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The ubiquity and ease with which microbial cells disperse over space is a key concept in microbiology, especially in microbial ecology. The phenomenon prompted Baas Becking's famous "everything is everywhere" statement that now acts as the null hypothesis in studies that test the dispersal limitation of microbial taxa. Despite covering the content in lectures, exam performance indicated that the concepts of dispersal and biogeography challenged undergraduate students in an upper-level Microbial Ecology course. Therefore, we iteratively designed a hands-on classroom activity to supplement the lecture content and reinforce fundamental microbial dispersal and biogeography concepts while also building quantitative reasoning and teamwork skills. In a class period soon after the lecture, the students formed three-to-five-person teams to engage in the activity, which included a hands-on dispersal simulation and worksheet to guide discussion. The simulation involved stepwise neutral immigration or emigration and then environmental selection on a random community of microbial taxa represented by craft poms. The students recorded the results at each step as microbial community data. A field guide was provided to identify the taxonomy based on the pom phenotype and a reference to each taxon's preferred environmental niches. The worksheet guided a reflection of student observations during the simulation. It also sharpened quantitative thinking by prompting the students to summarize and visualize their and other teams' microbial community data and then to compare the observed community distributions to the idealized expectation given only selection without dispersal. We found that the activity improved student performance on exam questions and general student satisfaction and comfort with the biogeography concepts. Activity instructions and a list of needed materials are included for instructors to reproduce for their classrooms.

BACKGROUND: Across sub-Saharan Africa, mid-level healthcare managers oversee implementation of national guidelines. It remains unclear whether leadership and management training can improve population health outcomes. METHODS: We sought to evaluate leadership/management skills among district-level health managers in Uganda participating in the SEARCH-IPT randomised trial to promote isoniazid preventive therapy (IPT) for persons with HIV (PWH). The intervention, which led to higher IPT rates, included annual leadership/management training of managers. We conducted a cross-sectional survey assessing leadership/management skills among managers at trial completion. The survey evaluated self-reported use of leadership/management tools and general leadership/management. We conducted a survey among a sample of providers to understand the interventions impact. Targeted minimum loss-based estimation (TMLE) was used to compare responses between trial arms. RESULTS: Of 163 managers participating in the SEARCH-IPT trial, 119 (73%) completed the survey. Intervention managers reported more frequent use of leadership/management tools taught in the intervention curriculum than control managers (+3.64, 95% CI 1.98-5.30, P < 0.001). There were no significant differences in self-reported leadership skills in the intervention as compared to the control group. Among providers, the average reported quality of guidance and supervision was significantly higher in intervention vs control districts (+1.08, 95% CI 0.63-1.53, P = 0.001). CONCLUSIONS: A leadership and management training intervention increased the use of leadership/management tools among mid-level managers and resulted in higher perceived quality of supervision among providers in intervention vs control districts in Uganda. These findings suggest improved leadership/management among managers contributed to increased IPT use among PWH in the intervention districts of the SEARCH-IPT trial.

IntroductionAlthough dementia-related proteinopathy has a strong negative impact on public health, and is highly heritable, understanding of the related genetic architecture is incomplete.MethodsWe applied multidimensional generalized partial credit modeling (GPCM) to test genetic associations with dementia-related proteinopathies. Data were analyzed to identify candidate single nucleotide variants for the following proteinopathies: Aβ, tau, α-synuclein, and TDP-43.ResultsFinal included data comprised 966 participants with neuropathologic and WGS data. Three continuous latent outcomes were constructed, corresponding to TDP-43-, Aβ/Tau-, and α-synuclein-related neuropathology endophenotype scores. This approach helped validate known genotype/phenotype associations: for example, TMEM106B and GRN were risk alleles for TDP-43 pathology; and GBA for α-synuclein/Lewy bodies. Novel suggestive proteinopathy-linked alleles were also discovered, including several (SDHAF1, TMEM68, and ARHGEF28) with colocalization analyses and/or high degrees of biologic credibility.DiscussionA novel methodology using GPCM enabled insights into gene candidates for driving misfolded proteinopathies.HighlightsLatent factor scores for proteinopathies were estimated using a generalized partial credit model. The three latent continuous scores corresponded well with proteinopathy severity. Novel genes associated with proteinopathies were identified. Several genes had high degrees of biologic credibility for dementia risk factors.

BACKGROUNDCOVID-19 convalescent plasma (CCP) virus-specific antibody levels that translate into recipient posttransfusion antibody levels sufficient to prevent disease progression are not defined.METHODSThis secondary analysis correlated donor and recipient antibody levels to hospitalization risk among unvaccinated, seronegative CCP recipients within the outpatient, double-blind, randomized clinical trial that compared CCP to control plasma. The majority of COVID-19 CCP arm hospitalizations (15/17, 88%) occurred in this unvaccinated, seronegative subgroup. A functional cutoff to delineate recipient high versus low posttransfusion antibody levels was established by 2 methods: (i) analyzing virus neutralization-equivalent anti-Spike receptor-binding domain immunoglobulin G (anti-S-RBD IgG) responses in donors or (ii) receiver operating characteristic (ROC) curve analysis.RESULTSSARS-CoV-2 anti-S-RBD IgG antibody was volume diluted 21.3-fold into posttransfusion seronegative recipients from matched donor units. Virus-specific antibody delivered was approximately 1.2 mg. The high-antibody recipients transfused early (symptom onset within 5 days) had no hospitalizations. A CCP-recipient analysis for antibody thresholds correlated to reduced hospitalizations found a statistical significant association between early transfusion and high antibodies versus all other CCP recipients (or control plasma), with antibody cutoffs established by both methods-donor-based virus neutralization cutoffs in posttransfusion recipients (0/85 [0%] versus 15/276 [5.6%]; P = 0.03) or ROC-based cutoff (0/94 [0%] versus 15/267 [5.4%]; P = 0.01).CONCLUSIONIn unvaccinated, seronegative CCP recipients, early transfusion of plasma units in the upper 30% of study donors antibody levels reduced outpatient hospitalizations. High antibody level plasma units, given early, should be reserved for therapeutic use.TRIAL REGISTRATIONClinicalTrials.gov NCT04373460.FUNDINGDepartment of Defense (W911QY2090012); Defense Health Agency; Bloomberg Philanthropies; the State of Maryland; NIH (3R01AI152078-01S1, U24TR001609-S3, 1K23HL151826NIH); the Mental Wellness Foundation; the Moriah Fund; Octapharma; the Healthnetwork Foundation; the Shear Family Foundation; the NorthShore Research Institute; and the Rice Foundation.

This study examined the role that cytokines may have played in the beneficial outcomes found when outpatient individuals infected with SARS-CoV-2 were transfused with COVID-19 convalescent plasma (CCP) early in their infection. We found that the pro-inflammatory cytokine IL-6 decreased significantly faster in patients treated early with CCP. Participants with COVID-19 treated with CCP later in the infection did not have the same effect. This decrease in IL-6 levels after early CCP treatment suggests a possible role of inflammation in COVID-19 progression. The evidence of IL-6 involvement brings insight into the possible mechanisms involved in CCP treatment mitigating SARS-CoV-2 severity.

OBJECTIVE: Despite advances in incorporating diversity and structural competency into medical education curriculum, there is limited curriculum for public health research professionals. We developed and implemented a four-part diversity, equity, and inclusion (DEI) training series tailored for academic health research professionals to increase foundational knowledge of core diversity concepts and improve skills. METHODS: We analyzed close- and open-ended attendee survey data to evaluate within- and between-session changes in DEI knowledge and perceived skills. RESULTS: Over the four sessions, workshop attendance ranged from 45 to 82 attendees from our 250-person academic department and represented a mix of staff (64%), faculty (25%), and trainees (11%). Most identified as female (74%), 28% as a member of an underrepresented racial and ethnic minority (URM) group, and 17% as LGBTQI. During all four sessions, attendees increased their level of DEI knowledge, and within sessions two through four, attendees perception of DEI skills increased. We observed increased situational DEI awareness as higher proportions of attendees noted disparities in mentoring and opportunities for advancement/promotion. An increase in a perceived lack of DEI in the workplace as a problem was observed; but only statistically significant among URM attendees. DISCUSSION: Developing applied curricula yielded measurable improvements in knowledge and skills for a diverse health research department of faculty, staff, and students. Nesting this training within a more extensive program of departmental activities to improve climate and address systematic exclusion likely contributed to the series success. Additional research is underway to understand the series longer-term impact on applying skills for behavior change.

We address the notion that different student grouping configurations in the classroom may provide different sets of opportunities for English learners (ELs) -- students whose home language is not English (the language of instruction in the U.S.) -- to both learn science and develop a second language through different forms of social interaction. We examined the frequency with which monolingual and bilingual (English-Spanish) teachers interacted with students working in four grouping configurations: Only ELs, Whole Class, Only Non-ELs, and Mixed (both ELs and non-ELs). We used a sample of 359 instructional episodes from 78 science lessons taught by bilingual and English-only teachers in the U.S. While we observed a considerable variation in the frequency of different classroom practices (e.g. those promoting critical thinking were less frequent than those involving factual knowledge), Whole Class was the grouping configuration most frequently observed for all classroom practices. The same frequency patterns were observed for monolingual and bilingual teachers. We argue that the low frequency of teachers' interactions with students working in small groups limits the opportunity for ELs to learn science through different forms of social interaction and for teachers to identify and address individual EL students' learning needs.

A summar y of the final progress achieved in two Metals Affordability Initiative (MAI) programs (RR-12 and RR-13) that were funded by the US Air Force to develop the necessary integrated computational materials engineering (ICME) framework, knowledge, and supporting database to model and predict location-specific fatigue properties across the entire titanium supply chain is presented. Validation of this ICME framework which allows for the prediction of location specific low cycle fatigue (LCF) and high cycle fatigue (HCF) behavior on complex production components in electro-polished and shot peened surface conditions will be presented. In addition, validation of a new shot peening capability embedded with the commercial software package DEFORM™ will be presented.

Nigeria has the third largest incidence of premature birth, after India and China. Most babies that will require treatment for retinopathy of prematurity (ROP) have birth weight (BW) less than 1500g and gestational age (GA) less than 32 weeks, with initial eye examination within the first 30 days of life. This report aims to present the findings in three babies with vision threatening ROP that developed at less than 30 days of life. Routine screening for ROP was conducted for three babies. One was born GA 33 weeks, BW 1.6kg, screened for ROP on the 13th day of life, while the other two were a set of twins born at GA of 33 weeks, both BW 1.3kg, screened for ROP first on the 16th day of life. The twins were found CC –BY 4.0 to have arborizing vessels at the initial exam, which progressed to stage 3 pre-plus ROP by the 23rd day of life. The 3rd child had stage -3 plus disease at the first screening, warranting immediate LASER therapy. The screening criteria of Nigeria ROP group is BW ≤ 1500g or GA of ≤ 34 weeks, with the first eye examination within the first 30 days of life. These case reports show that larger babies can also develop sight threatening ROP within the first two weeks of life. There is a need for constant review of ROP screening criteria and timing based on locally available data

Abstract Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

Post-COVID conditions (PCCs) are common and have significant morbidity. Risk factors for PCC include advancing age, female sex, obesity, and diabetes mellitus. Little is known about treatment, inflammation, and PCC. Among 882 individuals with confirmed SARS-CoV-2 infection participating in a randomized trial of COVID-19 convalescent plasma (CCP) vs control plasma with available biospecimens and symptom data, the association between early CCP treatment, cytokine levels, and PCC was evaluated. Cytokine and chemokine levels were assessed at baseline, day 14, and day 90 using a multiplexed sandwich immunoassay (Meso Scale Discovery). Presence of any self-reported PCC symptoms was assessed at day 90. Associations between CCP treatment, cytokine levels, and PCC were examined using multivariate logistic regression models. One third of the 882 participants had day 90 PCC symptoms, with fatigue (14.5%) and anosmia (14.5%) being most common. Cytokine levels decreased from baseline to day 90. In a multivariable analysis, female sex (adjusted odds ratio [AOR] = 2.69 [1.93-3.81]), older age (AOR = 1.32 [1.17-1.50]), and elevated baseline levels of IL-6 (AOR = 1.59 [1.02-2.47]) were independently associated with development of PCC. Those who received early CCP treatment (≤5 days after symptom onset) compared to late CCP treatment had statistically significant lower odds of PCC. IMPORTANCE Approximately 20% of individuals infected with SARS-CoV-2 experienced long-term health effects, as defined PCC. However, it is unknown if there are any early biomarkers associated with PCC or whether early intervention treatments may decrease the risk of PCC. In a secondary analysis of a randomized clinical trial, this study demonstrates that among outpatients with SARS-CoV-2, increased IL-6 at time of infection is associated with increased odds of PCC. In addition, among individuals treated early, within 5 days of symptom onset, with COVID-19 convalescent plasma, there was a trend for decreased odds of PCC after adjusting for other demographic and clinical characteristics. Future treatment studies should be considered to evaluate the effect of early treatment and anti-IL-6 therapies on PCC development.

