bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus
Authors: Torma Gábor , Tombácz Dóra , Moldován Norbert , Fülöp Ádám , Prazsák István , Csabai Zsolt , Snyder Michael , Boldogkői Zsolt 
Published: June 2021

Abstract
In this study, we used two long-read sequencing (LRS) techniques, Sequel from the Pacific Biosciences and MinION from Oxford Nanopore Technologies, for the transcriptional characterization of a prototype baculovirus, Autographacalifornica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby to distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcripts, of which 759 are novel and 116 have been annotated previously. These RNA molecules include 41 novel putative protein coding transcript (each containing 5’-truncated in-frame ORFs), 14 monocistronic transcripts, 99 multicistronic RNAs, 101 non-coding RNA, and 504 length isoforms. We also detected RNA methylation in 12 viral genes and RNA hyper-editing in the longer 5’-UTR transcript isoform of ORF 19 gene.
Capacity Building in Peer-Review: a Student-led Journal Experience
Authors: Campos Letícia Nunes , Yabrude Angela Theresa Zuffo , Medeiros Samantha Sartore Duque Estrada , Natividade Taiane do Socorro Silva , Luizeti Bárbara Okabaiasse , Cunha Moisés da Costa , Alves Rebeca Maria Gomes Guimarães , Bezerra Aristócles Hítallo , Ribeiro Lucas Loiola Ponte Albuquerque , Helal Lucas 
Published: June 2021

Abstract
Introduction: Peer-review plays a pivotal role in optimizing the quality of research articles. However, new strategies need to be implemented in the peer-review system to enhance research rigor, accurate reporting, and data reliability, such as increasing diversity among the reviewers through the inclusion of undergraduate students as reviewers. We aim to report the peer-review policies, procedures, and practices of a medical student-led journal editorial board in 2020, specifically detailing the challenges and the role of the students in the peer-review process. Methods: Through validated online training courses and peer education methodology, the students built capacity regarding the relevance of peer-review, its models, structure, and the publication process. The peer-review process was blinded for authors and reviewers, emphasizing the importance of impartiality and the minimization of identification bias. Guidelines for authors and reviewers were developed to add standardization to the submission and review processes, based on journals’ recommendations and reporting guidelines. Results: From July to August of 2020, the student-led journal received 254 submitted manuscripts from all five Brazilian geographic regions, compared to the 72 submissions received in the previous edition. After review, 50 manuscripts were accepted with major or minor corrections. Discussion: Peer-review contributes to the construction of content, and is the foundation for evidence-based medicine. In addition, it improves ethical thinking, communication skills, and critical appraisal abilities, also desirable in the academic and professional spheres. The medical student peer-review process has numerous benefits and should be promoted and further studied as a potential strategy for building capacity in peer-review.
ML of Striatum rs-fMRI Features Predicts TLE Diagnosis
Authors: Jiang Yanchun , Nie Liluo , zhang yanbo , Liu huihua , Zheng jinou 
Published: June 2021

Abstract
Objective: To determine whether patients with temporal lobe epilepsy (TLE) exhibit aberrant resting-state functional magnetic resonance imaging (rs-fMRI)-functional connectivity and build an individualized TLE prediction model using ML (ML). Methods: Sixty TLE patients and fifty-one controls underwent rs-fMRI scanning. The striatum was divided into 12 striatal seeds. rs-FC was compared between groups to enable TLE classification based on striatal FC using the SPM12, SVM and PRONTO softwares. Bilateral striatal FC values were extracted and significance values were obtained using leave-one-out (LOO) SVM analysis and permutation testing (2,000) for cross-validation.Results: Patients with TLE exhibited a significantly decreased rs-FC between the left inferior ventral striatum and the right posterior central gyrus, left superior frontal gyrus;and between the left dorsal rostral putamen and right superior parietal lobule, right middle frontal gyrus. And between right dorsal caudate And left prefrontal lobe, and right middle temporal gyrus. rs-fMRI analysis a revealed significantly increased FC between the left inferior ventral striatum seed and right anterior cingulate in TLE patients (p<0.05). Right dorsal caudate FC may distinguish individuals with TLE from controls with 79.08% Accuracy, including a 72.77% Sensitivity and 76.44% Specificity, resulting in an AUC of 0.71 (p <0 .01). The areas informing classification included left prefrontal lobe, right middle temporal gyrus, and left superior parietal lobule.Conclusion: Our findings demonstrate aberrant FC in certain brain regions, such as the right dorsal caudate, may play an important role as potential biomarkers of TLE and highlight the utility of ML-based models for clinical decision making.
ADAMTS4 or ADAMTS5: Which is the Key Enzyme in the Cartilage Degradation of Osteoarthritis and Kashin-Beck Disease?
Authors: Meng Peilin , Lammi Mikko J. , Yuan Linlin , Tan SiJia , Zhang Feng’e , Li Peilin , Zhang Yanan , Li Wenyu , Wang Sen , Guo Xiong 
Published: June 2021

Abstract
Background: This study aims to investigate the altered expression of a disintegrin and metalloproteinase with thrombospondin motifs 4（ADAMTS4）and a disintegrin and metalloproteinase with thrombospondin motifs 5（ADAMTS5）in the human articular cartilage between osteoarthritis(OA) and Kashin-Beck disease(KBD) and compare their roles in the cartilage injury. Methods: Articular samples were collected from confirmed OA patients and KBD patients then divided into three groups, and the articular cartilages from the normal donors were used as controls. The morphology，location and expression of ADAMTS4 and ADAMTS5 as well as aggrecan were detected by histochemical staining and immunohistochemical staining. Results: Compared to the control, the number of living cells in OA and KBD groups declined at three zones. Meanwhile, the results of toluidine blue staining showed that there was a loss of aggrecan in extracellular matrix of KBD and OA cartilages. The amounts of chondrocytes positively stained for ADAMTS4 were lower in the middle and deep zones of OA and KBD cartilages than those in the control samples. On the contrary, the immunostaining for ADAMTS5 significantly increased in OA and KBD group compared with control group at all three zones. Notably, although there was no statistical significance, the expression of ADAMST5 in KBD was slightly higher than the ones in OA in superficial, middle and deep zones. Conclusions: The role ADAMTS4 acted in aggrecan degradation was seemingly minor. It could be inferred that ADAMTS5 is the key enzyme in the cartilage destruction, particularly in KBD cartilage, which could explain the complex pathogenesis of KBD and provide a potential therapeutic target for KBD patients.
Correlation of In Vivo Imaging To Morphomolecular Pathology In Translational Research – Challenge Accepted
Authors: Ballke Simone , Heid Irina , Mogler Carolin , Braren Rickmer , Schwaiger Markus , Weichert Wilko , Steiger Katja 
Published: June 2021

Abstract
Correlation of in vivo imaging to histomorphological pathology in animal models requires comparative interdisciplinary expertise of different fields of medicine. From the morphological point of view, there is an urgent need to improve histopathological evaluation in animal model based research to expedite translation into clinical applications. While different other fields of translational science were standardized over the last years, little was done to improve the pipeline of experimental pathology to ensure reproducibility based on pathological expertise in experimental animal models with respect to defined guidelines and classifications. Additionally, longitudinal analyses of preclinical models often use a variety of imaging methods and much more attention should be drawn to enable for proper co-registration of in vivo imaging methods with the ex vivo morphological read-outs. Here we present the development of the Comparative Experimental Pathology (CEP) unit embedded in the Institute of Pathology of the Technical University of Munich during the Collaborative Research Center 824 (CRC824) funding period together with selected approaches of histomorphological techniques for correlation of in vivo imaging to morphomolecular pathology.
Parasitological, Serological and Molecular Survey of Camel Trypanosomosis (Surra) in Northern Nigeria
Authors: Mamman Shadrach , Dakul Anthony Danaan , Yohanna Jael Asabe , Dogo Goni Abraham , Reuben Rine Christopher , Ogunleye Oluyomi Oluniyi , Tyem Dinchin A , Peter Joana G , Kamani Joshua 
Published: June 2021

