An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance.

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

SUMMARY: Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. AVAILABILITY AND IMPLEMENTATION: https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Measuring positive and negative body talk in men and women: The development and validation of the Body Talk Scale.

Research suggests that positive and negative body talk are important factors in people's body image, however, the instruments designed to measure body talk are generally designed for use with a specific gender and primarily measure negative body talk. To address the shortcomings in the existing measures, the Body Talk Scale (BTS) was designed to measure both positive and negative body talk in men and women. The current study examines the development and psychometric properties of this new scale in two samples of adults, both including men and women. Study 1 focused on the development and examined the factor structure of the original scale items. Study 2 confirmed the factor structure and examined the concurrent validity, incremental validity, test-retest reliability of the scale, and also gender differences. The results indicated that the BTS is a 14-item scale that contains three subscales (Negative Fat Talk, Negative Muscle Talk, and Positive Body Talk) and demonstrates good concurrent validity, incremental validity, and test-retest reliability. Gender comparisons on all three subscales indicated that men engage in more positive body talk than women. The findings demonstrate that the BTS is a useful measure of positive and negative body talk in both men and women.

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.

The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.

A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays.

SUMMARY: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons. AVAILABILITY AND IMPLEMENTATION: The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics.org/#/assayValidation, https://github.com/jgans/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Single-Sided Deafness-Outcomes of Three Interventions for Profound Unilateral Sensorineural Hearing Loss: A Randomized Clinical Trial.

OBJECTIVE: A comparison of three interventions for profound unilateral sensorineural hearing loss. STUDY DESIGN: Prospective, crossover randomized clinical trial. PARTICIPANTS: Fifteen participants with profound unilateral sensorineural hearing loss. INTERVENTIONS: Three potential technical interventions were compared: Bone Conduction Device on softband, Contralateral Routing of Signal (CROS), and Remote Microphone . Each intervention was randomly trialed for a period of 3 weeks, separated by a 1 week washout period. OUTCOME MEASURES: Speech in noise recognition test performed under four conditions (lateral noise poorer ear, lateral noise better ear, speech poorer ear, speech better ear). Standardized questionnaires (Abbreviated Profile of Hearing Aid Benefit, Bern Benefit in Single Sided Deafness Questionnaire, and Speech, Spatial, and Other Qualities 12) were used to evaluate amplification benefit at baseline and following each intervention. RESULTS: The use of remote microphone provided the best results in the speech recognition in noise test. A benefit in some signal-to-noise ratios was presented of the CROS over bone conduction device on softband in the Speech Poor Ear condition. On questionnaires of benefit, participants did not rate a particular intervention as significantly better than any other. Following the study, CROS was the intervention preferred by the 8 of 15 participants (53%). The majority of participants (80%) chose to continue with an intervention rather than no treatment. CONCLUSION: The use of all interventions resulted in increased performance in speech recognition in noise and rated higher on subjective benefits in comparison with baseline. People with SSD are a heterogeneous population when considering perceived difficulties. Future research should focus on segmenting the population of SSD depending on factors such as etiology, high frequency loss in the better ear, and age of acquired loss for the poorer ear. This stratification may possibly increase the benefit for the patient in terms of more individual-based clinical routines.

A Multinational Cost-Consequence Analysis of a Bone Conduction Hearing Implant System-A Randomized Trial of a Conventional vs. a Less Invasive Treatment With New Abutment Technology.

Background: It is hypothesized that, for patients with hearing loss, surgically placing an implant/abutment combination whilst leaving the subcutaneous tissues intact will improve cosmetic and clinical results, increase quality of life (QoL) for the patient, and reduce medical costs. Here, incremental costs and consequences associated with soft tissue preservation surgery with a hydroxyapatite (HA)-coated abutment (test) were compared with the conventional approach, soft tissue reduction surgery with an all-titanium abutment (control). Methods: A cost-consequence analysis was performed based on data gathered over a period of 3 years in an open randomized (1:1) controlled trial (RCT) running in four European countries (The Netherlands, Spain, France, and Sweden). Subjects with conductive or mixed hearing loss or single-sided sensorineural deafness were included. Results: During the first year, in the Netherlands (NL), France (FR), and Spain (ES) a net cost saving was achieved in favor of the test intervention because of a lower cost associated with surgery time and adverse event treatments [NL €86 (CI -50.33; 219.20), FR €134 (CI -3.63; 261.30), ES €178 (CI 34.12; 97.48)]. In Sweden (SE), the HA-coated abutment was more expensive than the conventional abutment, which neutralized the cost savings and led to a negative cost (SE €-29 CI -160.27; 97.48) of the new treatment modality. After 3 years, the mean cost saving reduced to €17 (CI -191.80; 213.30) in the Netherlands, in Spain to €84.50 (CI -117.90; 289.50), and in France to €80 (CI -99.40; 248.50). The mean additional cost in Sweden increased to €-116 (CI -326.90; 68.10). The consequences in terms of the subjective audiological benefit and Health-related quality of life (HRQoL) were comparable between treatments. A trend was identified for favorable results in the test group for some consequences and statistical significance is achieved for the cosmetic outcome as assessed by the clinician. Conclusions: From this multinational cost-consequence analysis it can be discerned that health care systems can achieve a cost saving during the first year that regresses after 3 years, by implementing soft tissue preservation surgery with a HA-coated abutment in comparison to the conventional treatment. The cosmetic results are better. (sponsored by Cochlear Bone Anchored Solutions AB; Clinical and health economic evaluation with a new Baha® abutment design combined with a minimally invasive surgical technique, ClinicalTrials.gov NCT01796236).

