bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome
Authors: Rouse Warren B. , O’Leary Collin A. , Booher Nicholas J. , Moss Walter N. 
Published: May 2022

Abstract
RNA plays vital functional roles in almost every component of biology, and these functional roles are often influenced by its folding into secondary and tertiary structures. An important role of RNA secondary structure is in maintaining proper gene regulation; therefore, making accurate predictions of the structures involved in these processes is important. In this study, we have expanded on our previous work that led to the creation of the RNAStructuromeDB. Unlike this previous study that analyzed the human genome at low resolution, we have now scanned the protein-coding human transcriptome at high (single nt) resolution. This provides more robust structure predictions for over 100,000 isoforms of known protein-coding genes. Notably, we also utilize the motif identification tool, ScanFold, to model structures with high propensity for ordered/evolved stability. All data have been uploaded to the RNAStructuromeDB, allowing for easy searching of transcripts, visualization of data tracks (via the Integrative Genomics Viewer or IGV), and download of ScanFold data—including unique highly-ordered motifs. Herein, we provide an example analysis of MAT2A to demonstrate the utility of ScanFold at finding known and novel secondary structures, highlighting regions of potential functionality, and guiding generation of functional hypotheses through use of the data.
Molecular identification of Anisakis species (Nematoda: Anisakidae) in Scorpaena scrofa (Scorpaenidae) from the Aegean Sea
Authors: AYDIN Coskun , PEKMEZCI Gokmen Zafer 
Published: May 2022

Abstract
The red scorpionfish Scorpaena scrofa (Scorpaenidae) is a high commercial value marine fish species along the Mediterranean coasts. Anisakiasis is a fish‒borne parasitic zoonoses caused by Anisakis larvae in consumers. To date, there are only a few epidemiological studies on the presence and molecular identification of Anisakis larvae infecting the S. scrofa in the Mediterranean Sea. A total of 272 S. scrofa captured from the Aegean Sea (FAO 37.3.1) were examined for Anisakis larvae between March 2019 and March 2020. The prevalence, mean intensity, and mean abundance of Anisakis larvae was 9.6% (95% CI 6.5–13.7%), 2.8 (95% CI 1.88–5.19), and 0.27 (95% CI 0.15–0.56), respectively. Anisakis pegreffii, A. typica, A. ziphidarum, and A. simplex (s.s.)/A.pegreffii hybrid were identified by RFLP analysis of ITS region. Anisakis pegreffii, A. typica and A. ziphidarum larvae were also confirmed by cox2 sequence analysis. A weak positive and statistically significant correlation between total length (ρS 0.204; p = 0.001) and total weight (ρS 0.200; p = 0.001) of S. scrofa and the number of Anisakis larvae was observed. This survey presents the first molecular detection of A. typica and A. ziphidarum in S. scrofa. Thus, this fish species is a new host for A. typica and A. ziphidarum. This is also the first report of A. ziphidarum in the Aegean Sea.
Prevalence, Characteristics, and Risk of Exacerbation in Young patients with Chronic Obstructive Pulmonary Disease
Authors: Jo Yong Suk , Kim Kyung Joo , Rhee Chin Kook , Yoo Kwang Ha , Jung Ki-Suck , Park Yong-Bum 
Published: May 2022

Abstract
Background: Early identification of chronic obstructive pulmonary disease (COPD) in young individuals could be beneficial to attempt preventive interventions. The objective of this study was to investigate clinical features and outcomes of young individuals with COPD from the general population cohort. Methods: We included individuals from the Korean National Health and Nutrition Examination Survey (KNHANES) with spirometry and identifiable smoking status. Young subjects with COPD were defined as aged between 40 and 50 years and had baseline forced expiratory volume in 1 s [FEV1]/forced vital capacity [FVC] ratio less than 0.7. Outcomes include the risk of exacerbation and medical expenses during three years of follow-up. Results: Among 2,236 individuals aged between 40 and 50 years, 95 (4.2%) had COPD, including 47 who were non-smokers (smoking pack-year < 10) and 48 who were ever-smokers (smoking pack-year ≥ 10). Approximately 98% of COPD subjects had mild to moderate airflow limitation. Inhaler treatment was given to only 6.3% patients in the COPD group. Hazards ratio for exacerbation was 1.50 (95% confidence interval [CI]: 0.147-13.39) in the non-smoker COPD group and 1.83 (95% CI: 0.18-18.11) in the ever-smoker COPD group of young subjects. COPD related medical costs were not significantly different between non-COPD and COPD groups of young individuals. Conclusions: The risk of exacerbation showed an increasing trend in COPD patients regardless of smoking status compared to non-COPD. More attention to early identification and provision of preventive measures are needed to reduce disease progression and improve outcome.
Hearing loss and depressive symptoms in older Chinese: whether social isolation plays a role
Authors: Huang Hao , Wang Jiao , Jiang Chao Qiang , Zhu Feng , Jin Ya Li , Zhu Tong , Xu Lin , Zhang WS 
Published: May 2022

