ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

Development and validation of the Negative Attitudes towards CBT Scale

Background: Clinicians commonly fail to use cognitive-behavioural therapy (CBT) adequately, but the reasons for such omissions are not well understood. Aims: The objective of this study was to create and validate a measure to assess clinicians’ attitudes towards CBT - the Negative Attitudes towards CBT Scale (NACS). Method: The participants were 204 clinicians from various mental healthcare fields. Each completed the NACS, measures of anxiety and self-esteem, and a measure of therapists’ use of CBT and non-CBT techniques and their confidence in using those techniques. Exploratory factor analysis was used to determine the factor structure of the NACS, and scale internal consistency was tested. Results: A single, 16-item scale emerged from the factor analysis of the NACS, and that scale had good internal consistency. Clinicians’ negative attitudes and their anxiety had different patterns of association with the use of CBT and other therapeutic techniques. Conclusions: The findings suggest that clinicians’ attitudes and emotions each need to be considered when understanding why many clinicians fail to deliver the optimum version of evidence-based CBT. They also suggest that training effective CBT clinicians might depend on understanding and targeting such internal states

Peptides Derived from Vascular Endothelial Growth Factor B Show Potent Binding to Neuropilin-1

Vascular endothelial growth factors (VEGFs) regulate significant pathways in angiogenesis, myocardial and neuronal protection, metabolism, and cancer progression. The VEGF-B isoform is involved in cell survival, anti-apoptotic and antioxidant mechanisms, through binding to VEGF receptor 1 and neuropilin-1 (NRP-1). We employed surface plasmon resonance technology and X-ray crystallography to analyse the molecular basis of the interaction between VEGF-B and the b1 domain of NRP-1, and developed VEGF-B - C-terminus derived peptides to be used as chemical tools for studying VEGF-B - NRP-1 related pathways. Peptide lipidation was used as a means to stabilise the peptides. VEGF-B - derived peptides containing a C-terminal arginine show potent binding to NRP1-b1. Peptide lipidation increased binding residence time and improved plasma stability. A crystal structure of a peptide with NRP-1 demonstrated that VEGF-B peptides bind at the canonical C-terminal Arginine binding site. VEGF-B C-terminus imparts higher affinity for NRP-1 than the corresponding VEGF-A_{165} region. This tight binding may impact on the activity and selectivity of the full-length protein. The VEGF-B_{167} derived peptides were more effective than VEGF-A_{165} peptides in blocking functional phosphorylation events. Blockers of VEGF-B function have potential applications in diabetes and non-alcoholic fatty liver disease

Ferromagnetic resonances in single-crystal yttrium iron garnet nanofilms fabricated by metal-organic decomposition

Tunable microwave and millimeter wave oscillators and bandpass filters with ultra-low phase noise play a critical role in electronic devices, including wireless communication, microelectronics, and quantum computing. Magnetic materials, such as yttrium iron garnet (YIG), possess ultra-low phase noise and a ferromagnetic resonance tunable up to tens of gigahertz. Here, we report structural and magnetic properties of single-crystal 60 and 130 nm-thick YIG films prepared by metal-organic decomposition epitaxy. These films, consisting of multiple homoepitaxially grown monolayers, are atomically flat and possess magnetic properties similar to those grown with liquid-phase epitaxy, pulsed laser deposition, and sputtering. Our approach does not involve expensive high-vacuum deposition systems and is a true low-cost alternative to current commercial techniques that have the potential to transform the industry

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations]

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

Factors related to psychotherapists' self-assessment when treating anxiety and other disorders.

The aim of the study was to replicate and extend recent findings regarding therapists' self-assessment biases. This study examined clinicians' estimates of their abilities when working with general clinical groups and with anxious patients, and of the recovery/improvement rates of their clients. It also considered what clinician personality traits and clinical practice elements were associated with such estimates. A total of 195 out 801 clinicians completed a survey regarding self-ratings, team ratings, therapy outcomes for their clients, and their own personality traits. The great majority of clinicians rated themselves and their teams as being better clinicians than their peers, though not to as extreme a level as in the previous study. They also reported exceptionally positive therapy outcomes. Due to the large proportion of non-responders, it is possible that these findings do not reflect actual self-assessment bias, but a greater willingness to participate among clinicians who are more skilled and with particular personality styles. However, the data suggest that perceptions of skill and therapy outcome might be associated with clinician personality characteristics, though not with other clinical practice variables. These interpretations should be treated with caution due to the limited response rate. Different possible explanations for these patterns of self-assessment are outlined, including conscious and unconscious processes. Methods for enhancing accurate skill perception are discussed, including self-monitoring and supervision

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts