bluuebunny/crossref_metadata_2025_split huggingface dataset:
SynBioTools: a one-stop facility for searching and selecting synthetic biology tools
Authors: Cai Pengli , Liu Sheng , Zhang Dachuan , Xing Huadong , Han Mengying , Liu Dongliang , Gong Linlin , Hu Qian-Nan 
Published: April 2023

Abstract
Background
The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology.

Results
We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users’ understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system.

Conclusions
SynBioTools is freely available at https://synbiotools.lifesynther.com/. It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.
Using RNA-seq to identify suitable housekeeping genes for hypoxia studies in human adipose-derived stem cells
Authors: Ong Huan Ting , Prêle Cecilia M. , Dilley Rodney J. 
Published: April 2023

Abstract
Background
Hypoxic culture conditions have been used to study the impact of oxygen deprivation has on gene expression in a number of disease models. However, hypoxia response elements present in the promoter regions of some commonly used housekeeping genes, such as GAPDH and PGK1, can confound the relative gene expression analysis. Thus, there is ongoing debate as to which housekeeping gene is appropriate for studies investigating hypoxia-induced cell responses. Specifically, there is still contradicting information for which housekeeping genes are stable in hypoxia cultures of mesenchymal stem cells. In this study, candidate housekeeping genes curated from the literature were matched to RNAseq data of normoxic and hypoxic human adipose-derived stem cell cultures to determine if gene expression was modulated by hypoxia or not. Expression levels of selected candidates were used to calculate coefficient of variation. Then, accounting for the mean coefficient of variation, and normalised log twofold change, genes were ranked and shortlisted, before validating with qRT-PCR. Housekeeping gene suitability were then determined using GeNorm, NormFinder, BestKeeper, comparative$$\Delta Ct$$

Δ
C
t

, RefFinder, and the Livak method.

Results
Gene expression levels of 78 candidate genes identified in the literature were analysed in the RNAseq dataset generated from hADSC cultured under Nx and Hx conditions. From the dataset, 15 candidates with coefficient of variation ≤ 0.15 were identified, where differential expression analysis results further shortlisted 8 genes with least variation in expression levels. The top 4 housekeeping gene candidates, ALAS1, RRP1, GUSB, and POLR2B, were chosen for qRT-PCR validation. Additionally, 18S, a ribosomal RNA commonly used as housekeeping gene but not detected in the RNAseq method, was added to the list of housekeeping gene candidates to validate. From qRT-PCR results, 18S and RRP1 were determined to be stably expressed in cells cultured under hypoxic conditions.

Conclusions
We have demonstrated that 18S and RRP1 are suitable housekeeping genes for use in hypoxia studies with human adipose-derived stem cell and should be used in combination. Additionally, these data shown that the commonly used GAPDH and PGK1 are not suitable housekeeping genes for investigations into the effect of hypoxia in human adipose-derived stem cell.
Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.)
Authors: Kahie Mohamed Ali , Wang Yongjun , Fang Pingping , Qi Jianmin , Lei Rongjie , Xu Jiantang , Lin Lihui , Zhang Liwu , Zhang Jisen , Tao Aifen 
Published: April 2023

Abstract
Background
Jute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The potential functions of CCoAOMT in lignin biosynthesis of jute have been reported in several studies. However, little is known about the evolution of the CCoAOMT gene family, and either their expression level at different developing stages in different jute cultivars, as well as under abiotic stresses including salt and drought stress.

Results
In the present study, 66 CCoAOMT genes from 12 species including 12 and eight CCoAOMTs in Corchorus olitorius and C. capsularis were identified. Phylogenetic analysis revealed that CCoAOMTs could be divided into six groups, and gene expansion was observed in C. olitorius. Furthermore, gene expression analysis of developing jute fibers was conducted at different developmental stages (15, 30, 45, 60, and 90 days after sowing [DAS]) in six varieties (Jute-179 [J179], Lubinyuanguo [LB], and Qiongyueqing [QY] for C. capsularis; Funong No.5 [F5], Kuanyechangguo [KY], and Cvlv [CL] for C. olitorius). The results showed that CCoAOMT1 and CCoAOMT2 were the dominant genes in the CCoAOMT family. Of these two dominant CCoAOMTs, CCoAOMT2 showed a constitutive expression level during the entire growth stages, while CCoAOMT1 exhibited differential expression patterns. These two genes showed higher expression levels in C. olitorius than in C. capsularis. The correlation between lignin content and CCoAOMT gene expression levels indicated that this gene family influences the lignin content of jute. Using real-time quantitative reverse transcription PCR (qRT-PCR), a substantial up-regulation of CCoAOMTs was detected in stem tissues of jute 24 h after drought treatment, with an up to 17-fold increase in expression compared to that of untreated plants.

