OncoTree: A Cancer Classification System for Precision Oncology.

Purpose: Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research.

Methods: To meet these needs, we have developed OncoTree, an open-source cancer classification system.

An investigation of glutamate quantification with PRESS and MEGA-PRESS.

Glutamate is an important neurotransmitter. Although many studies have measured glutamate concentration in vivo using magnetic resonance spectroscopy (MRS), researchers have not reached a consensus on the accuracy of glutamate quantification at the field strength of 3 T. Besides, there is not an optimal MRS protocol for glutamate measurement.

Cross-coupling reactions with esters, aldehydes, and alcohols.

Cross-coupling reactions to form biaryls and π bond addition reactions to prepare substituted carbonyls or alcohols represent two of the most frequently performed families of chemical reactions. Recent progress in catalysis has uncovered substantial overlap between these two seemingly distinct topics. In particular, esters, aldehydes, and alcohols have been shown to act as carbon-based coupling partners in a range of Ni- and Pd-catalyzed reactions to prepare amides, ketones, substituted alcohols, alkanes, and more.

Trends and developments in hip and knee arthroplasty technology.

The developments in hip and knee arthroplasty over recent years have aimed to improve outcomes, reduce complications and improve implant survival. This review describes some of the most interesting trends and developments in this important and fast-moving field. Notable developments have included ceramic hip resurfacing, mini hip stems, cementless knee replacement and the wider adoption of the dual mobility articulation for hip arthroplasty.

Offshore pelagic subsidies dominate carbon inputs to coral reef predators.

Coral reefs were traditionally perceived as productive hot spots in oligotrophic waters. While modern evidence indicates that many coral reef food webs are heavily subsidized by planktonic production, the pathways through which this occurs remain unresolved. We used the analytical power of carbon isotope analysis of essential amino acids to distinguish between alternative carbon pathways supporting four key reef predators across an oceanic atoll.

Placing assistive technology and telecare in everyday practices of people with dementia and their caregivers: findings from an embedded ethnography of a national dementia trial.

Background: Policy makers and care providers see assistive technology and telecare as potential products to support people with dementia to live independently in their homes and communities. Previous research rarely examined how people with dementia and their caregivers actually use such technology. The study examined how and why people living with dementia and their caregivers used assistive technology and telecare in their own homes.

The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms.

Pediatric therapy-related myeloid neoplasms (tMN) occur in children after exposure to cytotoxic therapy and have a dismal prognosis. The somatic and germline genomic alterations that drive these myeloid neoplasms in children and how they arise have yet to be comprehensively described. We use whole exome, whole genome, and/or RNA sequencing to characterize the genomic profile of 84 pediatric tMN cases (tMDS: n = 28, tAML: n = 56).

Mammary carcinoma arising in an adenoma in a ewe.

A large, firm, multi-cystic mammary gland mass grew slowly over 4 y in a 12-y-old, female Finn-Shetland cross sheep. A diagnosis of epithelial malignancy was suspected following fine-needle aspiration cytology at 30 mo after initial observation. The sheep was euthanized when the flock was downsized 18 mo later.

Collegiate athlete brain data for white matter mapping and network neuroscience.

We describe a dataset of processed data with associated reproducible preprocessing pipeline collected from two collegiate athlete groups and one non-athlete group. The dataset shares minimally processed diffusion-weighted magnetic resonance imaging (dMRI) data, three models of the diffusion signal in the voxel, full-brain tractograms, segmentation of the major white matter tracts as well as structural connectivity matrices. There is currently a paucity of similar datasets openly shared.

In-home dementia caregiving is associated with greater psychological burden and poorer mental health than out-of-home caregiving: a cross-sectional study.

Introduction: Caregivers who live with a person with dementia who receives care, compared with those who live elsewhere, are often considered to experience greater levels of psychological and affective burden. The evidence for this is, however, only limited to studies employing small sample sizes and that failed to examine caregivers' psychological wellbeing. We address these issues in a large cohort of dementia caregivers.

Neural signatures of inhibitory control in intra-sentential code-switching: Evidence from fMRI.

In this study we examined the neural control mechanisms that are at play when habitual code-switchers read code-switches embedded in a sentence context. The goal was also to understand if and to what extent the putative control network that is engaged during the comprehension of code-switched sentences is modulated by the linguistic regularity of those switches. Towards that goal, we tested two different types of code switches (switches at the noun-phrase boundary and switches at the verb-phrase boundary) that despite being both represented in naturalistic corpora of code switching, show different distributional properties.

Quantifying the unreported and unaccounted domestic and foreign commercial catch of sharks and rays in Western Australia.

Reliable catch information is scarce for most sharks and rays worldwide, with almost half of the stocks considered to be Data Deficient due to limited species-specific catch statistics. Western Australia (WA) hosts a diverse number of shark and ray species, some of which are considered to be threatened with extinction at a global level. Commercial catch statistics only account for shark and ray landings.

