bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of self-reported sleep duration and quality with BaPWV levels in hypertensive patients
Authors: Hu Huan , Li Huan , Huang Xiao , Bao Huihui , Song Yun , Wang Binyan , Liu Chengzhang , Xu Richard , Liu Lishun , Wang Xiaobin , Huo Yong , Xu Xiping , Cheng Xiaoshu , Qin Xianhui , Li Ping 
Published: July 2020

AbstractThe association between sleep conditions and arterial stiffness remains inconclusive. We aimed to investigate the relationship of sleep duration and quality with brachial-ankle pulse-wave velocity (baPWV) in hypertensive patients. A total of 14,485 hypertensive adults were included in this cross-sectional analysis. Information about sleep duration and quality was obtained via questionnaire. A baPWV level ≥1800 cm/s was defined as indicative of arterial stiffness. Compared with participants with a sleep duration <8 h per day, participants with a sleep duration ≥8 h per day had a significantly higher baPWV level (β = 13.7 cm/s; 95% CI: 3.9, 23.5) and a nonsignificantly higher prevalence of arterial stiffness (39.7% vs. 33.0%; OR, 1.08; 95% CI: 0.99–1.19). Similarly, compared with participants with good or medium sleep quality, participants with poor sleep quality had a significantly higher baPWV level (β = 16.3 cm/s; 95% CI: 0.1, 32.6) and a nonsignificantly greater prevalence of arterial stiffness (36.6% vs. 35.3%; OR, 1.13; 95% CI: 0.97–1.32). When sleep duration and quality were examined jointly, participants with a sleep duration ≥8 h and/or poor sleep quality had a significantly higher baPWV level (β = 14.4 cm/s; 95% CI: 5.3, 23.4) and a greater prevalence of arterial stiffness (38.8% vs. 32.7%; OR, 1.10; 95% CI: 1.01–1.20) than those with a sleep duration <8 h and good/medium sleep quality. In summary, among hypertensive patients, a longer sleep duration (≥8 h per day) and poor sleep quality were associated with higher baPWV levels and a higher prevalence of arterial stiffness.
Using operando techniques to understand and design high performance and stable alkaline membrane fuel cells
Authors: Peng Xiong , Kulkarni Devashish , Huang Ying , Omasta Travis J. , Ng Benjamin , Zheng Yiwei , Wang Lianqin , LaManna Jacob M. , Hussey Daniel S. , Varcoe John R. , Zenyuk Iryna V. , Mustain William E. 
Published: July 2020

AbstractThere is a need to understand the water dynamics of alkaline membrane fuel cells under various operating conditions to create electrodes that enable high performance and stable, long-term operation. Here we show, via operando neutron imaging and operando micro X-ray computed tomography, visualizations of the spatial and temporal distribution of liquid water in operating cells. We provide direct evidence for liquid water accumulation at the anode, which causes severe ionomer swelling and performance loss, as well as cell dryout from undesirably low water content in the cathode. We observe that the operating conditions leading to the highest power density during polarization are not generally the conditions that allow for long-term stable operation. This observation leads to new catalyst layer designs and gas diffusion layers. This study reports alkaline membrane fuel cells that can be operated continuously for over 1000 h at 600 mA cm−2 with voltage decay rate of only 32-μV h−1 – the best-reported durability to date.
Automatic precursor recognition and real-time forecasting of sudden explosive volcanic eruptions at Whakaari, New Zealand
Authors: Dempsey D. E. , Cronin S. J. , Mei S. , Kempa-Liehr A. W. 
Published: July 2020

AbstractSudden steam-driven eruptions strike without warning and are a leading cause of fatalities at touristic volcanoes. Recent deaths following the 2019 Whakaari eruption in New Zealand expose a need for accurate, short-term forecasting. However, current volcano alert systems are heuristic and too slowly updated with human input. Here, we show that a structured machine learning approach can detect eruption precursors in real-time seismic data streamed from Whakaari. We identify four-hour energy bursts that occur hours to days before most eruptions and suggest these indicate charging of the vent hydrothermal system by hot magmatic fluids. We developed a model to issue short-term alerts of elevated eruption likelihood and show that, under cross-validation testing, it could provide advanced warning of an unseen eruption in four out of five instances, including at least four hours warning for the 2019 eruption. This makes a strong case to adopt real-time forecasting models at active volcanoes.
Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes
Authors: Mehnert Martin , Ciuffa Rodolfo , Frommelt Fabian , Uliana Federico , van Drogen Audrey , Ruminski Kilian , Gstaiger Matthias , Aebersold Ruedi 
Published: July 2020

AbstractRapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.
Five-year change in body mass index category of childhood and the establishment of an obesity prediction model
Authors: Sun Yuelin , Xing Yufang , Liu Junfeng , Zhang Xiaoxia , Liu Jingyu , Wang Zhaoxia , Bi Jingyang , Ping Xianghe , Shen Qiqiang , Zhao Zhouqiao , Xu Jinjie 
Published: July 2020

AbstractThe prevalence of childhood obesity in China has recently become increasingly severe, and intervention measures are needed to stop its growth. Currently, there is a lack of assessment and prediction methods for childhood obesity. We develop a predictive model that uses currently measured predictors [gender, age, urban/rural, height and body mass index (BMI)] to quantify children’s probabilities of belonging to one of four BMI category 5 years later and identify the high-risk group for possible intervention. A total of 88,980 students underwent a routine standard physical examination and were reexamined 5 years later to complete the study. The full model shows that boys, urban residence and height have positive effects and that age has a negative effect on transition to the overweight or obese category along with significant BMI effects. Our model correctly predicts BMI categories 5 years later for 70% of the students. From 2018 to 2023, the prevalence of obesity in rural boys and girls is expected to increase by 4% and 2%, respectively, while that in urban boys and girls is expected to remain unchanged. Predictive models help us assess the severity of childhood obesity and take targeted interventions and treatments to prevent it.
HIV X4 Variants Increase Arachidonate 5-Lipoxygenase in the Pulmonary Microenvironment and are associated with Pulmonary Arterial Hypertension
Authors: Almodovar Sharilyn , Wade Brandy E. , Porter Kristi M. , Smith Justin M. , Lopez-Astacio Robert A. , Bijli Kaiser , Kang Bum-Yong , Cribbs Sushma K. , Guidot David M. , Molehin Deborah , McNair Bryan K. , Pumarejo-Gomez Laura , Perez Hernandez Jaritza , Salazar Ethan A. , Martinez Edgar G. , Huang Laurence , Kessing Cari F. , Suarez-Martinez Edu B. , Pruitt Kevin , Hsue Priscilla Y. , Tyor William R. , Flores Sonia C. , Sutliff Roy L. 
Published: July 2020

AbstractPulmonary Arterial Hypertension (PAH) is overrepresented in People Living with Human Immunodeficiency Virus (PLWH). HIV protein gp120 plays a key role in the pathogenesis of HIV-PAH. Genetic changes in HIV gp120 determine viral interactions with chemokine receptors; specifically, HIV-X4 viruses interact with CXCR4 while HIV-R5 interact with CCR5 co-receptors. Herein, we leveraged banked samples from patients enrolled in the NIH Lung HIV studies and used bioinformatic analyses to investigate whether signature sequences in HIV-gp120 that predict tropism also predict PAH. Further biological assays were conducted in pulmonary endothelial cells in vitro and in HIV-transgenic rats. We found that significantly more persons living with HIV-PAH harbor HIV-X4 variants. Multiple HIV models showed that recombinant gp120-X4 as well as infectious HIV-X4 remarkably increase arachidonate 5-lipoxygenase (ALOX5) expression. ALOX5 is essential for the production of leukotrienes; we confirmed that leukotriene levels are increased in bronchoalveolar lavage fluid of HIV-infected patients. This is the first report associating HIV-gp120 genotype to a pulmonary disease phenotype, as we uncovered X4 viruses as potential agents in the pathophysiology of HIV-PAH. Altogether, our results allude to the supplementation of antiretroviral therapy with ALOX5 antagonists to rescue patients with HIV-X4 variants from fatal PAH.
Quantitative immunohistochemical analysis of myeloid cell marker expression in human cortex captures microglia heterogeneity with anatomical context
Authors: Swanson Molly E. V. , Murray Helen C. , Ryan Brigid , Faull Richard L. M. , Dragunow Mike , Curtis Maurice A. 
Published: July 2020