Conclusions
This study provides a basis for comprehensive genomic studies of the entire CCoAOMT gene family in C. capsularis and C. olitorius. Comparative genomics analysis among the CCoAOMT gene families of 12 species revealed the close evolutionary relationship among Corchorus, Theobroma cacao and Gossypium raimondii. This study also shows that CCoAOMTs are not only involved in lignin biosynthesis, but also are associated with the abiotic stress response in jute, and suggests the potential use of these lignin-related genes to genetically improve the fiber quality of jute.
Division of developmental phases of freshwater leech Whitmania pigra and key genes related to neurogenesis revealed by whole genome and transcriptome analysis
Authors: Liu Jiali , Liu Jinxin , Li Mingyue , Zhou Lisi , Kong Weijun , Zhang Hailin , Jin Panpan , Lu Fuhua , Lin Gufa , Shi Linchun 
Published: April 2023

AbstractThe freshwater leech Whitmania pigra (W. pigra) Whitman (Annelida phylum) is a model organism for neurodevelopmental studies. However, molecular biology research on its embryonic development is still scarce. Here, we described a series of developmental stages of the W. pigra embryos and defined five broad stages of embryogenesis: cleavage stages, blastocyst stage, gastrula stage, organogenesis and refinement, juvenile. We obtained a total of 239.64 Gb transcriptome data of eight representative developmental phases of embryos (from blastocyst stage to maturity), which was then assembled into 21,482 unigenes according to our reference genome sequenced by single-molecule real-time (SMRT) long-read sequencing. We found 3114 genes differentially expressed during the eight phases with phase-specific expression pattern. Using a comprehensive transcriptome dataset, we demonstrated that 57, 49 and 77 DEGs were respectively related to morphogenesis, signal pathways and neurogenesis. 49 DEGs related to signal pathways included 30 wnt genes, 14 notch genes, and 5 hedgehog genes. In particular, we found a cluster consisting of 7 genes related to signal pathways as well as synapses, which were essential for regulating embryonic development. Eight genes cooperatively participated in regulating neurogenesis. Our results reveal the whole picture of W. pigra development mechanism from the perspective of transcriptome and provide new clues for organogenesis and neurodevelopmental studies of Annelida species.
Predictive value of NoSAS questionnaire combined with the modified Mallampati grade for hypoxemia during routine sedation for gastrointestinal endoscopy
Authors: Li Nana , Wu Junbei , Lu Yunhong , Zhang Jigang , Sun Zhaochu , Cao Xiaofei , Liu Cunming 
Published: April 2023

Abstract
Background
The incidence of hypoxemia during painless gastrointestinal endoscopy remains a matter of concem. To date, there is no recognized simple method to predict hypoxemia in digestive endoscopic anesthesia. The NoSAS (neck circumference, obesity, snoring, age, sex) questionnaire, an objective and simple assessment scale used to assess obstructive sleep apnea (OSA), combined with the modified Mallampati grade (MMP), may have certain screening value. This combination may allow anesthesiologists to anticipate, manage, and consequently decrease the occurrence of hypoxemia.

Methods
This study was a prospective observational trial. The primary endpoint was the incidence of hypoxaemia defined as pulse oxygen saturation (SpO2) < 95% for 10 s. A total of 2207 patients admitted to our hospital for painless gastrointestinal endoscopy were studied. All patients were measured for age, height, weight, body mass index, neck circumference, snoring, MMP, and other parameters. Patients were divided into hypoxemic and non-hypoxemic groups based on the SpO2. The ROC curve was plotted to evaluate the screening value of the NoSAS questionnaire separately and combined with MMP for hypoxemia. The total NoSAS score was evaluated at cut-off points of 8 and 9.

Results
With a NoSAS score ≥ 8 as the critical value for analysis, the sensitivity for hypoxemia was 58.3%, the specificity was 88.4%, and the area under the ROC was 0.734 (P < 0.001, 95% CI: 0.708–0.759). With a NoSAS score ≥ 9 as a critical value, the sensitivity for hypoxemia was 36.50%, the specificity rose to 96.16%, and the area under the ROC was 0.663 (P < 0.001, 95% CI: 0.639–0.688). With the NoSAS Score combined with MMP for analysis, the sensitivity was 78.4%, the specificity was 84%, and the area under the ROC was 0.859 (P < 0.001, 95%CI:0.834–0.883).