BACKGROUND: COVID-19 convalescent plasma (CCP) is an important therapeutic option for outpatients at high risk of hospitalization from SARS-CoV-2 infection. We assessed the safety of outpatient CCP transfusions administered during clinical trials. STUDY DESIGN AND METHODS: We analyzed data pertaining to transfusion-related reactions from two randomized controlled trials in the U.S. that evaluated the efficacy of CCP versus control plasma in various ambulatory settings. Multivariable logistic regression was used to assess whether CCP was associated with transfusion reactions, after adjusting for potential confounders. RESULTS: The combined study reported 79/1351 (5.9%) adverse events during the transfusion visit, with the majority 62/1351 (4.6%) characterized by mild, allergic-type findings of urticaria, and/or pruritus consistent with minor allergic transfusion reactions; the other reported events were attributed to the patients underlying disease, COVID-19, or vasovagal in nature. We found no difference in the likelihood of allergic transfusion reactions between those receiving CCP versus control plasma (adjusted odds ratio [AOR], 0.75; 95% CI, 0.43-1.31). Risk of urticaria and/or pruritus increased with a pre-existing diagnosis of asthma (AOR, 2.33; 95% CI, 1.16-4.67). We did not observe any CCP-attributed antibody disease enhancement in participants with COVID-19 or increased risk of infection. There were no life-threatening severe transfusion reactions and no patients required hospitalization related to transfusion-associated complications. DISCUSSION: Outpatient plasma administration was safely performed for nearly 1400 participants. CCP is a safe therapeutic option for outpatients at risk of hospitalization from COVID-19.

BACKGROUND: Cytokines and chemokines play a critical role in the response to infection and vaccination. We aimed to assess the longitudinal association of COVID-19 vaccination with cytokine and chemokine concentrations and trajectories among people with SARS-CoV-2 infection. METHODS: In this longitudinal, prospective cohort study, blood samples were used from participants enrolled in a multi-centre randomised trial assessing the efficacy of convalescent plasma therapy for ambulatory COVID-19. The trial was conducted in 23 outpatient sites in the USA. In this study, participants (aged ≥18 years) were restricted to those with COVID-19 before vaccination or with breakthrough infections who had blood samples and symptom data collected at screening (pre-transfusion), day 14, and day 90 visits. Associations between COVID-19 vaccination status and concentrations of 21 cytokines and chemokines (measured using multiplexed sandwich immunoassays) were examined using multivariate linear mixed-effects regression models, adjusted for age, sex, BMI, hypertension, diabetes, trial group, and COVID-19 waves (pre-alpha or alpha and delta). FINDINGS: Between June 29, 2020, and Sept 30, 2021, 882 participants recently infected with SARS-CoV-2 were enrolled, of whom 506 (57%) were female and 376 (43%) were male. 688 (78%) of 882 participants were unvaccinated, 55 (6%) were partly vaccinated, and 139 (16%) were fully vaccinated at baseline. After adjusting for confounders, geometric mean concentrations of interleukin (IL)-2RA, IL-7, IL-8, IL-15, IL-29 (interferon-λ), inducible protein-10, monocyte chemoattractant protein-1, and tumour necrosis factor-α were significantly lower among the fully vaccinated group than in the unvaccinated group at screening. On day 90, fully vaccinated participants had approximately 20% lower geometric mean concentrations of IL-7, IL-8, and vascular endothelial growth factor-A than unvaccinated participants. Cytokine and chemokine concentrations decreased over time in the fully and partly vaccinated groups and unvaccinated group. Log10 cytokine and chemokine concentrations decreased faster among participants in the unvaccinated group than in other groups, but their geometric mean concentrations were generally higher than fully vaccinated participants at 90 days. Days since full vaccination and type of vaccine received were not correlated with cytokine and chemokine concentrations. INTERPRETATION: Initially and during recovery from symptomatic COVID-19, fully vaccinated participants had lower concentrations of inflammatory markers than unvaccinated participants suggesting vaccination is associated with short-term and long-term reduction in inflammation, which could in part explain the reduced disease severity and mortality in vaccinated individuals. FUNDING: US Department of Defense, National Institutes of Health, Bloomberg Philanthropies, State of Maryland, Mental Wellness Foundation, Moriah Fund, Octapharma, HealthNetwork Foundation, and the Shear Family Foundation.

BackgroundPeople with schizophrenia experience unique barriers to routine HIV testing, despite increased risk of HIV compared with the general US population. Little is known about how health care delivery system factors affect testing rates or whether there are testing differences for people with schizophrenia.SettingNationally representative sample of Medicaid enrollees with and without schizophrenia.MethodsUsing retrospective longitudinal data, we examined whether state-level factors were associated with differences in HIV testing among Medicaid enrollees with schizophrenia compared with frequency-matched controls during 2002-2012. Multivariable logistic regression estimated testing rate differences between and within cohorts.ResultsHigher HIV testing rates for enrollees with schizophrenia were associated with higher state-level Medicaid spending per enrollee, efforts to reduce Medicaid fragmentation, and higher federal prevention funding. State-level AIDS epidemiology predicted more frequent HIV testing for enrollees with schizophrenia versus controls. Living in rural settings predicted lower HIV testing, especially for people with schizophrenia.ConclusionOverall, state-level predictors of HIV testing rates varied among Medicaid enrollees, although rates were generally higher for those with schizophrenia than controls. Increased HIV testing for people with schizophrenia was associated with coverage of HIV testing when medically necessary, higher Centers for Disease Control and Prevention prevention funding, and higher AIDS incidence, prevalence, and mortality when compared with controls. This analysis suggests that state policymaking has an important role to play in advancing that effort. Overcoming fragmented care systems, sustaining robust prevention funding, and consolidating funding streams in innovative and flexible ways to support more comprehensive systems of care delivery deserve attention.