Abstract
Surra, a parasitic disease caused by Trypanosoma evansi and transmitted non-cyclically by biting flies significantly affects the health, productivity and market value of camels thereby constituting a major constraint to food safety, security and economy. This is the first study on the prevalence of surra in Northern Nigeria, using a broad variety of diagnostic tests along the parasitological-serological-molecular continuum hence, emphasizing it as a major enzootic risk for camels in Nigeria. In this cross-sectional study, 600 blood samples were collected from camels at major abattoirs in Northwestern Nigeria and evaluated for the prevalence of surra due to T. evansi using parasitological (Giemsa staining), serological (CATT/T.evansi) and molecular (VSG-PCR and sequencing) methods. The overall prevalence of surra recorded in this study was 5.3%, 11.5% and 22.5% using Giemsa stained blood smears, CATT/T.evansi and VSG-PCR respectively. However, higher prevalence of 6.0%, 13.7% and 26.7% by Giemsa stained blood smears, CATT/T. evansi and VSG-PCR was recorded in Katsina state when compared with Kano state. A significantly (p < 0.05) higher prevalence byVSG-PCR was observed when compared with both parasitological and serological methods used. Although age and body condition scores were associated (p < 0.05) with surra prevalence in sampled camels, no seasonal association (p > 0.05) was however recorded. Sequencing of the VSG region of Trypanosoma spp. Further confirmed the presence of T. evansi as the aetiological agent of surra from the sampled camels. Findings from this study call for the implementation of adequate control measures aimed at reducing the impact of T. evansi infections on camel production in Nigeria.
Analysis of Ionospheric Disturbance Associated With Earth Quakes In Papua New Guinea
Authors: Pereira Felix , Sekere Jessy 
Published: June 2021

Abstract
An analysis of the perturbations in the electron content up to the ionospheric F2 layer peak and F2 layer peak height (hmF2) variations during earthquake time has been done using ionosonde data observed in the equatorial station Vanimo, Papua New Guinea. Two earth quakes occurred, one of magnitude 7.1 in Sissano in 1998 and the other of magnitude 6.7 in Aitape in 2002 in the western province of Papua New Guinea, have been studied. A decrease in electron content was observed in both the cases a few days prior to the earthquakes. An increase in height of hmF2 during night time was also observed during this period. This can be explained in terms of the lithosphere- atmosphere-ionosphere coupling prior to earthquake period.
Identification of Molecular Biomarkers and Pathways for Risk Stratification in Human Papilloma Virus-Associated Cancers
Authors: Kwon Eun Jung , Lee Hye Ran , Lee Ju Ho , Ha Mihyang , Kim Yun Hak , Jang Jeon Yeob 
Published: June 2021

Abstract
Background: Human papillomavirus (HPV) is the major cause of cervical cancer (CC) etiology; its contribution to head and neck cancer (HNC) incidence is steadily increasing. As individual patients’ response to the treatment of HPV-associated cancer is variable, there is a pressing need for the identification of biomarkers for risk stratification that can help determine the intensity of treatment. Methods: We have previously reported a novel prognostic and predictive indicator (HPPI) scoring system in HPV-associated cancers regardless of the anatomical locations by analyzing the TCGA and GEO databases. In this study, we comprehensively investigated the association of group-specific expression patterns of common differentially expressed genes (DEGs) between high-risk and low-risk groups in HPV-associated CC and HNC, identifying a molecular biomarkers and pathways for the risk stratification. Results: Among the identified 174 DEGs, expression of the genes associated with extracellular matrix (ECM)-receptor interaction pathway (ITGA5, ITGB1, LAMB1, LAMC1) were increased in high-risk groups in both HPV-associated CC and HNC while expression of the genes associated with the T-cell immunity (CD3D, CD3E, CD8B, LCK, and ZAP70) were decreased vise versa. The individual genes showed statistically significant prognostic impact on HPV-associated cancers but not on HPV-negative cancers. The expression levels of identified genes were similar between HPV-negative and HPV-associated high-risk groups with distinct expression patterns only in HPV-associated low-risk groups. Each group of genes showed negative correlations, and distinct patterns of immune cell infiltration in tumor microenvironments. Conclusion: These results identify molecular biomarkers and pathways for risk stratification in HPV-associated cancers regardless of anatomical locations. The identified targets are selectively working in only HPV-associated cancers, but not in HPV-negative cancers indicating possibility of the selective targets governing HPV-infective tumor microenvironments.
Dysfunctional Insulin Resistant/mTOR Activation Is Involved In The Formation of Pulmonary Hypertension In Pressure Overload-Induced Heart Failure
Authors: Wu Xiaojing , Dong Bo , Ni Tongxin , Hu Junhao , Zhou Qi 
Published: June 2021

