bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk-focused Differences in Molecular Processes Implicated in SARS-CoV-2 Infection: Corollaries in DNA Methylation and Gene Expression
Authors: Konwar Chaini , Asiimwe Rebecca , Inkster Amy M. , Merrill Sarah M. , Negri Gian L. , Aristizabal Maria J. , Rider Christopher F. , MacIsaac Julie L. , Carlsten Christopher , Kobor Michael S. 
Published: August 2021

Abstract
Background Understanding the molecular basis of susceptibility factors to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global health imperative. It is well-established that males are more likely to acquire SARS-CoV-2 infection and exhibit more severe outcomes. Similarly, exposure to air pollutants and pre-existing respiratory chronic conditions like asthma and chronic obstructive respiratory disease (COPD) confer an increased risk to coronavirus disease 2019 (COVID-19). Methods We investigated molecular patterns associated with risk factors in 398 candidate genes relevant to COVID-19 biology. To accomplish this, we downloaded DNA methylation and gene expression datasets from publicly available repositories (GEO and GTEx portal) and utilized data from our unpublished controlled human exposure study. Results First, we observed sex-biased DNA methylation patterns in autosomal immune genes such as NLRP2, TLE1, GPX1, and ARRB2 (FDR <0.05, magnitude of DNA methylation difference Δβ >0.05). Second, our analysis on the X-linked genes identified sex associated DNA methylation profiles in genes such as ACE2, CA5B, and HS6ST2 (FDR <0.05, Δβ >0.05). These associations were observed across multiple respiratory tissues (lung, nasal epithelia, airway epithelia, and bronchoalveolar lavage) and in whole blood. Some of these genes, like NLRP2 and CA5B, also exhibited sex-biased expression patterns. Third, we identified modest DNA methylation changes in CpGs associated with PRIM2 and TATDN1 (FDR <0.1, Δβ >0.05) in response to particle-depleted diesel exhaust in bronchoalveolar lavage. Finally, we captured a DNA methylation signature associated with COPD diagnosis in a gene involved in nicotine dependence (COMT) (FDR <0.1, Δβ >0.05). Conclusion Our findings on sex differences are of clinical relevance given they potentially point to an exaggerated immune response in males. We also found tissue-specific DNA methylation differences in response to particulate exposure potentially capturing an NO2 effect – a contributor to COVID-19 susceptibility. While we identified a molecular signature associated with COPD, all COPD-affected individuals were smokers, which may either reflect an association with the disease, smoking, or may highlight a compounded effect of these two risk factors in COVID-19. Overall, the findings point towards the molecular basis of variation in susceptibility factors that may partly explain disparities in SARS-CoV-2 infection.
Design and Performance Analysis of Ultrathin Nanowire FET Ammonia GAS Sensor
Authors: Verma Chhaya , Singh Jeetendra , Tripathi Santosh Kumar , Kumar Rajeev 
Published: August 2021

Abstract
In this work, an ultrathin 3 nm nanowire field-effect transistor (NWFET) based ammonia gas sensor is designed, and its sensitivity is analyzed at room temperature. The designed NWFET for gas sensing is observed to have a higher ratio of ION to IOFF than 109, lower DIBL and better gate controlling due to a higher surface to volume ratio. The gas-sensing performance analysis has been done for three different catalysts, iridium (Ir), ruthenium (Ru), and palladium (Pd), by gradually increasing the work function by a difference of 50meV. The device showed higher OFF current sensitivity compared to ON current sensitivity. The power consumption and threshold voltage are observed to be least for palladium catalytic gate electrodes making palladium the most favorable catalytic for ammonia gas for the designed gas sensor.
Functional validation of Winged bean (Psophocarpus tetragonolobus (L.) DC.) anthocyanidin synthase (Wb ANS) gene through virus-induced gene silencing
Authors: Singh Vinayak , Kumar Verandra , Lone Rayees Ahmad , Mohanty Chandra Sekhar 
Published: August 2021