Low-cost interventions are needed to reduce alcohol use among persons with HIV (PWH) in low-income settings. Brief alcohol interventions hold promise, and technology may efficiently deliver brief intervention components with high frequency. We conducted a costing study of the components of a randomized trial that compared a counselling-based intervention with two in-person one-on-one sessions supplemented by booster sessions to reinforce the intervention among PWH with unhealthy alcohol use in southwest Uganda. Booster sessions were delivered twice weekly by two-way short message service (SMS) or Interactive Voice Response (IVR), i.e. via technology, or approximately monthly via live calls from counsellors. We found no significant intervention effects compared to the control, however the cost of the types of booster sessions differed. Start up and recurring costs for the technology-delivered booster sessions were 2.5 to 3 times the cost per participant of the live-call delivered booster intervention for 1000 participants. These results suggest technology-based interventions for PWH are unlikely to be lower cost than person-delivered interventions unless they are at very large scale.

Limbic-predominant age-related TDP-43 encephalopathy (LATE) affects approximately one-third of older individuals and is associated with cognitive impairment. However, there is a highly incomplete understanding of the genetic determinants of LATE neuropathologic changes (LATE-NC) in diverse populations. The defining neuropathologic feature of LATE-NC is TDP-43 proteinopathy, often with comorbid hippocampal sclerosis (HS). In terms of genetic risk factors, LATE-NC and/or HS are associated with single nucleotide variants (SNVs) in 3 genes-TMEM106B (rs1990622), GRN (rs5848), and ABCC9 (rs1914361 and rs701478). We evaluated these 3 genes in convenience samples of individuals of African ancestry. The allele frequencies of the LATE-associated alleles were significantly different between persons of primarily African (versus European) ancestry: In persons of African ancestry, the risk-associated alleles for TMEM106B and ABCC9 were less frequent, whereas the risk allele in GRN was more frequent. We performed an exploratory analysis of data from African-American subjects processed by the Alzheimer's Disease Genomics Consortium, with a subset of African-American participants (n = 166) having corroborating neuropathologic data through the National Alzheimer's Coordinating Center (NACC). In this limited-size sample, the ABCC9/rs1914361 SNV was associated with HS pathology. More work is required concerning the genetic factors influencing non-Alzheimer disease pathology such as LATE-NC in diverse cohorts.

Background & aimsThere are limited data regarding fibrosis progression in biopsy-proven nonalcoholic fatty liver disease (NAFLD) in people with type 2 diabetes mellitus (T2DM) compared with people without T2DM. We assessed the time to fibrosis progression in people with T2DM compared with people without T2DM in a large, multicenter, study of people with NAFLD who had paired liver biopsies.MethodsThis study included 447 adult participants (64% were female) with NAFLD who had paired liver biopsies more than 1 year apart. Liver histology was systematically assessed by a central pathology committee blinded to clinical data. The primary outcome was the cumulative incidence of a ≥1-stage increase in fibrosis in participants with T2DM compared with participants without T2DM.ResultsThe mean (SD) age and body mass index (calculated as weight in kilograms divided by the square of the height in meters) were 50.9 (11.5) years and 34.7 (6.3), respectively. The median time between biopsies was 3.3 years (interquartile range, 1.8-6.1 years). Participants with T2DM had a significantly higher cumulative incidence of fibrosis progression at 4 years (24% vs 20%), 8 years (60% vs 50%), and 12 years (93% vs 76%) (P = .005). Using a multivariable Cox proportional hazards model adjusted for multiple confounders, T2DM remained an independent predictor of fibrosis progression (adjusted hazard ratio, 1.69; 95% CI, 1.17-2.43; P = .005). The cumulative incidence of fibrosis regression by ≥1 stage was similar in participants with T2DM compared with participants without T2DM (P = .24).ConclusionsIn this large, multicenter cohort study of well-characterized participants with NAFLD and paired liver biopsies, we found that fibrosis progressed faster in participants with T2DM compared with participants without T2DM. These data have important implications for clinical practice and trial design.

ABSTRACT Microbiota that originate in the seed can have consequences for the education of the plant immune system, competitive exclusion of pathogens from the host tissue, and host access to critical nutrients. Our research objective was to investigate the consequences of the environmental conditions of the parent plant for bacterial seed microbiome assembly and transmission across plant generations. Using a fully factorial, three-generational experimental design, we investigated endophytic seed bacterial communities of common bean lines (Phaseolus vulgaris L.) grown in the growth chamber and exposed to either control conditions, drought, or excess nutrients at each generation. We applied 16S rRNA microbiome profiling to the seed endophytes and measured plant health outcomes. We discovered stable transmission of 22 bacterial members, regardless of the parental plant condition. This study shows the maintenance of bacterial members of the plant microbiome across generations, even under environmental stress. Overall, this work provides insights into the ability of plants to safeguard microbiome members, which has implications for crop microbiome management in the face of climate change.IMPORTANCESeed microbiomes initiate plant microbiome assembly and thus have critical implications for the healthy development and performance of crops. However, the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown, but this is critical information, given the intensifying stressors that crops face as the climate crisis accelerates. This study provides insights into the maintenance of plant microbiomes across generations, with implications for durable plant microbiome maintenance in agriculture on the changing planet.

BackgroundCoronavirus disease 2019 (COVID-19) convalescent plasma (CCP) reduces hospitalizations among outpatients treated early after symptom onset. It is unknown whether CCP reduces time to symptom resolution among outpatients.MethodsWe evaluated symptom resolution at day 14 by trial arm using an adjusted subdistribution hazard model, with hospitalization as a competing risk. We also assessed the prevalence of symptom clusters at day 14 between treatments. Clusters were defined based on biologic clustering, impact on ability to work, and an algorithm.ResultsAmong 1070 outpatients followed up after transfusion, 381 of 538 (70.8%) receiving CCP and 381 of 532 (71.6%) receiving control plasma were still symptomatic (P = .78) at day 14. Associations between CCP and symptom resolution by day 14 did not differ significantly from those in controls after adjustment for baseline characteristics (adjusted subdistribution hazard ratio, 0.99; P = .62). The most common cluster consisted of cough, fatigue, shortness of breath, and headache and was found in 308 (57.2%) and 325 (61.1%) of CCP and control plasma recipients, respectively (P = .16).ConclusionsIn this trial of outpatients with early COVID-19, CCP was not associated with faster resolution of symptoms compared with control. Overall, there were no differences by treatment in the prevalence of each symptom or symptom clusters at day 14.Clinical trials registrationNCT04373460.