Abstract
Background: Existing evidence links hearing loss to depressive symptoms, with the extent of association and underlying mechanisms remaining inconclusive. We conducted a cross-sectional study to examine the association of hearing loss with depressive symptoms and explored whether social isolation mediated the association.Methods: 8,962 participants from Guangzhou Biobank Cohort Study were included. Data on self-reported hearing status, the 15-item Geriatric Depression Scale (GDS-15), social isolation and potential confounders were collected by face-to-face interview.Results: The mean (standard deviation) age of participants was 60.2 (7.8) years. The prevalence of poor and fair hearing was 6.8% and 60.8%, respectively. After adjusting for age, sex, household income, education, occupation, smoking, alcohol use, self-rated health, comorbidities, compared with participants who had normal hearing, those with poor hearing (β=0.74, 95% confidence interval (CI) 0.54, 0.94) and fair hearing (β=0.59, 95% CI 0.48, 0.69) had higher scores of GDS-15. After similar adjustment, those with poor hearing (odds ratio (OR)=2.13, 95% CI 1.65, 2.74) or fair hearing (OR=1.68, 95% CI 1.43, 1.99) also showed higher odds of depressive symptoms. The association of poor and fair hearing with depressive symptoms attenuated slightly but not substantially after additionally adjusting for social isolation. In the mediation analysis, the adjusted proportion of the association mediated through social isolation was 9% (95% CI: 6%, 22%).Conclusion: Poor hearing was associated with a higher risk of depressive symptoms, which was only partly mediated by social isolation. Further investigation of the underlying mechanisms is warranted.
Car Black Box using Raspberry Pi
Authors: Deshmukh Shreya 
Published: May 2022

Abstract
Nowadays, people are facing one of the most and biggest problems which is an accident. Most people are dying because of accidents. The death rate or even the smallest accident rate is increasing day by day. Traveling is an important part of life, whether it is a workplace or any other. The main reason for death recorded is due to the lack of unavailability of medical services at the accident. Another cause that i personally think is the lack of co-operation of people to follow signals. Practically thinking one cannot prevent or stop any kind of accident but can lower the post-trauma. In present days we can see that every single person may come across with accidents and this is one of the critical situations. Few people can survive and few people may lose their lives, which occurs due to lack of information. To overcome these problems, a black box came into existence. The main objective of the car black box using raspberry pi is to develop a hardware system that will monitor image and video, motion detection, humidity & temperature in real-time continuously on an SD card. So any input can be logged into memory so that any authenticated person can observe the specific data from any place (here from the same place too. The data is stored in the SD card that is externally connected to the Raspberry pi. The information is collected by Raspberry Pi processors using a camera module and other sensors which are connected to the raspberry pi which is Linux based operating system that will give all the collected data information to the monitoring system. The monitoring system will display the data (if needed and wanted) in real-time which helps the investigation to find out the scenario of the accident that occurred.
Application of finite element Analysis in dynamic changes of Spinal Mechanics in Osteoporotic Lumbar fracture
Authors: Yan Jianwen , Liao Zhong , Yu Yafang 
Published: May 2022