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.

There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.

Hearing vs. engaging in negative body talk: an examination of adult men.

This study examined the negative body talk both engaged in and heard by adult men as separate constructs and how both constructs are related to men's body dissatisfaction and muscle dysmorphia. Data were collected from 260 adult men on negative body talk both engaged in and heard, body fat dissatisfaction, muscle dissatisfaction, and muscle dysmorphia. Results indicated that the muscle talk that men engaged in acted as a mediator between the relationship between the body talk men heard and muscle dissatisfaction. The same mediating relationship also existing for muscle dysmorphia symptoms. Similarly, the fat talk that men engaged in mediated the relationship between the fat talk that men heard from friends and body fat dissatisfaction. In addition, age was negatively related to muscle talk and body mass index was positively correlated with fat talk. These findings suggest that the relationship between the body talk that men hear from others and their body image may be explained by the body talk that men verbally engage in themselves.

Audiological and clinical outcomes of a transcutaneous bone conduction hearing implant: Six-month results from a multicentre study.

OBJECTIVES: To compare the hearing performance of patients with conductive and mild mixed hearing loss and single-sided sensorineural deafness provided with a new transcutaneous bone conduction hearing implant (the Baha Attract System) with unaided hearing as well as aided with a sound processor on a softband. Furthermore, to evaluate safety and subjective benefit before and after implantation of the test device. PARTICIPANTS: Fifty-four adult patients in five participating centres were enrolled in this prospective study. Baseline data were collected during a pre-operative visit, and after a softband trial, all patients were implanted unilaterally. Follow-up visits were scheduled at 10 days, 4, 6, 12 weeks and 6 months. MAIN OUTCOME MEASURES: Free-field hearing thresholds pure-tone average (PTA4 in dB HL; mean threshold at 500, 1000, 2000, 4000 Hz; primary outcome measure). Individual free-field hearing thresholds, speech recognition in quiet and in noise, soft tissue status during follow-up and subjective benefit as measured with the Abbreviated Profile of Hearing Aid Benefit (APHAB), Speech, Spatial and Qualities of Hearing Scale (SSQ) and Health Utilities Index (HUI) questionnaires. RESULTS: Implantation of the Baha Attract System resulted in favourable audiological outcomes compared to unaided conditions. On the primary outcome parameter, a statistically significant improvement was observed compared to unaided hearing for the patients with conductive/mixed hearing loss (mean PTA4 difference -20.8 dB HL, SD 9.8; P < 0.0001) and for the patients with single-sided sensorineural deafness (SSD) (mean PTA4 difference -21.6 dB HL, SD 12.2; P < 0.0001). During all audiology tests, the non-test ear was blocked. Statistically significant improvements were also recorded in speech tests in quiet and noise compared to unaided hearing for the conductive/mixed hearing loss group and for speech in quiet in the SSD group. Compared to the pre-operative measurement with softband, no significant differences were recorded in the PTA4 free-field hearing threshold or the other audiological outcomes in either of the groups (P > 0.05). Soft tissue-related issues observed during follow-up included numbness, pain/discomfort at the implant site and to a lesser extent pressure-related skin complications. A declining trend was noted in the rate of these complications during follow-up. Approximately 20% of patients reported some degree of numbness and 38% (slight) pain/discomfort at final follow-up of 6 months. Good results on the subjective benefit questionnaires were observed, with statistically significant improvements on APHAB and SSQ questionnaires, and on the hearing attribute of HUI3. CONCLUSIONS: The Baha Attract System provided a significant improvement in hearing performance and subjective benefit compared to the pre-operative unaided condition (with the non-test ear blocked). Hearing performance of the Baha Attract was similar to a test situation with the same sound processor on a softband. A proportion of the patients reported numbness and pain/discomfort at the implant site during follow-up, especially during the first post-operative weeks. Based on the results of the current multicentre study, the Baha Attract can be considered as a treatment option for patients with the aforementioned hearing losses. Especially in the SSD patients, a careful selection procedure is warranted. Therefore, a pre-operative trial should be part of the decision-making process before fitting a patient with the Baha Attract System.