Conclusions
As a new screening tool, the NoSAS questionnaire is simple, convenient, and useful for screening hypoxemia. This questionnaire, when paired withMMP, is likely to be helpful for the screening of hypoxemia.
A qualitative investigation of health benefits through a modified Taekwondo activity among nursing home residents
Authors: Kim Junhyoung , Kim Yongseop , Seo Dong-Chul , Han Sua 
Published: April 2023

Abstract
Background
A few studies suggest that Taekwondo is an effective intervention in increasing physical functions among older adults. This study is intended to focus on a multitude of health benefits of participation in a modified Taekwondo activity for nursing home residents in the U.S.

Methods
This qualitative study used semi-structured, in-depth interviews with seven participants consisting of 2 males and 5 females older adults from a community nursing home. The interview protocol included content mapping and content mining interview questions. The study followed the five steps of constant comparative analysis.

Results
Four main themes were identified as health benefits resulting from a modified Taekwondo participation: (a) promoting mental health, (b) increasing physical functions, (c) stimulating cognitive abilities, and (d) facilitating positive social interaction.

Discussion
This study indicates modified Taekwondo can be instrumental in promoting their physical functioning, cognitive functioning, social interactions, and mental health. Practical implications and further discussion are addressed in this paper.
A case report of brainstem hemorrhage due to Rhizopus delemar-induced encephalitis diagnosed by metagenomic next-generation sequencing (mNGS)
Authors: Xie Shuhua , Lai Zhaohui , Xia Han , Tang Mingze , Lai Jinxing , Liu Qing , Lu Zhijuan , He Dehai , Qi Jiangli , Liu Xianghong 
Published: April 2023

Abstract
Background
Rhizopus delemar is an invasive fungal pathogen that can cause fatal mucormycosis in immunodeficient individuals. Encephalitis caused by R. delemar is rare and difficult to diagnose early. Clinical detection methods for R. delemar include blood fungal culture, direct microscopic examination, and histopathological examination, but the detection is often inadequate for clinical diagnosis and can easily lead to missed diagnosis with delayed treatment.

Case presentation
We report a case of a 47-year-old male with brainstem hemorrhage caused by encephalitis due to R. delemar. The patient had a history of hypertension, type 2 diabetes, and irregular medication. No pathogens were detected in cerebrospinal fluid (CSF) and nasopharyngeal secretion cultures. R. delemar was identified by metagenomic next-generation sequencing (mNGS) in CSF, and in combination with the patient’s clinical characteristics, encephalitis caused by R. delemar was diagnosed. Antibiotic treatment using amphotericin B liposome in combination with posaconazole was given immediately. However, due to progressive aggravation of the patient’s symptoms, he later died due to brainstem hemorrhage after giving up treatment.

Conclusions
mNGS technique is a potential approach for the early diagnosis of infections, which can help clinicians provide appropriate antibiotic treatments, thus reducing the mortality and disability rate of patients.
Structural model of resilience based on parental support: the mediating role of hope and active coping
Authors: Cheraghian Hadis , Moradian Khadije , Nouri Tahere 
Published: April 2023

AbstractResilience is an essential trait in the academic and non-academic lives of students that has been associated with positive psychological and non-psychological outcomes. Given the importance and role of resilience, the main goal of this study was to create a structural model of resilience based on parental support and emphasizing the mediating role of hope and coping. The research design was correlational in nature and used structural equation modeling (SEM). The population of this study included high school students in Tehran city in 2019–2020 school year, and the sample consisted of 560 students selected by cluster sampling method. By applying Spearman correlation analysis and structural equation modeling, a significant relationship between hope, coping, resilience, and parental support was found. Both the SEM measurement and structural models provided a good fit. The significant findings of the present study include the direct and significant effect of parental support on resilience. The indirect and significant effect of parental support on resilience through the mediating role of hope and coping was also confirmed. Overall, the results of this study show that the effect of parental support on resilience can be improved by promoting hope and coping styles.
Potential mechanisms of osthole against bladder cancer cells based on network pharmacology, molecular docking, and experimental validation
Authors: Jiang Yunzhong , Zhang Mengzhao , Wang Lu , Zhang Lu , Ma Minghai , Jing Minxuan , Li Jianpeng , Song Rundong , Zhang Yuanquan , Yang Zezhong , Zhang Yaodong , Pu Yuanchun , Qu Xiaowei , Fan Jinhai 
Published: April 2023

Abstract
Background
Osthole was traditionally used in treatment for various diseases. However, few studies had demonstrated that osthole could suppress bladder cancer cells and its mechanism was unclear. Therefore, we performed a research to explore the potential mechanism for osthole against bladder cancer.