AbstractCurrent immunohistochemical methods of studying microglia in the post-mortem human brain do not capture the heterogeneity of microglial function in response to damage and disease. We therefore investigated the expression of eight myeloid cell proteins associated with changes in function alongside Iba1. To study the myeloid cells we used immunohistochemistry on post-mortem human middle temporal gyrus sections from neurologically normal individuals. First we investigated co-labelling between the classical ‘activation’ marker, HLA-DR and each of the other markers of interest. Significant co-labelling between HLA-DR with CD206, CD32, CD163, or L-Ferritin was observed, although complete overlap of expression of HLA-DR with aforementioned markers was not observed. A qualitative assessment also demonstrated that perivascular macrophages expressed higher levels of the markers of interest we investigated than microglia, suggesting perivascular macrophages show a more phagocytic and antigen presentation state in the human brain. To determine whether the markers of interest were expressed in different functional states, the immunoreactivity for each marker was qualitatively assessed on microglial morphologies. Degenerating marker, L-Ferritin, was specific for dystrophic microglia. We demonstrate that microglial heterogeneity can be investigated in immunohistochemically stain post-mortem human tissue by integrating the single-cell abundance of proteins and cell morphology to infer function.
RPmirDIP: Reciprocal Perspective improves miRNA targeting prediction
Authors: Kyrollos Daniel G. , Reid Bradley , Dick Kevin , Green James R. 
Published: July 2020

AbstractMicroRNAs (miRNAs) are short, non-coding RNAs that interact with messenger RNA (mRNA) to accomplish critical cellular activities such as the regulation of gene expression. Several machine learning methods have been developed to improve classification accuracy and reduce validation costs by predicting which miRNA will target which gene. Application of these predictors to large numbers of unique miRNA–gene pairs has resulted in datasets comprising tens of millions of scored interactions; the largest among these is mirDIP. We here demonstrate that miRNA target prediction can be significantly improved ($$p < 0.001$$p<0.001) through the application of the Reciprocal Perspective (RP) method, a cascaded, semi-supervised machine learning method originally developed for protein-protein interaction prediction. The RP method, aptly named RPmirDIP, augments the original mirDIP prediction scores by leveraging local thresholds from the two complimentary views available to each miRNA–gene pair, rather than apply a traditional global decision threshold. Application of this novel RPmirDIP predictor promises to help identify new, unexpected miRNA–gene interactions. A dataset of RPmirDIP-scored interactions are made available to the scientific community at cu-bic.ca/RPmirDIP and https://doi.org/10.5683/SP2/LD8JKJ.
Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images
Authors: Li Jiarui , Zarzar Tomás González , White Julie D. , Indencleef Karlijne , Hoskens Hanne , Matthews Harry , Nauwelaers Nele , Zaidi Arslan , Eller Ryan J. , Herrick Noah , Günther Torsten , Svensson Emma M. , Jakobsson Mattias , Walsh Susan , Van Steen Kristel , Shriver Mark D. , Claes Peter 
Published: July 2020

AbstractEstimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case–control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.
Fluorescent recognition of Fe3+ in acidic environment by enhanced-quantum yield N-doped carbon dots: optimization of variables using central composite design
Authors: Issa Mohammed Abdullah , Abidin Zurina Z. , Sobri Shafreeza , Rashid Suraya Abdul , Mahdi Mohd Adzir , Ibrahim Nor Azowa 
Published: July 2020

AbstractA versatile synthetic approach for development of highly fluorescent nitrogen-doped carbon dots (N-CDs) from carboxymethylcellulose in the presence of linear polyethyleneimine (LPEI) has been developed. According to single factor method, central composite design incorporated with response surface methodology matrix was applied to find and model optimal conditions for the temperature (220–260 °C), duration (1–3 h) and LPEI weight (0.5–1.5%). The statistical results show that duration was the most significant parameter for efficient carbonization conversion rate in comparison with temperature and LPEI weight. The reduced cubic model (R2 = 0.9993) shows a good correlation between the experimental data and predicted values. The optimal variables were temperature of 260 °C, duration of 2 h and LPEI weight of 1%. Under these conditions, quantum yield of up to 44% was obtained. The numerically optimized N-CDs have an average size of 3.4 nm with graphitic nature owing to the abundant amino species incorporated into the carbon core framework. The blue-green N-CDs possess emission dependent upon the solvent polarity, wide pH stability with enhanced emission in an acidic environment. Impressively, the N-CDs show long-shelf-life for up to 1 year with no noticeable precipitation. The N-CDs were able to recognize a high concentration of Fe3+ ions with a detection limit of 0.14 μM in acidic solution owing to the special coordination for Fe3+ to be captured by electron-donating oxygen/ amino groups around N-CDs. Moreover, the N-CDs can also be used as a new kind of fluorescent ink for imaging applications.
The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure
Authors: Mohan Ashwini V. , Orozco-terWengel Pablo , Shanker Kartik , Vences Miguel 
Published: July 2020