Background & aimsType 2 diabetes (T2D) is a growing problem in children. Children with NAFLD are at potentially high risk for developing T2D; however, the incidence of T2D in this population is unknown. This study aimed to determine the incidence of T2D in children with NAFLD and identify associated risk factors.MethodsChildren with NAFLD enrolled in the Nonalcoholic Steatohepatitis Clinical Research Network were followed longitudinally. Incidence of T2D was determined by using clinical history and fasting laboratory values. Cumulative incidence curves were developed for time to T2D. A Cox regression multivariable model was constructed using best subsets Akaike's Information Criteria selection.ResultsThis study included 892 children with NAFLD and with a mean age of 12.8 years (2.7) followed for 3.8 years (2.3) with a total 3234 person-years at risk. The incidence rate of T2D was 3000 new cases per 100,000 person-years at risk. At baseline, 63 children had T2D, and during follow-up, an additional 97 children developed incident T2D, resulting in a period prevalence of 16.8%. Incident T2D was significantly higher in females versus males (hazard ratio [HR], 1.8 [1.0-2.8]), associated with BMI z-score (HR, 1.8 [1.0-3.0]), and more severe liver histology including steatosis grade (HR, 1.3 [1.0-1.7]), and fibrosis stage (HR, 1.3 [1.0-1.5]).ConclusionsChildren with NAFLD are at high risk for existing and incident T2D. In addition to known risk factors for T2D (female and BMI z-score), severity of liver histology at the time of NAFLD diagnosis was independently associated with T2D development. Targeted strategies to prevent T2D in children with NAFLD are needed.

BACKGROUND: Adolescents and young adults living with HIV (AYAH) aged 14-24 years in Africa experience substantially higher rates of virological failure and HIV-related mortality than adults. We propose to utilize developmentally appropriate interventions with high potential for effectiveness, tailored by AYAH pre-implementation, in a sequential multiple assignment randomized trial (SMART) aimed at improving viral suppression for AYAH in Kenya. METHODS: Using a SMART design, we will randomize 880 AYAH in Kisumu, Kenya to either youth-centered education and counseling (standard of care) or electronic peer navigation in which a peer provides support, information, and counseling via phone and automated monthly text messages. Those with a lapse in engagement (defined as either a missed clinic visit by ≥14 days or HIV viral load ≥1000 copies/ml) will be randomized a second time to one of three higher-intensity re-engagement interventions: This study will evaluate which interventions and which dynamic sequence of interventions improve sustained viral suppression and HIV care engagement in AYAH at 24 months post-enrollment and assess the cost-effectiveness of successful strategies. DISCUSSION: The study utilizes promising interventions tailored to AYAH while optimizing resources by intensifying services only for those AYAH who need more support. Findings from this innovative study will offer evidence for public health programming to end the HIV epidemic as a public health threat for AYAH in Africa. TRIAL REGISTRATION: Clinicaltrials.govNCT04432571, registered June 16, 2020.

BACKGROUND: Optimizing retention in human immunodeficiency virus (HIV) treatment may require sequential behavioral interventions based on patients response. METHODS: In a sequential multiple assignment randomized trial in Kenya, we randomly assigned adults initiating HIV treatment to standard of care (SOC), Short Message Service (SMS) messages, or conditional cash transfers (CCT). Those with retention lapse (missed a clinic visit by ≥14 days) were randomly assigned again to standard-of-care outreach (SOC-Outreach), SMS+CCT, or peer navigation. Those randomly assigned to SMS or CCT who did not lapse after 1 year were randomly assigned again to either stop or continue the initial intervention. Primary outcomes were retention in care without an initial lapse, return to the clinic among those who lapsed, and time in care; secondary outcomes included adjudicated viral suppression. Average treatment effect (ATE) was calculated using targeted maximum likelihood estimation with adjustment for baseline characteristics at randomization and certain time-varying characteristics at rerandomization. RESULTS: Among 1809 participants, 79.7% of those randomly assigned to CCT (n=523/656), 71.7% to SMS (n=393/548), and 70.7% to SOC (n=428/605) were retained in care in the first year (ATE: 9.9%; 95% confidence interval [CI]: 5.4%, 14.4% and ATE: 4.2%; 95% CI: -0.7%, 9.2% for CCT and SMS compared with SOC, respectively). Among 312 participants with an initial lapse who were randomly assigned again, 69.1% who were randomly assigned to a navigator (n=76/110) returned, 69.5% randomly assigned to CCT+SMS (n=73/105) returned, and 55.7% randomly assigned to SOC-Outreach (n=54/97) returned (ATE: 14.1%; 95% CI: 0.6%, 27.6% and ATE: 11.4%; 95% CI: -2.2%, 24.9% for navigator and CCT+SMS compared with SOC-Outreach, respectively). Among participants without lapse on SMS, continuing SMS did not affect retention (n=122/180; 67.8% retained) versus stopping (n=151/209; 72.2% retained; ATE: -4.4%; 95% CI: -16.6%, 7.9%). Among participants without lapse on CCT, those continuing CCT had higher retention (n=192/230; 83.5% retained) than those stopping (n=173/287; 60.3% retained; ATE: 28.6%; 95% CI: 19.9%, 37.3%). Among 15 sequenced strategies, initial CCT, escalated to navigator if lapse occurred and continued if no lapse occurred, increased time in care (ATE: 7.2%, 95% CI: 3.7%, 10.7%) and viral suppression (ATE: 8.2%, 95% CI: 2.2%, 14.2%), the most compared with SOC throughout. Initial SMS escalated to navigator if lapse occurred, and otherwise continued, showed similar effect sizes compared with SOC throughout. CONCLUSIONS: Active interventions to prevent retention lapses followed by navigation for those who lapse and maintenance of initial intervention for those without lapse resulted in best overall retention and viral suppression among the strategies studied. Among those who remained in care, discontinuation of CCT, but not SMS, compromised retention and suppression. (Funded by National Institutes of Health grants R01 MH104123, K24 AI134413, and R01 AI074345; ClinicalTrials.gov number, NCT02338739.).

