Overview of the early campaign diagnostics for the SPARC tokamak (invited).

The SPARC tokamak is a high-field, Bt0 ∼12 T, medium-sized, R0 = 1.85 m, tokamak that is presently under construction in Devens, MA, led by Commonwealth Fusion Systems. It will be used to de-risk the high-field tokamak path to a fusion power plant and demonstrate the commercial viability of fusion energy.

Detecting Cholangiocarcinoma in the Setting of Primary Sclerosing Cholangitis: Is Biliary Tract Fluorescence In Situ Hybridization Helpful?

Introduction/objective: Biliary brushing cytology (BB) to detect cholangiocarcinoma (CCA) is integral in the surveillance of patients with primary sclerosing cholangitis (PSC). Since reactive changes can mimic carcinoma, indeterminant results are frequent. Fluorescence in situ hybridization (FISH) using the UroVysion probe set has been advocated to enhance the detection of CCA.

Overview of the neutron diagnostic systems for the SPARC tokamak.

Neutron measurement is the primary tool in the SPARC tokamak for fusion power (Pfus) monitoring, research on the physics of burning plasmas, validation of the neutronics simulation workflows, and providing feedback for machine protection. A demanding target uncertainty (10% for Pfus) and coverage of a wide dynamic range (>8 orders of magnitude going up to 5 × 1019 n/s), coupled with a fast-track timeline for design and deployment, make the development of the SPARC neutron diagnostics challenging. Four subsystems are under design that exploit the high flux of direct DT and DD plasma neutrons emanating from a shielded opening in a midplane diagnostic port.

Neutronics simulations for the design of neutron flux monitors in SPARC.

This paper presents the development and application of high-fidelity neutronic models of the SPARC tokamak for the design of neutron flux monitors (NFM) for application during plasma operations. NFMs measure the neutron flux in the tokamak hall, which is related to fusion power via calibration. We have explored Boron-10 gamma-compensated ionization chambers (ICs) and parallel-plate Uranium-238 fission chambers (FCs).

Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.

Insertions and deletions constitute the second most important source of natural genomic variation. Insertions and deletions make up to 25% of genomic variants in humans and are involved in complex evolutionary processes including genomic rearrangements, adaptation, and speciation. Recent advances in long-read sequencing technologies allow detailed inference of insertions and deletion variation in species and populations.

Setting Up the JBrowse 2 Genome Browser.

JBrowse 2 is a modular genome browser that can visualize many common genomic file formats. While JBrowse 2 supports a variety of different usages, it is particularly suited for deployment on websites, such as model organism databases or other web-based genomic data resources. This protocol provides detailed instructions for setting up JBrowse 2 on an Ubuntu Linux web server, loading a reference genome from a FASTA format file, and adding a gene annotation track from a GFF3 format file.

The mutuality account of parenthood: a subjective approach to parent-child relationships.

Stimulated by development of reproductive technologies, many current bioethical accounts of parenthood focus on defining parenthood at or around birth. They tend to exclude from their scope some parent-child relationships that develop later in a child's life. In reality, a parent-child relationship can emerge or dissolve over time: the parents of person A as an adolescent or adult may be different to her parents when she is a young child.

Performance of fluorescence in situ hybridization in biliary brushings with equivocal cytology: an institutional experience.

Introduction: Biliary brushing (BB) cytology has a sensitivity of 15%-65% and specificity approaching 100% for detecting malignancy. Fluorescence in-situ hybridization (FISH) using the UroVysion probe set has been advocated to enhance the detection of malignancies with reported sensitivity of 43%-84%. We sought to evaluate the performance of FISH in BB with equivocal cytology at our institution.

Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters.

Correctly identifying the strength of selection that parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes of host-parasite interactions. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can be used to identify infection-driven capture biases.

Perspectives of young adults diagnosed with early psychosis using coordinated specialty care in Texas on substance use and substance use interventions.

Aim: Despite known prevalence of substance use (SU) among young people experiencing early psychosis and increasing evidence for the relationship between certain substances (e.g., cannabis) and psychosis, there are no specialized interventions developed for effectively addressing substance use among young people participating in coordinated early psychosis services.

