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The practical application of new single molecule protein sequencing (SMPS) technologies requires accurate estimates of their associated sequencing error rates. Here, we describe the development and application of two distinct parameter estimation methods for analyzing SMPS reads produced by fluorosequencing. A Hidden Markov Model (HMM) based approach, extends whatprot, where we previously used HMMs for SMPS peptide-read matching. This extension offers a principled approach for estimating key parameters for fluorosequencing experiments, including missed amino acid cleavages, dye loss, and peptide detachment. Specifically, we adapted the Baum-Welch algorithm, a standard technique to estimate transition probabilities for an HMM using expectation maximization, but modified here to estimate a small number of parameter values directly rather than estimating every transition probability independently. We demonstrate a high degree of accuracy on simulated data, but on experimental datasets, we observed that the model needed to be augmented with an additional error type, N-terminal blocking. This, in combination with data pre-processing, results in reasonable parameterizations of experimental datasets that agree with controlled experimental perturbations. A second independent implementation using a hybrid of DIRECT and Powell's method to reduce the root mean squared error (RMSE) between simulations and the real dataset was also developed. We compare these methods on both simulated and real data, finding that our Baum-Welch based approach outperforms DIRECT and Powell's method by most, but not all, criteria. Although some discrepancies between the results exist, we also find that both approaches provide similar error rate estimates from experimental single molecule fluorosequencing datasets.

Social innovation in health is a ground-up, community-engaged process that draws on the diverse strengths of local individuals to drive social change and health improvement. Social innovation may be particularly useful in low and middle-income countries to ensure effective and sustainable health solutions. The purpose of this study is to describe the findings of a global youth (18-35 years old) crowdsourcing open call on social innovations, and to identify the levels of engagement in such innovations. We organized a global crowdsourcing open call (Go Youth!) to identify and recognize youth social innovations in health and adopted both quantitative and qualitative approaches to analyze our data. For quantitative analyses, we described the socio-demographic characteristics of youth who submitted innovations. For qualitative analyses, we adopted a deductive-inductive analytic approach utilizing an adapted Hart's Ladder as a conceptual framework for our thematic analysis of participants' submissions, which comprised four levels of youth engagement: none, minimal, moderate, and substantial. The open call received 99 eligible submissions. Most participants were 23 years of age or older (90.7%), resided in LMICs (98.0%), male (64.3%), and had a bachelor's or higher degree (72.4%). Most of the submissions were written in English (93.9%), located in Africa (69.7%), and had prior implementation (60.2%). A total of 39 innovations had substantial youth engagement and qualitative data suggested that youth leadership and peer mentorship of other youth in the community were important aspects of engagement. LMIC youth developed and implemented social innovations that had evidence of impact or effectiveness in their communities, illustrating how social innovation approaches may be feasible in LMICs. More efforts should be made to identify and empower youth in these settings to spark change.

Intimate partner violence (IPV) may have been exacerbated during the COVID-19 pandemic. Middle-aged and older adults, ages 45 years or older, are at higher risk of COVID-19 mortality and social isolation. However, most studies on IPV during the pandemic do not focus on this important subpopulation. Informed by the social-ecological theory, this study examines individual, household, community, and country-level correlates of IPV among middle-aged and older adults in multiple countries using a cross-sectional online survey. Data from 2867 participants aged 45 or older in the International Sexual Health and Reproductive Health (I-SHARE) survey from July 2020 to February 2021 were described using univariate analysis. IPV was defined using four validated WHO measures. Individual characteristics included self-isolation and food security. At the country-level, we examined social distancing stringency. Logistic regression models with a random intercept for country were conducted to explore IPV correlates among 1730 eligible individuals from 20 countries with complete data. Most participants were heterosexual (2469/2867), cisgender (2531/2867) females (1589/2867) between the ages of 45-54 (1539/2867). 12.1% (346/2867) of participants experienced IPV during social distancing measures. After adjustment, participants who self-isolated experienced 1.4 (95% CI 1.0, 2.0, p = 0.04) times the odds of IPV compared to those who had not isolated. Those who reported an increase in food insecurity compared to pre-pandemic experienced 2.2 times the odds (95% CI 1.6, 3.0, p

IntroductionToe brachial index (TBI), the ratio of toe pressure to systolic blood pressure (SBP), helps predict peripheral arterial disease. In patients with kidney failure this may be performed during haemodialysis for convenience. Until recently there has been little evaluation of the impact of haemodialysis in limb and systemic perfusion on these values. We aimed to determine if the values of TBI would change during and after dialysis compared to pre-dialysis assessments.MethodsUsing a repeated measures study, TBIs and toe pressures were measured using the Hadeco Smartop Vascular Ultrasound Doppler in 31 patients undergoing haemodialysis. TBI assessments were completed pre-dialysis and compared to values obtained at 1 hour, 2 hours, 3 hours, and post-dialysis to monitor change in TBI results. Comparison of values for each patient were tested for differences using paired t-tests. Linear mixed-effects models were used to test for the effect of patient and clinical factors on change in outcome measures.ResultsMean TBI decreased from pre-dialysis at 1 hour (0.72 to 0.63, p = 0.01) and remained lower at 2 hours and 3 hours, before returning to pre-dialysis levels at post-dialysis. Mean systolic blood pressure also declined during dialysis. Mean TBI results were lower in those with a history of lower limb ulceration and in females. Sixteen patients (51.6%) had a normal TBI at baseline, 14 (45.2%) had a mildly low TBI, and one (3.2%) had a severely low TBI. Between baseline and 1 h, five patient's results moved from normal to mildly abnormal and one from mildly abnormal to severely abnormal. As haemodialysis concluded (post-dialysis) there were 17 (56.7%) 'normal' TBIs, with no severely abnormal TBIs (p = 0.73). 0.30).ConclusionTBI and toe pressures are impacted significantly by dialysis. TBI and toe pressure assessments should be conducted before haemodialysis begins, or between dialysis sessions to avoid variability.

Mesenchymal stromal cells (MSCs) are promising therapeutic agents for cartilage regeneration, including the potential of cells to promote chondrogenesis in vivo. However, process development and regulatory approval of MSCs as cell therapy products benefit from facile in vitro approaches that can predict potency for a given production run. Current standard in vitro approaches include a 21 day 3D differentiation assay followed by quantification of cartilage matrix proteins. We propose a novel biophysical marker that is cell population-based and can be measured from in vitro monolayer culture of MSCs. We hypothesized that the self-assembly pattern that emerges from collective-cell behavior would predict chondrogenesis motivated by our observation that certain features in this pattern, namely, topological defects, corresponded to mesenchymal condensations. Indeed, we observed a strong predictive correlation between the degree-of-order of the pattern at day 9 of the monolayer culture and chondrogenic potential later estimated from in vitro 3D chondrogenic differentiation at day 21. These findings provide the rationale and the proof-of-concept for using self-assembly patterns to monitor chondrogenic commitment of cell populations. Such correlations across multiple MSC donors and production batches suggest that self-assembly patterns can be used as a candidate biophysical attribute to predict quality and efficacy for MSCs employed therapeutically for cartilage regeneration.

Microtubule-targeted agents are commonly used for cancer treatment, though many patients do not benefit. Microtubule-targeted drugs were assumed to elicit anticancer activity via mitotic arrest because they cause cell death following mitotic arrest in cell culture. However, we recently demonstrated that intratumoral paclitaxel concentrations are insufficient to induce mitotic arrest and rather induce chromosomal instability (CIN) via multipolar mitotic spindles. Here, we show in metastatic breast cancer and relevant human cellular models that this mechanism is conserved among clinically useful microtubule poisons. While multipolar divisions typically produce inviable progeny, multipolar spindles can be focused into near-normal bipolar spindles at any stage of mitosis. Using a novel method to quantify the rate of CIN, we demonstrate that cell death positively correlates with net loss of DNA. Spindle focusing decreases CIN and causes resistance to diverse microtubule poisons, which can be counteracted by addition of a drug that increases CIN without affecting spindle polarity. These results demonstrate conserved mechanisms of action and resistance for diverse microtubule-targeted agents. Trial registration: clinicaltrials.gov, NCT03393741.