BACKGROUND: Across sub-Saharan Africa, mid-level healthcare managers oversee implementation of national guidelines. It remains unclear whether leadership and management training can improve population health outcomes. METHODS: We sought to evaluate leadership/management skills among district-level health managers in Uganda participating in the SEARCH-IPT randomised trial to promote isoniazid preventive therapy (IPT) for persons with HIV (PWH). The intervention, which led to higher IPT rates, included annual leadership/management training of managers. We conducted a cross-sectional survey assessing leadership/management skills among managers at trial completion. The survey evaluated self-reported use of leadership/management tools and general leadership/management. We conducted a survey among a sample of providers to understand the intervention’s impact. Targeted minimum loss-based estimation (TMLE) was used to compare responses between trial arms. RESULTS: Of 163 managers participating in the SEARCH-IPT trial, 119 (73%) completed the survey. Intervention managers reported more frequent use of leadership/management tools taught in the intervention curriculum than control managers (+3.64, 95% CI 1.98–5.30, P < 0.001). There were no significant differences in self-reported leadership skills in the intervention as compared to the control group. Among providers, the average reported quality of guidance and supervision was significantly higher in intervention vs control districts (+1.08, 95% CI 0.63–1.53, P = 0.001). CONCLUSIONS: A leadership and management training intervention increased the use of leadership/management tools among mid-level managers and resulted in higher perceived quality of supervision among providers in intervention vs control districts in Uganda. These findings suggest improved leadership/management among managers contributed to increased IPT use among PWH in the intervention districts of the SEARCH-IPT trial.

Abstract Background Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. Results To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. Conclusions This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract

ObjectiveWe examine the efficacy of short message service (SMS) and SMS with peer navigation (SMS + PN) in improving linkage to HIV care and initiation of antiretroviral therapy (ART).DesignI-Care was a cluster randomized trial conducted in primary care facilities in North West Province, South Africa. The primary study outcome was retention in HIV care; this analysis includes secondary outcomes: linkage to care and ART initiation.MethodsEighteen primary care clinics were randomized to automated SMS ( n  = 7), automated and tailored SMS + PN ( n  = 7), or standard of care (SOC; n  = 4). Recently HIV diagnosed adults ( n  = 752) were recruited from October 2014 to April 2015. Those not previously linked to care ( n  = 352) contributed data to this analysis. Data extracted from clinical records were used to assess the days that elapsed between diagnosis and linkage to care and ART initiation. Cox proportional hazards models and generalized estimating equations were employed to compare outcomes between trial arms, overall and stratified by sex and pregnancy status.ResultsOverall, SMS ( n  = 132) and SMS + PN ( n  = 133) participants linked at 1.28 [95% confidence interval (CI): 1.01-1.61] and 1.60 (95% CI: 1.29-1.99) times the rate of SOC participants ( n  = 87), respectively. SMS + PN significantly improved time to ART initiation among non-pregnant women (hazards ratio: 1.68; 95% CI: 1.25-2.25) and men (hazards ratio: 1.83; 95% CI: 1.03-3.26) as compared with SOC.ConclusionResults suggest SMS and peer navigation services significantly reduce time to linkage to HIV care in sub-Saharan Africa and that SMS + PN reduced time to ART initiation among men and non-pregnant women. Both should be considered candidates for integration into national programs.Trial registrationNCT02417233, registered 12 December 2014; closed to accrual 17 April 2015.

BackgroundThe efficacy of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent plasma (CCP) for preventing infection in exposed, uninfected individuals is unknown. CCP might prevent infection when administered before symptoms or laboratory evidence of infection.MethodsThis double-blinded, phase 2 randomized, controlled trial (RCT) compared the efficacy and safety of prophylactic high titer (≥1:320 by Euroimmun ELISA) CCP with standard plasma. Asymptomatic participants aged ≥18 years with close contact exposure to a person with confirmed coronavirus disease 2019 (COVID-19) in the previous 120 hours and negative SARS-CoV-2 test within 24 hours before transfusion were eligible. The primary outcome was new SARS-CoV-2 infection.ResultsIn total, 180 participants were enrolled; 87 were assigned to CCP and 93 to control plasma, and 170 transfused at 19 sites across the United States from June 2020 to March 2021. Two were excluded for screening SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) positivity. Of the remaining 168 participants, 12/81 (14.8%) CCP and 13/87 (14.9%) control recipients developed SARS-CoV-2 infection; 6 (7.4%) CCP and 7 (8%) control recipients developed COVID-19 (infection with symptoms). There were no COVID-19-related hospitalizations in CCP and 2 in control recipients. Efficacy by restricted mean infection free time (RMIFT) by 28 days for all SARS-CoV-2 infections (25.3 vs 25.2 days; P = .49) and COVID-19 (26.3 vs 25.9 days; P = .35) was similar for both groups.ConclusionsAdministration of high-titer CCP as post-exposure prophylaxis, although appearing safe, did not prevent SARS-CoV-2 infection.Clinical trials registrationNCT04323800.

Mobile crisis services for people experiencing distress related to mental health or substance use are expanding rapidly across the US, yet there is little evidence to support these specific models of care. These new programs present a unique opportunity to expand the literature by utilizing implementation science methods to inform the future design of crisis systems. This mixed methods study will examine the effectiveness and acceptability of the Street Crisis Response Team (SCRT), a new 911-dispatched multidisciplinary mobile crisis intervention piloted in San Francisco, California. First, using quantitative data from electronic health records, we will conduct an interrupted time series analysis to quantitatively examine the impacts of the SCRT on people experiencing homelessness who utilized public behavioral health crisis services in San Francisco between November 2019 and August 2022, across four main outcomes within 30 days of the crisis episode: routine care utilization, crisis care reutilization, assessment for housing services, and jail entry. Second, to understand its impact on health equity, we will analyze racial and ethnic disparities in these outcomes prior to and after implementation of the SCRT. For the qualitative component, we will conduct semi-structured interviews with recipients of the SCRTs services to understand their experiences of the intervention and to identify how the SCRT influenced their health-related trajectories after the crisis encounter. Once complete, the quantitative and qualitative findings will be further analyzed in tandem to assist with more nuanced understanding of the effectiveness of the SCRT program. This evaluation of a novel mobile crisis response program will advance the field, while also providing a model for how real-world program implementation can be achieved in crisis service settings.