EUS-guided Gastroenterostomy: A Multicenter International Study Comparing Benign and Malignant Diseases.

Background: Endoscopic ultrasound (EUS)-guided gastroenterostomy (EUS-GE) is a minimally invasive therapy for patients with gastric outlet obstruction without the risks of surgical bypass and the limited long-term efficacy of enteral self-expanding metal stent placement. However, due to its novelty, there is a lack of significant data comparing long-term outcomes of patients with EUS-GE, based on the underlying disease. In this study, we compare outcomes of EUS-GE on benign versus malignant indications.

An Updated Contextual Approach to Mesothelial Proliferations in Pleural Effusion Cytology Leveraging Morphology, Ancillary Studies, and Novel Biomarkers.

Context.—: Pleural effusions are common cytologic specimens that can be leveraged to make diagnoses of malignancy that drive appropriate patient management. However, the overlap in morphologic features of reactive mesothelial proliferations, mesotheliomas, and adenocarcinomas can create diagnostic pitfalls in the cytologic evaluation of pleural fluids.

Randomized trial of gastric and colorectal endoscopic submucosal dissection defect closure comparing a novel through-the-scope suturing system with an over-the-scope suturing system (with video).

Background And Aims: Mucosal closure adds time but reduces adverse events associated with endoscopic submucosal dissection (ESD). We aimed to assess the closure time (CT), technical success, and cost-effectiveness between a novel through-the-scope helix tack suture system (TTSS) and the over-the-scope suturing system (OTSS).

Methods: In this single-center, prospective, randomized trial, all patients undergoing ESD with anticipated closure were randomized 1:1 to TTSS (study group) or OTSS (control group).

Is It Just for a Screening Program to Give People All the Information They Want?

Genomic screening at population scale generates many ethical considerations. One is the normative role that people's preferences should play in determining access to genomic information in screening contexts, particularly information that falls beyond the scope of screening. We expect both that people will express a preference to receive such results and that there will be interest from the professional community in providing them.

JBrowse 2: a modular genome browser with views of synteny and structural variation.

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views.

Comparison of Primary Care Patients' and Unannounced Standardized Patients' Perceptions of Care.

The objective of this study was to compare unannounced standardized patient (USP) and patient reports of care. Patient satisfaction surveys and USP checklist results collected at an urban, public hospital were compared to identify items included in both surveys. Qualitative commentary was reviewed to better understand USP and patient satisfaction survey data.

Salivary Antimicrobial Peptide Histatin-5 Does Not Display Zn(II)-Dependent or -Independent Activity against Streptococci.

Histatin-5 (Hst5) is a member of the histatin superfamily of cationic, His-rich, Zn(II)-binding peptides in human saliva. Hst5 displays antimicrobial activity against fungal and bacterial pathogens, often in a Zn(II)-dependent manner. In contrast, here we showed that under conditions that are characteristic of human saliva, Hst5 does not kill seven streptococcal species that normally colonize the human oral cavity and oropharynx.

Longitudinal outcomes of the endoscopic resection of nonpolypoid dysplastic lesions in patients with inflammatory bowel disease.

Background And Aims: Patients with inflammatory bowel disease (IBD) are at risk of developing dysplasia. According to the Surveillance for Colorectal Endoscopic Neoplasia Detection and Management in Inflammatory Bowel Disease Patients: International Consensus Recommendations, "After complete removal of endoscopically resectable nonpolypoid dysplastic lesions, surveillance colonoscopy is suggested rather than colectomy." We sought to add data to the literature and hypothesized that the endoscopic resection of nonpolypoid colorectal dysplasia (NP-CRD) is safe and effective.

JBrowse Jupyter: a Python interface to JBrowse 2.

Motivation: JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself.

Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community.

While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity.

Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes.

Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus .

Metastatic Anal Squamous Cell Carcinoma Presenting as an Indeterminate Biliary Stricture Diagnosed By Cholangioscopy.

Anal squamous cell carcinoma (SCC) rarely metastasizes outside the pelvis. Although liver involvement has been described, biliary strictures from metastatic disease are exceedingly rare. We report a case of a patient with metastatic anal SCC presenting as a biliary stricture, which was identified on endoscopic retrograde cholangiopancreatography with single-operator cholangioscopy.