity and clinical and surgical treatment characteristics.

Patients And Methods: A cross-sectional survey was administered to potential participants who were recruited through outpatient clinics and online.

Exploring the operating factors controlling Kouleothrix (type 1851), the dominant filamentous bacterial population, in a full-scale A2O plant.

This study reveals that the abundance of the filament Kouleothrix (Eikelboom type 1851) correlated positively with poor settleability of activated sludge biomass in a Japanese full-scale nutrient removal wastewater treatment plant sampled over a one-year period. 16S rRNA amplicon sequence data confirmed that Kouleothrix was the dominant filament in the plant, with a relative abundance of 3.06% positively correlated with sludge volume index (SVI) (R = 0.

Health expenditures and financial burden among patients with major gastrointestinal cancers relative to other common cancers in the United States.

Background: Gastrointestinal cancers contribute substantially to the cost of health care. We sought to quantify and compare the financial burden associated with treatment of gastrointestinal cancers versus other common nongastrointestinal cancers.

Methods: The Medical Expenditure Panel Survey from 2006 to 2015 was used to identify individuals with gastrointestinal cancer, other nongastrointestinal cancer (breast/prostate or lung), or no history of malignancy.

Complete Genome Sequence of Moraxella osloensis Strain YV1, Isolated from an Australian Wastewater Treatment Plant.

We report the complete genome sequence of strain YV1, which was isolated from a wastewater treatment plant in Australia. The YV1 genome comprises a 2,615,801-bp chromosome and four plasmids. strain YV1 displays the distinctive morphology of Eikelboom morphotype 1863.

Evaluation of costs and outcomes of physician-owned hospitals across common surgical procedures.

Introduction: The Affordable Care Act introduced restrictions on the creation of new physician-owned hospitals (POH). We sought to define whether POH status was associated with differences in care.

Methods: Patients undergoing one of ten surgical procedures were identified using Medicare Standard Analytic Files.

HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn's Disease.

Background & Aims: Anti-tumor necrosis factor (anti-TNF) therapies are the most widely used biologic drugs for treating immune-mediated diseases, but repeated administration can induce the formation of anti-drug antibodies. The ability to identify patients at increased risk for development of anti-drug antibodies would facilitate selection of therapy and use of preventative strategies.

Methods: We performed a genome-wide association study to identify variants associated with time to development of anti-drug antibodies in a discovery cohort of 1240 biologic-naïve patients with Crohn's disease starting infliximab or adalimumab therapy.

The Phylogeny, Biodiversity, and Ecology of the in Activated Sludge.

It is now clear that several of the filamentous bacteria in activated sludge wastewater treatment plants globally, are members of the phylum They appear to be more commonly found in treatment plants designed to remove nitrogen (N) and phosphorus (P), most of which operate at long sludge ages and expose the biomass to anaerobic conditions. The seem to play an important beneficial role in providing the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations. A few commonly extend beyond the floc surface, while others can align in bundles, which may facilitate interfloc bridging and hence generate a bulking sludge.

Bacteriophages in Natural and Artificial Environments.

Bacteriophages (phages) are biological entities that have attracted a great deal of attention in recent years. They have been reported as the most abundant biological entities on the planet and their ability to impact the composition of bacterial communities is of great interest. In this review, we aim to explore where phages exist in natural and artificial environments and how they impact communities.