Drug resistant HIV: Behaviors and characteristics among Los Angeles men who have sex with men with new HIV diagnosis.

Epidemiology of drug resistant HIV has focused on trends and less attention has been given to identification of factors, especially behaviors including substance use, in acquisition of drug-resistant HIV. From 2009 to 2012 The Metromates Study enrolled and followed for one year men who have sex with men (MSM) seeking testing for HIV in a community clinic in Los Angeles assessing those testing positive for acute and recent HIV infection. Behavioral data were collected via Computer-Assisted Self-Interview from 125 classified as newly HIV infected and 91 as chronically infected (newly HIV-diagnosed); specimens were available and viable for resistance testing for 154 of the 216 HIV positives with new diagnoses. In this community clinic we found prevalence of resistance among MSM with new HIV-diagnosis was 19.5% (n = 30/154) with no difference by recency of HIV infection. Sexual partnership characteristics were associated with resistance; those who reported transgendered sex partners had a higher prevalence of resistance as compared to those who did not report transgendered sex partners (40% vs. 17%; p value = 0.04), while those who reported having a main partner had a lower prevalence of drug resistance (12% vs. 24%; p value = 0.07). In multivariable analyses adjusting for HIV recency and antiviral use, reporting a main partner decreased odds [adjusted odds ratio (AOR) 0.34; 95% confidence interval (CI) 0.13-0.87], reporting a transgendered partnered increased odds (AOR = 3.37; 95% CI 0.95-12.43); and being African American increased odds of drug resistance (AOR = 5.63, 95%CI 1.41-22.38). This suggests African American MSM and TG individuals in Los Angeles represent pockets of exceptional risk that will require special approaches to prevention and care to enhance their own health and reduce their likelihood to support transmission of drug resistance in the US

Low prevalence of hepatitis C co-infection in recently HIV-infected minority men who have sex with men in Los Angeles: a cross-sectional study.

BackgroundGeographic and sociodemographic characterization of hepatitis C virus (HCV) transmission amongst men who have sex with men (MSM) has been limited. Our aim was to characterize HCV prevalence, risk factors for HCV co-infection, and patterns of HIV and HCV co-transmission and transmitted drug resistance mutations (DRMs) in newly HIV-diagnosed Los Angeles MSM.MethodsViral RNA was extracted from stored plasma samples from a Los Angeles cohort of newly diagnosed HIV-infected MSM with well-characterized substance use and sexual behavioral characteristics via computer-assisted self-interviewing surveys. Samples were screened for HCV by qPCR. HCV E1, E2, core, NS3 protease and NS5B polymerase and HIV-1 protease and reverse transcriptase regions were amplified and sequenced. Phylogenetic analysis was used to determine relatedness of HCV and HIV-1 isolates within the cohort and viral sequences were examined for DRMs.ResultsOf 185 newly HIV-diagnosed MSM, the majority (65%) were of minority race/ethnicity and recently infected (57.8%), with median age of 28.3 years. A minority (6.6%) reported injection drug use (IDU), whereas 96 (52.8%) reported recent substance use, primarily cannabis or stimulant use. High risk sexual behaviors included 132 (74.6%) with unprotected receptive anal intercourse, 60 (33.3%) with group sex, and 10 (5.7%) with fisting. Forty-five (24.3%) had acute gonorrhea or chlamydia infection. Only 3 (1.6%) subjects had detectable HCV RNA. Amongst these subjects, HIV and HCV isolates were unrelated by phylogenetic analysis and none possessed clinically relevant NS3 or NS5B HCV DRMs.ConclusionsPrevalence of HCV co-infection was low and there was no evidence of HIV-HCV co-transmission in this cohort of relatively young, predominantly minority, newly HIV-diagnosed MSM, most with early HIV infection, with high rates of high risk sexual behaviors, STI, and non-IDU. The low HCV prevalence in a group with high-risk behaviors for non-IDU HCV acquisition suggests an opportune time for targeted HCV prevention measures

Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men.