The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there have been important research advances since 2007, they have not been adopted in practice because of a lack of consensus in the conservation community. Here, building from an interdisciplinary workshop to update the existing EDGE approach, we present an "EDGE2" protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritising species conservation efforts. Key advances include methods for dealing with uncertainty and accounting for the extinction risk of closely related species. We describe EDGE2 in terms of distinct components to facilitate future revisions to its constituent parts without needing to reconsider the whole. We illustrate EDGE2 by applying it to the world's mammals. As we approach a crossroads for global biodiversity policy, this Consensus View shows how collaboration between academic and applied conservation biologists can guide effective and practical priority-setting to conserve biodiversity.

The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there have been important research advances since 2007, they have not been adopted in practice because of a lack of consensus in the conservation community. Here, building from an interdisciplinary workshop to update the existing EDGE approach, we present an “EDGE2” protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritising species conservation efforts. Key advances include methods for dealing with uncertainty and accounting for the extinction risk of closely related species. We describe EDGE2 in terms of distinct components to facilitate future revisions to its constituent parts without needing to reconsider the whole. We illustrate EDGE2 by applying it to the world’s mammals. As we approach a crossroads for global biodiversity policy, this Consensus View shows how collaboration between academic and applied conservation biologists can guide effective and practical priority-setting to conserve biodiversity. The Evolutionarily Distinct and Globally Endangered (EDGE) metric is used to prioritize threatened species for practical conservation. This Consensus View presents EDGE2, a protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritizing species conservation efforts.

A quasi-experimental study was conducted to evaluate the effectiveness of a pay-it-forward strategy for increasing influenza vaccination among children and older adults compared to a self-paid vaccination strategy in China. Pay-it-forward is an innovative community-engaged intervention in which participants receive a free influenza vaccination and are then asked if they would like to donate or create a message to support subsequent vaccinations. This economic evaluation used a decision-tree model to compare pay-it-forward to a standard of care arm in which patients had to pay for their own influenza vaccine. The analysis was performed from the healthcare provider perspective and costs were calculated with 2020 United States dollars. The time horizon was one year. In the base case analysis, pay-it-forward was more effective (111 vs 55 people vaccinated) but more costly than standard-of-care ($4477 vs $2725). Pay-it-forward spurred 96.4% (107/111) of individuals to voluntarily donate to support influenza vaccination for high-risk groups in China. Further costing and implementation research is needed to inform scale up.

BackgroundMobile health (mHealth) is a promising intervention mode for HIV prevention, but little is known about its feasibility and effects in promoting pre-exposure prophylaxis (PrEP) uptake among Chinese gay, bisexual and other men who have sex with men (GBMSM).MethodsWe evaluated an instant messaging application using a WeChat-based mini-app to promote PrEP uptake among GBMSM via a mixed-methods design that includes a 12-week, two-arm randomized controlled pilot trial and in-depth progress interviews in Guangzhou, China. Primary outcomes include the number of PrEP initiations, individual-level psychosocial variables related to PrEP initiation, and usability of the PrEP mini-app.ResultsBetween November 2020 and April 2021, 70 GBMSM were successfully enrolled and randomized into two arms at 2:1 ratio (46 to the intervention arm, 24 to the control arm). By the end of 12-week follow-up, 22 (31.4%) participants completed the initial consultation and lab tests for PrEP, and 13 (18.6%) filled their initial PrEP prescription. We observed modest but non-significant improvements in participants' intention to use PrEP, actual PrEP initiation, PrEP-related self-efficacy, stigma, and attitudes over 12 weeks when comparing the mini-app and the control arms. Qualitative interviews revealed the key barriers to PrEP uptake include anticipated stigma and discrimination in clinical settings, burden of PrEP care, and limited operating hours of the PrEP clinic. In-person clinic navigation support was highly valued.ConclusionsThis pilot trial of a mobile phone-based PrEP mini-app demonstrated feasibility and identified limitations in facilitating PrEP uptake among Chinese GBMSM. Future improvements may include diversifying the content presentation in engaging media formats, adding user engagement features, and providing off-line in-clinic navigation support during initial PrEP visit. More efforts are needed to understand optimal strategies to identify and implement alternative PrEP provision models especially in highly stigmatized settings with diverse needs.Trial registrationTrial registration: The study was prospectively registered on clinicaltrials.gov (NCT04426656) on 11 June, 2020.

IntroductionTo examine electroencephalogram (EEG) as a diagnostic tool for late-onset efavirenz (EFV) neurotoxicity syndrome (LENS), an uncommon but severe and potentially fatal complication of EFV therapy.MethodsWe conducted a Retrospective case-control study. EEGs from confirmed cases of LENS (clinical syndrome and plasma EFV >4ug/mL) recorded from June 2016 to May 2021 were compared with control EEGs from the same time-period. Controls were adults (18-70 years) with a similar indication for EEG (eg. encephalopathy or confusion), dysrhythmia generalised grade II, and LENS excluded. EEGs were reviewed by two blinded interpreters given a description of the characteristic EEG changes, ie. persistent, diffuse, high voltage, bisynchronous, monomorphic 4-7 Hz theta frequency waveforms with transient attenuation on eye opening. Interpreters were asked to determine whether EEGs showed definite, probable or no changes.ResultsThirteen LENS cases were compared with 50 control EEGs. Interpreter 1 labelled 11/13 LENS cases as having define or probable changes, and interpreter 2 labelled 10/13. Interpreter 1 labelled probable changes in 1/50 controls and interpreter 2 in 3/50. Neither interpreter labelled any controls as having definite changes. Interrater reliability was good with 95% agreement and a Cohen's kappa of 0.83. Sensitivity of EEG under these conditions for the diagnosis of LENS was 85% and 77% for interpreters 1 and 2 respectively, and specificity was 98% and 94%.ConclusionsEEG is a useful tool in the diagnosis of LENS which can be used to aid clinical decisions while awaiting EFV levels, or in low-resource settings where EFV levels are not available.

BackgroundInstitutional research mentorship is a form of mentorship whereby institutions foster mentor-mentee relationships. Research mentorship improves research effectiveness and supports relationships. However, resources are needed in order to institutionalize research mentorship tailored to low- and middle- income countries (LMICs). The aim of this study was to develop a consensus document on institutionalizing research mentorship through a modified Delphi process as part of the practical guide development process.MethodsThis study used a two-round modified Delphi process, which is an iterative, structured approach of consensus decision making. Each participant was asked about a series of items related to research mentorship using Likert scale questions. Agreement for each item was pre-defined as ≥80% of participants rating the item as "agree" or "strongly agree." The items that reached agreement, were then discussed during round two at an in-person conference in Ethiopia. A separate group of individuals only participated virtually. For the final consensus survey, response rates and commenting rates (participants who wrote two or more comments) were compared among conference and non-conference participants.ResultsThe Delphi process led to the inception of three main themes in terms of developing research mentorship: leveraging existing resources, measuring and evaluating institutional mentorship, and encouraging a research mentorship life cycle. During the virtual first round, 59% (36/61) participants who were emailed completed the survey. In the second round, conference participants had a response rate of 79% (11/14) compared to non-conference participants with a response rate of 45% (21/47). Conference participants had a 100% (11/11) commenting rate whereas non-conference participants had a 38% (8/21) commenting rate. This study achieved consensus in both survey rounds for all 35 items on the consensus document.ConclusionsThe data suggest that an in-person conference may increase participant engagement. The consensus developed through a modified Delphi method directly informed a practical guide on institutionalizing research mentorship in LMICs.