Abstract
Background: Heart failure (HF) usually presents with abnormal changes of metabolisms. Pulmonary hypertension (PH) is a frequent complication of left heart dysfunction. However, the association of serum metabolic changes with PH formation remains unknown. This study analyzed changes of serum metabolomic during the development of PH in a left heart pressure overload model. Methods: Male Sprague-Dawley rats were subjected to transverse aortic constriction (TAC) or sham surgery. Metabolomic analysis was performed on plasma samples of rats at 0 week, 3 weeks and 9 weeks after the surgery. Cardiac remodeling and heart function were determined by echocardiography. Right heart catheterization was performed to assay the mean pulmonary arterial pressure (mPAP). HE staining was performed to observe the remodeling of the myocardium and small pulmonary arteries.Results: The rats developed compensated cardiac hypertrophy with normal mPAP at 3 weeks and PH due to HF (PH-HF) at 9 weeks with distinct metabolic pattern after TAC. Twenty-five metabolites changed in the 9-week group compared with the 3-week group. KEGG analysis suggested abnormal insulin resistance and mTOR activation during the development of PH-HF. Acetylcarnitines related to insulin resistance increased about 3 folds from 4.14 ug/ml at 3 W group to 12.04μg/ml at 9-week group. L-leucine related to mTOR activation increased 1.6-fold with a VIP of 4.08 at 9 W when compared with that of the 3 W group.Conclusions: These results revealed distinct metabolic changes during the development of PH-HF. Dysfunctional insulin resistance and mTOR activation might be involved in the transition from compensated cardiac hypertrophy to PH-HF.
Real-World Study on Upper/Lower Respiratory Tract Microbiome Changes in AECOPD and COPD
Authors: Zhang Yunhui , Xu Yanyan , Liu Nailiang , Yan Dailing , Zhou Shiyi , He Meiyan , Shi Linfeng , Yang Zhiqin , Ma Mengjie , Dai Rufen , Li Xianli , Zhang Zhongyuan , Chen Liping , Wang Lina , Tian Kun , Duan Xingqiu , Yang Xiaohui , Huang Zhenming , Cai Bo , Su Jianyuan , Zhang Jingxin , Qin Jian , Yang Gang , Pan Quan , Yuan Bing 
Published: June 2021

Abstract
Background: Microbiome residing in the respiratory tract has emerged as an important player in the etiology and progression of COPD, but results are conflicting regarding the features of respiratory tract microbiome in COPD and at exacerbations and it is unknown whether these features differ by ethnicity and geography. To address these questions, we enrolled healthy individuals and patients with COPD, including healthy-COPD pairs from same households, from four geographical regions of Yunan province, representative of different ethnicities and/or environmental exposures. Sputum and oropharyngeal swabs were collected from these healthy individuals and from COPD patients at stable state (COPD) or exacerbations (AECOPD) and subjected to 16S amplicon sequencing. Results: We found that both COPD disease status and region had an impact on alpha-diversity of sputum and oropharyngeal microbiomes, with AECOPD having the lowest microbiome diversity. Shifts in the relative abundance (≥ 1.5 fold, adj.p < 0.05) of microbes at healthy, exacerbation and stable COPD. Microbes enriched at exacerbation COPD were primarily Proteobacteria and Firmicutes phylum in upper respiratory tract. In the lower respiratory tract, population-based study did not find any statistical differential abundance of microbe, however, paired-based study showed phylum of Proteobacteria, Chloroflexi, Bacteroidota, Acidobacteriota, Desulfobacterota, Firmicutes and Verrucomicrobiota enriched in exacerbation COPD. Conclusions: This study was the first attempt to combine the population-based and core-family-based to investigate the microbiome profiling in the upper and lower respiratory tract in COPD patients, and specific microbial flora characteristics may inform future study on the pathogenesis or management of COPD patients.
Analysis of Prognostic Factors of Nasopharyngeal Carcinoma and Construction of Risk Nomogram Prediction Model
Authors: zhang xuan hao , Jin LU , Cheng-yi JIANG , Mei-fang FANG , Hai-rong Liu 
Published: June 2021

Abstract
Objective To analyze the factors affecting the prognosis of nasopharyngeal carcinoma (NPC) patients and establish a risk nomogram prediction model for the diagnosis, treatment and prognosis of NPC. Methods A total of 1645 NPC patients (1470 survival) from 1973 to 2015 in the SEER database were included. The clinicopathological data of 180 NPC patients hospitalized in the First Affiliated Hospital of Bengbu Medical College since 2010 were collected. The spearman correlation analysis and COX regression analysis were used to identify the prognostic factors of NPC and establish the risk nomogram prediction model. Receiver operation characteristic (ROC) analysis and area under curves (AUC) were used to evaluate the ability of distinguishing the prognosis of NPC patients. The cross calibration was calculated to evaluate the external validation of established predictive model.Results The survival NPC had higher proportion in female, older age, degree of NPC differentiation, N and M stage (all P<0.05. The study factors including female, older age, and higher degree of differentiation were positively correlated with the prognosis of NPC patients (P<0.05), while N and M stage were negatively correlated with the prognosis of NPC patients (P<0.05). The factors including female (HR=4.92, 95%CI 3.58-6.75), age (HR=, 95%CI=), degree of differentiation (HR=, 95%CI=), N stage (HR=, 95%CI=) were independently associated with prognosis of NPC patients (P<0.05). Comparing with calibration curve, the constructed risk prediction model had good relations between predictive values and actual values (AUC=0.833). Additionally, the external verification results of 96 patients with NPC had a larger AUC in our established predictive model (AUC=0.851). Conclusions Female, degree of differentiation and N stage are independent factors for the prognosis of NPC patients. The risk nomogram prediction model has a good predictive ability for the survival of NPC patients, which can provide important insights into clinical prognosis for NPC patients.
Genome-wide Association Study Reveals Novel Quantitative Trait Loci and Candidate Genes of Lint Percentage in Upland Cotton Based on the CottonSNP80K Array
Authors: Chen Yu , Gao Yang , Chen Pengyun , Zhou Juan , Zhang Chuanyun , Song Zhangqiang , Huo Xuehan , Du Zhaohai , Gong Juwu , Zhao Chengjie , Wang Shengli , Zhang Jingxia , Wang Furong , Zhang Jun 
Published: June 2021

Abstract
Cotton (Gossypium spp.) is an important natural textile fiber and oilseed crop widely cultivated in the world. Lint percentage (LP, %) is one of the important yield factor, thus increasing lint percentage is a core goal of cotton breeding improvement. However, the underlying genetic and molecular mechanisms that control lint percentage in upland cotton remain largely unknown. Here, we performed a Genome-wide association study (GWAS) for LP based on phenotypic tests of 254 upland cotton accessions in four environments and BLUPs using the high-density CottonSNP80K array. A total of 41,413 high-quality single-nucleotide polymorphisms (SNPs) were screened and 34 SNPs within 22 QTLs were identified as significantly associated with lint percentage trait in different environments. In total, 175 candidate genes were identified from two major genomic loci (GR1 and GR2) of upland cotton and 50 hub genes were identified through GO enrichment and WGCNA analysis. Furthermore, two candidate/causal genes, Gh_D01G0162 and Gh_D07G0463, which pleiotropically increased lint percentage were identified and further verified its function through LD blocks, haplotypes and qRT-PCR analysis. Co-expression network analysis showed that the candidate/causal and hub gene, Gh_D07G0463, was significantly related to another candidate gene, Gh_D01G0162, and the simultaneous pyramid of the two genes lays the foundation for a more efficient increase in cotton production. Our study provides crucial insights into the genetic and molecular mechanisms underlying variations of yield traits and serves as an important foundation for lint percentage improvement via marker-assisted breeding.
Underlying IPEX Syndrome in a Patient With Idiopathic Juvenile Arthritis and Vitiligo
Authors: Mendonça Leonardo Oliveira , Chuster Adriana Ptichon dos Reis , Barros Samar Freschi , Alves Janaina Baptista , Gonçalves Victor Lucas , Yang Ariana Campos , Kalil Jorge , Toledo-Barros Myrthes Anna Maragna , Kokron Cristina Maria 
Published: June 2021

Abstract
IPEX syndrome (MIM #304790) also known as immune dysregulation, polyendocrinopathy, enteropathy, X-linked is a monogenic inborn error of immunity due to loss-of-function mutations in the forkhead box 3 (FOXP3) gene. This gene is crucial for the development, maturation and maintenance of CD4+ regulatory T (T-reg) cells. Various phenomenon mainly of autoimmune origin are characteristics of the syndrome such as enteropathy, endocrinopathies, cytopenias, renal disorders and skin manifestations (1).