bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes
Authors: Peng Jiao , Zhao Yunlin , Dong Meng , Liu Shiquan , Hu Zhiyuan , Zhong Xiaofen , Xu Zhenggang 
Published: July 2020

Abstract
Background: The cultivated tea is one of the most important economic and ecological trees distributing worldwide. The cultivated tea suffered from long-term targeted selection of traits and overexploitation of habitats by human beings, which may change the genetic structure. Chloroplast is an organelle with a conserved cyclic structure, and can help us better understand the evolutionary relationship of Camellia plants.Results: The study conducted comparative analysis and evolution analysis between cultivated tea and wild tea, and detected the evolution characteristic in cultivated tea. Chloroplast genome sizes of cultivated tea were slightly different, ranged from 157,025 bp to 157,085 bp. These cultivated species were more conservative than wild species, in terms of the genome length, genes number, genes arrangement and GC contents. However, the IRs length of cultivated species was about 20 bp shorter than that of C. sinensis var. sisnensis. We also found that the nucleotide diversity of 14 sequences in cultivated tea was higher than that of wild tea. These results provided the evidence on the variation of chloroplast genomes of cultivated tea. Detail analysis on the chloroplast genome variation and evolution of cultivated tea showed that 67 SNPs and 46 indels and 16 protein coding genes had nucleotide substitutions. The most comment variation gene was ycf1. It has the largest number of nucleotide substitutions. At the same time, in ycf1, five amino acid sites were exhibiting site-specific selection, and a 9 bp sequence insertion was found in the C. sinensis cultivar. Anhua. The phylogenetic tree constructed by ycf1 sequence shows that two cultivated tea were not completely clustered, and the evolutionary relationship between C. sinensis var. sisnensis and C. sinensis cultivar. Longjing is closer than that of C. sinensis cultivar. Anhua.Conclusions: The cultivated species were more conservative than wild species in terms of architecture and linear sequence order. The variation of chloroplast genome of cultivated tea was mainly manifested in the nucleotide polymorphism of some sequences. The ycf1 gene played an important role in the adaptive evolution of cultivated tea. These results provided evidence regarding the influence of human activities on tea.
Examining the quality of record linkage process using nationwide Brazilian administrative databases to build a large birth cohort
Authors: Almeida Daniela , Gorender David , Ichihara Maria Yury , Sena Samila , Menezes Luan , Barbosa George C. G. , Fiaccone Rosimeire L. , Paixao Enny , Pita Robespierre , Barreto Mauricio L. 
Published: July 2020

Abstract
Background : Research using linked routine population-based data collected for non-research purposes has increased in recent years because they are a rich and detailed source of information. The objective of this study is to present an approach to prepare and link data from administrative sources in a middle-income country, to estimate its quality and to identify potential sources of bias by comparing linked and no-linked case. Methods: We linked two administrative datasets with data covering the period 2001 to 2015, using maternal attributes (name, age, date of birth, and municipally of residence) from Brazil: live birth information system and the 100 Million Brazilian Cohort (created using administrative records from over 114 million individuals whose families applied for social assistance via the Unified Register for Social Programmes) implementing an in house developed linkage tool CIDACS-RL. We then estimated the proportion of highly probably link and examined the characteristics of missed-matches to identify any potential source of bias. Results: A total of 27,699,891 live births linked with maternal information recorded in the baseline of the 100 Million Brazilian Cohort dataset of those, 16,447,414 (59.4%) children were found registered in the 100 Million Brazilian Cohort dataset. The proportion of highly probably link ranged from 39.3% in 2001 to 82.1% in 2014. A substantial improvement in the linkage after the introduction of maternal date of birth attribute, in 2011, was observed. Our analyses indicated a slightly higher proportion of missing data among missed matches and a higher proportion of people living in an urban area and self-declared as Caucasian among linked pairs when compared with non-linked sets. Discussion: We demonstrated that CIDACS-RL is capable of performing high quality linkage even with a limited number of common attributes, using indexation as a blocking strategy in larg e routine databases from a middle-income country. However, residual records occurred more among people under worse living conditions. The results presented in this study reinforce the need of evaluating linkage quality and when necessary to take linkage error into account for the analyses of any generated dataset.
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.
Authors: Dissanayake Duminda S.B. , Holleley Clare , Hill Laura , O’Meally D. , Deakin J. , Georges Arthur 
Published: July 2020

Abstract
Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results: We generated 96.7 x 10 9 150 bp paired-end genomic sequence reads from a XY male and 81.4 x 10 9 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions: The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi . Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
Transcriptome-based Selection and Validation of Optimal House-keeping Genes for Skin Research in Goats (Capra hircus)
Authors: Zhang Jipan , Deng Chengchen , Li Jialu , Zhao Yong-Ju 
Published: July 2020