BACKGROUND: Economic inequity systematically affects Black emerging adults (BEA), aged 18-24, and their healthy trajectory into adulthood. Guaranteed income (GI)-temporary, unconditional cash payments-is gaining traction as a policy solution to address the inequitable distribution of resources sewn by decades of structural racism and disinvestment. GI provides recipients with security, time, and support to enable their transition into adulthood and shows promise for improving mental and physical health outcomes. To date, few GI pilots have targeted emerging adults. The BEEM trial seeks to determine whether providing GI to BEA improves financial wellbeing, mental and physical health as a means to address health disparities. METHODS/DESIGN: Using a randomized controlled crossover trial design, 300 low-income BEA from San Francisco and Oakland, California, are randomized to receive a $500/month GI either during the first 12-months of follow-up (Phase I) or during the second 12-months of a total of 24-months follow-up (Phase II). All participants are offered enrollment in optional peer discussion groups and financial mentoring to bolster financial capability. Primary intention-to-treat analyzes will evaluate the impact of GI at 12 months among Phase I GI recipients compared to waitlist arm participants using Generalized Estimating Equations (GEE). Primary outcomes include: (a) financial well-being (investing in education/training); (b) mental health status (depressive symptoms); and (c) unmet need for mental health and sexual and reproductive health services. Secondary analyzes will examine effects of optional financial capability components using GEE with causal inference methods to adjust for differences across sub-strata. We will also explore the degree to which GI impacts dissipate after payments end. Study outcomes will be collected via surveys every 3 months throughout the study. A nested longitudinal qualitative cohort of 36 participants will further clarify how GI impacts these outcomes. We also discuss how anti-racism praxis guided the intervention design, evaluation design, and implementation. DISCUSSION: Findings will provide the first experimental evidence of whether targeted GI paired with complementary financial programming improves the financial well-being, mental health, and unmet health service needs of urban BEA. Results will contribute timely evidence for utilizing GI as a policy tool to reduce health disparities. CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov, identifier NCT05609188.

BackgroundIn 2020, the Health Resources and Services Administration's HIV/AIDS Bureau funded an initiative to promote implementation of rapid antiretroviral therapy initiation in 14 HIV treatment settings across the U.S. The goal of this initiative is to accelerate uptake of this evidence-based strategy and provide an implementation blueprint for other HIV care settings to reduce the time from HIV diagnosis to entry into care, for re-engagement in care for those out of care, initiation of treatment, and viral suppression. As part of the effort, an evaluation and technical assistance provider (ETAP) was funded to study implementation of the model in the 14 implementation sites.MethodThe ETAP has used implementation science methods framed by the Dynamic Capabilities Model integrated with the Conceptual Model of Implementation Research to develop a Hybrid Type II, multi-site mixed-methods evaluation, described in this paper. The results of the evaluation will describe strategies associated with uptake, implementation outcomes, and HIV-related health outcomes for patients.DiscussionThis approach will allow us to understand in detail the processes that sites to implement and integrate rapid initiation of antiretroviral therapy as standard of care as a means of achieving equity in HIV care.

Introduction: Biological soil amendments of animal origin (BSAAO), including untreated amendments are often used to improve soil fertility and are particularly important in organic agriculture. However, application of untreated manure on cropland can potentially introduce foodborne pathogens into the soil and onto produce. Certified organic farms follow the USDA National Organic Program (NOP) standards that stipulate a 90- or 120-day interval between application of untreated manure and crop harvest, depending on whether the edible portion of the crop directly contacts the soil. This time-interval metric is based on environmental factors and does not consider a multitude of factors that might affect the survival of the main pathogens of concern. The objective of this study was to assess predictors for the prevalence of Shiga-toxin-producing Escherichia coli (non-O157 STEC) in soils amended with untreated manure on USDA-NOP certified farms. Methods: A longitudinal, multi-regional study was conducted on 19 farms in four USA regions for two growing seasons (2017–2018). Untreated manure (cattle, horse, and poultry), soil, and irrigation water samples were collected and enrichment cultured for non-O157 STEC. Mixed effects logistic regression models were used to analyze the predictors of non-O157 STEC in the soil up to 180 days post-manure application. Results and discussion: Results show that farm management practices (previous use with livestock, presence of animal feces on the field, season of manure application) and soil characteristics (presence of generic E. coli in the soil, soil moisture, sodium) increased the odds of STEC-positive soil samples. Manure application method and snowfall decreased the odds of detecting STEC in the soil. Time-variant predictors (year and sampling day) affected the presence of STEC. This study shows that a single metric, such as the time interval between application of untreated manure and crop harvest, may not be sufficient to reduce the food safety risks from untreated manure, and additional environmental and farm-management practices should also be considered. These findings are of particular importance because they provide multi-regional baseline data relating to current NOP wait-time standards. They can therefore contribute to the development of strategies to reduce pathogen persistence that may contribute to contamination of fresh produce typically eaten raw from NOP-certified farms using untreated manure.

