Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale ...studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. Here, we compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups. We test for differences in amplicon sequence variants and operational taxonomic units (ASVs) between these groups. Our findings confirm that these tools identified drastically different numbers and sets of significant ASVs, and that results depend on data pre-processing. For many tools the number of features identified correlate with aspects of the data, such as sample size, sequencing depth, and effect size of community differences. ALDEx2 and ANCOM-II produce the most consistent results across studies and agree best with the intersect of results from different approaches. Nevertheless, we recommend that researchers should use a consensus approach based on multiple differential abundance methods to help ensure robust biological interpretations.
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. ...Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results. We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space. By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Microbiome functional data are frequently analyzed to identify associations between microbial functions (e.g. genes) and sample groups of interest. However, it is challenging to distinguish between ...different possible explanations for variation in community-wide functional profiles by considering functions alone. To help address this problem, we have developed POMS, a package that implements multiple phylogeny-aware frameworks to more robustly identify enriched functions.
The key contribution is an extended balance-tree workflow that incorporates functional and taxonomic information to identify functions that are consistently enriched in sample groups across independent taxonomic lineages. Our package also includes a workflow for running phylogenetic regression. Based on simulated data we demonstrate that these approaches more accurately identify gene families that confer a selective advantage compared with commonly used tools. We also show that POMS in particular can identify enriched functions in real-world metagenomics datasets that are potential targets of strong selection on multiple members of the microbiome.
These workflows are freely available in the POMS R package at https://github.com/gavinmdouglas/POMS.
Supplementary data are available at Bioinformatics online.
Colleges and universities should serve as inclusive environments positioned to provide a strong education to all students. However, bias and discrimination mar the college atmosphere for many. ...Simultaneously, there is a paucity of research that examines student views of diversity and inclusion in both higher education and sport management. Employing mixed methods, this research examined the perceptions of diversity and inclusion among undergraduate students in sport management programs. Data demonstrate that student perceptions differ across measures of sex, race/ethnicity, upbringing, internship experiences, and transfer status. Findings suggest implications for embedding diversity and inclusion topics within sport management curricula to develop competencies crucial to students' educational success and future in the sport industry.
This study’s main purpose was to extend the current understanding of sport management intern satisfaction by investigating how it is related to students’ perceived learning. Undergraduate students (n ...= 139) from 13 sport management programs in the United States completed the surveys while enrolled in their full-time, senior-level capstone internships. The study’s results show a positive, significant relationship between internship satisfaction and perceived learning in personal development and career development. Further, satisfaction with duties at the internship worksite predicted perceived learning in both personal and career development; satisfaction with academic elements of the internship also predicted perceived learning in career development. Interns who engaged in more internships prior to the capstone internship experience had higher levels of satisfaction with their job duties in their capstone internship than students with fewer numbers of early internships. These findings are examined with respect to Kolb’s experiential learning theory and practical implications are outlined.
Background
Breast cancer is the most common cancer among women globally. Recovery from breast cancer treatment can be mentally and physically challenging. SMS text message programs offer a novel way ...to provide health information and support, but few programs are co-designed with consumer representatives.
Objective
This study aims to report the procedures and outcomes of a co-design process of a lifestyle-focused SMS text message program to support women’s mental and physical health after breast cancer treatment.
Methods
We followed an iterative mixed methods two-step process: (1) co-design workshop with consumers and health professionals and researchers to draft text messages and (2) evaluation of message content, which was scored (5-point Likert scale; 1=strongly disagree to 5=strongly agree) for ease of understanding, usefulness, and appropriateness, and readability (Flesch-Kincaid score). Additional free-text responses and semistructured interviews were coded into themes. Messages were edited or deleted based on the evaluations, with consumers’ evaluations prioritized.
Results
In step 1, co-designed text messages (N=189) were semipersonalized, and the main content themes were (1) physical activity and healthy eating, (2) medications and side effects, (3) mental health, and (4) general breast cancer information. In step 2, consumers (n=14) and health professionals and researchers (n=14) provided 870 reviews of 189 messages and found that most messages were easy to understand (799/870, 91.8%), useful (746/870, 85.7%), and appropriate (732/870, 84.1%). However, consumers rated 50 messages differently from health professionals and researchers. On the basis of evaluations, 37.6% (71/189) of messages were deleted, 36.5% (69/189) were edited, and 12 new messages related to fatigue, self-care, and cognition were created. The final 130 text messages had a mean 7.12 (SD 2.8) Flesch-Kincaid grade level and 68.9 (SD 15.5) ease-of-reading score, which represents standard reading ease.
Conclusions
Co-designing and evaluating a bank of evidence-based mental and physical health-themed text messages with breast cancer survivors, health professionals, and researchers was feasible and resulted in a bank of 130 text messages evaluated highly by participants. Some consumer evaluations differed from health professionals and researchers, supporting the importance of co-design.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
COVID-19 lockdowns caused widespread closures of supportive care services for breast cancer survivors in Australia. In a randomized controlled trial, our team's lifestyle-focused, evidence-based SMS ...text message support program (EMPOWER-SMS COVID-19) was found to be acceptable and useful for breast cancer survivors, and it was ready for rapid widespread delivery.
