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Phylogenetic trees provide a framework for organizing evolutionary histories across the tree of life and aid downstream comparative analyses such as metagenomic identification. Methods that rely on single-marker genes such as 16S rRNA have produced trees of limited accuracy with hundreds of thousands of organisms, whereas methods that use genome-wide data are not scalable to large numbers of genomes. We introduce updating trees using divide-and-conquer (uDance), a method that enables updatable genome-wide inference using a divide-and-conquer strategy that refines different parts of the tree independently and can build off of existing trees, with high accuracy and scalability. With uDance, we infer a species tree of roughly 200,000 genomes using 387 marker genes, totaling 42.5 billion amino acid residues.

BACKGROUND: Buprenorphine is an effective treatment for opioid use disorder (OUD); however, buprenorphine initiation can be complicated by withdrawal symptoms including precipitated withdrawal. There has been increasing interest in using low dose initiation (LDI) strategies to reduce this withdrawal risk. As there are limited data on withdrawal symptoms during LDI, we characterize withdrawal symptoms in people with daily fentanyl use who underwent initiation using these strategies as outpatients. METHODS: We conducted a retrospective chart review of patients with OUD using daily fentanyl who were prescribed 7-day or 4-day LDI at 2 substance use disorder treatment clinics in San Francisco. Two addiction medicine experts assessed extracted chart documentation for withdrawal severity and precipitated withdrawal, defined as acute worsening of withdrawal symptoms immediately after taking buprenorphine. A third expert adjudicated disagreements. Data were analyzed using descriptive statistics. RESULTS: There were 175 initiations in 126 patients. The mean age was 37 (SD 10 years). 71% were men, 26% women, and 2% non-binary. 21% identified as Black, 16% Latine, and 52% white. 60% were unstably housed and 75% had Medicaid insurance. Substance co-use included 74% who used amphetamines, 29% cocaine, 22% benzodiazepines, and 19% alcohol. Follow up was available for 118 (67%) initiations. There was deviation from protocol instructions in 22% of these initiations with follow up. 31% had any withdrawal, including 21% with mild symptoms, 8% moderate and 2% severe. Precipitated withdrawal occurred in 10 cases, or 8% of initiations with follow up. Of these, 7 had deviation from protocol instructions; thus, there were 3 cases with follow up (3%) in which precipitated withdrawal occurred without protocol deviation. CONCLUSIONS: Withdrawal was relatively common in our cohort but was mostly mild, and precipitated withdrawal was rare. Deviation from instructions, structural barriers, and varying fentanyl use characteristics may contribute to withdrawal. Clinicians should counsel patients who use fentanyl that mild withdrawal symptoms are likely during LDI, and there is still a low risk for precipitated withdrawal. Future studies should compare withdrawal across initiation types, seek ways to support patients in initiating buprenorphine, and qualitatively elicit patients withdrawal experiences.

The composition of the microbial community in the intestine may influence the functions of distant organs such as the brain, lung, and skin. These microbes can promote disease or have beneficial functions, leading to the hypothesis that microbes in the gut explain the co-occurrence of intestinal and skin diseases. Here, we show that the reverse can occur, and that skin directly alters the gut microbiome. Disruption of the dermis by skin wounding or the digestion of dermal hyaluronan results in increased expression in the colon of the host defense genes Reg3 and Muc2, and skin wounding changes the composition and behavior of intestinal bacteria. Enhanced expression Reg3 and Muc2 is induced in vitro by exposure to hyaluronan released by these skin interventions. The change in the colon microbiome after skin wounding is functionally important as these bacteria penetrate the intestinal epithelium and enhance colitis from dextran sodium sulfate (DSS) as seen by the ability to rescue skin associated DSS colitis with oral antibiotics, in germ-free mice, and fecal microbiome transplantation to unwounded mice from mice with skin wounds. These observations provide direct evidence of a skin-gut axis by demonstrating that damage to the skin disrupts homeostasis in intestinal host defense and alters the gut microbiome.

AbstractAlthough numerous studies have demonstrated the impact of microbiome manipulation on human health, research on the microbiome's influence on female health remains relatively limited despite substantial disease burden. In light of this, we present a selected review of clinical trials and preclinical studies targeting both the vaginal and gut microbiomes for the prevention or treatment of various gynecologic conditions. Specifically, we explore studies that leverage microbiota transplants, probiotics, prebiotics, diet modifications, and engineered microbial strains. A healthy vaginal microbiome for females of reproductive age consists of lactic acid-producing bacteria predominantly of the Lactobacillus genus, which serves as a protective barrier against pathogens and maintains a balanced ecosystem. The gut microbiota's production of short-chain fatty acids, metabolism of primary bile acids, and modulation of sex steroid levels have significant implications for the interplay between host and microbes throughout the body, ultimately impacting reproductive health. By harnessing interventions that modulate both the vaginal and gut microbiomes, it becomes possible to not only maintain homeostasis but also mitigate pathological conditions. While the field is still working toward making broad clinical recommendations, the current studies demonstrate that manipulating the microbiome holds great potential for addressing diverse gynecologic conditions.Lay summaryManipulating the microbiome has recently entered popular culture, with various diets thought to aid the microbes that live within us. These microbes live in different locations of our body and accordingly help us digest food, modulate our immune system, and influence reproductive health. The role of the microbes living in and influencing the female reproductive tract remains understudied despite known roles in common conditions such as vulvovaginal candidiasis (affecting 75% of females in their lifetime), bacterial vaginosis (25% of females in their lifetime), cervical HPV infection (80% of females in their lifetime), endometriosis (6-10% of females of reproductive age), and polycystic ovary syndrome (10-12% of females of reproductive age). Here, we review four different approaches used to manipulate the female reproductive tract and gastrointestinal system microbiomes: microbiota transplants, probiotics, prebiotics, and dietary interventions, and the use of engineered microbial strains. In doing so, we aim to stimulate discussion on new ways to understand and treat female reproductive health conditions.