Understanding factors that influence those who are initially COVID-19 vaccine hesitant to accept vaccination is valuable for the development of vaccine promotion strategies. Using Ipsos KnowledgePanel®, we conducted a national survey of adults aged 18 and older in the United States. We created a questionnaire to examine factors associated with COVID-19 vaccine uptake over a longitudinal period ("Wave 1" in April 2021 and "Wave 2" in February 2022), and utilized weighted data provided by Ipsos to make the data nationally representative. Overall, 1189 individuals participated in the Wave 1 survey, and 843 participants completed the Wave 2 survey (71.6% retention rate). Those who intended to be vaccinated as soon as possible ("ASAP") were overwhelmingly vaccinated by Wave 2 (96%, 95% CI: 92% to 100%). Of those who initially wished to delay vaccination until there was more experience with it ("Wait and See"), 57% (95% CI: 47% to 67%) were vaccinated at Wave 2. Within the "Wait and See" cohort, those with income

Crowdsourcing is an interactive process that has a group of individuals attempt to solve all or part of a problem and then share solutions with the public. Crowdsourcing is increasingly used to enhance training through developing learning materials and promoting mentorship. This scoping review aims to assess the literature on crowdsourcing for training in public health. We searched five medical and public health research databases using terms related to crowdsourcing and training. For this review, the concept of crowdsourcing included open calls, designathons, and other activities. We used a PRISMA checklist for scoping reviews. Each full-text was assessed by two independent reviewers. We identified 4,071 citations, and 74 studies were included in the scoping review. This included one study in a low-income country, 15 studies in middle-income countries, 35 studies in high-income countries, and 11 studies conducted in multiple countries of varying income levels (the country income level for 12 studies could not be ascertained). Nine studies used open calls, 35 used a hackathon, designathon or other "a-thon" event, and 30 used other crowdsourcing methods, such as citizen science programs and online creation platforms. In terms of crowdsourcing purpose, studies used crowdsourcing to educate participants (20 studies), develop learning materials (17 studies), enhance mentorship (13 studies) and identify trainees (9 studies). Fifteen studies used crowdsourcing for more than one training purpose. Thirty-four studies were done in-person, 31 were conducted virtually and nine used both meeting options for their crowdsourcing events. Seventeen studies generated open access materials. Our review found that crowdsourcing has been increasingly used to support public health training. This participatory approach can be a useful tool for training in a variety of settings and populations. Future research should investigate the impact of crowdsourcing on training outcomes.

Background Health systems are under pressure to maintain services within limited resources. The Evidence-Based Interventions (EBI) programme published a first list of guidelines in 2019, which aimed to reduce inappropriate use of interventions within the NHS in England, reducing potential harm and optimising the use of limited resources. Seventeen procedures were selected in the first round, published in April 2019. Methods We evaluated changes in the trends for each procedure after its inclusion in the EBI’s first list of guidelines using interrupted time series analysis. We explored whether there was any evidence of spill-over effects onto related or substitute procedures, as well as exploring changes in geographical variation following the publication of national guidance. Results Most procedures were experiencing downward trends in the years prior to the launch of EBI. We found no evidence of a trend change in any of the 17 procedures following the introduction of the guidance. No evidence of spill-over increases in substitute or related procedures was found. Geographic variation in the number of procedures performed across English CCGs remained at similar levels before and after EBI. Conclusions The EBI programme had little success in its aim to further reduce the use of the 17 procedures it deemed inappropriate in all or certain circumstances. Most procedure rates were already decreasing before EBI and all continued with a similar trend afterwards. Geographical variation in the number of procedures remained at a similar level post EBI. De-adoption of inappropriate care is essential in maintaining health systems across the world. However, further research is needed to explore context specific enablers and barriers to effective identification and de-adoption of such inappropriate health care to support future de-adoption endeavours.

BackgroundIncreasing numbers of opioid-overdose deaths have been witnessed among Hispanics and other underserved populations in Massachusetts. Puerto Rican adults (PRs) have a disproportionately higher prevalence of chronic diseases than non-Hispanic White adults-conditions linked to increased prescription opioid use and misuse. Stress indicators, including low acculturation, low social support, and perceived discrimination, have been recognized as correlates of chronic diseases. However, little research has been undertaken on how these socio-cultural factors relate to persistent prescription opioid use among PRs. This study evaluated the prevalence of prescription opioid use and socio-cultural factors associated with persistent prescription opioid use among PRs.MethodsData from the prospective population-based Boston Puerto Rican Health Study, at baseline, ~2-year, and ~ 6-year follow-up, were used to estimate prescription opioid use prevalence and its associations with acculturation, social support, and perceived discrimination. Analyses were conducted using multivariable binary logistic regression modeling.ResultsThe study sample was comprised of 798 PRs (age 56.5 ± 7.5y) with data at all three-time points. A high prevalence of prescription opioid use was observed and was associated with lower household income. PRs with experiences of perceived discrimination had higher odds of persistent prescription opioid use (y/n; OR = 2.85, 95% CI: 1.46-5.58). No significant associations were found between acculturation, social support, and persistent prescription opioid use.ConclusionOur study reported a high prevalence of prescription opioid use in PRs, with persistent prescription opioid use significantly associated with perceived discrimination. Future programs to limit discrimination practices may reduce persistent prescription opioid use and opioid-related complications among PRs.

A quasi-experimental study was conducted to evaluate the effectiveness of a pay-it-forward strategy for increasing influenza vaccination among children and older adults compared to a self-paid vaccination strategy in China. Pay-it-forward is an innovative community-engaged intervention in which participants receive a free influenza vaccination and are then asked if they would like to donate or create a message to support subsequent vaccinations. This economic evaluation used a decision-tree model to compare pay-it-forward to a standard of care arm in which patients had to pay for their own influenza vaccine. The analysis was performed from the healthcare provider perspective and costs were calculated with 2020 United States dollars. The time horizon was one year. In the base case analysis, pay-it-forward was more effective (111 vs 55 people vaccinated) but more costly than standard-of-care ($4477 vs $2725). Pay-it-forward spurred 96.4% (107/111) of individuals to voluntarily donate to support influenza vaccination for high-risk groups in China. Further costing and implementation research is needed to inform scale up.

Intensifying macrovertebrate reconnaissance together with refined age-dating of mid-Cretaceous assemblages in recent decades is producing a more nuanced understanding of the impact of the Cretaceous Thermal Maximum on terrestrial ecosystems. Here we report discovery of a new early-diverging ornithopod, Iani smithi gen. et sp. nov., from the Cenomanian-age lower Mussentuchit Member, Cedar Mountain Formation of Utah, USA. The single known specimen of this species (NCSM 29373) includes a well-preserved, disarticulated skull, partial axial column, and portions of the appendicular skeleton. Apomorphic traits are concentrated on the frontal, squamosal, braincase, and premaxilla, including the presence of three premaxillary teeth. Phylogenetic analyses using parsimony and Bayesian inference posit Iani as a North American rhabdodontomorph based on the presence of enlarged, spatulate teeth bearing up to 12 secondary ridges, maxillary teeth lacking a primary ridge, a laterally depressed maxillary process of the jugal, and a posttemporal foramen restricted to the squamosal, among other features. Prior to this discovery, neornithischian paleobiodiversity in the Mussentuchit Member was based primarily on isolated teeth, with only the hadrosauroid Eolambia caroljonesa named from macrovertebrate remains. Documentation of a possible rhabdodontomorph in this assemblage, along with published reports of an as-of-yet undescribed thescelosaurid, and fragmentary remains of ankylosaurians and ceratopsians confirms a minimum of five, cohabiting neornithischian clades in earliest Late Cretaceous terrestrial ecosystems of North America. Due to poor preservation and exploration of Turonian-Santonian assemblages, the timing of rhabdodontomorph extirpation in the Western Interior Basin is, as of yet, unclear. However, Iani documents survival of all three major clades of Early Cretaceous neornithischians (Thescelosauridae, Rhabdodontomorpha, and Ankylopollexia) into the dawn of the Late Cretaceous of North America.

