bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic Profiling of Cotton Leaves in Response to Cotton Aphid Damage
Authors: Yang Yazhen , Zhong Xiao , Feng Pei , Ma Qiqi , Su Qi , Wang Xiangping , Zhang Jianmin 
Published: January 2020

Abstract
Background Cotton aphids (Aphis gossypii Glover) are regarded as one of the most harmful insect pests for cotton production. They are usually capable of causing severe yield loss through sucking cotton liquids, secreting honeydew and transmitting plant viral diseases. However, the molecular mechanism of the interaction between cotton and cotton aphids remains unclear currently. Therefore, the RNA-Seq study of cotton leaves was performed in response to cotton aphid damage at different time points (0 h, 6 h, 12 h, 24 h, 48 h and 72 h).Results A total of 9, 103 new genes were identified, and 7, 510 of them were annotated functionally. Based on the comparison results, the gene expression was analyzed according to the expression amount of genes in different samples. 24,793 differentially expressed genes were authenticated in all and their functional annotation and enrichment analysis were conducted. Compared with 0 h (without aphid damage, CK), the amount of down-regulated DEGs was largely more than that of the up-regulated genes at different time points under cotton aphid attack except for 48h. As revealed by the functional annotation of DEGs, these genes were involved in all kinds of plant biological process, including various resistance to abiotic and biotic stress, hormone metabolism, signaling transduction and transcriptional regulation.Conclusions The results revealed the molecular mechanism of the interaction between cotton and cotton aphids and would facilitate the development of plant aphid resistant cultivars.
Heart Sound Segmentation Based on Personalized Gaussian Mixture Model and Convolutional Neural Network
Authors: Xu Chun Dong , Zhou Jing , Ying Dong Wen , Hou Lei Jing , Long Qing Hua 
Published: January 2020

Abstract
Background: Heart sound segmentation is a long-standing problem in heart analysis, and it is mainly caused by noise interference and diversification of heart sounds. Faced with the challenging of heart sound segmentation, a more applicable segmentation model was studied. Methods: In this process, the optimal modified Log-spectral amplitude and wavelet were used to suppress the noise in the heart sound, and used the duration-dependent hidden Markov model based on personalized Gaussian mixture model (PGMM-DHMM) to segment the fundamental heart sound (FHS) and the non-fundamental heart sound (non-FHS). Then used the optimized Mel frequency cepstral coefficient (MFCC) to realize the classification of S1 and S2 heart sound frames through the Convolutional neural network (CNN) classifier, which can avoid the errors caused by the ambiguity of the time domain features. Results: PGMM-DHMM can segment FHS more effectively, and the accuracy is 94.3%. The CNN classifier obtained the best results in the S1 and S2 classifications, the accuracy is 90.92%, the precision of S1 is 90.76%, the recall is 91.05%, the F-measure is 90.9%, and the precision of S2 is 91.07%, the recall is 90.79%, the F-measure is 90.93%. The final segmentation accuracy is 92.92%. In addition, the experimental results further indicate that CNN has more robust performance when classifying abnormal S1 and abnormal S2. Conclusions: The PGMM-DHMM model can better segment FHS and Non-FHS. The optimization of MFCC improves the classification effect of S1 and S2, and the improvement effect by the CNN classifier is significant, especially for abnormal heart sounds. The proposed algorithm is better than other algorithms at this stage.
Factors Associated With Late Presentation to HIV Care Among Patients Attending in Public Hospitals of Mekelle City, Tigray, Ethiopia, 2018/19. Case- Control Study.
Authors: Tesfay Teklay Araya , Aregawi Desta Hailu , Geltu Hiwotea Melese , Gebrekidan Kiros Belay 
Published: January 2020

Abstract
Background The European Late Presenter Consensus Working Group, defines “late presentation” as initial presentation to HIV care with a CD4 cell count of <200 cells/μl. Globally, 36.9 million people were living with HIV, African region remains most severely affected, with nearly 1 in every 25 adults. In 2017, around 940,000 people died from AIDS-related illnesses worldwide.Methods Hospital based case control study was conducted from Nov 2018-June 2019 in public hospitals of Mekelle city. Using simple random sampling technique 114 cases and 229 controls were included in the study. Data was coded and entered to Statistical Package for Social Science version 23 for data analysis. Variables with p-value<0.25 in bivariate logistic regression were selected for multivariable logistic regression to identify factors of HIV presentation. Odds ratio was estimated with 95% CI to show strength of association and p-value <0.005 was used to declare stastical significance in multivariable analysis. Results was summarized and presented by tables, and charts. Percentage, frequency, standard deviation and mean was calculated.Result The mean age among cases, controls was 39.7(sd + 11.5), 34 (SD+10.2) respectively. Prior HIV related teaching before enrolment to care 3.48(AOR=3.48(1.57-7.70), having symptoms while starting care 3.85(AOR=3.85(1.91-774), presence of chronic illness 4.59(AOR=4.59, 95%CI: 2.17-9.74) and Being challenged during care 1.84(AOR=1.84, 95%CI: 0.13-0.77) were independent predictors of late presentation to HIV care and support.Conclusion and recommendation Prior HIV related teaching before enrolment to care, symptom while starting care, presence of chronic illness and challenge faced during care were significantly associated with late presentation. It is better to give emphasis in providing prior HIV related teaching and cousling.
The impact of parents' health behaviours on their preferences regarding vaccinations
Authors: Kulak Wojciech , Kraśnicka Jolanta , Krajewska-Kułak Elżbieta , Klimaszewska Krystyna , Cybulski Mateusz , Guzowski Andrzej , Lewko Jolanta , Łukaszuk Cecylia , Kowalczuk Krystyna , Doroszkiewicz Halina , Baranowska Anna , Krajewska-Ferishah Katarzyna , Rolka Hanna 
Published: January 2020