In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2-12]. Given this impact, we carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested batch correction by comparing raw and Voom-SNM-corrected data per-batch, finding predictive equivalence and significantly similar features. We found consistent results with a modern microbiome-specific method (ConQuR [14]), and when restricting to taxa found in an independent, highly-decontaminated cohort. (2) Using Conterminator [15], we found low levels of human contamination in our original databases (~1% of genomes). We demonstrated that the increased detection of human reads in Gihawi et al. [13] was due to using a newer human genome reference. (3) We developed Exhaustive, a method twice as sensitive as Conterminator, to clean RefSeq. We comprehensively host-deplete TCGA with many human (pan)genome references. We repeated all analyses with this and the Gihawi et al. [13] pipeline, and found cancer type-specific microbiomes. These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.

Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.

In this study, we aimed to understand the potential role of the gut microbiome in the development of Alzheimers disease (AD). We took a multi-faceted approach to investigate this relationship. Urine metabolomics were examined in individuals with AD and controls, revealing decreased formate and fumarate concentrations in AD. Additionally, we utilised whole-genome sequencing (WGS) data obtained from a separate group of individuals with AD and controls. This information allowed us to create and investigate host-microbiome personalised whole-body metabolic models. Notably, AD individuals displayed diminished formate microbial secretion in these models. Additionally, we identified specific reactions responsible for the production of formate in the host, and interestingly, these reactions were linked to genes that have correlations with AD. This study suggests formate as a possible early AD marker and highlights genetic and microbiome contributions to its production. The reduced formate secretion and its genetic associations point to a complex connection between gut microbiota and AD. This holistic understanding might pave the way for novel diagnostic and therapeutic avenues in AD management.

South Africa has low literacy levels and teachers face multiple challenges in their endeavours to elevate levels of literacy. This is especially prevalent in rural and township schools where teachers face the additional challenges of isolation, limited resources and access to professional development. This article reports on the findings and learning from a preliminary research study which piloted a handheld mobile phone App. This collaborative project, between a university in KwaZulu-Natal and one in England, aimed to support in-service and preservice teachers in rural and township settings to use the App to assess and match books to learners' (aged 9-12) stage of reading development in order to facilitate their independent reading and provide teachers with a range of strategies for teaching comprehension that could supplement other professional development available. In-service teachers (n = 120) and preservice teachers (n = 93) took part in this mixed-methods study. The main finding from the study was that whilst participants were positive about the App, many did not access the App independently. This article discusses the broader issues, including participants' foundational knowledge and literacy research participation considerations, that may have underpinned this finding in this collaborative Global North and South research.

Background: Engineering curricula are built around faculty and accreditors' perceptions of what knowledge, skills, and abilities graduates will need in engineering careers. However, the people making these decisions may not be fully aware of what industry employers require for engineering graduates. Purpose/Hypothesis: The purpose of this study is to determine how industry employer-sought professional and technical skills vary among engineering disciplines and levels of education. Design/Method: Using a large sample (n = 26,103) of mined job advertisements, we use the O*NET skills database to determine the frequencies of different professional and technical skills for biomedical, civil, chemical, electrical, environmental, and mechanical engineers with bachelor's, master's, and PhD degrees. Results: The most frequently sought professional skill is problem-solving; the most frequently sought technical skills across disciplines are Microsoft Office software and computer-aided design software. Although not the most frequently requested skills, job advertisements including the Python and MATLAB programming languages paid significantly higher salaries than those without. Conclusions: The findings of this study have important implications for engineering program leaders and curriculum designers choosing which skills to teach students so that they are best prepared to get and excel in engineering jobs. The results also show which skills students can prioritize investing their time in so that they receive the largest financial return on their investment.

In this article, we focus on dance as intra- and intergenerational learning that cultivates corporeal knowledge held in common. Three interrelated projects reveal how danced connections between life stages develops an aesthetics of complex interaction and a mutuality of learning that enacts citizenry through communities in motion in the urban-scape. The projects approach dance practice through an expanded concept of choreography that takes into account the site, situation and life stage of dancers. We propose that moving together is a social choreography, a method for developing body-place awareness and civic participation, sharing experiences and bodily practices and performing relational complexity.

