bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and evaluation of recombinant GRA8 protein for the serodiagnosis of Toxoplasma gondii infection in goats
Authors: Jirapattharasate Charoonluk , Udonsom Ruenruetai , Prachasuphap Apichai , Jongpitisub Kodcharad , Dhepakson Panadda 
Published: December 2020

Abstract
Background The development of sensitive and specific methods for detecting Toxoplasma gondii infection is critical for preventing and controlling toxoplasmosis in humans and other animals. Recently, various recombinant proteins have been used in serological tests for diagnosing toxoplasmosis. The production of these antigens is associated with live tachyzoites obtained from cell cultures or laboratory animals for genomic extraction to amplify target genes. Synthetic genes have gained a key role in recombinant protein production. For the first time, we demonstrated the production of the recombinant protein of the T. gondii dense granular antigen 8 (TgGRA8) gene based on commercial gene synthesis. Recombinant TgGRA8 plasmids were successfully expressed in an Escherichia coli system. The recombinant protein was affinity-purified and characterized via sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting. Furthermore, the diagnostic potential of the recombinant protein was assessed using 306 field serum samples from goats via indirect enzyme-linked immunosorbent assay (iELISA) and the latex agglutination test (LAT).Results Western blotting using known positive serum samples from goats identified a single antigen at the expected molecular weight of TgGRA8 (27 kDa). iELISA illustrated that 15.40% of goat samples were positive for T. gondii-specific IgG antibodies. In addition, TgGRA8 provided high sensitivity and specificity, with significant concordance (91.83) and kappa values (0.69) compared with the results obtained using LAT.Conclusion Our findings highlight the production of a recombinant protein from a synthetic TgGRA8 gene and the ability to detect T. gondii infection in field samples. The sensitivity and specificity of TgGRA8 demonstrated that this protein could be a good serological marker for detecting specific IgG in goat sera
Identification of DNA repair-related genes predicting pathogenesis and prognosis for liver cancer
Authors: Zhu Wenjing , Zhang Qiliang , Liu Min , Yan Meixing , Chu Xiao , Li Yongchun 
Published: December 2020

Abstract
Background Liver cancer (LC) is one of the most fatal cancers throughout the world. More efficient and sensitive gene signatures that could accurately predict survival in LC patients are vitally needed to promote a better individualized and effective treatment. Material/Methods 422 LC and adjacent normal tissues with both RNA-Seq and clinical data in TCGA were embedded in our study. Gene set enrichment analysis (GSEA) was applied to identify genes and hallmark gene sets that are more valuable for liver cancer therapy. Cox regression analysis was used to identify genes related to overall survival (OS) and build the prediction model. cBioPortal database was used to examine the alterations of the panel mRNA signature. ROC curves and Kaplan–Meier curves were used to validate the prediction model. Besides, the expression of the genes in the model were validated using quantitative real-time PCR in clinical tissue specimens.Results The panel of DNA repair-related mRNA signature consisted of seven mRNAs: RFC4 (replication factor C subunit 4), ZWINT (ZW10 interacting kinetochore protein), UPF3B (UPF3B regulator of nonsense mediated mRNA decay), NCBP2 (nuclear cap binding protein subunit 2), ADA (adenosine deaminase), SF3A3 (splicing factor 3a subunit 3) and GTF2H1 (general transcription factor IIH subunit 1). On-line analysis of cBioPortal database found that the expression of the panel mRNA has a wide variation ranging from 7% to 10%. All the mRNAs were significantly upregulated in LC tissues compared to normal tissues (P < 0.05). The risk model is closely related to the OS of LC patients. The hazard ratio (HR) is 2.184 (95%CI [confidence interval]:1.523-3.132) and log-rank P-value<0.0001. For clinical specimen validation, we found that all of the genes in the model upregulated in liver cancer tissues versus normal liver tissues, which was consistent with the results predicted.Conclusions Our study demonstrated a mRNA signature including seven mRNA for prognosis prediction of LC. This panel gene signature provides a new criterion for accurate diagnosis and therapeutic target of LC.
Investigating the molecular control of deer antler extract on articular cartilage
Authors: Yao Baojin , Zhou Zhenwei , Zhang Mei , Leng Xiangyang , Zhao Daqing 
Published: December 2020