Abstract
Background

Histochemical and microscopic observations of various tissues of the underutilized legume winged bean (Psophocarpus tetragonolobus (L.) DC.) indicated that the plant and its various parts are highly infested with condensed tannin (CT). Characterization of CT was carried out through the quantification of its structural-monomeric units catechin and epicatechin. The responsible candidate gene for anthocyanidin synthase (ANS) biosynthesis was identified, phylogenetically mapped and manipulated for lowering the CT-content.
Results

Virus-induced gene silencing (VIGS) was employed for silencing of WbANS transcript. WbANS-VIGS induction resulted in four-fold decrease in condensed tannin biosynthesis in P. tetragonolobus.
Conclusion

As condensed tannin adversely affects digestion and considered as an anti-nutrient, so this study might be helpful in future for altering the biosynthesis of condensed tannin by manipulating the ANS-encoding molecular factors.
Detection of Sepsis Patients Using Biomarkers Based on Machine Learning
Authors: Eskandari Mahsa Amin , Moridani Mohammad Karimi , Mohammadi Salar 
Published: August 2021

Abstract
Objective: Sepsis is the second most common cause of death in patients with non-cardiovascular diseases admitted to the ICU. It is one of the top ten reasons for death among all hospitalized patients. This study aimed to compare the value of some blood parameters in the diagnosis of sepsis and investigate their relationship to select a more practical diagnostic method.Method: In this descriptive-analytical study, 208 patients with sepsis admitted to the ICU were selected. Then the physiological parameters of patients and normal individuals were measured. Data analysis was performed using the P-value and effect size methods and MATLAB software. To classify the disease, the MLP, RBF, and KNN methods were used.Result: The values of the HR, O­2Sat, and SBP in patients with sepsis have changed significantly compared to normal conditions. The classification results using different classifications showed that the values of specificity, sensitivity, and accuracy in the classifier are more than MLP and RBF and are equal to 98%,100%, and 99%, respectively.Conclusion: Clinically, accurate detection of sepsis and the prediction of the patients at risk of developing sepsis is useful for improving treatment. Given the significant differences between HR, O­2Sat, and SBP between normal and sepsis patients in this study, it may be possible to use these tests as simple tests instead of the complement protein 3 (C3) and Procalcitonin (PCT) tests to diagnose sepsis in the ICU.
Selected Ideal Natural Ligand Against TNBC by Inhibiting CDC20, Using Bioinformatics and Molecular Biology
Authors: Liu Naimeng , Wang Xinhui , Lv Xiaye , Li Duo , Xie Haoqun , Guo Zhen , Song Dong 
Published: August 2021

Abstract
Background: Triple-negative breast cancer (TNBC), as the most aggressive kinds of breast tumor, still cannot get effective targeted therapy. Recently, techniques of bioinformatics and molecular biology were hot topics in drug development. We want to find potential therapeutic targets of triple-negative breast cancer (TNBC) patients by bioinformatics and screen ideal natural ligand that can bind with the potential target and inhibit it by using molecular biology.Methods: Bioinformatics and molecular biology were combined to analyze potential therapeutic targets. Differential expression analysis identified the differentially expressed genes (DEGs) between TNBC tissues and normal tissues. The functional enrichment analyses of DEGs shown the important gene ontology (GO) terms and pathways of TNBC. Protein-protein interaction (PPI) network construction screened 20 hub genes, while Kaplan website was used to analyze the relationship between the survival curve and expression of hub genes. Then Discovery Studio 4.5 screened ideal natural inhibitors of the potential therapeutic target by LibDock, ADME, toxicity prediction, CDOCKER and molecular dynamic simulation.Results: 1,212 and 353 DEGs were respectively found between TNBC tissues and normal tissues, including 88 up-regulated and 141 down-regulated DEGs in both databases. 20 hub genes were screened, and the higher expression of CDC20 was associated with a poor prognosis. Therefore, we chose CDC20 as the potential therapeutic target. 7,416 natural ligands were conducted to bind firmly with CDC20, and among these ligands, ZINC000004098930 was regarded as the potential ideal ligand, owing to its non-hepatotoxicity, more solubility level and less carcinogenicity than the reference drug, apcin. The ZINC000004098930-CDC20 could exist stably in natural environment.Conclusion: 20 genes were regarded as hub genes of TNBC and most of them were relevant to the survival curve of breast cancer patients, especially CDC20. ZINC000004098930 was chosen as the ideal natural ligand that can targeted and inhibited CDC20, which may give great contribution to TNBC targeted treatment.
Computational Study of Halogen-Halogen Interactions in Polyhalide Ionic Liquids
Authors: Xu Yanmin , Zhang Jiaqiang , Yang La , Zhang Yifei , Xu Zhijian , Lu Yunxiang 
Published: August 2021

