Classification of crystallization outcomes using deep convolutional neural networks

The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications

The central policy unit in the governance of Hong Kong : a study of institutional dynamics

published_or_final_versionPolitics and Public AdministrationMasterMaster of Public Administratio

Insomnia as an Independent Predictor of Incident Cardiovascular Disease in HIV: Data from the Veterans Aging Cohort Study

Background: Insomnia is associated with increased cardiovascular disease (CVD) risk in the general population and is highly prevalent in people with HIV. The CVD risk conferred by insomnia in the HIV population is unknown. Methods: Using the Veterans Aging Cohort Study-Survey Cohort, insomnia symptoms were measured and dummy coded with the item, “Difficulty falling or staying asleep?” (5-point scale from no difficulty to bothers a lot). Incident CVD event ICD-9 codes (acute myocardial infarction, stroke, or coronary artery revascularization) were identified with VA and Medicare administrative data and VA fee-for-service data. Those with baseline CVD were excluded. Results: HIV-infected (N=3,108) veterans had a median follow-up time of 10.8 years, during which 267 CVD events occurred. Compared to HIV-infected veterans with no difficulty falling or staying asleep, HIV-infected veterans bothered a lot by insomnia symptoms had an increased risk of incident CVD after adjusting for demographics (HR=1.64, 95%CI=1.16-2.31, p=.005), CVD risk factors (HR=1.62, 95%CI=1.14-2.30, p=.007), additional potential confounders (hepatitis C infection, renal disease, anemia, alcohol use, cocaine use; HR=1.70, 95%CI=1.19-2.43, p=.003), and HIV-specific factors (HIV-1 RNA, CD4+ T-cell count, ART; HR=1.66, 95%CI=1.16-2.37, p=.005). Additional adjustment for non-benzodiazepine sleep medication (HR=1.62, 95%CI=1.13-2.32, p=.009) did not attenuate the association; however, it fell short of significance at p < .01 after adjustment for depressive symptoms (HR=1.51, 95%CI=0.98-2.32, p=.060) or antidepressant medication (HR=1.51, 95%CI=1.04-2.19, p=.031). Conclusion: Highly bothersome insomnia symptoms were significantly associated with incident CVD in HIV-infected veterans, suggesting that insomnia may be a novel, modifiable risk factor for CVD in HIV

Sex and authorship in global cancer research

Introduction Research is an essential pillar of cancer control and key in shaping regional cancer control agendas. Imbalances in science and technology in terms of lack of female participation have been well documented. However, there is little evidence about country-level female participation in cancer research. Methodology Through a complex filter, cancer research papers were identified and grouped by countries and sex of the first and last authors of each paper and analysed by the percentage of females in these positions alongside other parameters. Results Our analysis of 56 countries’ outputs, in 2009, revealed that females were the first authors in 37.2% and last authors in 23.3% of papers. In 2019, females were the first author in 41.6% and last author in 29.4% of papers. Females increased as first authors by 26%, and as last authors by 12% between these two time periods. The top performing countries in terms female/male parity for first or last authorship were in Eastern and Southern Europe as well as Latin American countries.From 2009 to 2019, the highest proportion of females as first and last authors were from low-income and middle-income countries in Latin America and Eastern Europe.Females were more likely to publish in lower impact journals and were less likely to be cited compared to males. Conclusions Globally, progress in female’s authorship in oncology research has been uneven. More research is needed to understand the reasons behind this. Advancing diversity and equity in research leadership and authorship will be essential to address the complex challenges of cancer globally

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status.

DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing

HIV infection and cardiovascular disease in women

Background HIV infection is associated with increased risk of cardiovascular disease (CVD) in men. Whether HIV is an independent risk factor for CVD in women has not yet been established. Methods and Results We analyzed data from the Veterans Aging Cohort Study on 2187 women (32% HIV infected [HIV+]) who were free of CVD at baseline. Participants were followed from their first clinical encounter on or after April 01, 2003 until a CVD event, death, or the last follow‐up date (December 31, 2009). The primary outcome was CVD (acute myocardial infarction [AMI], unstable angina, ischemic stroke, and heart failure). CVD events were defined using clinical data, International Classification of Diseases, Ninth Revision, Clinical Modification codes, and/or death certificate data. We used Cox proportional hazards models to assess the association between HIV and incident CVD, adjusting for age, race/ethnicity, lipids, smoking, blood pressure, diabetes, renal disease, obesity, hepatitis C, and substance use/abuse. Median follow‐up time was 6.0 years. Mean age at baseline of HIV+ and HIV uninfected (HIV−) women was 44.0 versus 43.2 years (PP=0.11). There were 86 incident CVD events (53%, HIV+): AMI, 13%; unstable angina, 8%; ischemic stroke, 22%; and heart failure, 57%. Incident CVD/1000 person‐years was significantly higher among HIV+ (13.5; 95% confidence interval [CI]=10.1, 18.1) than HIV−women (5.3; 95% CI=3.9, 7.3; P+ women had an increased risk of CVD, compared to HIV− (hazard ratio=2.8; 95% CI=1.7, 4.6; P\u3c0.001). Conclusions HIV is associated with an increased risk of CVD in women