Abstract
Background: Deer antler is considered as a precious traditional Chinese medicinal material, and has been widely used to reinforce kidney’s yang, nourish essence and strengthen bone function. The most prominent bioactive components in deer antler are water-soluble proteins that play potential roles in bone formation and repair. The aim of this study was to explore the molecular control and therapeutic targets of deer antler extract (DAE) on articular cartilage.Methods: DAE was prepared as previously described. All rats were randomly divided into Blank group and DAE group (10 rats per group) after 7-day adaptive feeding. The rats in DAE group were orally administrated with DAE at a dose of 0.2 g/kg per day for 3 weeks and the rats in Blank group were fed with drinking water. Total RNA was isolated from the articular cartilage of knee joints. RNA sequencing (RNA-seq) experiment combined with quantitative real-time polymerase chain reaction (qRT-PCR) verification assay were carried out to explore the molecular control and therapeutic targets of DAE on articular cartilage.Results: We demonstrated that DAE significantly increased the expression levels of functional genes involved in cartilage formation, growth and repair, and decreased the expression levels of susceptibility genes involved in the pathophysiology of osteoarthritis.Conclusions: DAE might serve as a candidate supplement for maintaining cartilage homeostasis, and preventing cartilage degeneration and inflammation. These effects were possibly achieved by accelerating the expression of functional genes involved in chondrocyte commitment, survival, proliferation and differentiation, and suppressing the expression of susceptibility genes involved in the pathophysiology of osteoarthritis. Thus, our findings will contribute towards deepening the knowledge about the molecular control and therapeutic targets of DAE on the treatment of cartilage related diseases.
Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines
Authors: Weißbach Stephan , Sys Stanislav Jur`Evic , Hewel Charlotte , Todorov Hristo , Schweiger Susann , Winter Jennifer , Pfenninger Markus , Torkamani Ali , Evans Doug , Burger Joachim , Everschor-Sitte Karin , May-Simera Helen , Gerber Susanne 
Published: December 2020

Abstract
Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform's impact.Results The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (InDels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in InDel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups.Conclusion We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies.
The German Corona Consensus Dataset (GECCO): A standardized dataset for COVID-19 research in university medicine and beyond
Authors: Sass Julian , Bartschke Alexander , Lehne Moritz , Essenwanger Andrea , Rinaldi Eugenia , Rudolph Stefanie , Heitmann Kai U. , Vehreschild Jörg J. , von Kalle Christof , Thun Sylvia 
Published: December 2020

Abstract
Background: The current COVID-19 pandemic has led to a surge of research activity. While this research provides important insights, the multitude of studies results in an increasing fragmentation of information. To ensure comparability across projects and institutions, standard datasets are needed. Here, we introduce the “German Corona Consensus Dataset” (GECCO), a uniform dataset that uses international terminologies and health IT standards to improve interoperability of COVID-19 data, in particular for university medicine. Methods: Based on previous work (e.g., the ISARIC-WHO COVID-19 case report form) and in coordination with experts from university hospitals, professional associations and research initiatives, data elements relevant for COVID-19 research were collected, prioritized and consolidated into a compact core dataset. The dataset was mapped to international terminologies, and the Fast Healthcare Interoperability Resources (FHIR) standard was used to define interoperable, machine-readable data formats. Results: A core dataset consisting of 81 data elements with 281 response options was defined, including information about, for example, demography, medical history, symptoms, therapy, medications or laboratory values of COVID-19 patients. Data elements and response options were mapped to SNOMED CT, LOINC, UCUM, ICD-10-GM and ATC, and FHIR profiles for interoperable data exchange were defined. Conclusion: GECCO provides a compact, interoperable dataset that can help to make COVID-19 research data more comparable across studies and institutions. The dataset will be further refined in the future by adding domain-specific extension modules for more specialized use cases.
Survey of Perceptions and Educational Needs of Primary Care Providers Regarding Management of Patients with Class II and III Obesity in Ontario, Canada
Authors: Zevin Boris , Martin Mary Imelda , Dalgarno Nancy , Chan Linda , Sivapalan Nardhana , Houlden Robyn , Birtwhistle Richard , Smith Karen , Barber David 
Published: December 2020

Abstract
Background: Primary care providers (PCPs) are typically the primary contact for patients with obesity seeking medical and surgical weight loss interventions; however, previous studies suggest that fewer than 7% of eligible adult patients are referred to publically funded medical and surgical weight loss interventions (MSWLI).Methods: We performed an anonymous survey study between October 2017 and June 2018 to explore the knowledge, experiences, perceptions, and educational needs of PCPs in Southeastern Ontario in managing patients with class II and III obesity. Results: Surveys were distributed to 591 PCPs (n=538 family physicians; n=53 nurse practitioners) identified as practicing in the Southeastern Ontario and 103 (15.6%) participated. PCPs serving a rural population estimated that 14.2±10.9% of patients would qualify for MSWLI compared to 9.9±8.5% of patients of PCPs serving an urban population (p=.049). Overall, 57.5% of respondents did not feel competent prescribing MSWLI to patients with class II/III obesity, while 69.8% stated they had ‘good’ knowledge of the referral criteria for MSWLI. 22.2% of respondents were hesitant to refer patients for bariatric surgery (BS) due to concerns about postoperative surgical complications and risks associated with surgery. Only 25% of respondents were comfortable providing long-term follow up after BS, and only 39.1% had participated in continuing education on management of patients with class II/III obesity in the past five years. Conclusion: The majority of PCPs believe there is a need for additional education about MSWLI for patients with class II/III obesity. Future studies are needed to develop and compare the effectiveness of additional education and professional development around risks of contemporary BS, indications to consider referral for MSWLI, management and long-term follow-up of patients after BS.
CD9 is a leukemic stem cell-specific marker in human acute myeloid leukemia
Authors: Liu Yongliang , Wang Guiqin , Zhang Jiasi , Chen Xue , Xu Huailong , Heng Gang , Chen Jun , Zhao Yongchun , Li Jiatao , Ni Yuanli , Zhang Yingzi , Shan Juanjuan , Qian Cheng 
Published: December 2020