Students with disabilities continue to experience barriers to accessing tertiary (i.e., postsecondary) education in Australia. Using the principles of Universal Design for Learning (UDL) may help educators proactively address barriers through the design of more accessible and inclusive educational experiences. However, at present, references to UDL appear in only a small number of Australian educational policies and tertiary institute websites, and few tertiary educators use UDL in practice. In this article, we describe how a team of educators, learning designers, accessibility advocates, and people with disabilities from multiple institutions across Australia collaborated to co-create a free, accessible eLearning program to build workforce knowledge and skill in UDL. We first describe how the advisory group was established, how the Knowledge to Action cycle was used to guide the activities of the advisory group, and the evaluation framework that was used to assess the outcomes of the eLearning program. We share potential future activities to raise awareness of UDL and influence policy and practice in local contexts and propose directions for future work in this area.

The focus of ethics in learning analytics (LA) frameworks and guidelines is predominantly on procedural elements of data management and accountability. Another, less represented focus is on the duty to act and LA as a moral practice. Data feminism as a critical theoretical approach to data science practices may offer LA research and practitioners a valuable lens through which to consider LA as a moral practice. This paper examines what data feminism can offer the LA community. It identifies critical questions for further developing and enabling a responsible stance in LA research and practice taking one particular case -- algorithmic decision-making -- as a point of departure.

Research in mentoring has shown that students may at times be more willing and able to absorb information that is delivered to them by their near-peers, rather than by traditional figures of authority, like teachers and professors. In this study, underrepresented minority high school students participated in an informal learning experience that was led by college students who were "near-peers" to the high schoolers. Students were engaged by participating in interactive MathShows, following a Math Social Media Campaign, and attending a summer Math Internship. Participants in the quantitative component of the study included N = 559 U.S. high schoolers who were from predominantly (>99%) Hispanic ethnic backgrounds. The qualitative component of the study involved another 19 students from the same school. The mixed methods study addresses associations between high schoolers' attitudes toward mathematics and their identity alignment, as well as classes of reasons that students gave for their identity alignment. Interactions with the college near-peers that occurred during the experiential learning intervention are also discussed. Results of this study address the goal of broadening participation of underrepresented student groups in STEM careers.

Student pre-departure preparation has been identified as essential if study abroad programs involving work-integrated learning are to deliver the numerous benefits they intend, while mitigating the many risks they involve. However, little is known about what preparation is provided to the academic and professional staff who implement these programs, and the community members who host the students. Interviews with 16 academic and professional staff involved in preparing students, staff, and host communities for Australian study abroad programs reveal inconsistencies in the preparation provided to students, and very limited preparation to staff and host communities. The limited preparation that is offered, is designed and developed in an organic (not structured) and inconsistent manner. Our findings suggest that institutions should consider implementing a more structured, consistent and institutionally driven approach to preparation for students, staff, and host communities to reduce the substantial risks associated with these programs while maximizing the benefits.

This study contributes to a better understanding of instructors' perceptions of equity issues within online teaching and learning. The researchers conducted interviews with 21 instructors at one university across disciplines regarding their experience with, and recommendations for, attending to issues of inclusion, diversity, equity, and access (IDEA) in online teaching. Findings revealed that instructors characterized online teaching and IDEA issues as distinct skillsets and that they were not necessarily prepared to apply IDEA issues in online teaching. Participants also focused their attention much more on access and inclusion--with access as a baseline expectation and inclusion operationalized as relationship building--rather than on equity and diversity, areas in which faculty efforts often translated (or not) from their face-to-face teaching experience. We conclude the paper with implications for faculty, educational developers, administrators, and institutions.

Therapy dogs positively impact students mental and emotional well-being, which can improve the student's academic performance. Therapy dogs can reduce stress and anxiety levels, which leads to better concentration and improved learning outcomes. Canines can also help improve social skills and behavior, which fosters a more productive classroom environment. School accountability becomes more critical each year. Student performance on state assessments determines accountability ratings. This study investigated therapy dogs' impact on academic achievement in a rural middle school math classroom. By addressing this issue through learning motivational theory, the quantitative research sheds light on how incorporating canine animal-assisted interventions into the daily classroom routine can increase student achievement.

This systematic literature review synthesizes empirical evidence to comprehensively examine factors driving international students' choice of Australia as their preferred destination for tertiary education. Deductive analysis of findings from the 46 selected studies, framed within the push and pull framework, identified 27 factors that revealed Australia's distinctive attractiveness to international students. The results of this review reaffirmed the strengths of Australia's environmental images in the international tertiary education market, highlighting that it could be a double-edged sword. The review discusses Australia's attractiveness, especially after the COVID-19 crisis and suggests strategies to make the international education sector more sustainable. This review provides implications for policy, practice, and future research that are of importance to work towards enhancing Australia's intake of international education. Additionally, it serves as a valuable resource for those seeking guidance on effectively attracting international students in the post-pandemic era.

This article presents an interdisciplinary collaboration to address the needs of older adults at risk of social isolation exacerbated by the COVID-19 pandemic. An intergenerational service-learning program developed by the Pennsylvania Department of Aging was offered to several universities across the state of Pennsylvania. The authors share their experience and lessons learned from pairing older adults with graduate students studying in the fields of Gerontology, Public Health, and Social Work.