PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes.

Background: One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence and shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain. More importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it.

Using Performance Status to Identify Risk of Acute Care Transfer in Inpatient Cancer Rehabilitation.

Objective: To identify patient factors associated with acute care transfer (ACT) among cancer survivors admitted for inpatient medical rehabilitation.

Design: An exploratory, observational design was used to analyze retrospective data from electronic medical records.

Setting: Data were obtained from 3 separate inpatient rehabilitation hospitals within a private rehabilitation hospital system in the Northeast.

Host interactions of novel species belonging to multiple families infecting bacterial host, WH2.

Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the order. Despite identifying over 600 genomes computationally, only few have been successfully isolated.

Compounding Phages for Therapeutic Applications.

species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by CF418 or CF116 experienced fatal exacerbations. spp.

Women's perceptions and preferences for cervical cancer screening in light of updated guidelines.

Background: Updated risk-based guidelines for cervical cancer screening (CCS) allow for individualized screening that minimizes unnecessary testing. However, these guidelines are complex and may not be easily understandable to patients.

Purpose: To describe women's perceptions and preferences about CCS in light of recent guideline changes.

Establishing thresholds for cytokine storm and defining their relationship to disease severity in respiratory viral infections.

Previous studies have identified cytokines associated with respiratory virus infection illness outcome. However, few studies have included comprehensive cytokine panels, longitudinal analyses, and/or simultaneous assessment across the severity spectrum. This, coupled with subjective definitions of cytokine storm syndrome (CSS), have contributed to inconsistent findings of cytokine signatures, particularly with COVID severity.

PRFect: A tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes.

Background: One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence, shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain, but more importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the original amino acids, followed by all the alternate frame amino acids.

The Promise and Pitfalls of Prophages.

Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains.

A geospatial approach to identify patterns of antibiotic susceptibility at a neighborhood level in Wisconsin, United States.

The global threat of antimicrobial resistance (AMR) varies regionally. This study explores whether geospatial analysis and data visualization methods detect both clinically and statistically significant variations in antibiotic susceptibility rates at a neighborhood level. This observational multicenter geospatial study collected 10 years of patient-level antibiotic susceptibility data and patient addresses from three regionally distinct Wisconsin health systems (UW Health, Fort HealthCare, Marshfield Clinic Health System [MCHS]).

Host interactions of novel species belonging to multiple families infecting bacterial host, WH2.

Unlabelled: Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the order. Despite identifying over 600 genomes computationally, only few have been successfully isolated.

Creating an Extraordinary Experience for Women Undergoing Cystoscopy: A Patient-Centered Approach to Process Improvement.

Objective: To re-examine and improve the cystoscopy process for women based on patient input. While cystoscopy is a common urological procedure, women perceive it as invasive, personal, and fear-inducing. Patients want to be treated as individuals and not just another "procedure.

Longitudinal Analysis of the Microbiome and Metabolome in the 5xfAD Mouse Model of Alzheimer's Disease.

Recent reports implicate gut microbiome dysbiosis in the onset and progression of Alzheimer's disease (AD), yet studies involving model animals overwhelmingly omit the microbial perspective. Here, we evaluate longitudinal microbiomes and metabolomes from a popular transgenic mouse model for familial AD (5xfAD). Cecal and fecal samples from 5xfAD and wild-type B6J (WT) mice from 4 to 18 months of age were subjected to shotgun Illumina sequencing.

Predicting the capsid architecture of phages from metagenomic data.

Tailed phages are viruses that infect bacteria and are the most abundant biological entities on Earth. Their ecological, evolutionary, and biogeochemical roles in the planet stem from their genomic diversity. Known tailed phage genomes range from 10 to 735 kilobase pairs thanks to the size variability of the protective protein capsids that store them.

Translation of Karnofsky Performance Status (KPS) for use in inpatient cancer rehabilitation.

Background: Better tools are needed to predict functional decline and oncologic prognosis in inpatient cancer rehabilitation. The Karnofky Performance Status (KPS) is a widely used scale of functional performance in oncology, although the scale differs from current rehabilitation terminology. Use of the KPS in inpatient rehabilitation may support a shared method of communication between cancer rehabilitation providers and the primary oncology teams.

MultiPhATE2: code for functional annotation and comparison of phage genomes.

To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations.

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes.

One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before.

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes.

Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the family have been shown to produce only one type of CIS-a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term injection systems (BIS).

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome.

The approximately 10 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction.

PHANOTATE: a novel approach to gene identification in phage genomes.

Motivation: Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments.

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates.

Summary: To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline: multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric databases.

Perspectives and preferences for a mobile health tool designed to facilitate HPV vaccination among young men who have sex with men.

We sought to understand young men who have sex with men (YMSM) perspectives and preferred features for a mobile health (mHealth) tool designed to facilitate human papillomavirus (HPV) vaccination. YMSM were recruited on a popular social/sexual networking app to participate in online focus groups. Discussions were designed to elicit what the men would want in a mHealth tool specific for sexual health and HPV.

Sexual Misconduct Policies at Institutes of Higher Education: An Integrative Review.

Although federal legislation designed to advance sexual misconduct policies at institutes of higher education (IHEs) has been in effect for decades, recent national attention has put more pressure on IHEs to combat sexual violence on their campuses. Thus, the past few years have yielded significant research that examines federal compliance, dissemination, and perception of IHE sexual misconduct policies. This integrative review was conducted to assess sexual misconduct policies in the United States and the potential to prevent and combat sexual violence at IHEs through these policies.

Serine protease modulation of Dependence Receptors and EMT protein expression.

Expression of the tumour suppressor Deleted in Colorectal Cancer (DCC) and the related protein neogenin is reduced by the mammalian serine protease chymotrypsin or the bacterial serine protease subtilisin, with increased cell migration. The present work examines whether these actions are associated with changes in the expression of cadherins, β-catenin and vimentin, established markers of the Epithelial-Mesenchymal Transition (EMT) which has been linked with cell migration and tumour metastasis. The results confirm the depletion of DCC and neogenin and show that chymotrypsin and subtilisin also reduce expression of β-catenin in acutely prepared tissue sections but not in human mammary adenocarcinoma MCF-7 or MDA-MB-231 cells cultured in normal media, or primary normal human breast cells.

A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage.

Background: Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hypervariable phage tail fiber that enables host tropism switching. Subsequent surveys for DGRs conclude that the majority identified to date are bacterial or archaeal in origin.