Abstract
Recent years have seen many specific applications of polyhalide ionic liquids (ILs) such as oxidizing solvents for metals and alloys, immersion fluids for optical mineralogy, and electrolyte components for dye-sensitized solar cells. In this work, interhalogen interactions in a set of polyhalide ILs composed of polyhalide anions, [X3]−, [X5]− and [X7]− (X = I or Br), with two typical cations, tetramethylammonium [NMe4]+ and 1,3-dimethylimidazolium [DMIM]+, were thoroughly studied from a computational point of view. In addition, a halogen-bonded supramolecular anion, [C6F13-I∙∙∙I∙∙∙I-C6F13]−, was also taken into account for comparison. Unlike those in bare polyhalide ions, halogen-halogen interactions in ionic pairs for the investigated ILs are somewhat asymmetric caused by the interactions between the cations and the anions. Most interhalogen contacts in ionic pairs have some covalent content, while I∙∙∙I interactions in the complexes of the supramolecular anion are purely noncovalent. In general, there are two classes of interhalogen bonds in ionic pairs: one class with longer X∙∙∙X distances shows primarily ionic character, while the other with shorter distances has a larger degree of covalency, i.e. intermediate ionic/covalent nature.
Distinct Composition and Assembly Processes of Bacterial Communities in a River From The Arid Area: Ecotypes or Habitat Types?
Authors: Qi Ran , Xue Nana , Zhou Xiaobin , Zhao Li , song Wen juan , Yang Yuyi 
Published: August 2021

Abstract
The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, function, and assembly mechanism of the bacterial community in the arid river were analyzed. Four ecotypes were recognized across the three habitats (biofilm, water, and sediment) by Dirichlet multinomial mixture method. The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of Water II to Water I. Significant differences in the composition and function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and function of plastic degradation in Water I than those in Water II. Habitat filtering may play a more important role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominated the assembly process of bacterial communities in water and sediment. In Water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in the Water II. These results would provide conceptual frameworks about how to choose habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.
Chinese Patent Medicine As An Adjuvant Treatment for Idiopathic Pulmonary Fibrosis Patients: A Protocol for A Systematic Review and Meta-Analysis
Authors: Sun Fang , Wu Zhaochu , Jiang Fengli , Huang Mao , Wang Jine , Sun Wenli , Zhang Lishan 
Published: August 2021