AbstractThe Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genusPhelsumalikely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genusPhelsuma,and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name ‘North’ (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and ‘South’ (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.
Probiotics have beneficial metabolic effects in patients with type 2 diabetes mellitus: a meta-analysis of randomized clinical trials
Authors: Kocsis Tícia , Molnár Bálint , Németh Dávid , Hegyi Péter , Szakács Zsolt , Bálint Alexandra , Garami András , Soós Alexandra , Márta Katalin , Solymár Margit 
Published: July 2020

AbstractProbiotics have been reported to have a positive impact on the metabolic control of patients with type 2 diabetes. We aimed to systematically evaluate the effects of probiotics on cardiometabolic parameters in type 2 diabetes based on randomized controlled studies. MEDLINE, Embase, and CENTRAL databases were reviewed to search for randomized controlled trials that examined the effects of probiotic supplementation on cardiometabolic parameters in patients with type 2 diabetes. 32 trials provided results suitable to be included in the analysis. The effects of probiotics were calculated for the following parameters: BMI, total cholesterol levels, LDL, triglycerides, HDL, CRP, HbA1c levels, fasting plasma glucose, fasting insulin levels, systolic and diastolic blood pressure values. Data analysis showed a significant effect of probiotics on reducing total cholesterol, triglyceride levels, CRP, HbA1c, fasting plasma glucose, fasting insulin levels, and both systolic and diastolic blood pressure values. Supplementation with probiotics increased HDL levels however did not have a significant effect on BMI or LDL levels. Our data clearly suggest that probiotics could be a supplementary therapeutic approach in type 2 diabetes mellitus patients to improve dyslipidemia and to promote better metabolic control. According to our analysis, probiotic supplementation is beneficial in type 2 diabetes mellitus.
Segregation dynamics with reinforcement learning and agent based modeling
Authors: Sert Egemen , Bar-Yam Yaneer , Morales Alfredo J. 
Published: July 2020

AbstractSocieties are complex. Properties of social systems can be explained by the interplay and weaving of individual actions. Rewards are key to understand people’s choices and decisions. For instance, individual preferences of where to live may lead to the emergence of social segregation. In this paper, we combine Reinforcement Learning (RL) with Agent Based Modeling (ABM) in order to address the self-organizing dynamics of social segregation and explore the space of possibilities that emerge from considering different types of rewards. Our model promotes the creation of interdependencies and interactions among multiple agents of two different kinds that segregate from each other. For this purpose, agents use Deep Q-Networks to make decisions inspired on the rules of the Schelling Segregation model and rewards for interactions. Despite the segregation reward, our experiments show that spatial integration can be achieved by establishing interdependencies among agents of different kinds. They also reveal that segregated areas are more probable to host older people than diverse areas, which attract younger ones. Through this work, we show that the combination of RL and ABM can create an artificial environment for policy makers to observe potential and existing behaviors associated to rules of interactions and rewards.
Global distribution of epidemic-related Shiga toxin 2 encoding phages among enteroaggregative Escherichia coli
Authors: Kimata Keiko , Lee Kenichi , Watahiki Masanori , Isobe Junko , Ohnishi Makoto , Iyoda Sunao 
Published: July 2020

AbstractSince the Shiga toxin-producing enteroaggregative Escherichia coli (Stx-EAEC) O104:H4 strain caused a massive outbreak across Europe in 2011, the importance of Stx-EAEC has attracted attention from a public health perspective. Two Stx-EAEC O86 isolates were obtained from patients with severe symptoms in Japan in 1999 and 2015. To characterize the phylogeny and pathogenic potential of these Stx-EAEC O86 isolates, whole-genome sequence analyses were performed by short-and long-read sequencing. Among genetically diverse E. coli O86, the Stx-EAEC O86 isolates were clustered with the EAEC O86:H27 ST3570 subgroup. Strikingly, there were only two loci with single nucleotide polymorphisms (SNPs) between the Stx2a phage of a Japanese O86:H27 isolate and that of the European epidemic-related Stx-EAEC O104:H4 isolate. These results provide evidence of global distribution of epidemic-related Stx2a phages among various lineages of E. coli with few mutations.