Voluntary male medical circumcision (VMMC) reduces HIV acquisition by up to 60%. Kenya has successfully scaled up VMMC to an estimated 91% of eligible men and boys in certain regions in combination due to VMMC and cultural circumcisions. VMMC as a program is implemented regionally in traditionally non-circumcising counties where the prevalence is still below 91%, ranging from 56.4% to 66.7%. Given that funding toward VMMC is expected to decline in the coming years, it is important to identify what models of service delivery are most appropriate and efficient to sustainably meet the VMMC needs of new cohorts' eligible men. To this end, we compared the costs of facility-based VMMC and one within a rapid results initiative (RRI), a public health service scheduled during school holidays to perform many procedures over a short period. We employed activity-based micro-costing to estimate the costs, from the implementer perspective, of facility-based VMMC and RRI-based VMMC conducted between October 2017 and September 2018 at 41 sites in Kisumu County, Kenya supported by the Family AIDS care & Education Services (FACES). We conducted site visits and reviewed financial ledger and programmatic data to identify and quantify resources consumed and the number of VMMC procedures performed during routine care and RRIs. Ledger data were used to estimate fixed costs, recurring costs, and cost per circumcision (CPC) in United States dollar (USD). A sensitivity analysis was done to estimate CPC where we allocated 6 months of the ledger to facility-based and 6 months to RRI. Overall, FACES spent $3,092,891 toward VMMC services and performed 42,139 procedures during the funding year. This included $2,644,910 in stable programmatic costs, $139,786 procedure costs, and $308,195 for RRI-specific activities. Over the year, 49% (n = 20,625) of procedures were performed as part of routine care and 51% (n = 21,514) were performed during the RRIs. Procedures conducted during facility-based cost $99.35 per circumcision, those conducted during the RRIs cost $48.51 per circumcision, and according to our sensitivity analysis, CPC for facility-based ranges from $99.35 to $287.24 and for RRI costs ranged from $29.81 to $48.51. The cost of VMMC during the RRI was substantially lower than unit costs reported in previous costing studies. We conclude that circumcision campaigns, such as the RRI, offer an efficient and sustainable approach to VMMC.

The study assessed petroleum systems in the southern Bida Basin, Nigeria, focusing on the Cretaceous sediments. Reservoirs comprise Lokoja and Patti Formation sandstones, while shales, claystone, and siltstone serve as source rocks and stratigraphic traps/seals. Detailed studies delineating the key elements of the petroleum systems in the basin have not been conducted due to a lack of subsurface data. The goal of the current study was to use field observations, Scanning Electron Microscopy (SEM), X-ray diffraction (XRD), and geochemical and geomechanical data to evaluate key components of petroleum systems in the southern Bida Basin. The results presented in this investigation are intended to attain specific objectives, especially those lacking in the basin's study sections. Petrophysical analysis revealed that the Lokoja Sandstone has porosity of 37%–39.5% and moderate permeability of 23.22–42.29 mD. The Patti Formation sandstone reservoirs exhibited high porosity (38%–42%) and moderate to good permeability (31.54–66.48 mD), suggesting good potential reservoirs. SEM results revealed intragranular pores and micro-fractures in the Patti Shale, whereas the sandstone reservoirs in the Lokoja and Patti formations displayed fractures, facilitating hydrocarbon migration. Quartz was the dominant mineral in the sandstone units of both formations. XRD analysis revealed that brittle and clay minerals influenced the microstructure of Patti Shale. Geochemical analysis indicated promising petroleum potential in the Patti Shale, with a total organic carbon (TOC) content of 1.87 wt%, free hydrocarbon from kerogen (S1) of 0.41 mg/g, hydrogen index (HI) of 0.75 mg HC/g TOC, and production index (PI) of 0.17. The Patti and Lokoja formations' shale, claystone, and siltstone exhibited sealing potential, with a plasticity index of 24–35 and coefficient permeability of 2.8 × 10−4- 3.6 × 10−4 cm/s. Field studies, XRD, geochemical data, and geomechanical index values have confirmed the key components of the petroleum system, which in turn facilitate hydrocarbon generation, migration, accumulation, and entrapment in the basin.

IntroductionThere is a high burden of hypertension (HTN) among HIV-infected people in Uganda. However, capacity to prevent, diagnose and treat HTN is suboptimal. This study seeks to leverage the existing HIV-related infrastructure in primary care health facilities (HFs) using the integrated HIV/HTN care model to improve health outcomes of patients with HIV and HTN.Methods and analysisIntegrated HIV/HTN study a type-1 effectiveness/implementation cluster randomised trial, will evaluate the effectiveness of a multicomponent model intervention in 13 districts randomised to the intervention arm compared with 13 districts randomised to control. Two randomly selected HFs per district and their patients will be eligible to participate. The intervention will comprise training of primary healthcare (PHC) providers followed by regular supervision, integration of HTN care into HIV clinics, improvement of the health management information system, IT-based messaging to improve communication among frontline PHCs and district-level managers. HTN care guidelines, sphygmomanometers, patient registers and a buffer stock of essential drugs will be provided to HFs in both study arms. We will perform cross-sectional surveys at baseline, 12 and 24 months, on a random sample of patients attending HFs to measure effectiveness of the integrated care model between 2021 and 2024. We will perform in-depth interviews of providers, patients and healthcare managers to assess barriers and facilitators of integrated care. We will measure the cost of the intervention through microcosting and time-and-motion studies. The outcomes will be analysed taking the clustered structure of the data set into account.Ethics and disseminationEthics approval has been obtained from the Research Ethics Committees at London School of Hygiene and Tropical Medicine, and Makerere University School of Medicine. All participants will provide informed consent prior to study inclusion. Strict confidentiality will be applied throughout. Findings will be disseminated to public through meetings, and publications.Trial registration numberNCT04624061.

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

PURPOSE: Nonmuscle myosin II complexes are master regulators of actin dynamics that play essential roles during embryogenesis with vertebrates possessing 3 nonmuscle myosin II heavy chain genes, MYH9, MYH10, and MYH14. As opposed to MYH9 and MYH14, no recognizable disorder has been associated with MYH10. We sought to define the clinical characteristics and molecular mechanism of a novel autosomal dominant disorder related to MYH10. METHODS: An international collaboration identified the patient cohort. CAS9-mediated knockout cell models were used to explore the mechanism of disease pathogenesis. RESULTS: We identified a cohort of 16 individuals with heterozygous MYH10 variants presenting with a broad spectrum of neurodevelopmental disorders and variable congenital anomalies that affect most organ systems and were recapitulated in animal models of altered MYH10 activity. Variants were typically de novo missense changes with clustering observed in the motor domain. MYH10 knockout cells showed defects in primary ciliogenesis and reduced ciliary length with impaired Hedgehog signaling. MYH10 variant overexpression produced a dominant-negative effect on ciliary length. CONCLUSION: These data presented a novel genetic cause of isolated and syndromic neurodevelopmental disorders related to heterozygous variants in the MYH10 gene with implications for disrupted primary cilia length control and altered Hedgehog signaling in disease pathogenesis.