Abstract
Background: Leukemia stem cells (LSCs) are responsible for the initiation, progressing and relapse of acute myeloid leukemia (AML). Therefore, the therapy strategy of targeting LSCs is hopeful to eradicate AML. In this study, we aimed to identify LSCs-specific surface markers and uncover the underlying mechanism of AML LSCs.Methods: Microarray gene expression data were used to investigate the candidate AML-LSCs specific markers. CD9 expression was evaluated by flow cytometry (FC) in AML cell lines, patients with AML and normal donors. The biological characteristics of CD9-positive (CD9+) cells were analyzed by in vitro proliferation, chemotherapeutic drug resistance, migration and in vivo xenotransplantation assays. The molecular mechanism involved in CD9+ cell function was investigated by gene expression profiling. Effects of alpha-2-macroglobulin (A2M) on CD9+ cells were analyzed in the aspects of proliferation, drug resistance and migration.Results：CD9, as a cell surface protein, is specifically expressed on AML LSCs, but barely can be detected on normal hematopoietic stem cells (HSCs). CD9+ cells exhibits more resistance to chemotherapy drugs and higher migration potential than CD9-negative (CD9-) cells. More importantly, CD9+ cells possess the ability to reconstitute human AML in immunocompromised mice and promote leukemia growth, suggesting CD9+ cells define the LSCs population. Furthermore, we identified A2M as an important role in CD9+ LSCs stemness maintenance. Knock down of A2M impairs drug-resistance and migration of CD9+ cells.Conclusion: Our findings suggested that CD9 is a new biomarker of AML LSCs and may serve as a promising therapeutic target.
Bile acid, glucose, lipid profile, and liver enzyme changes in prediabetic patients 1 year after sleeve gastrectomy
Authors: Mak Tsz Kin , Huang Shifang , Guan Bingsheng , Au Hoyin , Chong Tsz Hong , Peng Juzheng , Chen Fazhi , Liang Chuqiao , Lai Wanjing , Ho LongLam , Wang Cunchuan , yang jingge 
Published: December 2020

Abstract
Background: Few articles have studied individuals with prediabetes after sleeve gastrectomy. Bile acid and lipid levels remain inconsistent in postbariatric patients. The purpose of this study was to explore bile acid, glucose, lipid, and liver enzyme changes in patients with different diabetes statuses who underwent sleeve gastrectomy. The impact of bariatric surgery and its potential benefits for prediabetic patients was also discussed.Methods: A total of 202 overweight and obese patients who underwent bariatric surgery in our hospital between January 2016 and October 2018 were retrospectively reviewed. Patients were divided into prediabetes (n=32), nondiabetes (n=144), and diabetes (n=26) groups and analysed. Glucose and lipid data were collected from medical records at baseline and at each follow-up visit.Result: Significant improvements in body weight, glucose and lipid levels, and liver enzymes (P≤0.05) in prediabetic patients were found throughout the first year postoperatively. Improvement in glycaemic control was first seen one month postoperatively, followed by persistent improvement in the next 12 months. Total bile acid (TBA) decreased, which was associated with ALT improvement in prediabetic patients 1-year post-surgery. There were no significant differences in HbA1c, glucose, or triglycerides (TGs) between prediabetic and T2DM patients or between prediabetic and nondiabetic patients at 12 months post-surgery.Conclusion: LSG is highly effective at interfering with glucose and lipid levels as well as total bile acid levels in prediabetic patients in the first year postoperatively. Thus, LSG is indeed an alternative for overweight and obese prediabetic patients.
Sociodemographic, health-related, and social predictors of subjective well-being among Chinese oldest-old: a national community-based cohort study
Authors: Cheng Gang , Yan Yan 
Published: December 2020