Animals raised in environments that prevent natural foraging opportunities may have difficulty adapting to novelty, such as feeding and management changes. Our objective was to evaluate how early provision and presentation of forage in dairy calves affected response to novel TMR (total mixed ration; grain and alfalfa) at weaning. Holstein heifer calves were housed individually in a covered outdoor hutch with an attached uncovered wire-fenced pen on sand bedding. Calves were fed a diet of starter grain and milk replacer (5.7-8.4L/d step-up) via a bottle (Control, n = 9) or given additional access to mountaingrass hay presented either in a bucket (Bucket, n = 9), or PVC pipe feeder (Pipe, n = 9). Treatments were applied from birth through 50 d of age, when step-down weaning began. All calves had 3 buckets and a pipe feeder provided in their uncovered pen area. On d 50, each calf was briefly blocked inside their hutch. TMR was put in the 3rd bucket that previously contained hay (Bucket) or was empty (Control, Pipe). The calf was released from the hutch and video-recorded for 30 min. Neophobia towards TMR was affected by prior experience with presentation: Bucket calves began eating TMR faster than Pipe and Control (P≤0.012) and showed the fewest number of startle responses (P = 0.004). Intake was similar across groups (P = 0.978), suggesting this apparent neophobia was transient, but Control calves took longer to eat than Bucket (P

IntroductionMany patients with growth hormone-secreting pituitary adenoma (GHPA) fail to achieve biochemical remission, warranting investigation into epigenetic and molecular signatures associated with tumorigenesis and hormonal secretion. Prior work exploring the DNA methylome showed Myc-Associated Protein X (MAX), a transcription factor involved in cell cycle regulation, was differentially methylated between GHPA and nonfunctional pituitary adenoma (NFPA). We aimed to validate the differential DNA methylation and related MAX protein expression profiles between NFPA and GHPA.MethodsDNA methylation levels were measured in 52 surgically resected tumors (37 NFPA, 15 GHPA) at ~100,000 known MAX binding sites derived using ChIP-seq analysis from ENCODE. Findings were correlated with MAX protein expression using a constructed tissue microarray (TMA). Gene ontology analysis was performed to explore downstream genetic and signaling pathways regulated by MAX.ResultsGHPA had more hypomethylation events across all known MAX binding sites. Of binding sites defined using ChIP-seq analysis, 1,551 sites had significantly different methylation patterns between the two cohorts; 432 occurred near promoter regions potentially regulated by MAX, including promoters of TNF and MMP9. Gene ontology analysis suggested enrichment in genes involved in oxygen response, immune system regulation, and cell proliferation. Thirteen MAX binding sites were within coding regions of genes. GHPA demonstrated significantly increased expression of MAX protein compared to NFPA.ConclusionGHPA have significantly different DNA methylation and downstream protein expression levels of MAX compared to NFPA. These differences may influence mechanisms involved with cellular proliferation, tumor invasion and hormonal secretion.

Introduction Many patients with growth hormone-secreting pituitary adenoma (GHPA) fail to achieve biochemical remission, warranting investigation into epigenetic and molecular signatures associated with tumorigenesis and hormonal secretion. Prior work exploring the DNA methylome showed Myc-Associated Protein X (MAX), a transcription factor involved in cell cycle regulation, was differentially methylated between GHPA and nonfunctional pituitary adenoma (NFPA). We aimed to validate the differential DNA methylation and related MAX protein expression profiles between NFPA and GHPA. Methods DNA methylation levels were measured in 52 surgically resected tumors (37 NFPA, 15 GHPA) at ~100,000 known MAX binding sites derived using ChIP-seq analysis from ENCODE. Findings were correlated with MAX protein expression using a constructed tissue microarray (TMA). Gene ontology analysis was performed to explore downstream genetic and signaling pathways regulated by MAX. Results GHPA had more hypomethylation events across all known MAX binding sites. Of binding sites defined using ChIP-seq analysis, 1,551 sites had significantly different methylation patterns between the two cohorts; 432 occurred near promoter regions potentially regulated by MAX, including promoters of TNF and MMP9. Gene ontology analysis suggested enrichment in genes involved in oxygen response, immune system regulation, and cell proliferation. Thirteen MAX binding sites were within coding regions of genes. GHPA demonstrated significantly increased expression of MAX protein compared to NFPA. Conclusion GHPA have significantly different DNA methylation and downstream protein expression levels of MAX compared to NFPA. These differences may influence mechanisms involved with cellular proliferation, tumor invasion and hormonal secretion.

Asymptomatic carriage of Staphylococcus aureus is a major risk factor for subsequent clinical infection. Diminishing returns from mitigation efforts emphasize the need to better understand colonization, spread, and transmission of this opportunistic pathogen. While contact with other people presents opportunities for pathogen exposure and transmission, diversity of social connections may be protective against pathogens such as the common cold. This study examined whether social relationship resources, including the amount and diversity of social contacts, are associated with S. aureus colonization. Participants were community members (N = 443; 68% Hispanic) in naturally occurring social groups in southwestern Arizona. Four types of social relationships and loneliness were assessed, and samples from the skin, nose and throat were obtained to ascertain S. aureus colonization. Overall S. aureus prevalence was 64.8%. Neither the amount nor the diversity of social contacts were associated with S. aureus colonization. The concurrent validity of the social relationship assessments was supported by their moderate intercorrelations and by their positive association with self-rated health. The results suggest that the association of social network diversity and susceptibility to the common cold does not extend to S. aureus colonization. Conversely, colonization prevalence was not higher among those with more social contacts. The latter pattern suggests that social transmission may be relatively infrequent or that more intimate forms of social interaction may drive transmission and colonization resulting in high community prevalence of S. aureus colonization. These data inform communicable disease control efforts.

BackgroundStudies conducted in regions consisting of low and middle income and developing countries often report high prevalence of mental health problems among children and young people (CYP). To identify some of the contributing factors we examined the available evidence from research in one such setting.MethodsMultiple academic databases and grey literature sources were searched until January 2022. We then identified primary research focusing on CYP's mental health in the English-speaking Caribbean region. Data was extracted and summarized to form a narrative synthesis of the factors associated with CYP's mental health. The synthesis was then organised according to the social-ecological model. The Joanna Briggs Institute's critical appraisal tools were used to examine the quality of the reviewed evidence. The study protocol was registered with PROSPERO, CRD42021283161.ResultsFrom 9684 records, 83 publications representing CYP ages 3 to 24 years from 13 countries met our inclusion criteria. The evidence was varied in quality, quantity and consistency for 21 factors associated with CYP's mental health. Adverse events and negative peer to peer and sibling relationships were consistently associated with mental health problems, while helpful coping strategies were associated with better mental health. There were mixed findings for age, sex/gender, race/ethnicity, academic level, comorbidity, positive affect, health risks behaviours, religion/prayer, parent history, parent to parent and parent to child relationships, school/employment, geography and social status. There was also some limited evidence for associations between sexuality, screen time and policies/procedures and CYP's mental health. At least 40% of the evidence contributing to each of the factors was judged as high quality.ConclusionIndividual, relationship, community and societal factors may influence CYP's mental health outcomes in the English-speaking Caribbean. Knowledge of these factors is useful to inform early identification and early interventions. More research is needed to explore inconsistent findings and understudied areas.

Asymptomatic carriage of Staphylococcus aureus is a major risk factor for subsequent clinical infection. Diminishing returns from mitigation efforts emphasize the need to better understand colonization, spread, and transmission of this opportunistic pathogen. While contact with other people presents opportunities for pathogen exposure and transmission, diversity of social connections may be protective against pathogens such as the common cold. This study examined whether social relationship resources, including the amount and diversity of social contacts, are associated with S. aureus colonization. Participants were community members (N = 443; 68% Hispanic) in naturally occurring social groups in southwestern Arizona. Four types of social relationships and loneliness were assessed, and samples from the skin, nose and throat were obtained to ascertain S. aureus colonization. Overall S. aureus prevalence was 64.8%. Neither the amount nor the diversity of social contacts were associated with S. aureus colonization. The concurrent validity of the social relationship assessments was supported by their moderate intercorrelations and by their positive association with self-rated health. The results suggest that the association of social network diversity and susceptibility to the common cold does not extend to S. aureus colonization. Conversely, colonization prevalence was not higher among those with more social contacts. The latter pattern suggests that social transmission may be relatively infrequent or that more intimate forms of social interaction may drive transmission and colonization resulting in high community prevalence of S. aureus colonization. These data inform communicable disease control efforts.