Abstract
Aim: To explore the effect of finite element biomechanical properties of different methods in the treatment of osteoporotic thoracolumbar fractures.Methods: Based on the ultra-thin CT scan data of a volunteer's thoracolumbar spine, the finite element method was used to simulate the treatment of osteoporotic thoracolumbar fracture. The images of thoracolumbar region were obtained by spiral CT scanning, and the three-dimensional geometric model was obtained by importing Mimics software, the finite element model of normal T11 ~ L2 segment was established by finite element software Abaqus, and the validity of the model loading was verified. Based on the finite element model of T11 vertebral compression fracture based on normal raw data, the clinical overextension reduction manipulation was simulated by different treatment methods, and the changes of stress and displacement in different parts of injured vertebrae were analyzed.Results: In this study, an effective finite element model of T11-L2 segment is established. The maximum stress, axial compression strength, axial compression stiffness (EF) and transverse shear stiffness (GF) of PKP and PVP treatment group were significantly better than those of conservative treatment group and open treatment group, and the difference was statistically significant. There was no significant difference between open treatment group and conservative treatment group, and there was no significant difference between PKP and PVP treatment group.Conclusion: The results of finite element analysis show that PKP and PVP in the treatment of osteoporotic thoracolumbar fractures can effectively improve the condition of patients, relieve their clinical symptoms, have a good prognosis and have a good long-term effect, and its biomechanical properties are good, the application effect is remarkable.
Immunoinformatics and structural vaccinology approach to design a Multi-Epitope Subunit Vaccine against Francisella tularensis through In Silico modeling
Authors: Hayat Chandni , Sikandar Haris , Shahab Muhammad , Liang Chaoqun , Duan Xiuyuan , Zheng Guojun , Junaid Muhammad 
Published: May 2022

Abstract
BackgroundFrancisella tularensis is a category A pathogen with the maximum infectious and death rates, demanding the development of a vaccine. In the last eight years, growing interest in F. tularensis has resulted in the generation of data about the pathogen and its host binding method. So far, extensive information is available, but there is no authorized vaccination on the market.MethodUsing in silico techniques, present study design to develop multi-epitope vaccine. From F. tularensis, B-cell and T-cell epitopes were predicted to design a vaccine. The selection of epitope was selected on basis of lower percentile score, antigenicity, Non-toxicity, and immunogenicity scores. The 193 amino-acid long vaccine construct was obtained by joining the epitopes through EAAAK, CPGPG and AAY Linkers.ResultOur vaccine represented overall the good stability, expression, immunostimulatory capabilities and solubility. Moreover, molecular docking and MD simulation exhibited strong interaction and stability of polypeptide vaccine construct. Conclusion:Design vaccine was verified as efficient in different computer-based immune response investigations and population coverage was good. But designed vaccines require scientific consensus and require in vitro experimental work also.
Comparing the effect of modified ureterosigmoidostomy（MainzⅡ）in the treatment of bladder cancer after open and laparoscopic radical cystectomy
Authors: Zhang Bin , He Yang , Zheng Duo , Liu Junyao , Qi Peng , Han Dali , yue Zhongjin , Shang Panfeng 
Published: May 2022

Abstract
Background
To analyze perioperative conditions and long-term efficacy of open modified ureterosigmoidostomy urinary diversion (OMUUD) in patients with bladder cancer who underwent open radical cystectomy (ORC) or laparoscopic radical cystectomy (LRC).
Methods
In this retrospective study, the clinical data of patients who underwent open and laparoscopic radical cystectomy plus open modified ureterosigmoidostomy urinary diversion in our hospital were collected from January 2011 to December 2019. In addition, perioperative data of 56 patients who underwent ORC and OMUUD were compared with those of 118 patients who underwent laparoscopic radical cystectomy (LRC) plus OMUUD. A long-term follow-up was performed to compare the overall survival (OS) and progression-free survival (PFS) rate between the two groups.
Results
Results showed that the mean operation time in the open group was shorter than that in the laparoscopic group (P < 0.001). Moreover, the estimated intraoperative blood loss༈P < 0.001༉and postoperative hospital stay༈P = 0.023༉were better in the laparoscopic group than in the open group. The incidence of complications between 30 days (P = 0.665) and 90 days (P = 0.211) time-points after surgery was not significantly different. Similarly, the OS (P = 0.237) and PFS (P = 0.307) between the two groups were comparable.
Conclusion
This study shows that the LRC group has long operation time, but less estimated intraoperative blood loss, short postoperative hospital stay, small trauma, and fast postoperative recovery compared to open surgery. Moreover, the incidence of complications at 30-and 90-days postoperation, as well as the OS and PFS is not different between laparoscopy and open surgery.
Current HIV/AIDS Trends among General Public in Telangana: A Cross-sectional Study
Authors: Reddy Adila , Reddy Sunitha 
Published: May 2022