Abstract
Background: There is still a lack of a relatively comprehensive multifactor analysis of subjective well-being (SWB) among Chinese oldest-old. This study aimed to explore sociodemographic, health-related, and social predictors of SWB among Chinese oldest-old using a large and representative sample.Methods: The study included 49,069 individuals aged 80 and older from the Chinese Longitudinal Healthy Longevity Survey, a prospective, nationwide, community-based study conducted from 1998 to 2014. SWB was measured by eight items covering life satisfaction, positive affect (optimism, happiness, personal control, and conscientiousness), and negative affect (anxiety, loneliness, and uselessness). Generalized estimating equation models were used to explore the predictors of SWB.Results: We found that age, gender, ethnic group, education, primary occupation before retirement, current marital status, and place of residence were sociodemographic predictors of SWB among the Chinese oldest-old. The health-related predictors included self-rated health, visual function, hearing function, diet quality, smoking status, drinking status, and exercise status. SWB was influenced by some social factors, such as the number of biological siblings, the number of children, leisure activities, financial independence, and access to adequate medical service. In particular, self-rated health, access to adequate medical services, exercise status, and place of residence exert a stronger effect than other factors.Conclusions: SWB in the oldest-old is influenced by a large number of complex sociodemographic, health-related, and social factors. Special attention should be paid to the mental health of centenarians, women, rural residents, widowed, physically disabled, and childless oldest-old people. Relevant agencies can improve physical activities, leisure activities, financial support, and medical services to promote the well-being of the oldest-old.
Screening of plant species for phytoremediation of synthetic textile dye wastewater
Authors: Kaur Navjeet , Kaushal Jyotsna , Mahajan Pooja , Srivas Arun Lal 
Published: December 2020

Abstract
Most of the dyes are carcinogenic and mutagenic in nature. Plants are potential candidates to remediate textile dye wastewater from contaminated sites. The present study aimed to screen potential plant species for removal of synthetic dye solution of triarylmethane dye Methylene Blue (MB) and diazo dye Congo Red (CR). The six plants selected for screening are Trachyspermum ammi (T. ammi), Tagetes erecta (T. erecta), Hibiscus rosa-sinensis (H. rosa- sinensis), Chrysanthemum indicum (C. indicum), Bryophyllum fedtschenkoi (B. fedtschenkoi), and Catharanthus roseus (C. roseus). The phytotreatment of dyes was done up to 40 h for two different concentrations of dyes i.e. 10 and 20 mg L−1. Among screened plant species, the maximum decolorization was obtained from T. ammi followed by B. fedtschenkoi. Both of these plant species showed active growth even after the phytoremediation process. T. ammi decolorized the MB dye 99 (10 mg L−1) and 86% (20 mg L−1) while the decolorization of the CR dye solution was up to 95 (10 mg L−1) and 84% (20 mg L−1). T. ammi found to have maximum potential among screened plants for the removal of MB and CR dye from synthetic dye solution and can be used for phytoremediation of wastewater contaminated with synthetic dyes.
Exploring Equity and Inclusion in Malawi’s National Disability Mainstreaming Strategy and Implementation Plan
Authors: Ebuenyi Ikenna D , Smith Emma M. , Munthali Alister , Msowoya Steven W. , Kafumba Juba , Jamali Monica Z. , MacLachlan Malcolm 
Published: December 2020

Abstract
Background: Equity and inclusion are important principles in policy development and implementation. The aim of this study is to explore the extent to which equity and inclusion were considered in the development of Malawi’s National Disability Mainstreaming Strategy and Implementation Plan. Methods: We applied an analytical methodology to review the Malawi’s National Disability Mainstreaming Strategy and Implementation Plan using the EquIPP (Equity and Inclusion in Policy Processes) tool. The EquIPP tool assesses 17 Key Actions to explore the extent of equity and inclusion. Results: The development of the Malawi National Disability Mainstreaming Strategy and Implementation Plan was informed by a desire to promote the rights, opportunities and wellbeing of persons with disability in Malawi. The majority (58%) of the Key Actions received a rating of three, indicating evidence of clear, but incomplete or only partial engagement of persons with disabilities in the policy process. Three (18%) of the Key Actions received a rating of four indicating that all reasonable steps to engage in the policy development process were observed. Four (23%) of the Key Actions received a score five indicating a reference to Key Action in the core documents in the policy development process. Conclusion: The development of disability policies and associated implementation strategies requires equitable and inclusive processes that consider input from all stakeholders especially those whose wellbeing depend on such policies. It is pivotal for government and organisations in the process of policy or strategy development and implementation, to involve stakeholders in a virtuous process of co-production – co-implementation – co-evaluation, which may strengthen both the sense of inclusion and the effectiveness of the policy life-cycle.