BackgroundTo inform policy and implementation that can enhance prevention and improve tuberculosis (TB) care cascade outcomes, this review aimed to summarize the impact of various interventions on care cascade outcomes for active TB.Methods and findingsIn this systematic review and meta-analysis, we retrieved English articles with comparator arms (like randomized controlled trials (RCTs) and before and after intervention studies) that evaluated TB interventions published from January 1970 to September 30, 2022, from Embase, CINAHL, PubMed, and the Cochrane library. Commentaries, qualitative studies, conference abstracts, studies without standard of care comparator arms, and studies that did not report quantitative results for TB care cascade outcomes were excluded. Data from studies with similar comparator arms were pooled in a random effects model, and outcomes were reported as odds ratio (OR) with 95% confidence interval (CI) and number of studies (k). The quality of evidence was appraised using GRADE, and the study was registered on PROSPERO (CRD42018103331). Of 21,548 deduplicated studies, 144 eligible studies were included. Of 144 studies, 128 were from low/middle-income countries, 84 were RCTs, and 25 integrated TB and HIV care. Counselling and education was significantly associated with testing (OR = 8.82, 95% CI:1.71 to 45.43; I2 = 99.9%, k = 7), diagnosis (OR = 1.44, 95% CI:1.08 to 1.92; I2 = 97.6%, k = 9), linkage to care (OR = 3.10, 95% CI = 1.97 to 4.86; I2 = 0%, k = 1), cure (OR = 2.08, 95% CI:1.11 to 3.88; I2 = 76.7%, k = 4), treatment completion (OR = 1.48, 95% CI: 1.07 to 2.03; I2 = 73.1%, k = 8), and treatment success (OR = 3.24, 95% CI: 1.88 to 5.55; I2 = 75.9%, k = 5) outcomes compared to standard-of-care. Incentives, multisector collaborations, and community-based interventions were associated with at least three TB care cascade outcomes; digital interventions and mixed interventions were associated with an increased likelihood of two cascade outcomes each. These findings remained salient when studies were limited to RCTs only. Also, our study does not cover the entire care cascade as we did not measure gaps in pre-testing, pretreatment, and post-treatment outcomes (like loss to follow-up and TB recurrence).ConclusionsAmong TB interventions, education and counseling, incentives, community-based interventions, and mixed interventions were associated with multiple active TB care cascade outcomes. However, cost-effectiveness and local-setting contexts should be considered when choosing such strategies due to their high heterogeneity.

[This corrects the article DOI: 10.1371/journal.pmed.1003930.].

Recent meta-analyses combining direct genome-wide association studies (GWAS) with those of family history (GWAX) have indicated very low SNP heritability of Alzheimer's disease (AD). These low estimates may call into question the prospects of continued progress in genetic discovery for AD within the spectrum of common variants. We highlight dramatic downward biases in previous methods, and we validate a novel method for the estimation of SNP heritability via integration of GWAS and GWAX summary data. We apply our method to investigate the genetic architecture of AD using GWAX from UK Biobank and direct case-control GWAS from the International Genomics of Alzheimer's Project (IGAP). We estimate the liability scale common variant SNP heritability of Clinical AD outside of APOE region at ~7-11%, and we project the corresponding estimate for AD pathology to be up to approximately 23%. We estimate that nearly 90% of common variant SNP heritability of Clinical AD exists outside the APOE region. Rare variants not tagged in standard GWAS may account for additional variance. Our results indicate that, while GWAX for AD in UK Biobank may result in greater attenuation of genetic effects beyond that conventionally assumed, it does not introduce appreciable contamination of signal by genetically distinct traits relative to direct case-control GWAS in IGAP. Genetic risk for AD represents a strong effect of APOE superimposed upon a highly polygenic background.

Nontuberculous mycobacteria (NTM) infection is common in patients with structural lung damage. To address how NTM infection is established and causes lung damage, we established an NTM mouse model by intranasal inoculation of clinical isolates of M. intracellulare. During the 39-week course of infection, the bacteria persistently grew in the lung and caused progressive granulomatous and fibrotic lung damage with mortality exceeding 50%. Lung neutrophils were significantly increased at 1 week postinfection, reduced at 2 weeks postinfection and increased again at 39 weeks postinfection. IL-17A was increased in the lungs at 1-2 weeks of infection and reduced at 3 weeks postinfection. Depletion of neutrophils during early (0-2 weeks) and late (32-34 weeks) infection had no effect on mortality or lung damage in chronically infected mice. However, neutralization of IL-17A during early infection significantly reduced bacterial burden, fibrotic lung damage, and mortality in chronically infected mice. Since it is known that IL-17A regulates matrix metalloproteinases (MMPs) and that MMPs contribute to the pathogenesis of pulmonary fibrosis, we determined the levels of MMPs in the lungs of M. intracellulare-infected mice. Interestingly, MMP-3 was significantly reduced by anti-IL-17A neutralizing antibody. Moreover, in vitro data showed that exogenous IL-17A exaggerated the production of MMP-3 by lung epithelial cells upon M. intracellulare infection. Collectively, our findings suggest that early IL-17A production precedes and promotes organized pulmonary M. intracellulare infection in mice, at least in part through MMP-3 production.

BackgroundLow syphilis testing uptake is a major public health issue among men who have sex with men (MSM) in many low- and middle-income countries. Syphilis self-testing (SST) may complement and extend facility-based testing. We aimed to evaluate the effectiveness and costs of providing SST on increasing syphilis testing uptake among MSM in China.Methods and findingsAn open-label, parallel 3-arm randomized controlled trial (RCT) was conducted between January 7, 2020 and July 17, 2020. Men who were at least 18 years of age, had condomless anal sex with men in the past year, reported not testing for syphilis in the last 6 months, and had a stable residence with mailing addresses were recruited from 124 cities in 26 Chinese provinces. Using block randomization with blocks of size 12, enrolled participants were randomly assigned (1:1:1) into 3 arms: standard of care arm, standard SST arm, and lottery incentivized SST arm (1 in 10 chance to win US$15 if they had a syphilis test). The primary outcome was the proportion of participants who tested for syphilis during the trial period and confirmed with photo verification and between arm comparisons were estimated with risk differences (RDs). Analyses were performed on a modified intention-to-treat basis: Participants were included in the complete case analysis if they had initiated at least 1 follow-up survey. The Syphilis/HIV Duo rapid test kit was used. A total of 451 men were enrolled. In total, 136 (90·7%, 136/150) in the standard of care arm, 142 (94·0%, 142/151) in the standard of SST arm, and 137 (91·3%, 137/150) in the lottery incentivized SST arm were included in the final analysis. The proportion of men who had at least 1 syphilis test during the trial period was 63.4% (95% confidence interval [CI]: 55.5% to 71.3%, p = 0.001) in the standard SST arm, 65.7% (95% CI: 57.7% to 73.6%, p = 0.0002) in the lottery incentivized SST arm, and 14.7% (95% CI: 8.8% to 20.7%, p < 0.001) in the standard of care arm. The estimated RD between the standard SST and standard of care arm was 48.7% (95% CI: 37.8% to 58.4%, p < 0.001). The majority (78.5%, 95% CI: 72.7% to 84.4%, p < 0.001) of syphilis self-testers reported never testing for syphilis. The cost per person tested was US$26.55 for standard SST, US$28.09 for the lottery incentivized SST, and US$66.19 for the standard of care. No study-related adverse events were reported during the study duration. Limitation was that the impact of the Coronavirus Disease 2019 (COVID-19) restrictions may have accentuated demand for decentralized testing.ConclusionsCompared to standard of care, providing SST significantly increased the proportion of MSM testing for syphilis in China and was cheaper (per person tested).Trial registrationChinese Clinical Trial Registry: ChiCTR1900022409.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.

