Novel Genetic Risk and Metabolic Signatures of Insulin Signaling and Androgenesis in the Anovulation of Polycystic Ovary Syndrome

Funding Information: The authors are grateful to all staff in the PCOSAct group for their effort in the collection of blood samples and clinical dataset which used in current study. Special thanks to Prof. Attila Toth from Institute of Physiological Chemistry, Dresden, Germany for the REC114 antibody. This study was supported by the National key Research and Development Program of China (2019YFC1709500); the National Collaboration Project of Critical Illness by Integrating Chinese Medicine and Western Medicine; the Project of Heilongjiang Province Innovation Team “TouYan;” the Yi-Xun Liu and Xiao-Ke Wu Academician Workstation; the Innovation Team of Reproductive Technique with Integrative Chinese Medicine and Western Medicine in Xuzhou City, China; Heilongjiang University of Chinese Medicine from the National Clinical Trial Base; Heilongjiang Provincial Clinical Research Center for Ovary Diseases; the Research Grant Council (T13-602/21-N, C5045-20EF, and 14122021); and Food and Health Bureau in Hong Kong, China (06171026). Ben Willem J. Mol is supported by a National Health and Medical Research Council (NHMRC) Investigator grant (GNT1176437). Ben Willem J. Mol reports consultancy for ObsEva and Merck and travel support from Merck. Xiaoke Wu, Yongyong Shi, and Chi Chiu Wang developed the research question and designed the study. Xiaoke Wu, Yongyong Shi, Yijuan Cao, and Chi Chiu Wang designed the analysis. Yongyong Shi and Zhiqiang Li contributed to the design of the experiment of whole-exome plus targeted SNP sequencing and the analysis, and interpreted the results. Jingshu Gao, Hui Chang, Duojia Zhang, Jing Cong, Yu Wang, Qi Wu, Xiaoxiao Han, Pui Wah Jacqueline Chung, Yiran Li, and Lin Zeng contributed to the experiment of metabolic profile and immunofluorescent staining and the analysis, and interpreted the results. Astrid Borchert and Hartmut Kuhn provided antibody support and advice. Xu Zheng and Lingxi Chen contributed to create the predictive model with deep machine learning. Jian Li, Qi Wu, Hongli Ma, Xu Zheng, and Lingxi Chen contributed to the analysis of the clinical characteristics and interpreted the results. Jian Li, Hongli Ma, Hui Chang, Jing Cong, and Chi Chiu Wang drafted the manuscript. All authors reviewed and revised the manuscript. Xiaoke Wu is the guarantor of this work and, as such, had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. Xiaoke Wu, Chi Chiu Wang, Yijuan Cao, Jian Li, Zhiqiang Li, Hongli Ma, Jingshu Gao, Hui Chang, Duojia Zhang, Jing Cong, Yu Wang, Qi Wu, Xiaoxiao Han, Pui Wah Jacqueline Chung, Yiran Li, Xu Zheng, Lingxi Chen, Lin Zeng, Astrid Borchert, Hartmut Kuhn, Zijiang Chen, Ernest Hung Yu Ng, Elisabet Stener-Victorin, Heping Zhang, Richard S. Legro, Ben Willem J. Mol, and Yongyong Shi declare that they have no conflict of interest or financial conflicts to disclose. Funding Information: This study was supported by the National key Research and Development Program of China ( 2019YFC1709500 ); the National Collaboration Project of Critical Illness by Integrating Chinese Medicine and Western Medicine ; the Project of Heilongjiang Province Innovation Team “TouYan;” the Yi-Xun Liu and Xiao-Ke Wu Academician Workstation; the Innovation Team of Reproductive Technique with Integrative Chinese Medicine and Western Medicine in Xuzhou City , China; Heilongjiang University of Chinese Medicine from the National Clinical Trial Base ; Heilongjiang Provincial Clinical Research Center for Ovary Diseases ; the Research Grant Council ( T13-602/21-N , C5045-20EF , and 14122021 ); and Food and Health Bureau in Hong Kong, China ( 06171026 ). Publisher Copyright: © 2023Peer reviewedPublisher PD

Spinor Bose-Einstein condensates

An overview on the physics of spinor and dipolar Bose-Einstein condensates (BECs) is given. Mean-field ground states, Bogoliubov spectra, and many-body ground and excited states of spinor BECs are discussed. Properties of spin-polarized dipolar BECs and those of spinor-dipolar BECs are reviewed. Some of the unique features of the vortices in spinor BECs such as fractional vortices and non-Abelian vortices are delineated. The symmetry of the order parameter is classified using group theory, and various topological excitations are investigated based on homotopy theory. Some of the more recent developments in a spinor BEC are discussed.Comment: To appear in Physics Reports. The PDF file with high resolution figures is available from the following website: http://cat.phys.s.u-tokyo.ac.jp/publication/review_of_spinorBEC.pd

Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology

<p>Abstract</p> <p>Background</p> <p>In the literature, there are fruitful algorithmic approaches for identification functional modules in protein-protein interactions (PPI) networks. Because of accumulation of large-scale interaction data on multiple organisms and non-recording interaction data in the existing PPI database, it is still emergent to design novel computational techniques that can be able to correctly and scalably analyze interaction data sets. Indeed there are a number of large scale biological data sets providing indirect evidence for protein-protein interaction relationships.</p> <p>Results</p> <p>The main aim of this paper is to present a prior knowledge based mining strategy to identify functional modules from PPI networks with the aid of Gene Ontology. Higher similarity value in Gene Ontology means that two gene products are more functionally related to each other, so it is better to group such gene products into one functional module. We study (i) to encode the functional pairs into the existing PPI networks; and (ii) to use these functional pairs as pairwise constraints to supervise the existing functional module identification algorithms. Topology-based modularity metric and complex annotation in MIPs will be used to evaluate the identified functional modules by these two approaches.</p> <p>Conclusions</p> <p>The experimental results on Yeast PPI networks and GO have shown that the prior knowledge based learning methods perform better than the existing algorithms.</p

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens

© 2014 The Authors. Published by Elsevier Inc. Background A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of human allergies. Objective We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens. Methods A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests. Results The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome. Conclusion An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.Link_to_subscribed_fulltex

Atomic Layer Deposition of 2D Metal Dichalcogenides for Electronics, Catalysis, Energy Storage, and Beyond

2D transition metal dichalcogenides (TMDCs) are among the most exciting materials of today. Their layered crystal structures result in unique and useful electronic, optical, catalytic, and quantum properties. To realize the technological potential of TMDCs, methods depositing uniform films of controlled thickness at low temperatures in a highly controllable, scalable, and repeatable manner are needed. Atomic layer deposition (ALD) is a chemical gas-phase thin film deposition method capable of meeting these challenges. In this review, the applications evaluated for ALD TMDCs are systematically examined, including electronics and optoelectonics, electrocatalysis and photocatalysis, energy storage, lubrication, plasmonics, solar cells, and photonics. This review focuses on understanding the interplay between ALD precursors and deposition conditions, the resulting film characteristics such as thickness, crystallinity, and morphology, and ultimately device performance. Through rational choice of precursors and conditions, ALD is observed to exhibit potential to meet the varying requirements of widely different applications. Beyond the current state of ALD TMDCs, the future prospects, opportunities, and challenges in different applications are discussed. The authors hope that the review aids in bringing together experts in the fields of ALD, TMDCs, and various applications to eventually realize industrial applications of ALD TMDCs.Peer reviewe

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead