bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics and mechanism of spatial-temporal changes of fluorosis in typical high fluoride areas of Northwest China over the past 40 years
Authors: Liu Xinlei , Li Xuxiang , Fu Hao , Zhou Pengyun 
Published: November 2022

Abstract

Since the 1980s, China, especially the northwest part had carried out extensive water-improving project to reduce fluoride, but the fluorosis has not been completely eliminated. Through historical data comparison, on-site investigation and sample detection, combined with hydrochemical analysis and spatial analysis, this paper studied the 40 years’ changes of water fluoride and the control effect of fluorosis in the typical fluorosis areas Dali County of northwest China. Results show that from 1980 to 2017, benefited from the water-improving project, the fluoride in local residents' drinking water significantly decreased, with the median value declined from 2.40 to 1.26 mg/L, which further reduced fluorosis. As a typical water-improving area by low-fluoride water sources developing, in Dali, the generally dropped fluoride of groundwater is the root cause for the controlled endemic fluorosis. The enrichment of fluoride in groundwater here is controlled by the fluoride-rich geological background, landform and evaporative climate. The water environment characterized by slight alkalinity, rich sodium and low calcium is also an important factor. For the temporal changes of groundwater, human irrigation activities were considered as the primary role. Although the fluorosis has improved significantly, low residents' satisfaction and the rise of fluoride concentration in some water sources have led to a continuous high fluoride water drinking and fluorosis in some areas. It is suggested that the local government should strengthen water quality improvement from the aspects of low fluoride water source development and water supply management to consolidate the effect of fluorosis prevention and control.
Contribution of rare coding variants to complex trait heritability
Authors: Pathan Nazia , Deng Wei Q. , Khan Mohammad , Scipio Matteo Di , Mao Shihong , Morton Robert W. , Lali Ricky , Pigeyre Marie , Chong Michael R. , Paré Guillaume 
Published: November 2022

Abstract
It has been postulated that rare coding variants (RVs; MAF<0.01) contribute to the “missing” heritability of complex traits. We developed a novel framework, the Rare variant heritability (RARity) estimator, to assess RV heritability (h2RV) without assuming a particular genetic architecture. We applied RARity to 31 complex traits in the UK Biobank (N=167,348) and showed that gene-level RV aggregation suffers from 79% (95% CI: 68-93%) loss of h2RV. Using unaggregated variants, 27 traits had h2RV>5%, with height having the highest h2RV at 21.9% (95% CI: 19.0-24.8%). The total heritability, including common and rare variants, recovered pedigree-based estimates for 11 traits. RARity can estimate gene-level h2RV, enabling the assessment of gene-level characteristics and revealing 12 novel gene-phenotype relationships. Finally, we demonstrated that in silico pathogenicity prediction (variant-level) and gene-level annotations do not generally enrich for RVs that over-contribute to complex trait variance, and thus, novel methods are needed to predict RV functionality.
Relationship between depressive disorders and biochemical indicators in adult men and women
Authors: Li Xinyuan , Mao Yafei , Zhu Shumin , Gao Shichao , Jin Xiuyu , Geng Yulan , Ma Jin , Wei Zishuan 
Published: November 2022

Abstract
Background Depression is a psychiatric disorder with global public health concerns. In spite of the fact that a number of risk factors have been identified for depression, there is no clear relationship between biochemistry and depression. In this study, we assessed whether depressive disorders are significantly associated with biochemical indicators.
Methods Our study included 17561 adults (age ≥18 years) participating in the 2009-2018 National Health and Nutrition Examination Survey (NHANES). The relationship between depression and biochemical and obesity indicators was analyzed by logistic regression
Results As compared to the control group, men with depression showed significantly higher levels of gamma-glutamyl transferase, glucose, and triglycerides, and lower levels of albumin and total bilirubin. The depressed group had higher levels of alkaline phosphatase, bicarbonate, and sodium than the control group.
Conclusion A number of biochemical and anthropometric indices were associated with depression in this study. It would be interesting to further analyze their cause-effect relationship
Limitations This study is a cross-sectional study. The population is less restricted and does not exclude people with diabetes, pregnancy, etc., so it is less significant for a specific population. Dietary information was not included, as diet plays an important role in many indicators.
Epithelial Plasticity and Innate Immune Activation
Promote Lung Tissue Remodeling following Respiratory Viral Infection.
Authors: Beppu Andrew , Zhao Juanjuan , Yao Changfu , Carraro Gianni , Israely Edo , Coelho Ana Lucia , Hogaboam Cory , Parks William , Kolls Jay , Stripp Barry 
Published: November 2022

Abstract
Epithelial plasticity has been suggested in lungs of mice following genetic depletion of stem cells but is of unknown physiological relevance. Viral infection and chronic lung disease share similar pathological features of stem cell loss in alveoli, basal cell (BC) hyperplasia in small airways, and innate immune activation, that contribute to epithelial remodeling and loss of lung function. We show that a novel subset of distal airway secretory cells, intralobar serous (IS) cells, are activated to assume BC fates following influenza virus infection. Injury-induced hyperplastic BC (hBC) differ from pre-existing BC by high expression of IL-22Ra1 and undergo IL-22-dependent expansion for colonization of injured alveoli. Resolution of virus-elicited inflammation resulted in BC>IS re-differentiation in repopulated alveoli, and increased local expression of antimicrobial factors, but failed to replace normal alveolar epithelium. Epithelial plasticity therefore protects against mortality from acute respiratory viral infection but results in distal lung remodeling and loss of lung function.
Dual-signal readout paper-based wearable biosensor for multiplexed analyte detection in sweat with 3D origami structure
Authors: WANG KAN , Cheng Yuemeng , Feng Shaoqing , Ning Qihong , Li Tangan , Xu Hao , Sun Qingwen , Cui Daxiang 
Published: November 2022

Abstract

In this research, we designed and implemented a small, convenient, and non-invasive paper-based microfluidic sweat sensor that can simultaneously detect multiple key biomarkers in human sweat. The origami structure of the chip includes colorimetric and electrochemical sensing regions. Different colorimetric sensing regions are modified with specific chromogenic reagents to selectively identify glucose, lactate, uric acid, and magnesium ions in sweat, as well as its pH value. The regions of electrochemical sensing identify cortisol in sweat by molecular imprinting. The entire chip is composed of hydrophilic- and hydrophobically-treated filter paper, and 3D microfluidic channels are constructed by using folding paper. The thread-based channels formed after hydrophilic and hydrophobic modifications are used to control the rate of flow of sweat, which in turn can be used to control the sequence of reactions in the differently colored regions of development to ensure that signals of the best color can be captured simultaneously in the colorimetric sensing regions. Finally, the results of on-body experiments verified the reliability of the proposed sweat sensor and its potential for the non-invasive identification of a variety of sweat biomarkers.
Response to Medicines and Healthcare products Regulatory Agency’s “Consultation on proposals for legislative changes for clinical trials”
Authors: Law Martin , Couturier Dominique-Laurent , Choodari-Oskooei Babak , Crout Phillip , Gamble Carrol , Pallmann Philip , Pilling Mark , Robertson David , Robling Michael , Sydes Matthew R. , Villar Sofía S. , Wason James , Wheeler Graham , Williamson S. Faye , Yap Christina , Jaki Thomas 
Published: November 2022

Abstract
In the United Kingdom, the Medicines and Healthcare products Regulatory Agency consulted on proposals “to improve and strengthen the UK clinical trials legislation to help us make the UK the best place to research and develop safe and innovative medicines”. The purpose of the consultation was to help finalise the proposals and contribute to the drafting of secondary legislation. We discussed these proposals as members of the Trials Methodology Research Partnership Adaptive Designs Working Group, which is jointly funded by the Medical Research Council and the National Institute for Health and Care Research. Two topics arose frequently in the discussion: the emphasis on legislation, and data sharing. It is our opinion that the proposals rely heavily on legislation to change practice. However, clinical trials are heterogeneous, and as a result some trials will struggle to comply with all of the proposed legislation. Furthermore, adaptive design clinical trials are even more heterogeneous than their non-adaptive counterparts, and face more challenges. Consequently, it is possible that increased legislation could have a greater negative impact on adaptive designs than non-adaptive designs. Overall, we are skeptical that the introduction of legislation will achieve the desired outcomes, with some exceptions. Meanwhile the topic of data sharing – making anonymised individual-level clinical trial data available to other investigators for further use – is entirely absent from the proposals. However, as an aspect of the wider concept of open science and reproducible research, data sharing is an increasingly important aspect of clinical trials. The benefits of data sharing include faster innovation, improved surveillance of drug safety and effectiveness and decreasing participant exposure to unnecessary risk. There are already a number of UK-focused documents that discuss and encourage data sharing, for example, the Concordat on Open Research Data and the Medical Research Council’s Data Sharing Policy. We strongly suggest that data sharing should be the norm rather than the exception, and hope that the forthcoming proposals on clinical trials  address this important topic.
Rapid TCR:Epitope Ranker (RAPTER): A primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution
Authors: Deering Raquel P. , Blumenberg Lili , Li Lianjie , Dhanik Ankur , Jeong Se , Pourpe Stephane , Song Hang , Boucher Lauren , Ragunathan Shoba , Li Yanxia , Zhong Maggie , Kuhnert Jessica , Adler Christina , Hawins Peter G. , Gupta Namita T. , Moore Michael , Ni Min , Hansen Johanna , Wei Yi , Thurston Gavin 
Published: November 2022