Abstract
Aim: This cross-sectional study aims to investigate the knowledge, attitude, beliefs and practices (KABP) concerning Human Immunodeficiency Virus (HIV) and Acquired Immunodeficiency Syndrome (AIDS) among the general public in the state of Telangana.Introduction: HIV was first reported on June 5, 1981 and has since affected every country across the globe. Worldwide over 37.7 million people are seropositive for Human Immunodeficiency Virus (HIV). Despite large awareness campaigns, inclusive educational curriculum and increased access to healthcare; mainstream understanding about the disease continues to be incomplete. Much of the misunderstanding comes not from the lack of access to information but from the omnipresent misinformation at the community level.Methods: Multiple college campuses were presented with a survey to assess their KABP about HIV/AIDS. The assessment form contained 4 sections as follows, Section 1: Socio-demographic data, Section 2: Knowledge of HIV/AIDS, Section 3: Personal beliefs towards HIV/AIDS, Section 4: Personal Beliefs on Blood Donation and HIV.
The different characteristic of chronic liver damage in patients with metabolic-(dysfunction) associated fatty liver disease in different subtypes
Authors: Wang Yu , Liu Zi-yu , Ji Fang , Dai Ming-jia , Li Jian-zhong , Huang Rui , Wu Chao , Yan Xue-bing 
Published: May 2022

Abstract
BACKGROUND and AIMS: This study aimed to compare the difference on liver damage among MAFLD subgroup classification in MAFLD.METHODS: A cross-sectional study of 882 Chinese patients who underwent ultrasonography or biopsy with metabolic-(dysfunction)-associated fatty liver disease (MAFLD) involved a cohort from a health screening program during the years 2018-2020. The liver damage characteristics of different MAFLD subtypes were compared. Liver damage was assessed based on the inflammation indicators and non-invasive diagnostic model.RESULTS: The median age was 43 years, and 490 (55.56%) patients were male. There was significant difference among three MAFLD subgroups (Group1, 2, and 3) in age, BMI, GGT, TG, CHO, LDL, HDL, FPG, NFS, and FIB-4 (p < 0.05). The FIB-4 and NFS were higher in the Group 2 and the abnormal FPG-level Group than in the other groups to which they were compared (p < 0.05). The age, BMI, and GGT were lower in the only overweight/obese Group than the Concomitant metabolic dysregulation Group (p < 0.05).CONCLUSION: There was statistically difference in liver inflammation and liver fibrosis among different subtypes in MAFLD. It’s urgent to improve substantially in health care for patients and advance disease awareness, public health policy for MAFLD. [197 words]
Comparative chloroplast genomes of six Magnoliaceae species provides new insight into intergeneric relationship and phylogeny
Authors: Yang Lin , Tian Jinhong , Xu Liu , Zhao Xueli , Song Yuyang , Wang Dawei 
Published: May 2022

Abstract
The Magnoliaceae plants are industrial tree species with high medicinal value. We published the 6 complete chloroplast genomes of the family Magnoliaceae by using Illumina sequencing. These 6 chloroplast genomes showed a typical quadripartite structure of angiosperm and were 159,901 − 160,008 bp in size, respectively. A total of 324 microsatellite loci and 6 variable intergenic regions (Pi > 0.01) were identified in 6 genomes. Compare with other 5 genomes, the contraction and expansion of the IR regions were significantly different in Manglietia grandis. For having more thorough understanding of the intergeneric relationship of family Magnoliaceae, we also included 31 published chloroplast genomes of close relative species for phylogenetic analyses. The new insights into intergeneric relationship of family Magnoliaceae was provided based on the combination of our result and the previous morphological, phytochemical and anatomygical information. We suggest that the genus Yulania should be separated from the genus Michelia, and restore systematic position of the genus Yulania; the genera Paramichelia and Tsoongiodendron should be merged into the genera Michelia; the genera Pachylarnax and Parakmeria should be combined into one genus. These findings will provide a theoretical basis for adjustment phylogenetic position of family Magnoliaceae at the molecular level.
DNA Methylation Diagnosis Markers Detection on Lung Adenocarcinoma with Deep Learning
Authors: Yuan Xinyang 
Published: May 2022

Abstract
Lung Adenocarcinoma (LUAD) is one of the most fatal malignant tumors which has led to millions of deaths yearly all around the world. Arouse from new topic of selecting DNA methylation markers in cancer therapy diagnosis, we explore relationship between gene expression and DNA methylation, we applied machine learning unsupervised algorithms in narrowing the range of candidate DNA methylation probes and create a deep-learning-based diagnosis model which has high accuracy in predicting cells into malignant and benign.
The oncogene EIF3c promotes esophageal squamous cell carcinoma tumorigenesis by inhibiting cell proliferation and inducing cell apoptosis
Authors: lu zhengyang , Sheng Binwu , yang Ganghua , Xu Qinhong 
Published: May 2022