This study aims to evaluate the reach (uptake) of an adapted 3-month lifestyle-focused SMS text message program (EMPOWER-SMS COVID-19) and barriers and enablers to implementation using the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework.
A mixed methods pre-post study was conducted to evaluate the EMPOWER-SMS COVID-19 program. The study evaluated the following aspects: (1) reach/representativeness, which refers to the proportion of participant enrollment (ie, number enrolled/number that visited the study website) and demographics (eg, age, sex, ethnicity, time since completing treatment, Index of Relative Socio-economic Advantage and Disadvantage IRSAD; quintile 1, which refers to most disadvantaged areas, to quintile 5, which refers to least disadvantaged areas, and remoteness); (2) effectiveness, in which participant engagement and acceptability were evaluated using SMS text message reply data and a feedback survey (5-point Likert scale and free-text responses); (3) adoption, which corresponds to the proportion of organizations or health professionals who agreed to promote the program; (4) implementation fidelity and maintenance, which evaluated SMS text message delivery data, opt-outs, costs, and adaptations. Quantitative data were summarized using means and SDs or frequencies and percentages, while qualitative data were analyzed thematically.
With regard to the reach/representativeness of the program, 841/1340 (62.8%) participants enrolled and provided electronic consent. Participants had a mean age of 58.8 (SD 9.8; range 30-87) years. According to the data collected, most participants identified as female (837/840, 99.6%) and White (736/840, 87.6%) and nearly half (418/841, 49.7%) finished treatment ≤18 months ago. Most resided in major cities (574/838, 68.5%) and 30% (251/838) in IRSAD quintile 1 or 2. In terms of effectiveness, 852 replies were received from 511 unique participants (median 1; range 1-26). The most common replies were participants stating how they heard about the program (467/852, 54.8%) or "thank you" (131/852, 15.4%). None of the replies contained urgent safety concerns. Among participants who provided feedback (449/841, 53.4%), most "(strongly) agreed" the SMS text messages were easy to understand (445/448, 99.3%), useful (373/440, 84.8%), helped participants feel supported (388/448, 86.6%), and motivated participants to be physically active (312/445, 70.1%) and eat healthier (313/457, 68.5%). Free-text responses revealed 5 factors influencing engagement: (1) feeling supported and less alone, (2) motivation and reassurance for health self-management, (3) the variety of information, (4) weblinks to information and resources, and (5) the option to save the SMS text messages. Concerning adoption, 50% (18/36) of organizations/health professionals agreed to promote the program. With regard to implementation/maintenance, SMS text messages were delivered as planned (97.43% 41,257/42,344 of SMS text messages were successfully delivered) with minimal opt-outs (62/838, 7.4%) and low cost (Aus $15.40/participant; Aus $1=US $0.67). No adaptations were made during the intervention period. Postintervention adaptations included adding weblinks and participant-selected customizations.
EMPOWER-SMS COVID-19 was implemented quickly, had a broad reach, and had high engagement and acceptability among socioeconomically diverse participants. The program had high fidelity, low cost, and required minimal staff oversight, which may facilitate future implementation. However, further research is needed to evaluate barriers and enablers to adoption and implementation for health professionals and strategies for long-term maintenance.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Male undergraduate sport management majors substantially outnumber females, suggesting that the path to a career in the sport industry is male dominated and gender stereotypes may exist. ...Simultaneously, there is a dearth of research on females’ experiences while enrolled in higher education and within sport management career development. Through qualitative focus groups conducted at two institutions with female sport management majors, this research sought to understand the barriers and sources of support that female students perceive while engaged in this academic discipline. The authors identified four themes—otherness, roles and credibility, prior experiences, and people of influence—all of which help illuminate the lived experience of gender bias among women in the sport management major and generate suggestions for the creation of more inclusive environments that foster persistence.
Two species of endangered, primarily lake-dwelling sucker are endemic to the Upper Klamath Basin in southern Oregon: shortnose sucker (Chasmistes brevirostris) and Lost River sucker (Deltistes ...luxatus). A third unlisted species, Klamath largescale sucker (Catostomus snyderi), also occurs in the basin. Apart from a small group of adult Lost River suckers documented in a tributary to Upper Klamath Lake in the late 1990s, it is generally believed that though the listed sucker species spawn in tributaries, the larvae out-migrate within days of swim-up, and therefore, there is no juvenile residence in the tributaries. We used X-ray imaging and vertebral counts to identify 347 juvenile suckers collected from tributaries to Upper Klamath Lake between 2006 and 2008. We positively identified 13 individuals as Lost River sucker. Our finding of juvenile endangered suckers rearing in tributaries to Upper Klamath Lake challenges the previous finding that larval and juvenile suckers only spend a small portion of their lives in rivers. This finding may have broader implications for future research and management of endangered suckers in the Klamath Basin.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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