BackgroundDigital network-based methods may enhance peer distribution of HIV self-testing (HIVST) kits, but interventions that can optimize this approach are needed. We aimed to assess whether monetary incentives and peer referral could improve a secondary distribution program for HIVST among men who have sex with men (MSM) in China.Methods and findingsBetween October 21, 2019 and September 14, 2020, a 3-arm randomized controlled, single-blinded trial was conducted online among 309 individuals (defined as index participants) who were assigned male at birth, aged 18 years or older, ever had male-to-male sex, willing to order HIVST kits online, and consented to take surveys online. We randomly assigned index participants into one of the 3 arms: (1) standard secondary distribution (control) group (n = 102); (2) secondary distribution with monetary incentives (SD-M) group (n = 103); and (3) secondary distribution with monetary incentives plus peer referral (SD-M-PR) group (n = 104). Index participants in 3 groups were encouraged to order HIVST kits online and distribute to members within their social networks. Members who received kits directly from index participants or through peer referral links from index MSM were defined as alters. Index participants in the 2 intervention groups could receive a fixed incentive ($3 USD) online for the verified test result uploaded to the digital platform by each unique alter. Index participants in the SD-M-PR group could additionally have a personalized peer referral link for alters to order kits online. Both index participants and alters needed to pay a refundable deposit ($15 USD) for ordering a kit. All index participants were assigned an online 3-month follow-up survey after ordering kits. The primary outcomes were the mean number of alters motivated by index participants in each arm and the mean number of newly tested alters motivated by index participants in each arm. These were assessed using zero-inflated negative binomial regression to determine the group differences in the mean number of alters and the mean number of newly tested alters motivated by index participants. Analyses were performed on an intention-to-treat basis. We also conducted an economic evaluation using microcosting from a health provider perspective with a 3-month time horizon. The mean number of unique tested alters motivated by index participants was 0.57 ± 0.96 (mean ± standard deviation [SD]) in the control group, compared with 0.98 ± 1.38 in the SD-M group (mean difference [MD] = 0.41),and 1.78 ± 2.05 in the SD-M-PR group (MD = 1.21). The mean number of newly tested alters motivated by index participants was 0.16 ± 0.39 (mean ± SD) in the control group, compared with 0.41 ± 0.73 in the SD-M group (MD = 0.25) and 0.57 ± 0.91 in the SD-M-PR group (MD = 0.41), respectively. Results indicated that index participants in intervention arms were more likely to motivate unique tested alters (control versus SD-M: incidence rate ratio [IRR = 2.98, 95% CI = 1.82 to 4.89, p-value < 0.001; control versus SD-M-PR: IRR = 3.26, 95% CI = 2.29 to 4.63, p-value < 0.001) and newly tested alters (control versus SD-M: IRR = 4.22, 95% CI = 1.93 to 9.23, p-value < 0.001; control versus SD-M-PR: IRR = 3.49, 95% CI = 1.92 to 6.37, p-value < 0.001) to conduct HIVST. The proportion of newly tested testers among alters was 28% in the control group, 42% in the SD-M group, and 32% in the SD-M-PR group. A total of 18 testers (3 index participants and 15 alters) tested as HIV positive, and the HIV reactive rates for alters were similar between the 3 groups. The total costs were $19,485.97 for 794 testers, including 450 index participants and 344 alter testers. Overall, the average cost per tester was $24.54, and the average cost per alter tester was $56.65. Monetary incentives alone (SD-M group) were more cost-effective than monetary incentives with peer referral (SD-M-PR group) on average in terms of alters tested and newly tested alters, despite SD-M-PR having larger effects. Compared to the control group, the cost for one more alter tester in the SD-M group was $14.90 and $16.61 in the SD-M-PR group. For newly tested alters, the cost of one more alter in the SD-M group was $24.65 and $49.07 in the SD-M-PR group. No study-related adverse events were reported during the study. Limitations include the digital network approach might neglect individuals who lack internet access.ConclusionsMonetary incentives alone and the combined intervention of monetary incentives and peer referral can promote the secondary distribution of HIVST among MSM. Monetary incentives can also expand HIV testing by encouraging first-time testing through secondary distribution by MSM. This social network-based digital approach can be expanded to other public health research, especially in the era of the Coronavirus Disease 2019 (COVID-19).Trial registrationChinese Clinical Trial Registry (ChiCTR) ChiCTR1900025433.

In response to the global pandemic of COVID-19, South Africa implemented a strict lockdown in March 2020 before its first COVID-19 wave started, gradually lifted restrictions between May and September 2020, and then re-imposed restrictions in December 2020 in response to its second wave. There is concern that COVID-19-related morbidity and mortality, the deprioritization of TB activities, fear of transmission, and societal restrictions led to a reduction in tuberculosis (TB) treatment initiations. We analysed monthly public sector, facility-level data from South Africa's District Health Information System (DHIS) from January 2019 to April 2021 to quantify changes in TB treatment initiation numbers stratified by province, setting, and facility type and compared the timing of these changes to COVID-19 case numbers and government lockdown levels. At the 1189 facilities that reported observations for all 28 months of our study period, TB treatment initiations in 2020 were 20.4% lower than in 2019 and 21.9% lower in the first four months of 2021 than in 2019. At the 3669 facilities that reported observations in ≤28 months, numbers of TB treatment initiations declined sharply in all provinces in May-August 2020, compared to the same months in 2019. After recovering somewhat in the last four months of 2020, numbers plummeted again in early 2021. Percentage reductions were somewhat larger in urban and peri-urban areas than in rural areas. Most provinces experienced a clear inverse relationship between COVID-19 cases and TB treatment initiations but little relationship between TB treatment initiations and lockdown level. The COVID-19 pandemic and responses to it resulted in substantial declines in the number of individuals starting treatment for TB in South Africa and risked progress toward achieving TB management goals. Exceptional effort will be needed to sustain gains in combating TB.

In response to the global pandemic of COVID-19, South Africa implemented a strict lockdown in March 2020 before its first COVID-19 wave started, gradually lifted restrictions between May and September 2020, and then re-imposed restrictions in December 2020 in response to its second wave. There is concern that COVID-19-related morbidity and mortality, the deprioritization of TB activities, fear of transmission, and societal restrictions led to a reduction in tuberculosis (TB) treatment initiations. We analysed monthly public sector, facility-level data from South Africa’s District Health Information System (DHIS) from January 2019 to April 2021 to quantify changes in TB treatment initiation numbers stratified by province, setting, and facility type and compared the timing of these changes to COVID-19 case numbers and government lockdown levels. At the 1189 facilities that reported observations for all 28 months of our study period, TB treatment initiations in 2020 were 20.4% lower than in 2019 and 21.9% lower in the first four months of 2021 than in 2019. At the 3669 facilities that reported observations in ≤28 months, numbers of TB treatment initiations declined sharply in all provinces in May-August 2020, compared to the same months in 2019. After recovering somewhat in the last four months of 2020, numbers plummeted again in early 2021. Percentage reductions were somewhat larger in urban and peri-urban areas than in rural areas. Most provinces experienced a clear inverse relationship between COVID-19 cases and TB treatment initiations but little relationship between TB treatment initiations and lockdown level. The COVID-19 pandemic and responses to it resulted in substantial declines in the number of individuals starting treatment for TB in South Africa and risked progress toward achieving TB management goals. Exceptional effort will be needed to sustain gains in combating TB.