Methamphetamine (MA) use is a major public health problem in the United States, especially among people living with HIV (PLWH). Many MA-induced neurotoxic effects are mediated by inflammation and gut microbiota may play a role in this process, yet the effects of MA on the microbiome have not been adequately explored. Therefore, we performed 16S rRNA gene sequencing on rectal swab samples from 381 men who have sex with men, 48% of whom were PLWH and 41% of whom used MA. We compared microbiome composition between MA users and non-users while testing for potential interactions with HIV and controlling for numerous confounders using inverse probability of treatment weighting. We found that MA use explained significant variation in overall composition (R2 = 0.005, p = 0.008) and was associated with elevated Finegoldia, Parvimonas, Peptoniphilus, and Porphyromonas and reduced Butyricicoccus and Faecalibacterium, among others. Genera including Actinomyces and Streptobacillus interacted with HIV status, such that they were increased in HIV+ MA users. Finegoldia and Peptoniphilus increased with increasing frequency of MA use, among others. In summary, MA use was associated with a microbial imbalance favoring pro-inflammatory bacteria, including some with neuroactive potential and others that have previously been associated with poor HIV outcomes

Influence of the Kuroshio interannual variability on the summertime precipitation over the East China Sea and adjacent area

Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 32(8), (2019): 2185-2205. doi:10.1175/JCLI-D-18-0538.1.Much attention has been paid to the climatic impacts of changes in the Kuroshio Extension, instead of the Kuroshio in the East China Sea (ECS). This study, however, reveals the prominent influences of the lateral shift of the Kuroshio at interannual time scale in late spring [April–June (AMJ)] on the sea surface temperature (SST) and precipitation in summer around the ECS, based on high-resolution satellite observations and ERA-Interim. A persistent offshore displacement of the Kuroshio during AMJ can result in cold SST anomalies in the northern ECS and the Japan/East Sea until late summer, which correspondingly causes anomalous cooling of the lower troposphere. Consequently, the anomalous cold SST in the northern ECS acts as a key driver to robustly enhance the precipitation from the Yangtze River delta to Kyushu in early summer (May–August) and over the central ECS in late summer (July–September). In view of the moisture budget analysis, two different physical processes modulated by the lateral shift of the Kuroshio are identified to account for the distinct responses of precipitation in early and late summer, respectively. First, the anomalous cold SST in the northern ECS induced by the Kuroshio offshore shift is likely conducive to the earlier arrival of the mei-yu–baiu front at 30°–32°N and its subsequent slower northward movement, which may prolong the local rainy season, leading to the increased rain belt in early summer. Second, the persistent cold SST anomalies in late summer strengthen the near-surface baroclinicity and the associated strong atmospheric fronts embedded in the extratropical cyclones over the central ECS, which in turn enhances the local rainfall.We appreciate three anonymous reviewers for their thoughtful and constructive comments. This work is supported by the National Key Research and Development Program of China (2016YFA0601804), the National Natural Science Foundation of China (NSFC) Projects (91858102, 41490643, 41490640, 41506009, U1606402) and the OUC–WHOI joint research program (21366).2019-10-0

High-precision high-coverage functional inference from integrated data sources

<p>Abstract</p> <p>Background</p> <p>Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge about protein function. The result is a weighted functional linkage network (FLN) in which linked neighbors share at least one function with high probability. Precision is, however, low. Aiming to provide precise functional annotation for as many proteins as possible, we explore and propose a two-step framework for functional annotation (1) construction of a high-coverage and reliable FLN via machine learning techniques (2) development of a decision rule for the constructed FLN to optimize functional annotation.</p> <p>Results</p> <p>We first apply this framework to <it>Saccharomyces cerevisiae</it>. In the first step, we demonstrate that four commonly used machine learning methods, Linear SVM, Linear Discriminant Analysis, Naïve Bayes, and Neural Network, all combine heterogeneous data to produce reliable and high-coverage FLNs, in which the linkage weight more accurately estimates functional coupling of linked proteins than use individual data sources alone. In the second step, empirical tuning of an adjustable decision rule on the constructed FLN reveals that basing annotation on maximum edge weight results in the most precise annotation at high coverages. In particular at low coverage all rules evaluated perform comparably. At coverage above approximately 50%, however, they diverge rapidly. At full coverage, the maximum weight decision rule still has a precision of approximately 70%, whereas for other methods, precision ranges from a high of slightly more than 30%, down to 3%. In addition, a scoring scheme to estimate the precisions of individual predictions is also provided. Finally, tests of the robustness of the framework indicate that our framework can be successfully applied to less studied organisms.</p> <p>Conclusion</p> <p>We provide a general two-step function-annotation framework, and show that high coverage, high precision annotations can be achieved by constructing a high-coverage and reliable FLN via data integration followed by applying a maximum weight decision rule.</p

