bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes following acute poor-grade aneurysmal subarachnoid bleed – Is early definitive treatment better than delayed management?
Authors: Gittins Adam , Talbott Nick , Gilani Ahmed A , Packer Greg , Browne Richard , Mullhi Randeep , Khan Zaheed , Whitehouse T , Belli Antonio , Mehta Rajnikant L , Gao-Smith Fang , Veenith Tonny 
Published: September 2020

Background/objective Patients with poor-grade subarachnoid bleed (World Federation of Neurosurgical Societies grades 4–5) often improve their neurocognitive function months after their ictus. However, it is essential to explore the timing of intervention and its impact on long-term outcome. We compared the long-term outcomes between immediate management within 24 h and delayed management after 24 h in patients following poor-grade subarachnoid bleed. Methods This was a retrospective population-based study, including patients with poor-grade subarachnoid bleed who received definitive management between 1 January 2011 and 31 December 2016 in a large tertiary neurocritical care unit. The primary outcome was adjusted odds ratio of favourable outcome (Glasgow Outcome Scale 4–5) for survivors at 12 months following discharge, as measured by the Glasgow Outcome Scale. The secondary outcomes included adjusted odds ratio of a favourable outcome at discharge, 3 months and 6 months following discharge and survival rate at 28 days, 3 months, 6 months and 12 months following haemorrhage. Results A total of 111 patients were included in this study: 53 (48%) received immediate management and 58 (52%) received delayed management. The mean time delay from referral to intervention was 14.9 ± 5.8 h in immediate management patients, compared to 79.6 ± 106.1 h in delayed management patients. At 12 months following discharge, the adjusted odds ratio for favourable outcome in immediate management versus delayed management patients was 0.96 (confidence interval (CI) = 0.17, 5.39; p = 0.961). At hospital discharge, 3 months and 6 months, the adjusted odds ratio for favourable outcome was 3.85 (CI = 1.38, 10.73; p = 0.010), 1.04 (CI = 0.22, 5.00; p = 0.956) and 0.98 (CI = 0.21, 4.58; p = 0.982), respectively. There were no differences in survival rate between the groups at 28 days, 3 months, 6 months and 12 months (71.7% in immediate management group vs. 82.8% in delayed management group at 12 months, p = 0.163). Conclusions Immediate management and delayed management after poor-grade subarachnoid bleed are associated with similar morbidity and mortality at 12 months. Therefore, delaying intervention in poor-grade patients may be a reasonable approach, especially if time is needed to plan the procedure or stabilise the patient adequately.
Zinc ameliorates lead toxicity by reducing body Pb burden and restoring Pb-induced haematological and biochemical derangements
Authors: Ugwuja Emmanuel Ike , Vincent Nweze , Ikaraoha Ikechukwu C , Ohayi Samuel R 
Published: September 2020

Background: Studies on nutritional factors, including zinc in ameliorating the deleterious effects of potentially toxic elements have been scarce and the findings have been inconsistent. Aim: The aim of the present study was to evaluate the ameliorative potential of zinc against lead-induced toxicity in rats. Materials and methods: Male albino rats (n = 24) assigned into four groups of six/group: normal control (NC), zinc control (ZnC; 20 mg/kg ZnCl2), lead control (PbC; 50 mg/kg PbCl2) and lead plus zinc (Pb + Zn; 50 mg/kg PbCl2 plus 20 mg/kg ZnCl2), respectively were investigated. All administrations were through oral route and lasted for 42 days after which blood samples were collected for haematological and biochemical analyses using standard techniques. Results: Results showed that packed cell volume (PCV), haemoglobin concentration (HBC), red blood cell count (RBC) were significant (p < 0.05) reduced while total white blood cell count (TWBC), mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC) and platelets were significantly elevated in PbC group in comparison with NC and ZnC. Also liver and renal function parameters as well as the liver and kidney malondialdehyde (MDA) were elevated while antioxidant enzymes; catalase (CAT) and superoxide dismutase (SOD) were significantly (p < 0.05) reduced in PbC group in comparison with NC and ZnC. Concentrations of lead were in the order: blood > liver > kidney in the PbC group. In addition to restoration of the altered parameters, administration of zinc in Pb + Zn group significantly reduced the raised lead concentrations in the plasma and organs. Conclusion: Reduction in body Pb burden and restoration of Pb-induced derangements in haematological and biochemical parameters by Zn strongly support the ameliorative property of Zn against Pb-induced toxicity.
Allergen inhalation generates pro-inflammatory oxidised phosphatidylcholine associated with airway dysfunction
Authors: Pascoe Christopher D. , Jha Aruni , Ryu Min Hyung , Ragheb Mirna , Vaghasiya Jignesh , Basu Sujata , Stelmack Gerald L. , Srinathan Sadeesh , Kidane Biniam , Kindrachuk Jason , O'Byrne Paul M. , Gauvreau Gail M. , Ravandi Amir , Carlsten Christopher , Halayko Andrew J. 
Published: September 2020

Oxidised phosphatidylcholines (OxPCs) are produced under conditions of elevated oxidative stress and can contribute to human disease pathobiology. However, their role in allergic asthma is unexplored. The aim of this study was to characterise the OxPC profile in the airways after allergen challenge of people with airway hyperresponsiveness (AHR) or mild asthma. The capacity of OxPCs to contribute to pathobiology associated with asthma was also to be determined.Using bronchoalveolar lavage fluid from two human cohorts, OxPC species were quantified using ultra-high performance liquid chromatography-tandem mass spectrometry. Murine thin-cut lung slices were used to measure airway narrowing caused by OxPCs. Human airway smooth muscle (HASM) cells were exposed to OxPCs to assess concentration-associated changes in inflammatory phenotype and activation of signalling networks.OxPC profiles in the airways were different between people with and without AHR and correlated with methacholine responsiveness. Exposing patients with mild asthma to allergens produced unique OxPC signatures that associated with the severity of the late asthma response. OxPCs dose-dependently induced 15% airway narrowing in murine thin-cut lung slices. In HASM cells, OxPCs dose-dependently increased the biosynthesis of cyclooxygenase-2, interleukin (IL)-6, IL-8, granulocyte−macrophage colony-stimulating factor and the production of oxylipinsviaprotein kinase C-dependent pathways.Data from human cohorts and primary HASM cell culture show that OxPCs are present in the airways, increase after allergen challenge and correlate with metrics of airway dysfunction. Furthermore, OxPCs may contribute to asthma pathobiology by promoting airway narrowing and inducing a pro-inflammatory phenotype and contraction of airway smooth muscle. OxPCs represent a potential novel target for treating oxidative stress-associated pathobiology in asthma.
“METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI’s sequence read archive”
Authors: Quiñones Mariam , Liou David T. , Shyu Conrad , Kim Wongyu , Vujkovic-Cvijin Ivan , Belkaid Yasmine , Hurt Darrell E. 
Published: September 2020

Abstract
Background
The improvements in genomics methods coupled with readily accessible high-throughput sequencing have contributed to our understanding of microbial species, metagenomes, infectious diseases and more. To maximize the impact of these genomics studies, it is important that data from biological samples will become publicly available with standardized metadata. The availability of data at public archives provides the hope that greater insights could be obtained through integration with multi-omics data, reproducibility of published studies, or meta-analyses of large diverse datasets. These datasets should include a description of the host, organism, environmental source of the specimen, spatial-temporal information and other relevant metadata, but unfortunately these attributes are often missing and when present, they show inconsistencies in the use of metadata standards and ontologies.

Results
METAGENOTE (https://metagenote.niaid.nih.gov) is a web portal that greatly facilitates the annotation of samples from genomic studies and streamlines the submission process of sequencing files and metadata to the Sequence Read Archive (SRA) (Leinonen R, et al, Nucleic Acids Res, 39:D19-21, 2011) for public access. This platform offers a wide selection of packages for different types of biological and experimental studies with a special emphasis on the standardization of metadata reporting. These packages follow the guidelines from the MIxS standards developed by the Genomics Standard Consortium (GSC) and adopted by the three partners of the International Nucleotides Sequencing Database Collaboration (INSDC) (Cochrane G, et al, Nucleic Acids Res, 44:D48-50, 2016) - National Center for Biotechnology Information (NCBI), European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). METAGENOTE then compiles, validates and manages the submission through an easy-to-use web interface minimizing submission errors and eliminating the need for submitting sequencing files via a separate file transfer mechanism.