Does prospective acceptability of an intervention influence refusal to participate in a randomised controlled trial? An interview study.

Background: The generalizability of findings of Randomised Controlled Trials (RCTs) is undermined by low or biased recruitment. Reasons for participant refusal are infrequently reported in published literature.

Aims: To apply the Theoretical Framework of Acceptability (TFA) to: (1) explore patient-reported reasons for declining to participate in a RCT comparing a new service model (patient-initiated appointments) with standard care (appointments scheduled by clinician) for managing blepharospasm and hemifacial spasm; (2) to explore associations between decliners' perceptions of acceptability and non-participation.

Increasing Intracellular Levels of Iron with Ferric Ammonium Citrate Leads to Reduced P-glycoprotein Expression in Human Immortalised Brain Microvascular Endothelial Cells.

Purpose: P-glycoprotein (P-gp) at the blood-brain barrier (BBB) precludes the brain penetration of many xenobiotics and mediates brain-to-blood clearance of β-amyloid, which accumulates in the Alzheimer's disease (AD) brain. Zinc and copper are reported to modulate BBB expression and function of P-gp; however, the impact of exogenous iron, which accumulates in AD, on P-gp dynamics remains unknown.

Methods: P-gp protein and MDR1 transcript levels were assessed in immortalised human cerebral microvascular endothelial (hCMEC/D3) cells treated with ferric ammonium citrate (FAC; 250 μM, 72 h), by Western blotting and RT-qPCR, respectively.

COVID-19 Adaptations in the Care of Patients with Opioid Use Disorder: a Survey of California Primary Care Clinics.

Background: With the onset of the COVID-19 crisis, many federal agencies relaxed policies regulating opioid use disorder treatment. The impact of these changes has been minimally documented. The abrupt nature of these shifts provides a naturalistic opportunity to examine adaptations for opioid use disorder treatment in primary care.

The effectiveness and cost-effectiveness of assistive technology and telecare for independent living in dementia: a randomised controlled trial.

Objectives: The use of assistive technology and telecare (ATT) has been promoted to manage risks associated with independent living in people with dementia but with little evidence for effectiveness.

Methods: Participants were randomly assigned to receive an ATT assessment followed by installation of all appropriate ATT devices or limited control of appropriate ATT. The primary outcomes were time to institutionalisation and cost-effectiveness.

Inflammation Is Associated with Worse Outcome in the Whole Cohort but with Better Outcome in Triple-Negative Subtype of Breast Cancer Patients.

Inflammation has been linked with cancer, but whether it is part of the problem or part of the solution remains to be a matter of debate in breast cancer. Our group and others have demonstrated that inflammation aggravates cancer progression; however, some claim that inflammation may support immune cell infiltration and suppress cancer. We defined the gene set variation analysis of the Molecular Signatures Database Hallmark inflammatory response gene set as the inflammatory pathway score and analyzed 3632 tumors in total from 4 breast cancer cohorts (METABRIC, TCGA, GSE25066, and GSE21094).

Embracing diversity and inclusivity in an academic setting: Insights from the Organization for Human Brain Mapping.

Scientific research aims to bring forward innovative ideas and constantly challenges existing knowledge structures and stereotypes. However, women, ethnic and cultural minorities, as well as individuals with disabilities, are systematically discriminated against or even excluded from promotions, publications, and general visibility. A more diverse workforce is more productive, and thus discrimination has a negative impact on science and the wider society, as well as on the education, careers, and well-being of individuals who are discriminated against.

Histological characterization of the gastrointestinal tract of the adult horseshoe crab (Limulus polyphemus) with special reference to the stomach.

The American horseshoe crab (Limulus polyphemus) is one of four extant species in the Order Xiphosura, subphylum Chelicerata, and are evolutionarily more closely related to scorpions and spiders, than crabs. The basic structure, function, and physiology of these invertebrates and their internal organs are not well documented in the literature. In this study, the gastrointestinal system, with a focus on the stomach, of adult L.

SCISSOR: a framework for identifying structural changes in RNA transcripts.

High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile.

Reaction screening in multiwell plates: high-throughput optimization of a Buchwald-Hartwig amination.

Chemical space is vast, and chemical reactions involve the complex interplay of multiple variables. As a consequence, reactions can fail for subtle reasons, necessitating screening of conditions. High-throughput experimentation (HTE) techniques enable a more comprehensive array of data to be obtained in a relatively short amount of time.

St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem.

Effective data sharing is key to accelerating research to improve diagnostic precision, treatment efficacy, and long-term survival in pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.

Site-Level Variation in the Characteristics and Care of Infants With Neonatal Opioid Withdrawal.

Background And Objectives: Variation in pediatric medical care is common and contributes to differences in patient outcomes. Site-to-site variation in the characteristics and care of infants with neonatal opioid withdrawal syndrome (NOWS) has yet to be quantified. Our objective was to describe site-to-site variation in maternal-infant characteristics, infant management, and outcomes for infants with NOWS.