Methods
Internet web servers SwissTargetPrediction, PharmMapper, SuperPRED, and TargetNet were used to predict the Osthole targets. GeneCards and the OMIM database were used to indicate bladder cancer targets. The intersection of two target gene fragments was used to obtain the key target genes. Protein–protein interaction (PPI) analysis was performed using the Search Tool for the Retrieval of Interacting Genes (STRING) database. Furthermore, we used gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to explore the molecular function of target genes. AutoDock software was then used to perform molecular docking of target genes,osthole and co-crystal ligand. Finally, an in vitro experiment was conducted to validate bladder cancer inhibition by osthole.

Results
Our analysis identified 369 intersection genes for osthole, the top ten target genes included MAPK1, AKT1, SRC, HRAS, HASP90AA1, PIK3R1, PTPN11, MAPK14, CREBBP, and RXRA. The GO and KEGG pathway enrichment results revealed that the PI3K-AKT pathway was closely correlated with osthole against bladder cancer. The osthole had cytotoxic effect on bladder cancer cells according to the cytotoxic assay. Additionally, osthole blocked the bladder cancer epithelial-mesenchymal transition and promoted bladder cancer cell apoptosis by inhibiting the PI3K-AKT and Janus kinase/signal transducer and activator of transcription (JAK/STAT3) pathways.

Conclusions
We found that osthole had cytotoxic effect on bladder cancer cells and inhibited invasion, migration, and epithelial-mesenchymal transition by inhibiting PI3K-AKT and JAK/STAT3 pathways in in vitro experiment. Above all, osthole might have potential significance in treatment of bladder cancer.

Subjects
Bioinformatics, Computational Biology, Molecular Biology.
Nigella sativa powder for helicobacter pylori infected patients: a randomized, double-blinded, placebo-controlled clinical trial
Authors: Yousefnejad Hedieh , Mohammadi Farzaneh , Alizadeh-naini Mahvash , Hejazi Najmeh 
Published: April 2023

AbstractObjectiveThis double-blind, placebo-controlled, clinical trial was conducted to define the effects of Nigella sativa (N. Sativa) powder plus conventional medical treatment ofHelicobacter pylori(H. pylori) on serum ghrelin level and appetite inH. pylori-infected patients.MethodsIn the present study, 51H. pylori-positive patients were randomly allocated to treatment (n = 26) or placebo (n = 25) groups. They received 2 g/dayN. Sativawith quadruple therapy or 2 g/day placebo plus quadruple therapy for 8 weeks. The serum level of ghrelin was assessed before and after the intervention. Appetite was evaluated at the onset and at the end of the intervention.ResultsAt the end of the study, the appetite of the treatment group improved significantly compared with the placebo group (P = 0.02). Statistically, the difference in serum ghrelin levels between the study’s groups was insignificant (P > 0.05).ConclusionSupplementation withN. Sativapowder may be a beneficial adjunctive therapy inH. pylori-infected patients.Trial registrationThis study was registered in the Iranian Registry of Clinical Trials (IRCT20170916036204N7) on 08/08/2018.
Development and evaluation of an online surgical elective for medical students
Authors: Goble Mary , Chapman Neil 
Published: April 2023

Abstract
Background
Decreased experiential learning opportunities exacerbated by the COVID-19 pandemic have increased development of online surgical educational courses. To what extent may such courses provide exposure to broad and accessible surgical education?

Methods
Surge is a 6-week online surgical elective hosted within a virtual learning environment, covering all surgical specialties. Course content is mapped to the Royal College of Surgeons’ Undergraduate Curriculum in Surgery. Each week consultant surgeons discuss their specialty in short videos on anatomy, pathology and lifestyle of a surgeon. Students also engage with learning activities; further reading lists; formative quizzes and live sessions including suturing practice. Participants were medical students undertaking third-year electives at the University of Sheffield. Pre- and post-course questionnaires investigated student interest in surgery, understanding of steps required to pursue a surgical career and confidence in surgical environments. Qualitative data was collected via free-text responses and analysed with content analysis. Quantitative data was collected using 5-point Likert scales (1 = Strongly Disagree; 5 = Strongly Agree) and analysed using the Wilcoxon signed-rank test.

Results
Twenty-two students participated in Surge over five 6-week cohorts. Examination of free-text responses revealed students gained increased understanding of available surgical career options. Students felt better informed regarding different surgical specialties (median score 2.5 vs. 4, p = 0.000) and steps required to develop a surgical portfolio (median score 2 vs. 5, p = 0.000). Additionally, confidence in understanding of relevant intraoperative steps improved (median score 3 vs. 4, p = 0.000).

Conclusion
These data demonstrate Surge increased student confidence and understanding of surgical careers despite reduced in-person opportunities to engage with surgical education. Surge will continue to be developed and evaluated on a larger scale.