Let's Get Involved! The Impact of Service Learning on Drinking Perceptions, Alcohol Use, and Protective Behaviors in College Students.

While there is mounting support for the efficacy of alcohol-based curriculum infusion (CI) programs, studies have yielded mixed results. Insufficient attention has been given to nuances in the types of CI. Using a two-group pretest-posttest quasi-experimental design, this study assessed two forms of CI, information-only (IO) and service learning (SL), on drinking perceptions, drinking behavior, and protective behaviors. When the entire sample was considered, CI significantly improved participants' drinking perceptions and behavior. SL was more effective than IO for one measure of drinking behavior and for protective behaviors. Interestingly, there was a greater decrease in men's drinking behavior and increase in women's protective behaviors in the SL group. This study may help guide health professionals, educators, and faculty members interested in developing alcohol-focused CI programs.

Effects of acute high-intensity exercise on cognitive performance in trained individuals: A systematic review.

BACKGROUND: High-intensity exercise is generally considered to have detrimental effects on cognition. However, high fitness levels are suggested to alleviate this effect. OBJECTIVES: The specific objective of this review was to evaluate the literature on the effect of acute high-intensity exercise on cognitive performance in trained individuals. METHODS: Studies were sourced through electronic databases, reference lists of retrieved articles, and manual searches of relevant reviews. Included studies examined trained participants, included a high-intensity exercise bout, used a control or comparison group/condition, and assessed cognitive performance via general laboratory tasks during or ≤10min following exercise cessation. RESULTS: Ten articles met the inclusion criteria. Results indicated that the effect of acute high-intensity exercise on cognitive performance in trained individuals is dependent on the specific cognitive domain being assessed. Generally, simple tasks were not affected, while the results on complex tasks remain ambiguous. Accuracy showed little tendency to be influenced by high-intensity exercise compared to measures of speed. CONCLUSION: Multiple factors influence the acute exercise-cognition relationship and thus future research should be highly specific when outlining criteria such as fitness levels, exercise intensity, and exercise mode. Furthermore, greater research is needed assessing more cognitive domains, greater exercise durations/types, and trained populations at high intensities.

An exploratory evaluation of the feasibility, acceptability, and efficacy of the mental fitness disordered eating program in schools.

The present study examines the feasibility, acceptability, and efficacy of a tiered professional development disordered eating prevention program. A pretest/posttest quasi-experimental design assessed elementary and junior high school faculty and staff's disordered eating knowledge and attitudes. Findings indicate participants experienced increased awareness of students' susceptibility to and the severity of disordered eating, increased self-efficacy about referring students to appropriate resources, and overall perceived acceptability of the training. Improved knowledge and attitudes suggest faculty and staff are better equipped to identify at-risk individuals at an early stage, increasing the likelihood of recovery from disordered eating behaviors or disordered eating.

"Drunk in Love": The Portrayal of Risk Behavior in Music Lyrics.

The current study investigated the prevalence of multiple risk behaviors in popular music lyrics as well as the contexts within which they occur. We conducted a content analysis of the top 20 Billboard songs from 2009 to 2013 in the genres of rap, country, adult contemporary, rock, R&B/hip-hop, and pop, coding for the presence of alcohol, marijuana, nonmarijuana drugs, and sex as well as the contexts intoxication, binging/addiction, partying/socializing, disregard for consequences, and emotional states. The contexts relationship status and degradation were also coded for when sex was present. Of the 600 songs, 212 mentioned sexual behaviors, which were most frequent in rap and R&B/hip-hop. Alcohol was the next most frequent risk behavior, again with greatest mention in rap and R&B/hip-hop. Alcohol, marijuana, and nonmarijuana drugs were most often associated with positive emotions, and sex was most often described within the context of casual relationships. Alcohol and sex were associated with disregard for consequences most often in 2011, when the "you only live once" motto was most popular. These findings are concerning because exposure to popular music is associated with increased risk behaviors for adolescents and young adults, who are the greatest consumers of music.

Stability, Survival, and Tolerability of an Auditory Osseointegrated Implant for Bone Conduction Hearing: Long-Term Follow-Up of a Randomized Controlled Trial.