Abstract
Background
Idiopathic pulmonary fibrosis (IPF) is a progressive, chronic, irreversible, and lethal interstitial lung disease (ILD) with unknown etiology occurring mainly in elderly. In recent years, the morbidity and mortality of IPF steady increase. However, there are currently no therapies that reverse fibrosis, the median survival time reported ranging from 2 to 5 years from diagnosis. The purpose of this systematic review and meta-analysis is to evaluate the effectiveness and safety of Chinese patent medicines as an adjuvant treatment in combination with Western medicines in the treatment of patients with IPF.
Methods
We will search electronic databases including PubMed, EMBASE, Cochrane Central, Web of Science, Chinese Biomedical Database (SinoMed), Chinese National Knowledge Infrastructure (CNKI), Chongqing VIP information (CQVIP), and Wanfang database using keywords related to IPF and Chinese patent medicine. Search was also carried out on ClinicalTrials.gov, International Clinical Trials Registry Platform (ICTRP) and the Chinese Clinical Trials Register (ChiCTR). Reference lists of literature included and relevant systematic reviews will be checked. Two independent reviewers will involved in screening studies, extracting data, and evaluating works. Any disagreements will be resolved by discussion or in consultation with a third reviewer. Data analysis will be conducted using the Review Manager software (version 5.4.1). The risk of bias of each study and the quality of evidence will be respectively assessed using Cochrane Risk of Bias tools and GRADE system.
Discussion
This review will integrate the current evidence and provide evidence regarding use of Chinese patent medicine as an adjuvant treatment in idiopathic pulmonary fibrosis to provide clarity regarding the potential benefits and best practice.
Trial registration:
PROSPERO CRD42021252806
Inequality in Financing and Distribution of Noncommunicable Diseases in China: Evidence From 2017-2019
Authors: Fang Quan , Ma Guoliang , Zhang Shunli , Zhang Qin , Xu Xinzhou , Wang Xin 
Published: August 2021

Abstract
Background: Noncommunicable diseases (NCDs) are the leading causes of morbidity and mortality worldwide. Understanding the financing and distribution of diseases can provide a basis for policy formulation and intervention. This study analyses the expenditure of NCDs in China to provide health policy advice.Methods: Data were collected by multi-stage stratified random sampling from 2017-2019. The medical expenses of patients with NCDs were calculated based on “System of Health Accounts 2011”(SHA 2011), Analyze from funding sources, dimensions of institutional flow, and financing scheme. Linear regression analysis was conducted by controlling factors influencing hospitalization expenses. All analyses were performed by STATA 15.0.Results: 408 institutions and 8,104,233 valid items were included in the study. The current curative expenditure (CCE) of NCDs was 14.205 billion China Yuan (CNY) in 2017, 15.914 billion CNY in 2018, and 18.055 billion CNY in 2019. More than 60% came from public financing. The proportion of family health financing continued to decline, reaching 31.16% in 2019. The expenditures were mainly in general hospitals, above 70%. Elderly patients account for the majority. Diseases of the circulatory system, Diseases of the digestive system, and Neoplasms were the main NCDs. Year, age, gender, length of stay, surgery, insurance, and institution level were the factors affecting hospitalization expenses.Conclusions: NCDs are the main economic burden of diseases in China, and their financing and distribution are inequality. To reduce the economic burden of NCDs, the government needs to optimize resource allocation and rationalize institutional flows and functions.
Cementless Hemiarthroplasty Without Femoral Calcar Reconstruction Versus Cemented Hemiarthroplasty for Unstable Intertrochanteric Fractures in octogenarians
Authors: Sun Chang , Cai Meng , Meng Jia , Zhang Yu , Jiang Hui , Zhao Jianning , Guo Ting 
Published: August 2021

Abstract
Background

The aim of this study was to compare the mid-term outcomes of cementless hemiarthroplasty without femoral calcar reconstruction with cemented hemiarthroplasty in patients aged 80 years or more.
Methods

From January 2015 to December 2017, 135 patients with unstable intertrochanteric fractures were retrospectively investigated, 70 patients were treated with the cemented hemiarthroplasty while 65 patients were treated with a modular long-stem cementless hemiarthroplasty without rebuilding calcar. Clinical and radiological results were analyzed.
Results

The 106 alive patients were followed for 62.1 ± 8.3 months, and 29 patients died during the follow-up period. No significant differences were found in terms of demographic and clinical characters of patients, weight training time, postoperative hospital stay length, postoperative ambulatory status and Harris hip score. Patients treated with cementless hemiarthroplasty had a shorter operative time, less estimated blood loss, less amount of blood transfusion and a lower one-year mortality compared with patients treated with cemented hemiarthroplasty.
Conclusions