Global emergency remote education in secondary schools during the COVID-19 pandemic: A systematic review

The worldwide shift to emergency remote education in 2020 as a result of the COVID-19 pandemic impacted billions of students and teachers. A range of teaching and learning strategies were employed by schools as a result, despite confusing and sometimes contradictory government guidance, with systemic issues such as equity and access impacting heavily on disadvantaged students. In light of the findings of a recent IPPO evidence snapshot and roundtable event, and in order to gain further insight into how emergency remote education was experienced by secondary school students, parents and educators, a systematic review was conducted that collates and synthesises primary empirical studies across five key research questions focusing on student engagement, online assessment, peer collaboration, parent engagement, and future directions for online learning. Studies were searched for in May 2021 using Web of Science, Scopus, ERIC, Microsoft Academic Graph, ResearchGate and the COVID-19 living map, and were included if they focused on teaching and learning using blended or online approaches in secondary schools during the pandemic, that were published in English. Following quality assessment on scope and methodological rigour, 81 studies were included for narrative synthesis. The research studies were conducted in 38 countries, with 37% of studies from low or lower-middle income countries, and 63% from upper-middle income or high-income countries. Most of the evidence came from students (64%), followed by teachers (53%), with very few studies exploring the perceptions and experiences of parents (6%) or school leaders (5%). Findings reveal that self-regulation and understanding were the most frequently reported indicators of student engagement, with online assessment tools, learning management systems with collaborative tools, live synchronous lessons with peer and teacher interaction, and teacher-made videos considered particularly engaging. Social isolation was the most frequently reported indicator of disengagement, characterised by poor attendance in live lessons, a lack of opportunities to seek help with challenges and difficulties facilitating peer collaboration. Although many articles reported that assessment online was particularly challenging, 21 different types of online assessments strategies were identified, with online quizzes and formative online feedback the most frequently used. Live marking or recorded feedback and assessment were found to be particularly beneficial, as providing feedback during live lessons was sometimes challenging. Peer collaboration was facilitated through peer assessment, inquiry-based group work and experiments, aided by the use of collaborative software and combining multiple applications. Parental involvement and support contributed to student learning, although issues of equity impacted the extent to which they could engage with their children's learning, alongside gaps in family content knowledge and technological skills. Numerous implications for future policy relating to online and blended learning are provided

Spirulina is an effective dietary source of zeaxanthin to humans

Zeaxanthin is a predominant xanthophyll in human eyes and may reduce the risk of cataracts and age-related macular degeneration. Spirulina is an algal food that contains a high concentration of zeaxanthin. In order to determine the zeaxanthin bioavailability of spirulina for dietary supplementation in humans, spirulina was grown in nutrient solution with 2H2O for carotenoid labelling. Single servings of 2H-labelled spirulina (4·0-5·0g) containing 2·6-3·7mg zeaxanthin were consumed by fourteen healthy male volunteers (four Americans and ten Chinese) with 12g dietary fat. Blood samples were collected over a 45d period. The serum concentrations of total zeaxanthin were measured using HPLC, and the enrichment of labelled zeaxanthin was determined using LC-atmospheric pressure chemical ionisation-MS (LC-APCI-MS). The results showed that intrinsically labelled spirulina zeaxanthin in the circulation was detected at levels as low as 10% of the total zeaxanthin for up to 45d after intake of the algae. A single dose of spirulina can increase mean serum zeaxanthin concentration in humans from 0·06 to 0·15μmol/l, as shown in our study involving American and Chinese volunteers. The average 15 d area under the serum zeaxanthin response curve to the single dose of spirulina was 293nmol×d/μmol (range 254-335) in American subjects, and 197nmol×d/μmol (range 154-285) in Chinese subjects. It is concluded that the relative bioavailability of spirulina zeaxanthin can be studied with high sensitivity and specificity using 2H labelling and LC-APCI-MS methodology. Spirulina can serve as a rich source of dietary zeaxanthin in human