Breast cancer is heterogenous in development and cell population with prognoses being highly dependent on numerous factors from driving mutations, biomarker expression and variation in extracellular environment, all affecting response to therapies. Recently, much attention has been given to the role of metabolic alteration in cancers, expanding from the Warburg effect to highlight unique patterns in different cancer cell populations for improving diagnostic and therapeutic approaches. We recently reported on modulation of mannosylation of α-dystroglycan with the metabolite ribitol in breast cancer lines. Here we investigate the effects of pentose sugars ribitol, ribose, and xylitol media supplementation in breast cancer cells by metabolomics and differential gene expression profiling. This combined approach revealed distinctive patterns of alterations in metabolic pathways by ribitol, contrasted with the closely related pentose ribose and pentitol xylitol. Significantly, ribitol supplementation enhances utilization of glucose by glycolysis, whereas ribose improves oxidative phosphorylation and fatty acid synthesis. Ribitol supplementation also increased levels of reduced glutathione (associated with a decrease in oxidative phosphorylation, gluconeogenesis), where ribose supplementation elevated levels of oxidized glutathione (GSSG) indicating an increase in oxidative stress. Treatment with ribitol also enhanced nucleotide biosynthesis. The apparent TCA cycle dysregulation, with distinctive pattern in response to the individual pentitol and pentose, such as ribitol increasing succinate and fumarate while decreasing citrate, demonstrate the adaptive capability of cancer cells to nutritional environment. This metabolic reprogramming presents new avenues for developing targeted therapies to cancers with metabolites, especially in combination with other drug treatments.

Limb Girdle Muscular Dystrophy 2I (LGMDR9) is one of the most common LGMD characterized by defects in glycosylation of α-dystroglycan (matriglycan) resulting from mutations of Fukutin-related protein (FKRP). There is no effective therapy currently available. We recently demonstrated that ribitol supplement increases levels of matriglycan in cells in vitro and in FKRP-P448L (P448L) mutant mouse model through drinking water administration. To be clinically relevant, we have now conducted a dose-escalating efficacy study by gavage in P448L mutant mice. Six months of ribitol treatment daily significantly rescued functions of skeletal, respiratory, and cardiac muscles dose-dependently. This was associated with a dose dependent increase in matriglycan and improvement in muscle pathology with reductions in muscle degeneration, inflammatory infiltration and fibrosis. Importantly, ribitol significantly increased life span and muscle functions of the female animals receiving treatment from 10 months of age. The only observed side effect was gastrointestinal tract bloating with loose stool and this effect is also dose dependent. The results validate the mechanism that ribitol as a pre-substrate of glycosyltransferase is able to compensate for the decreased function of mutant FKRP with restoration of matriglycan expression and provide a guidance for future clinical trial design.

Breast cancer is heterogenous in development and cell population with prognoses being highly dependent on numerous factors from driving mutations, biomarker expression and variation in extracellular environment, all affecting response to therapies. Recently, much attention has been given to the role of metabolic alteration in cancers, expanding from the Warburg effect to highlight unique patterns in different cancer cell populations for improving diagnostic and therapeutic approaches. We recently reported on modulation of mannosylation of α-dystroglycan with the metabolite ribitol in breast cancer lines. Here we investigate the effects of pentose sugars ribitol, ribose, and xylitol media supplementation in breast cancer cells by metabolomics and differential gene expression profiling. This combined approach revealed distinctive patterns of alterations in metabolic pathways by ribitol, contrasted with the closely related pentose ribose and pentitol xylitol. Significantly, ribitol supplementation enhances utilization of glucose by glycolysis, whereas ribose improves oxidative phosphorylation and fatty acid synthesis. Ribitol supplementation also increased levels of reduced glutathione (associated with a decrease in oxidative phosphorylation, gluconeogenesis), where ribose supplementation elevated levels of oxidized glutathione (GSSG) indicating an increase in oxidative stress. Treatment with ribitol also enhanced nucleotide biosynthesis. The apparent TCA cycle dysregulation, with distinctive pattern in response to the individual pentitol and pentose, such as ribitol increasing succinate and fumarate while decreasing citrate, demonstrate the adaptive capability of cancer cells to nutritional environment. This metabolic reprogramming presents new avenues for developing targeted therapies to cancers with metabolites, especially in combination with other drug treatments.

Limb Girdle Muscular Dystrophy 2I (LGMDR9) is one of the most common LGMD characterized by defects in glycosylation of α-dystroglycan (matriglycan) resulting from mutations of Fukutin-related protein (FKRP). There is no effective therapy currently available. We recently demonstrated that ribitol supplement increases levels of matriglycan in cells in vitro and in FKRP-P448L (P448L) mutant mouse model through drinking water administration. To be clinically relevant, we have now conducted a dose-escalating efficacy study by gavage in P448L mutant mice. Six months of ribitol treatment daily significantly rescued functions of skeletal, respiratory, and cardiac muscles dose-dependently. This was associated with a dose dependent increase in matriglycan and improvement in muscle pathology with reductions in muscle degeneration, inflammatory infiltration and fibrosis. Importantly, ribitol significantly increased life span and muscle functions of the female animals receiving treatment from 10 months of age. The only observed side effect was gastrointestinal tract bloating with loose stool and this effect is also dose dependent. The results validate the mechanism that ribitol as a pre-substrate of glycosyltransferase is able to compensate for the decreased function of mutant FKRP with restoration of matriglycan expression and provide a guidance for future clinical trial design.

To address a major knowledge gap for flatback sea turtles (Natator depressus), a species endemic to Australia and considered 'Data Deficient' for IUCN Red List assessment, we present the first-ever skeletochronology-derived age and growth rate estimates for this species. Using a rare collection of bone samples gathered from across northern Australia, we applied skeletochronology and characterized the length-at-age relationship, established baseline growth rates from the hatchling to adult life stages, and produced empirical estimates of age-at- and size-at-sexual-maturation (ASM, SSM). We analyzed humeri from 74 flatback sea turtles ranging in body size from 6.0-96.0 cm curved carapace length (CCL), and recovered from Western Australia (n = 48), Eastern Australia (n = 13), central Australia (n = 8; Northern Territory n = 3, the Gulf of Carpentaria n = 5), and unknown locations (n = 5). We identified the onset of sexual maturity for 29 turtles, based on rapprochement growth patterns in the bones. Estimates for ASM ranged from 12.0 to 23.0 years (mean: 16.3 ± 0.53 SE), SSM ranged from 76.1 to 94.0 cm CCL (mean: 84.9 ± 0.90 SE), and maximum observed reproductive longevity was 31 years for a 45-year old male flatback. Growth was modeled as a smoothing spline fit to the size-at-age relationship and at the mean SSM (84.9 cm CCL) corresponded with a spline-predicted maturity age of 18 years (95% CI: 16 to 24), while mean nesting sizes reported in the literature (86.4 to 94 cm CCL) corresponded to estimated ages of 24+ years. A bootstrapped von Bertalanffy growth model was also applied and showed consistencies with the spline curve, yielding an estimated upper size limit, Linf, at 89.2 ± 0.04 cm (95% CI: 85.5 to 95.9 cm) with the intrinsic growth rate parameter, k, at 0.185 ± 0.0004 (0.16 to 0.22); at the same mean SSM (84.9 cm CCL) the estimated ASM was 16.3 ± 0.05 years (95% CI: 12.8 to 27.7 years). Lastly, four of the samples analyzed were collected from deceased adult females that had previous sizes known from on-going mark/recapture studies at nesting sites in Western Australia. The paired CCL data (measured at nesting and back-calculated) did not significantly differ (p = 0.875). This first skeletochronology study for flatback sea turtles generates valuable empirical estimates for ongoing conservation and management efforts.

Background Ruminant livestock are a major contributor to Australian agricultural sector carbon emissions. Variation in methane (CH4) produced from enteric microbial fermentation of feed in the reticulo-rumen of sheep differs with different digestive functions. Method We isolated rumen epithelium enzymatically to extract membrane and cytosol proteins from sheep with high (H) and low (L) CH4 emission. Protein abundance was quantified using SWATH-mass spectrometry. Results The research found differences related to the metabolism of glucose, lactate and processes of cell defence against microbes in sheep from each phenotype. Enzymes in the methylglyoxal pathway, a side path of glycolysis, resulting in D-lactate production, differed in abundance. In the H CH4 rumen epithelium the enzyme hydroxyacylglutathione hydrolase (HAGH) was 2.56 fold higher in abundance, whereas in the L CH4 epithelium lactate dehydrogenase D (LDHD) was 1.93 fold higher. Malic enzyme 1 which converts D-lactate to pyruvate via the tricarboxylic cycle was 1.57 fold higher in the L CH4 phenotype. Other proteins that are known to regulate cell defence against microbes had differential abundance in the epithelium of each phenotype. Conclusion Differences in the abundance of enzymes involved in the metabolism of glucose were associated with H and L CH4 phenotype sheep. Potentially this represents an opportunity to use protein markers in the rumen epithelium to select low CH4 emitting sheep.