Abstract
Identifying epitopes that T cells respond to is critical to understanding T cell-mediated immunity. Traditional multimer and other single cell assays often require large blood volumes and/or expensive HLA-specific reagents and provide limited phenotypic and functional information. Here, we present the Rapid TCR:Epitope Ranker (RAPTER) assay, a single cell RNA sequencing (scRNA-SEQ) method that uses primary human T cells and antigen presenting cells (APCs) to assess functional T cell reactivity at single cell resolution. Using hash-tag oligonucleotide (HTO) coding and T cell activation-induced markers (AIM), RAPTER defines paired epitope specificity and TCR sequence and can include RNA- and protein-level T cell phenotype information. We demonstrate that RAPTER identified specific reactivities to viral and tumor antigens at sensitivities as low as 0.15% of total CD8+ T cells, and deconvoluted low-frequency circulating HPV16-specific T cell clones from a cervical cancer patient. The specificities of TCRs identified by RAPTER for MART1, EBV, and influenza epitopes were functionally confirmed in vitro. In summary, RAPTER identifies low-frequency T cell reactivities using primary cells from low blood volumes, and the resulting paired TCR: ligand information can directly enable immunogenic antigen selection for vaccine epitope inclusion, antigen-specific TCR tracking, and TCR cloning for further therapeutic development.
Cloning and functional analysis of the promoter of a UDP-glycosyltransferase gene from Panax quinquefolium L.
Authors: chen jing xian , LU CHAO , Cruz Reggie Yadao de la , LI YUHUA , ZHENG JUNPING , ZHANG YAOGUANG , WANG YANLU 
Published: November 2022

Abstract
In order to explore the function of the Pq3-O-UGT2 promoter, chromosome walking technology was used to isolate the 1399 bp sequence upstream of the ATG initiation codon of Pq3-O-UGT2 from Panax quinquefolium L. Bioinformatics analysis shows that the nucleic acid sequence contains a large number of typical structures unique to eukaryotic promoters and many other important cis-acting regulatory elements, including light responsive elements, hormone-responsive elements and stress-responsive elements, etc. Seven fragments including the full-length promoter and six 5′ terminal series deleted fragments were fused with the GUS reporter gene to test their activities. The results of histochemical staining show that a strong GUS activity were observed in flowers, siliques, leaves, stems and roots of transgenic Arabidopsis containing the full length Pq3-O-UGT2 promoter. Different GUS activity were also observed in the seedlings of transgenic Arabidopsis containing the full length promoter and six 5′ terminal series deleted fragments. Fluorometric assays show that seven fragments were found to drive GUS expression, and the highest enzyme activity is the full-length fragment with 4370 pmol 4-MU/min/mg protein, which is 80.01% of the CaMV35S promoter. Followed by P-801::GUS with 2162 pmol 4-MU/min/mg protein, and the shortest promoter containing P-198::GUS with 45 pmol 4-MU/min/mg protein was sufficient to activate GUS expression. In addition, extended light, low temperatures, Methyl jasmonate(MeJA), Abscisic acid(ABA), NAA and GA3 were selected to investigate the Pq3-O-UGT2 promoter in response to abiotic stress and hormone treatment. The promoter activity of the full length can be enhanced much more than the other six 5′ terminal series deleted fragments, and the most significant change was detected in MeJA treatment with 2.12 times increased. Furthermore, it was found that the promoter activity of P-998::GUS can be enhanced by ABA with 1.47 times. Above results show that the GUS activity of different promoter fragments had different response to different environmental factors. This article provides a great understanding of complex regulatory mechanisms of Pq3-O-UGT2 and the molecular mechanisms of triterpene biosynthesis.
Micropropagation of Brassavola nodosa (L.) Lindl. using SETIS™ bioreactor
Authors: Vendrame Wagner , Xu JianJian , Beleski David G. 
Published: November 2022