Conclusions
METAGENOTE is a public resource that focuses on simplifying the annotation and submission process of data with its corresponding metadata. Users of METAGENOTE will benefit from the easy to use annotation interface but most importantly will be encouraged to publish metadata following standards and ontologies that make the public data available for reuse.
Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana
Authors: Chu Duan , Wei Lai 
Published: September 2020

AbstractBackgroundC-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at genome-wide level, the cis and trans determinants affecting the occurrence or editing levels of these C-to-U events are relatively less studied. What is known is that the PPR (pentatricopeptide repeat) proteins are the main trans-regulatory elements responsible for the C-to-U conversion, but other determinants especially the cis-regulatory elements remain largely uninvestigated.ResultsBy analyzing the transcriptome and translatome data inArabidopsis thalianaroots and shoots, combined with RNA-seq data from hybrids ofArabidopsis thalianaandArabidopsis lyrata, we perform genome-wide investigation on the cis elements and trans-regulatory elements that potentially affect C-to-U editing events. An upstream guanosine or double-stranded RNA (dsRNA) regions are unfavorable for editing events. Meanwhile, many genes including the transcription factors may indirectly play regulatory roles in trans.ConclusionsThe 5-prime thymidine facilitates editing and dsRNA structures prevent editing in cis. Many transcription factors affect editing in trans. Although the detailed molecular mechanisms underlying the cis and trans regulation remain to be experimentally verified, our findings provide novel aspects in studying the botanical C-to-U RNA editing events.
Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape
Authors: Wang Huiling , Yan Ailing , Sun Lei , Zhang Guojun , Wang Xiaoyue , Ren Jiancheng , Xu Haiying 
Published: September 2020

Abstract
Background
Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, the information about their genetic mechanisms is limited, which results in low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits.

Results
In the present work, a final integrated map consisting of 3411 SLAF markers on 19 linkage groups (LGs) with an average distance of 0.98 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. A total of 9 significant stable QTLs for Muscat flavor, berry firmness and berry shape were identified on two linkage groups among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new stable QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes (VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350) related to berry firmness and 3 genes (VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200) linked to berry shape were highlighted. Overexpression of VIT_08s0032g01110 in transgenic Arabidopsis plants caused the change of pod shape.

Conclusions
A new high-density genetic map with total 3411 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine. VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350 were found to be related to berry firmness, while VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200 were linked to berry shape.
A new randomization procedure based on multiple covariates and applicable to parallel studies with simultaneous enrollment of all subjects prior to intervention
Authors: Schoen Eric D. , Wopereis Suzan 
Published: September 2020

AbstractBackgroundParallel intervention studies involving volunteers usually require a procedure to allocate the subjects to study-arms. Statistical models to evaluate the different outcomes of the study-arms will include study-arm as a factor along with any covariate that might affect the results. To ensure that the effects of the covariates are confounded to the least possible extent with the effects of the arms, stratified randomization can be applied. However, there is at present no clear-cut procedure when there are multiple covariates.MethodsFor parallel study designs with simultaneous enrollment of all subjects prior to intervention, we propose a D-optimal blocking procedure to allocate subjects with known values of the covariates to the study arms. We prove that the procedure minimizes the variances of the baseline differences between the arms corrected for the covariates. The procedure uses standard statistical software.ResultsWe demonstrate the potential of the method by an application to a human parallel nutritional intervention trial with three arms and 162 healthy volunteers. The covariates were gender, age, body mass index, an initial composite health score, and a categorical indicator called first-visit group, defining groups of volunteers who visit the clinical centre on the same day (17 groups). Volunteers were allocated equally to the study-arms by the D-optimal blocking procedure. The D-efficiency of the model connecting an outcome with the study-arms and correcting for the covariates equals 99.2%. We simulated 10,000 random allocations of subjects to arms either unstratified or stratified by first-visit group. Intervals covering the middle 95% of the D-efficiencies for these allocations were [82.0, 92.0] and [93.2, 98.4], respectively.ConclusionsAllocation of volunteers to study-arms with a D-optimal blocking procedure with the values of the covariates as inputs substantially improves the efficiency of the statistical model that connects the response with the study arms and corrects for the covariates.Trial registrationDutch Trial Register NL7054 (NTR7259). Registered May 15, 2018.
Smart home for elderly care: development and challenges in China
Authors: Zhang Quan , Li Meiyu , Wu Yijin 
Published: September 2020

Abstract
Background
China’s smart home for elderly care emerged in 2008, and had went through four developmental stages which consists of seed stage, start-up stage, development stage and popularization stage.

Main text
The status quo and development of smart home for elderly care in China is reviewed, and suggestions are provided on how to further develop China’s smart home for elderly care. The focus of China’s policies on smart home for elderly care were different during those four developmental stages. Compared with Western countries, China’s smart home for elderly care is a policy-driven product rather than technology-driven or demand-driven one. In addition, it is quasi-public goods rather than private goods. These unique characteristics of China’s smart home for elderly care not only become the driving force of its rapid development, but also bring many challenges to its development, such as the insufficient demand, the disorderly development, and the waste of public and private resources.