OBJECTIVE: To compare implant stability, survival, and soft tissue reactions for a novel (test) and previous generation (control) percutaneous auditory osseointegrated implant for bone conduction hearing at long-term follow-up of 5 years. STUDY DESIGN: Single follow-up visit of a previously completed multicenter, randomized, controlled trial. PATIENTS: Fifty-seven of the 77 participants of a completed randomized controlled trial on a new auditory osseointegrated implant underwent a single follow-up visit 5 years after implantation, which comprised implant stability measurements and collection of Holgers scores. Additionally, implant survival was recorded for all 77 patients from the original trial. RESULTS: The test implant showed significantly higher implant stability quotient (ISQ) values compared with the control implant throughout the 5-year follow-up. Mean area under the curve of ISQ high from baseline to 5 years was 71.6 (standard deviation [SD] ±2.0) and 66.7 (SD ±3.4) for the test and control implant, respectively (p < 0.0001). For both implants, the mean ISQ value recorded at 5 years was higher compared with implantation (test group +2.03 [SD ±2.55, within group p < 0.0001] and control group +2.25 [SD ±4.95, within group p = 0.12]). No difference was noticed in increase from baseline between groups (p = 0.64). Furthermore, evaluation of soft tissue reactions continued to show superiority of the test implant. At the 5-year follow-up visit, one patient (2.5%) presented with a Holgers grade 2 in the test group, compared with four patients (23.5%) in the control group (p = 0.048); no patient presented with more severe soft tissue reactions. Excluding explantations, the survival rate was 95.8% for the test group and 95.0% for the control group. The corresponding rates including explantations were 93.9 and 90.0%. CONCLUSION: The test implant showed superiority in terms of higher mean ISQ values and less adverse soft tissue reactions, both at the single 5-year follow-up visit and during the complete follow-up. In addition, both implants showed an equally high implant survival.

The Effects of Profile Pictures and Friends' Comments on Social Network Site Users' Body Image and Adherence to the Norm.

This study sought to explore the effects of exposure to Facebook body ideal profile pictures and norm conforming comments on users' body image. In addition, the social identity and self-categorization theoretical frameworks were used to explore users' endorsement of a body ideal norm. A mock Facebook page was used to conduct a pretest posttest 2 × 2 between-group web-based experiment that featured body ideal profile pictures (body ideal vs. no body) and body ideal comments (conforming vs. nonconforming). Five hundred and one participants completed the experiment and passed all manipulation checks. Participants viewed pictures and comments on the status page and were able to leave their own comment before exiting. Results demonstrated no significant main effects. However, predispositional body satisfaction significantly moderated the relationship between body ideal pictures and body satisfaction. Most comments supported the body ideal norm. However, in support of self-categorization theory, participants exposed to nonconforming comments made nonconforming comments themselves significantly more than those exposed to conforming comments. The findings demonstrated the importance of continued body image research in social network sites, as well as the potential for self-categorization theory to guide such research.

Estimating the benefit of a second bone anchored hearing implant in unilaterally implanted users with a testband.

Conclusion Using a second bone anchored hearing implant (BAHI) mounted on a testband in unilaterally implanted BAHI users to test its potential advantage pre-operatively under-estimates the advantage of two BAHIs placed on two implants. Objectives To investigate how well speech understanding with a second BAHI mounted on a testband approaches the benefit of bilaterally implanted BAHIs. Method Prospective study with 16 BAHI users. Eight were implanted unilaterally (group A) and eight were implanted bilaterally (group B). Aided speech understanding was measured. Speech was presented from the front and noise came either from the left, right, or from the front in two conditions for group A (with one BAHI, and with two BAHIs, where the second device was mounted on a testband) and in three conditions for group B (same two conditions as group A, and in addition with both BAHIs mounted on implants). Results Speech understanding in noise improved with the additional device for noise from the side of the first BAHI (+0.7 to +2.1 dB) and decreased for noise from the other side (-1.8 dB to -3.9 dB). Improvements were highest (+2.1 dB, p = 0.016) and disadvantages were smallest (-1.8 dB, p = 0.047) with both BAHIs mounted on implants. Testbands yielded smaller advantages and higher disadvantages of the additional BAHI (average difference = -0.9 dB).

"Let's Get This Party Started!": An Analysis of Health Risk Behavior on MTV Reality Television Shows.

Past research has examined portrayals of risk behavior in various media, including television, advertising, and film. To address an underexplored area, this study analyzed drinking, smoking, and sexual activities in MTV reality programming popular among adolescent viewers from 2004 to 2011. Cast members' demographic attributes were also examined in relation to their risk behaviors. Results demonstrated that drinking and casual sexual behaviors were pervasive among cast members. Smoking and more intense sexual behaviors were also present, but to a smaller degree. Men and young adult cast members were more likely to engage in risk behaviors than women and teenage cast members. Also, ethnic/racial minority characters were shown drinking more often than were White cast members. Interpretations of these findings are discussed based in social cognitive theory and the concept of super peers. Implications for future research are provided.