Voluntary movement frequencies in submaximal one- and two-legged knee extension exercise and pedaling

Understanding of behavior and control of human voluntary rhythmic stereotyped leg movements is useful in work to improve performance, function, and rehabilitation of exercising, healthy, and injured humans. The present study aimed at adding to the existing understanding within this field. To pursue the aim, correlations between freely chosen movement frequencies in relatively simple, single-joint, one- and two-legged knee extension exercise were investigated. The same was done for more complex, multiple-joint, one- and two-legged pedaling. These particular activities were chosen because they could be considered related to some extent, as they shared a key aspect of knee extension, and because they at the same time were different. The activities were performed at submaximal intensities, by healthy individuals (n=16, thereof 8 women; 23.4±2.7 years; 1.70±0.11 m; 68.6±11.2 kg).High and fair correlations (R-values of 0.99 and 0.75) occurred between frequencies generated with the dominant leg and the nondominant leg during knee extension exercise and pedaling, respectively. Fair to high correlations (R-values between 0.71 and 0.95) occurred between frequencies performed with each of the two legs in an activity, and the two-legged frequency performed in the same type of activity. In general, the correlations were higher for knee extension exercise than for pedaling. Correlations between knee extension and pedaling frequencies were of modest occurrence.The correlations between movement frequencies generated separately by each of the legs might be interpreted to support the following working hypothesis, which was based on existing literature. It is likely that involved central pattern generators (CPGs) of the two legs share a common frequency generator or that separate frequency generators of each leg are attuned via interneuronal connections. Further, activity type appeared to be relevant. Thus, the apparent common rhythmogenesis for the two legs appeared to be stronger for the relatively simple single-joint activity of knee extension exercise as compared to the more complex multi-joint activity of pedaling. Finally, it appeared that the shared aspect of knee extension in the related types of activities of knee extension exercise and pedaling was insufficient to cause obvious correlations between generated movement frequencies in the two types of activities

The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator

Mdc1 is a large modular phosphoprotein scaffold that maintains signaling and repair complexes at double-stranded DNA break sites. Mdc1 is anchored to damaged chromatin through interaction of its C-terminal BRCT-repeat domain with the tail of γH2AX following DNA damage, but the role of the N-terminal forkhead-associated (FHA) domain remains unclear. We show that a major binding target of the Mdc1 FHA domain is a previously unidentified DNA damage and ATM-dependent phosphorylation site near the N-terminus of Mdc1 itself. Binding to this motif stabilizes a weak self-association of the FHA domain to form a tight dimer. X-ray structures of free and complexed Mdc1 FHA domain reveal a ‘head-to-tail’ dimerization mechanism that is closely related to that seen in pre-activated forms of the Chk2 DNA damage kinase, and which both positively and negatively influences Mdc1 FHA domain-mediated interactions in human cells prior to and following DNA damage

Epstein-Barr Virus-Induced Gene 3 (EBI3): A Novel Diagnosis Marker in Burkitt Lymphoma and Diffuse Large B-Cell Lymphoma

The distinction between Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), two types of mature aggressive B-cell lymphomas that require distinct treatments, can be difficult because of forms showing features intermediate between DLBCL and BL (here called BL/DLBCL). They can be discriminated by the presence of c-myc translocations characteristic of BL. However, these are not exclusive of BL and when present in DLBCL are associated with lower survival. In this study, we show that Epstein-Barr virus-induced gene 3 (EBI3) is differentially expressed among BL and DLBCL. Analysis of gene expression data from 502 cases of aggressive mature B-cell lymphomas available on Gene Expression Omnibus and immunohistochemical analysis of 184 cases of BL, BL/DLBCL or DLBCL, showed that EBI3 was not expressed in EBV-positive or -negative BL cases, whereas it was expressed by over 30% of tumoral cells in nearly 80% of DLBCL cases, independently of their subtypes. In addition, we show that c-myc overexpression represses EBI3 expression, and that DLBCL or BL/DLBCL cases with c-myc translocations have lower expression of EBI3. Thus, EBI3 immunohistochemistry could be useful to discriminate BL from DLBCL, and to identify cases of BL/DLBCL or DLBCL with potential c-myc translocations

Integration of water, sanitation, and hygiene for the prevention and control of neglected tropical diseases: a rationale for inter-sectoral collaboration.

Improvements of water, sanitation, and hygiene (WASH) infrastructure and appropriate health-seeking behavior are necessary for achieving sustained control, elimination, or eradication of many neglected tropical diseases (NTDs). Indeed, the global strategies to fight NTDs include provision of WASH, but few programs have specific WASH targets and approaches. Collaboration between disease control programs and stakeholders in WASH is a critical next step. A group of stakeholders from the NTD control, child health, and WASH sectors convened in late 2012 to discuss opportunities for, and barriers to, collaboration. The group agreed on a common vision, namely "Disease-free communities that have adequate and equitable access to water and sanitation, and that practice good hygiene." Four key areas of collaboration were identified, including (i) advocacy, policy, and communication; (ii) capacity building and training; (iii) mapping, data collection, and monitoring; and (iv) research. We discuss strategic opportunities and ways forward for enhanced collaboration between the WASH and the NTD sectors