Abstract
Background : In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat ( Capra hircus ) is an economically important livestock species and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology. Results: Based on the transcriptome dataset of 39 goat skin tissue samples, 8 genes ( SRP68 , NCBP3 , RRAGA , EIF4H , CTBP2 , PTPRA , CNBP , and EEF2 ) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes ( ACTB and GAPDH ) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was shown that NCBP3+SDHA+PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released. Conclusion: This study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3+SDHA+PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.
Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites
Authors: Song Jiali , Chen Changming , Zhang Shuanglin , Wang Juntao , Huang Zhubin , Chen Muxi , Cao Bihao , Zhu Zhangsheng , Lei Jianjun 
Published: July 2020

Abstract
Background: ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results: In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion: This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.
The Prevalence of Pathogenic Bacteria from Different Clinical Samples, Northern Part of Iraq.
Authors: MIYASAR ALLAA 
Published: July 2020

Abstract
Background Bacteria are prokaryotic which causes a wide range of diseases in human and animals as well, thus, early diagnosis of bacterial infection is an important step for their management. The vast majority of bacteria are harmless to human and some strains are even beneficial. However, some strains cause infections including pneumonia, meningitis and urinary tract infection…etc. The present study aimed to describe and determine the prevalence rate of pathogenic bacteria in different clinical samples from Duhok city, Kurdistan region of Iraq, as there are no available data of bacterial infections.Methods Totally, 200 adult patients enrolled in the present study during July 2017-July 2018. We collected different clinical specimens including (SFA, Bronchial Lavage, catheter, cerebrospinal fluid, body fluids, blood, semen, stool pus, urine, sputum and ear swabs). Standard microbiological techniques used for isolation and identification. All samples collected before antibiotic uses by specialized physician.Results The result reported that forty-six samples (23%) obtained from male and one hundred fifty-four samples (77%) obtained from females. A high diversity of pathogens was found but Staphylococcus aureus recorded the highest infection rate by (33.3%) which observed in 32 urine samples by and followed by E. coli (27.3%) and Coagulase-Negative Staphylococci (25.3%), which observed in 36 and 29 urine samples, respectively. Alternatively, Klebsiella, Streptococcus, Enterobacteriaceae and Pseudomonas aeruginosa were founded in few samples.Conclusion The highest diversity of potential pathogens observed in urine samples was E.coi. Over all, Staphlococcus aureus was predominant and recorded the highest prevalence rate by (33.3%) in 50 samples which followed by E. coli recorded in 41 samples (27.3%) and Coagulase-Negative Staphylococci observed in 38 samples (25.3%).
Molecular epidemiology and risk factors of Stenotrophomonas maltophilia infections in a Chinese teaching hospital
Authors: Duan Zhongliang , Qin Juanxiu , Liu Yao , Li Cui , Ying Chunmei 
Published: July 2020

Abstract
Background: Stenotrophomonas maltophilia ( S. maltophilia ) is an important opportunistic pathogen obtained in hospitals. With the abuse of broad spectrum antibiotics and invasive surgical devices, the rate of S . maltophilia infections is increasing every year. This study is an epidemiological analysis of the clinical and molecular characteristics of S . maltophilia infections in a Chinese teaching hospital. The goal is to obtain a comprehensive understanding of the status of S . maltophilia infections in order to provide strong epidemiological data for the prevention and treatment of S . maltophilia infections. Results: A total of 93 isolates from the Renji Hospital were included, in which 81 isolates were cultured from sputum samples, and 86 patients had underlying diseases. All of the patients had received antibiotic therapeutics. The multilocus sequence typing (MLST) analysis indicated that 61 different sequence types (STs) were found (including 45 novel STs), and the MLST did not show significantly dominant STs. The resistant rates to Trimethoprim/sulfamethoxazole (TMP/SMX) and levofloxacin were 9.7% and 4.3%. All of the strains were susceptible to minocycline. The positive rates of the four virulence genes Stmpr1 , Stmpr2 , Smf-1 , and Smlt3773 locus were 79.6%, 91.4%, 94.6% and 52.7%, respectively. The positive rates of the three biofilm genes rmlA , spgM, and rpfF were 82.8%, 92.5%, and 64.5%, respectively. The mean biofilm forming level of OD 492 was 0.54 ± 0.49, and there was no significant difference between different genders and age groups. Data from patients in the intensive care unit (ICU) and the control group were analyzed, and the independent risk factors of those who were infected in the ICU included immunosuppression and the increased of the use of antibiotics. Conclusions : Most of the patients had prior medical usage histories and baseline diseases. The carrying rate of virulence genes was high, the drug resistance rate of S . maltophilia was low, and the biofilm formation ability was strong. The increased use of antibiotics was an independent risk factor for S . maltophilia infection, which should receive more attention. No obvious clonal transmission was found in the same department.
Consolidating strategic information to monitor progress against the UNAIDS 90-90-90 targets: evaluating the operational feasibility of an electronic HIV testing register in Cape Town, South Africa
Authors: Jacob Nisha , Rice Brian , Kalk Emma , Heekes Alexa , Morgan Jennie , Brinkmann Samantha , Hargreaves James , Orgill Marsha , Boulle Andrew 
Published: July 2020