Abstract
Background: It has been reported that EIF3c (Eukaryotic initiation factor 3c) was associated with carcinogenesis of several cancer. However, the role of EIF3c in human esophageal squamous cell carcinoma (ESCC) is still unknown. The aim of present study was to explore the relationship between EIF3c and ESCC, and further investigate the effect of EIF3c in ESCC cells and potential molecular mechanism.Methods: The MRNA expression data and the clinical information of ESCC patients was obtained from TCGA and used for the analysis of association between EIF3c and ESCC. SiRNA transfection was performed to knock down EIF3c in ESCC cells. Cellomics ArrayScan, colony formation and CCK-8 assay was used to test cell proliferation. Flow cytometry assay was used to test apoptosis and cell cycle. Western blot assay was used to measure protein expression. Microarray assay and Ingenuity Pathway Analysis (IPA) was used to profile gene expression and physiological processes effected by EIF3c in ESCC cells. Results: Firstly, EIF3c exhibited higher expression in ESCC tissue compared with normal esophageal tissue. Furthermore, silencing EIF3c resulted in cell proliferation inhibition in ESCC cells. In addition, EIF3c knockdown induced cell apoptosis and cell cycle arrest. Moreover, microarray assay and Ingenuity Pathway Analysis (IPA) revealed 1081 differentially expressed genes (DEGS) including 593 upregulated genes and 488 downregulated genes, and the related canonical pathways and possible up-regulators after silencing EIF3c in ESCC cells.Conclusion: Our study for the first time demonstrated the role of EIF3C as oncogene in ESCC and the underlying molecular mechanism.
Distinct patterns of gene expression changes in the colon and striatum of young mice overexpressing alpha-synuclein support Parkinson Disease as a multi-system process
Authors: Videlock Elizabeth Jane , Hatami Asa , Zhu Chunni , Kawaguchi Riki , Chen Han , Khan Tasnin , Joshi Swapna , Hoffman Jill M. , Law Ka Man , Rankin Carl Robert , Chang Lin , Maidment Nigel T. , John Varghese , Geschwind Daniel H. , Pothoulakis Charalabos 
Published: May 2022

Abstract
Background
Parkinson Disease (PD) is increasingly being recognized as a disease of the gut-brain axis. Overexpression of human wild type α–synuclein under the neuron-specific Thy1 promoter (Thy1-haSyn) is a well-characterized mouse model of PD. In addition to a progressive motor phenotype, Thy1-haSyn mice have delayed colonic transit at three months of age mirroring prodromal constipation common in human PD. Identification of initial molecular changes in the gastrointestinal tract in PD could lead to early detection of PD and/or gut-targeted therapies to prevent motor symptoms in PD.
Methods
Colon and striatum gene expression profiling was performed in Thy1-haSyn and wild type (WT) mice aged 1 month and 3 months using 3′ RNA sequencing. Analysis of transcriptomic data included identification of differentially expressed genes, gene set enrichment analysis and weighted gene co-expression network analysis (WGCNA). WGCNA results were further analyzed by linear regression to identify modules most strongly associated with Thy1-haSyn in the colon and striatum, as well as in a combined multivariate model. Module annotation included enrichment for gene ontology terms, cell type signatures and risk genes.
Results
Differential gene expression in Thy1-haSyn vs WT was greater at one vs three months in both the colon and striatum. There was an opposite pattern of enrichment of mitochondrial genes related to PD (KEGG PD pathway) in striatum (enriched in WT) and colon (enriched in Thy1-haSyn). Colon Thy1-haSyn-associated WGCNA modules were enriched for PD risk genes and PD-relevant pathways including inflammation, autophagy, and oxidative stress. When combined with striatum modules, colon modules remained independent predictors of Thy1-haSyn genotype and increased the model fit (p = 0.048).
Conclusions
Overexpression of alpha synuclein acutely disrupts gene expression in the colon. While changes in colon gene expression are highly related to known PD-relevant mechanisms, they are distinct from brain changes and in some cases opposite in direction. These findings are in line with the emerging view of PD as a multi-system disease.