Conclusions
Although great progress has been made in China’s smart home care, much efforts are still needed to further advance its development. The technical standards for the elderly care services should be formulated as soon as possible and the existing public and private smart home for elderly care platforms should be combined. Enterprises involved in smart home care services should be encouraged to develop new technologies to reduce the cost of products and services provided by smart home for elderly care.
A novel Cys328-terminator mutant implicated in severe coagulation factor XIII deficiency: a case report
Authors: Cai Ruimin , Li Yi , Wang Wenyang , Feng Qiang 
Published: September 2020

Abstract
Background
Factor XIII (FXIII) deficiency is an extremely rare bleeding disorder that is commonly due to mutations in the FXIIIA subunit gene (F13A1), and it has been reported to have a prevalence of one per 2 million. We describe a new genetic variant in the F13A1 gene that caused a patient to suffer from lifelong hemorrhagic diathesis.

Case presentation
We evaluated a 20-year-old female with umbilical cord bleeding after birth, an intracerebral hemorrhage at age 6, and other bleeding episodes, including hematuria and cephalohematoma, who suffered from a lifelong hemorrhagic diathesis. The clot solubility test showed that the clot of the patient was dissolved in urea solution at 10 h. Genetic testing identified a novel homozygous mutation, c.984C > A(p. Cys328stop), resulting in a premature stop codon in exon 8 of the F13A1 gene. The results obtained with ClusterX software showed that Cys328 of exon 8 in the F13A1 gene is highly conserved among species.

Conclusion
We reported a novel homozygous mutation in the F13A1 gene in a factor XIII (FXIII)-deficient patient, which adds a new point mutation to the mutant library. In this paper, we discuss other aspects of the disease, including laboratory examination, homogeneous sequence alignment and molecular modeling.
Metastatic renal cell carcinoma patients of T4 stage who are in status of N1 stage or older than 76 years cannot benefit from cytoreductive nephrectomy
Authors: Zhang Zhao , Wu Hongliang , Yang Tong , Wu Yaohai , Yu Nengwang , Xu Zhonghua 
Published: September 2020

Abstract
Background
We aimed to identify which part of the patients with metastatic renal cell carcinoma (mRCC) is not suitable for cytoreductive nephrectomy (CN).

Methods
The data of mRCC patients was acquired from the Surveillance, Epidemiology, and End Results (SEER) database. Multivariate cox regression analysis and nomogram were performed for selecting factors independently associated with survival. Propensity score matching (PSM) was applied to reduce potential bias when comparing survival of mRCC patients treated by CN or non-surgery (NS). The survival analysis of subgroups was estimated by the Kaplan–Meier method and compared by log-rank testing. The summary of subgroup analysis was showed by forest plots.

Results
The records of 21,411 patients with mRCC were obtained from the SEER database. After screening, a total of 6532 patients were included for further analysis, of which 6043 underwent CN and 489 underwent NS. Age, T stage, N stage and tumor size were involved in subgroup analysis by PSM according to the result of multivariate cox regression analysis and clinical experience. Survival benefit was not found in T4 stage patients. Further analysis showed that T4&N1 and T4&age ≥ 76 yr subgroups could not obtain survival benefit from CN.

Conclusion
CN should not be performed in T4 stage mRCC patients who were in status of N1 stage or older than 76 years, because surgery cannot take significant survival benefit for them.
Ecological factors associated with suicide mortality among non-Hispanic whites
Authors: Graetz Nick , Preston Samuel H. , Peele Morgan , Elo Irma T. 
Published: September 2020

Abstract
Background
In this paper, we examine the ecological factors associated with death rates from suicide in the United States in 1999 and 2017, a period when suicide mortality increased in the United States. We focus on Non-Hispanic Whites, who experienced the largest increase in suicide mortality. We ask whether variation in suicide mortality among commuting zones can be explained by measures of the social and economic environment and access to lethal means used to kill oneself in one’s area of residence.

Methods
We use vital statistics data on deaths and Census Bureau population estimates and define area of residence as one of 704 commuting zones. We estimate separate models for men and women at ages 20–64 and 65 and above. We measure economic environment by percent of the workforce in manufacturing and the unemployment rate and social environment by marital status, educational attainment, and religious participation. We use gun sellers and opioid prescriptions as measures of access to lethal means.

Results
We find that the strongest contextual predictors of higher suicide mortality are lower rates of manufacturing employment and higher rates of opiate prescriptions for all age/sex groups, increased gun accessibility for men, and religious participation for older people.

Conclusions
Socioeconomic characteristic and access to lethal means explain much of the variation in suicide mortality rates across commuting zones, but do not account for the pervasive national-level increase in suicide mortality between 1999 and 2017.