Abstract
Brassavola nodosa (L.) Lindl. is a tropical epiphytic orchid showing characteristics of interest for the ornamental nursery industry. However, problems with traditional propagation methods limit the development of a large-scale commercial production system. In addition, this species is considered endangered due to the reduction in population caused by habitat destruction, climate change and over-collection from native areas. The use of micropropagation has been investigated for this species, and the use of liquid in vitro systems showed potential for use of temporary immersion bioreactors for micropropagation of B. nodosa. This study evaluated the efficiency of the SETIS™ bioreactor system for the micropropagation of B. nodosa by adjusting parameters of immersion (frequency and duration) and by comparing it to conventional semi-solid culture systems. Results indicate that temporary immersion of B. nodosa explants with a frequency of 2 h and duration of 2 min returned the highest multiplication rates, with 4.6 shoots produced per explant compared with 2.8 shoots per explant in semi-solid agar-based systems. The use of bioreactors also promoted increased growth and development and in vitro rooting, therefore improving survival and facilitating acclimatization of in vitro-derived plantlets. This is the first study demonstrating a successful protocol for large-scale micropropagation of B. nodosa using SETIS™ bioreactors, which could have significant value and impact for the commercial production of this species as well as for conservation purposes.
Field Experiment Reveals Unintended Consequences of Organic Matter Amendments in Restoring Wetlands
Authors: Baldwin Andrew H. , Yarwood Stephanie A. , Scott Brian 
Published: November 2022

Abstract
Wetlands are identified as key ecosystems in the UN Decade on Restoration initiative because of their water management and global warming benefits. Wetland restoration sometimes includes adding organic matter (+ OM) to accelerate hydric soil development and provide nutrients for new vegetation. We conducted a manipulative field experiment to identify the most effective type of + OM and loading rate for soil and vegetation development in a freshwater wetland restoration site that was a former agricultural field. The + OM included municipal waste biosolids, composted wood chips, and cow manure at various application rates. We found that + OM had little influence on soil bulk density or hydric soil indicators, and resulted in the growth of undesirable vegetation and increased greenhouse gas flux. For example, manure, which contains nitrogen (N) and phosphorus (P), increased aboveground biomass but favored non-native species that lowered plant diversity and floristic quality. All + OM increased methane (CH4), but the range varied greatly (1.04–7.3 times). Hydrology also had a strong influence on CH4 emissions, and areas that experienced wet-dry cycles had 1.7–3.0 times more estimated annual CH4 emissions that those that were constantly inundated. Organic soil amendments were not necessary to support wetland plant growth or develop hydric soils, and may unnecessarily exacerbate atmospheric warming and invasive species spread.
Identification of Serotypes of Mannheimia haemolytica and Pasteurella multocida from pneumonic cases of sheep and goats and their antimicrobial sensitivity profiles in Borana and Arsi zones, Ethiopia
Authors: Girma Sisay , Getachew Latera , Beyene Ayele , Tegegne Desiye Tesfaye , Tesgera Takele , Debelo Motuma , Debano Jarso , Teshome Dereje , Abdisa Kebede , Wirtu Abebe , Tekle Muluken , Abera Birhanu , Tafess Ketema , Dandecha Morka , Abayneh Takele , Getachew Belayneh , Tufa Takele Beyene , Tolera Teshale S.. 
Published: November 2022