Compared with cemented hemiarthroplasty, cementless hemiarthroplasty using a long modular stem without reconstruction of femoral calcar was a good choice for octogenarians with unstable intertrochanteric fractures.
Research on the Mechanism of Main Roof Advanced Breaking and Supporting Technology When Long-wall Face Passing Through Abandoned Roadways
Authors: Weidong Pan , Cang Deng , Boyang Li , Kunming Zhang , Shan Gao 
Published: August 2021

Abstract
Unlike general long-wall mining, the roof activity is more intense when long-wall face passes through the abandoned roadway. Technically, the coal pillar between the abandoned roadway and the long-wall face will suddenly fail with a certain critical value of its width, leading to the roof breaks in advance and other production-restricted problems because of the support loss, which will be a great threat to underground mining activities. In order to guarantee a safe mining condition, therefore, it is greatly necessary to uncover how the roof breaks in advance and how to cope with it. From the stability maintaining of the key block perspective, this paper took for research that the 12404-1 long-wall face of Wulanmulun coal mine, China. The critical value of the coal pillar’s width was determined to be about 5m by theoretical analysis, likely, the appropriate support force of the abandoned roadway’s roof is about 4020KN per meter. Meanwhile, a numerical simulation method was adopted to study the ground pressure when the long-wall face passing through the abandoned roadway. Correspondingly, a compound supporting technology involving the roof presplit technique, anchor cable supporting and pumping pillar supporting were proposed for the roof of the abandoned roadway, and it practically worked well.
Influence of Indirect Solar Irradiance on Satellite Observation
Authors: Wang Xia , LI Zhi , Xu Can , Huo Yurong , Wu Yifan 
Published: August 2021

Abstract
With the development of Space Domain Awareness(SDA), satellites’ optical characteristics are becoming attention-grabbing. Sunlight was usually considered the only light source for the satellites. However, in the actual observation, researchers have found that earthshine and moonlight would increase errors of the observation results, which have greatly influence the estimation of the satellite’s state. In order to avoid this influence, we propose an observation strategy. Firstly, we propose an accurate earthshine model, which considers the earth’s volume and favors long-time continuous satellite observation. Then, we explore the earthshine and moonlight’s impact on satellite observation results and find that this impact varies with the satellite attributes. Furthermore, we Figure out the law of this impact and establish a connection between this law and observation geometry. Finally, a Period Contribution model is proposed to provide a corresponding observation strategy to avoid the influence of earthshine and moonlight.
Fast Machine Learning Annotation in the Medical Domain: A Semi-Automated Video Annotation Tool for Gastroenterologists
Authors: Krenzer Adrian , Makowski Kevin , Hekalo Amar , Fitting Daniel , Troya Joel , Zoller Wolfram G. , Hann Alexander , Puppe Frank 
Published: August 2021

Abstract
Background: Machine learning, especially deep learning, is becoming more and more relevant in research and development in the medical domain. For all of the supervised deep learning applications, data is the most critical factor in securing successful implementation and sustaining the progress of the machine learning model. Especially gastroenterological data, which often involves endoscopic videos, are cumbersome to annotate. Domain experts are needed to interpret and annotate the videos. To support those domain experts, we generated a framework. With this framework, instead of annotating every frame in the video sequence, experts are just performing key annotations at the beginning and the end of sequences with pathologies, e.g. visible polyps. Subsequently, non-expert annotators supported by machine learning add the missing annotations for the frames in-between. Results: Using this framework we were able to reduce work load of domain experts on average by a factor of 20. This is primarily due to the structure of the framework, which is designed to minimize the workload of the domain expert. Pairing this framework with a state-of-the-art semi-automated pre-annotation model enhances the annotation speed further. Through a study with 10 participants we show that semi-automated annotation using our tool doubles the annotation speed of non-expert annotators compared to a well-known state-of-the-art annotation tool. Conclusion: In summary, we introduce a framework for fast expert annotation for gastroenterologists, which reduces the workload of the domain expert considerably while maintaining a very high annotation quality. The framework incorporates a semi-automated annotation system utilizing trained object detection models. The software and framework are open-source.