At Our Own Peril: DoD Risk Assessment in a Post-Primacy World

The U.S. Department of Defense (DoD) faces persistent fundamental change in its strategic and operating environments. This report suggests this reality is the product of the United States entering or being in the midst of a new, more competitive, post-U.S. primacy environment. Post-primacy conditions promise far-reaching impacts on U.S. national security and defense strategy. Consequently, there is an urgent requirement for DoD to examine and adapt how it develops strategy and describes, identifies, assesses, and communicates corporate-level risk. This report takes on the latter risk challenge. It argues for a new post-primacy risk concept and its four governing principles of diversity, dynamism, persistent dialogue, and adaptation. The authors suggest that this approach is critical to maintaining U.S. military advantage into the future. Absent change in current risk convention, the report suggests DoD exposes current and future military performance to potential failure or gross under-performance.https://press.armywarcollege.edu/monographs/1410/thumbnail.jp

Biosolids application and soil organic carbon dynamics: a meta-analysis.

Soil carbon sequestration has been recognized as a potential “direct action” tool in mitigating climate change. Organic matter rich biosolids from wastewater industry has been applied to soils as one of the strategies to the carbon sequestration. However, most of the short- and long-term studies as influenced by land application of biosolids have been showed quite inconsistent results in carbon increments in soils. Therefore, soil carbon sequestration resulted by biosolids application is yet to be needed further studies to elucidate. This study presents a comprehensive MetaAnalysis (MA) on soil carbon sequestration as influenced by biosolids application. Datasets comprised with 175 independent paired-treatments across 25 countries were fed in to Comprehensive Meta-Analysis (version 3) programme and modelled. The MA compared Soil Organic Carbon (SOC as g/kg) changes as the functions of time after biosolids application and its rate over twelve groups under two categories: application age (time after application) as 11 year, and cumulative application rate as 251 tonnes/ha.The fixed model is applied to explicate overall effects of analysed data derived from the MA. The MA showed overall positive influences on soil carbon sequestration towards increasing SOC. For example, the highest effect on SOC was observed at 1-3 age group suggesting the need of short term biosolids application to develop carbon storage in soils. Overall, this study shows that land application of biosolids can be used to increase soil carbon storage and therefore has the potential to be a strategy for mitigating climate change towards carbon sequestration in soils

Simulating carbon capture by enhanced weathering with global croplands: an overview of key processes highlighting areas of future model development

Enhanced weathering (EW) aims to amplify a natural sink for CO2 by incorporating powdered silicate rock with high reactive surface area into agricultural soils. The goal is to achieve rapid dissolution of minerals and release of alkalinity with accompanying dissolution of CO2 into soils and drainage waters. EW could counteract phosphorus limitation and greenhouse gas (GHG) emissions in tropical soils, and soil acidification, a common agricultural problem studied with numerical process models over several decades. Here, we review the processes leading to soil acidification in croplands and how the soil weathering CO2 sink is represented in models. Mathematical models capturing the dominant processes and human interventions governing cropland soil chemistry and GHG emissions neglect weathering, while most weathering models neglect agricultural processes. We discuss current approaches to modelling EW and highlight several classes of model having the potential to simulate EW in croplands. Finally, we argue for further integration of process knowledge in mathematical models to capture feedbacks affecting both longer-term CO2 consumption and crop growth and yields