BackgroundRuminant livestock are a major contributor to Australian agricultural sector carbon emissions. Variation in methane (CH4) produced from enteric microbial fermentation of feed in the reticulo-rumen of sheep differs with different digestive functions.MethodWe isolated rumen epithelium enzymatically to extract membrane and cytosol proteins from sheep with high (H) and low (L) CH4 emission. Protein abundance was quantified using SWATH-mass spectrometry.ResultsThe research found differences related to the metabolism of glucose, lactate and processes of cell defence against microbes in sheep from each phenotype. Enzymes in the methylglyoxal pathway, a side path of glycolysis, resulting in D-lactate production, differed in abundance. In the H CH4 rumen epithelium the enzyme hydroxyacylglutathione hydrolase (HAGH) was 2.56 fold higher in abundance, whereas in the L CH4 epithelium lactate dehydrogenase D (LDHD) was 1.93 fold higher. Malic enzyme 1 which converts D-lactate to pyruvate via the tricarboxylic cycle was 1.57 fold higher in the L CH4 phenotype. Other proteins that are known to regulate cell defence against microbes had differential abundance in the epithelium of each phenotype.ConclusionDifferences in the abundance of enzymes involved in the metabolism of glucose were associated with H and L CH4 phenotype sheep. Potentially this represents an opportunity to use protein markers in the rumen epithelium to select low CH4 emitting sheep.

Background Prior studies have documented lower cardiovascular disease (CVD) risk among people with a higher adherence to a plant-based dietary pattern. Non-Hispanic black Americans are an understudied group with high burden of CVD, yet studies of plant-based diets have been limited in this population. Methods and findings We conducted an analysis of prospectively collected data from a community-based cohort of African American adults (n = 3,635) in the Jackson Heart Study (JHS) aged 21–95 years, living in the Jackson, Mississippi, metropolitan area, US, who were followed from 2000 to 2018. Using self-reported dietary data, we assigned scores to participants’ adherence to 3 plant-based dietary patterns: an overall plant-based diet index (PDI), a healthy PDI (hPDI), and an unhealthy PDI (uPDI). Cox proportional hazards models were used to estimate associations between plant-based diet scores and CVD incidence and all-cause mortality. Over a median follow-up of 13 and 15 years, there were 293 incident CVD cases and 597 deaths, respectively. After adjusting for sociodemographic characteristics (age, sex, and education) and health behaviors (smoking, alcohol intake, margarine intake, physical activity, and total energy intake), no significant association was observed between plant-based diets and incident CVD for overall PDI (hazard ratio [HR] 1.06, 95% CI 0.78–1.42, p-trend = 0.72), hPDI (HR 1.07, 95% CI 0.80–1.42, p-trend = 0.67), and uPDI (HR 0.95, 95% CI 0.71–1.28, p-trend = 0.76). Corresponding HRs (95% CIs) for all-cause mortality risk with overall PDI, hPDI, and uPDI were 0.96 (0.78–1.18), 0.94 (0.76–1.16), and 1.06 (0.86–1.30), respectively. Corresponding HRs (95% CIs) for incident coronary heart disease with overall PDI, hPDI, and uPDI were 1.09 (0.74–1.61), 1.11 (0.76–1.61), and 0.79 (0.52–1.18), respectively. For incident total stroke, HRs (95% CIs) for overall PDI, hPDI, and uPDI were 1.00 (0.66–1.52), 0.91 (0.61–1.36), and 1.26 (0.84–1.89) (p-trend for all tests > 0.05). Limitations of the study include use of self-reported dietary intake, residual confounding, potential for reverse causation, and that the study did not capture those who exclusively consume plant-derived foods. Conclusions In this study of black Americans, we observed that, unlike in prior studies, greater adherence to a plant-based diet was not associated with CVD or all-cause mortality. In a cohort study, Leah J. Weston and colleagues investigate the associations between consumption of plant-based diets and incident cardiovascular disease and all-cause mortality in African Americans. Author summary Why was this study done? Plant-based diets have been linked, largely through studies of “vegetarian” diets, with health benefits, including lower risk of heart disease; however, studies of these associations among more general populations have produced mixed results. Investigating plant-based dietary patterns has allowed researchers to study how levels of adherence to plant-based dietary patterns and the healthfulness of plant-based diets correlate with cardiovascular disease (CVD) risk. This study was conducted to expand the generalizability of conclusions about plant-based diets and CVD risk in African American men and women in the US who were following a southern dietary pattern. What did the researchers do and find? We used data on 3,635 African American adults from the Jackson Heart Study with a mean follow-up of 13 years to assess the association of 3 plant-based dietary patterns (overall, healthy, and unhealthy) with CVD incidence and all-cause mortality. Overall diet quality was low for all participants, and participants with the most plant-rich diets still regularly included animal-based foods. Incidence of CVD and all-cause mortality was the same among participants whose diets were most similar to a plant-based dietary pattern and among those whose diets were least plant-based. Among individual food groups, legumes were associated with a lower risk for CVD, while vegetable oils were associated with higher risk for CVD, and whole grains and sugar-sweetened beverages were associated with higher all-cause mortality. What do these findings mean? Plant-based diet index scores have gained popularity among researchers for their ability to characterize overall dietary patterns; however, their use may be limited in populations with minimal gradations in the plant richness of participants’ diets. Health benefits linked to plant-based diets may depend on the overall healthfulness of an individual’s diet and might require higher levels of adherence to a plant-based diet than what is typically practiced among those with the most plant-rich diets in this cohort of African Americans residing in the southern region of the US.

Background Social relationships play a key role in both substance use and homelessness. Transitioning out of homelessness often requires reduction in substance use as well as changes in social networks. A social network-based behavior change intervention that targets changes personal social networks may assist the transition out of homelessness. Most behavior change interventions that incorporate social networks assume a static network. However, people experiencing homelessness who transition into housing programs that use a harm reduction approach experience many changes in their social networks during this transition. Changes may include disconnecting from street-based network contacts, re-connecting with former network contacts, and exposure to new network members who actively engage in substance use. An intervention that helps people transitioning out of homelessness make positive alterations to their social networks may compliment traditional harm reduction housing program services. Methods We conducted a pilot randomized controlled trial (RCT) of an innovative Social Network Intervention (MI-SNI), which combines network visualization and Motivational Interviewing to assist adults transitioning out of homelessness. The MI-SNI provides feedback to new residents about their social environments and is designed to motivate residents to make positive changes in both their individual behavior and their personal network. In a sample of 41 adult housing program residents with past year risky substance use, we examined whether participants randomized to receive a MI-SNI showed greater changes in their personal networks over 3 months compared to those receiving usual care. Results There were significant differences in the networks of the MI-SNI group compared to the group receiving usual care at follow-up, controlling for baseline network characteristics. The MI-SNI group had greater reductions in the proportion of their network members who influenced alcohol or other drug use (AOD) use, such as drinking partners, and more frequently changed their relationships in the direction of lower AOD risk with network members who were retained in their networks across waves. Conclusions This study is the first pilot test of a MI-SNI customized for assisting the transition out of homelessness to test for personal network changes. Results indicate that MI-SNIs can have a positive impact on short-term network changes and thus may serve as a useful adjunct to behavioral change interventions. These findings suggest that a MI-SNI approach may help individuals experiencing homelessness and risky AOD use positively restructure their social networks while transitioning into supportive housing. These promising results suggest the need for a larger RCT test of this innovative intervention approach. Trial registration ClinicalTrials.gov Identifier: NCT02140359.