Abstract

Respiratory diseases caused by M. haemolytica and P. multocida have been known to result in a considerable loss due to mortality and reduced production. This study aimed at isolation and identification of M. haemolytica and P. multocida associated with pneumonic pasteurellosis in sheep and goats using bacteriological and molecular techniques. Identification of serotypes of M. haemolytica and P. multocida was done using indirect haemagglutination test (IHAT). The in vitro antimicrobial sensitivity profiles of the M. haemolytica were tested using standard disk diffusion method. A total of 52 and 78 nasal swabs were collected from pneumonic cases for bacterial isolation and identification in Borana and Arsi zone, respectively. Four hundred sera samples were collected for identification of serotypes. The results showed that 17 of 52 (32.69%; 95% CI: 20.33, 47.11) nasal swabs collected from pneumonic animals in Borana yielded positive results for Pasteurella / Mannheimia species, 13 (25.00%; 95% CI: 14.03, 38.95) of which were M. haemolytica. None of the samples yielded P. multocida. Twenty-three of 78 (29.49%; 95% CI: 19.69, 40.89) nasal swabs collected from pneumonic animals yielded positive results for M. haemolytica (17) and P. multocida (6). Secondary biochemical characterization revealed that 14 of the 17 isolates conform to M. haemolytica whereas none of the 6 isolates suspected to be P. mutocida were confirmed. Eleven (84.62%) isolates from Borana and 4 (28.57%) from Arsi were confirmed to be M. haemolytica using PCR targeting the Rpt2 genes. None of the isolates with cultural and morphological features of P. multocida gave positive results by molecular assay. Serological assay identified three serotypes of M. haemolytica namely A1, A2 and A7 almost in all of the samples whereas P. multocida serotype A was detected in 78.75% of the samples. The M. haemolytica isolates tested for susceptibility to antibiotics showed resistance against Bacitracin (83.33%) and Penicillin (50.00%) while were found susceptible to Gentamycin, Chloramphenicol and Sulfamethoxazole (100%) and Tetracycline (83.33%). In conclusion, the results of the present study revealed the association of M. haemolytica with pneumonic pasteurellosis in sheep and goats and can be of use in vaccine development in Ethiopia. Nevertheless, further investigations and continuous monitoring of antimicrobial resistance and appropriate selection and prudent use of antimicrobials in livestock sector are required.
A Genetic Algorithm for Simultaneous Route and Path Planning in a Road Network
Authors: Sakazaki Kota , Shen Tielong 
Published: November 2022

Abstract
We consider the problem of deploying a connected car, capable of V2X communication, to propagate data to groups of evacuation shelters that have lost mobile network connectivity. The problem is a combination of two subproblems: first of finding the optimal order in which the destinations should be visited, and second of finding the optimal path in a road network that allows a connected car to deliver information to all prescribed shelters. We develop a genetic algorithm with double chromosome encoding to simultaneously solve both subproblems. One chromosome encodes the solution to the routing problem, the other to the path-planning problem. Experimental results demonstrate that our algorithm is capable of finding the optimal solution with reasonable accuracy and precision.
LASSO regression combined with SVM-REF to screen the characteristic genes of pancreatic cancer and its immune correlation analysis
Authors: chen yiyang , zhou wanbang , gong yiju , ou xi 
Published: November 2022

Abstract
Background
Pancreatic cancer is a malignant tumor of the digestive tract, and its mortality, recurrence, and morbidity are still increasing year by year. At the same time, due to the lack of typical clinical manifestations in its early stage, pancreatic cancer is often diagnosed at an advanced stage.
Methods
In this study, the differential genes of pancreatic cancer and normal tissues were first analyzed from 4 datasets in the GEO database. GO function, DO disease and GSEA enrichment analysis of differential genes was performed. Screening of characteristic genes of pancreatic cancer using LASSO regression combined with SVM-REF. Differential analysis and ROC curve analysis were performed on the eigengenes. Meanwhile, another dataset from the GEO database is used for validation. Finally, differences and correlations between pancreatic cancer characteristic genes and immune cells were analyzed.
Results
90 differential genes were obtained by screening, and 6 characteristic genes of pancreatic cancer were obtained by taking the intersection of the two characteristic genes of pancreatic cancer screened by machine learning. Validation of signature genes further increases its reliability. Finally, immunoassays yielded multiple immune cells associated with pancreatic cancer signature genes.
Conclusion
The six characteristic genes of pancreatic cancer screened by the combination of LASSO regression and SVM-REF may be new biomarkers for early diagnosis and prognosis of pancreatic cancer, and may be a new potential therapeutic target for pancreatic cancer. point.