Abstract
Background HIV diagnosis in South Africa is based on a point-of-care testing (PoCT) algorithm with paper-based record-keeping. Aggregated testing data are reported routinely. To facilitate improved HIV case-based surveillance, the Western Cape Province implemented a unique pilot intervention to digitise PoCT results, at an individual level, and generate an electronic register using the newly developed Provincial Health Data Centre (PHDC). We describe the intervention (phased) and present an evaluation of the operational feasibility of the intervention. We also offer implementation insights into establishing electronic capture of individual level testing data. Methods Cross-sectional analyses were conducted on records of all patients attending a local Community Health Centre who had an HIV-PoCT during the study period. Data from the intervention were linked to the PHDC using a unique identifier and compared with aggregate data from the paper-based register. Correlation coefficients were calculated to quantify the correlation between the two monthly datasets. To support an understanding of the findings, the Department of Health project management team generated reflections on the implementation process, which were then grouped thematically into implementation lessons. Results In total, 11 337 PoCT records were digitised (70% (7954) during Phase I; and 30% (3383) during Phase II). Linkage of forms to the PHDC was 96% in Phase I and 98% in Phase II. Comparison with aggregate data showed high correlation during Phase I, but notable divergence during Phase II. Divergence in Phase II was due to stringent data quality requirements and high clinical staff turnover. Factors supporting implementation success in Phase I included direct oversight of data capturing by a manager with clinical and operational insight. Implementation challenges included operational, health system, and high cost-related issues. Conclusions We demonstrate that rapid digitisation of HIV PoCT data, without compromising currently collected aggregate data, is operationally feasible, and can contribute to person-level longitudinal HIV case-based surveillance. To take to scale, we will need to improve PoCT platforms and clerical and administrative systems. Although we highlight challenges, we demonstrate that electronic HIV testing registers can successfully replace manual registers and improve efforts to monitor and evaluate HIV testing strategies.
Albumin-bound paclitaxel and gemcitabine combination therapy in soft tissue sarcoma
Authors: Tian Zhichao , Zhang Fan , Li Po , Wang Jiaqiang , Yang Jinpo , Zhang Peng , Yao Weitao , Wang Xin 
Published: July 2020

Abstract
Background: The evidence that albumin-bound paclitaxel (nab-paclitaxel) is safe and efficacious for the treatment of many types of malignant tumors is continuously increasing. However, the clinical data and evidence of nab-paclitaxel and gemcitabine in metastatic soft tissue sarcoma (STS) treatment are rare.Methods: The data of 17 patients with metastatic STS who received nab-paclitaxel/ gemcitabine chemotherapy between January 2019 and February 2020 were retrospectively reviewed. All patients were treated with nab-paclitaxel/ gemcitabine only after doxorubicin-based chemotherapy had failed. We evaluated the median progression-free survival (m-PFS), disease control rate (DCR), objective response rate (ORR) and adverse events (AEs) in these patients. Results: The m-PFS was 6 months (95% CI, 2–9 months), ORR was 41.2% and DCR was 70.6%. The average change in target lesion diameter from baseline was -19.06±45.74%. While the majority of the treatment patients experienced grade 1 or 2 AEs, grade 3 or 4 AEs were not common, but included neutropenia (17.6%), fatigue (11.8%), anemia (11.8%), leukopenia (11.8%), nausea (5.9%), peripheral neuropathy (5.9%), diarrhea (5.9%), and thrombocytopenia (5.9%). No treatment-related deaths occurred. Conclusion: Nab-paclitaxel/ gemcitabine combination chemotherapy is comparatively effective in the treatment of STS, demonstrates low toxicity, and is worthy of further study.
PM2.5 exposure induced renal injury via the activation of the autophagic pathway in the rat and HK-2 cell
Authors: Huang Xiaoliu , Zhou Zhitong , Liu Xinwen , Li Jue , Zhang Lijuan 
Published: July 2020

Abstract
Background: Exposure to airborne fine particulate matter (PM2.5) has been declared to be harmful to human kidney. However, whether activation of the autophagic pathway plays key roles in the nephrotoxicity caused by PM2.5 exposure is still poorly understood. The aim of this study was to explore the mechanism of kidney damage after PM2.5 exposure in vivo and in vitro.Results: In the present study, statistically significant alterations in water intake, urine flow rate and mean blood pressure were observed between the concentrated PM2.5 (PM2.5) group and the filtered air (FA) group. Exposed animals showed severe edema of renal tubular epithelial cells, capillary congestion, reduction of the glomerular urinary space and early pro-fibrotic state. Moreover, significant increases in the levels of early kidney damage markers were observed in the exposed rats and these animals exhibited more apoptosis rate in kidney cells. In addition, PM2.5 exposure activated the autophagic pathway, as evidenced by LC3-I to LC3-II conversion, activation of P62 and beclin-1. All of these effects are in concurrence with the presence of more autophagosomes both in vivo and in vitro after PM2.5 exposure. Conclusions: Taken together, our findings indicated that PM2.5-induced renal function impairment via the activation of the autophagic pathway in renal tubular epithelial cells.