Abstract
Background. Health behaviours are very important factors of human life. Currently, as the number of vaccinated children in Poland and throughout Europe is decreasing, parents’ health behaviours may affect the frequency of vaccinations. The aim of this study was to assess the impact of parents’ preferred health behaviours regarding vaccinations.Methods. The study was carried out using a diagnostic survey method with an original questionnaire and the Inventory of Health Behaviours. The study included 300 parents.Results: The level of health behaviours was average in 42.3% of the respondents, low in 33%, and high in 24.7%. Convictions about immunity after contracting a disease, the need to vaccinate for all diseases, the vaccination system, the quality of the vaccines used in Poland, the universal obligation to vaccinate, and the admission of unvaccinated children to crèches and kindergartens were not statistically related to health behaviours. Significant differences in health behaviours, mainly the level of normal eating habits (p = 0.038) and positive mental attitude (p = 0.022), were found in relation to views on the toxicity of vaccines. Participants who reported that vaccines can cause autism engaged in a higher level of prophylactic behaviours. Respondents who vaccinated their children with combined vaccines had a significantly higher level of health practices. Significant or near-significant differences in health behaviour levels in various areas were found between those who sought the recommended vaccinations and those who did not.Conclusions: The health behaviour levels of the majority of the respondents were average, and the most frequent category was "positive mental attitude.” Parents who believed in the toxicity of vaccines were more concerned about proper nutrition, had a positive mental attitude, and engaged in a higher level of preventive behaviours and health practices. Parents who did not vaccinate their children had lower levels of normal eating habits. Parents who vaccinated their children with additional vaccines had a higher level of health behaviours, especially in terms of health practices.
Genetic diversity analysis and the genetic fingerprinting of 33 DUS test standard tobacco varieties
Authors: He Binbin , Geng Ruimei , Cheng Lirui , Yang Xianbin , Ge Hongmei , Ren Min 
Published: January 2020

Abstract
BackgroundAt present, the distinctness, uniformity, and stability (DUS) test of tobacco varieties still depends on the field phenotype identification, lack of simple and reliable molecular marker technology. To improve the efficiency and reliability of the identification of tobacco varieties, a molecular marker-based method was developed for the DUS test of tobacco varieties.ResultsIn total, 91 simple sequence repeats (SSR) markers with clear, polymorphic amplification bands were obtained, with polymorphism information content, Nei’s index, and Shannon’s information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties could all be distinguished from each other. Further analysis showed that a minimum of 25 markers was required to reveal the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers.ConclusionsGenetic fingerprints of the 33 study varieties were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.
Integrated analyses of early responses to radiation in glioblastoma identify new alterations in RNA processing and candidate targets to improve treatment outcomes
Authors: Choudhary Saket , Burns Suzanne , Mirsafian Hoda , LI Whenzheng , Vo Dat , Mei Qiao , Smith Andrew , Penalva Luiz 
Published: January 2020

Abstract
BackgroundHigh-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. Methods: We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. ResultsChanges at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio- resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. ConclusionsOur integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.
KRAS and BRAF Mutations as survival prognostic factors for Metastatic Colorectal Cancer patients after Lung metastasectomy: A Systematic Review and Meta-Analysis
Authors: Shahramian Iraj , Parooie Fateme , salarzaei morteza 
Published: January 2020

Abstract
Introduction While knowledge has grown extensively regarding the impact of mutations on colorectal cancer prognosis, their role in outcomes after pulmonary metastasectomy (PM) remains minimally understood. Therefore, in this paper, we conduct a systematic review and meta-analysis of retrospective and prospective studies to evaluate whether KRAS or BRAF mutation status can be independent predictors in colorectal cancer patients undergoing complete lung metastasis surgery.Methods A systematic literature review was performed to identify articles reporting overall survival (OS) of patients who underwent lung metastasectomy for colorectal cancer lung metastases (CRLM), stratified according to KRAS and BRAF mutational status. Hazard ratios (HRs) from multivariate analyses were pooled in the meta-analysis.Results 9 studies, including 1833 patients, were eligible for the meta-analysis. Based on the random effect model, the total frequency of KRAS mutations in 1305 patients who had undergone the lung metastasectomy was 45% and the total 5-year OS in these patients was 55.7%. five of them reported OS stratified according to KRAS mutation. The pooled analysis revealed that KRAS mutation was negatively associated with OS (HR, 1.674; 95% confidence interval [CI], 1.341-2.089; P < .001). the rate of KRAS mutations were lower in the studies with higher male to female ratio. There was statistically significant linear trend in univariate meta-regression to explain effect size variation by male to female ratio of study with coefficient = 0.47 (95% CI 0.03, 0.91), P = 0.03. disease free survival (DFS), thoracic metastases and origin of primary tumor were significantly influenced by KRAS mutation status.Conclusions Our meta-analysis confirms the KRAS mutation as a strong and predictive biomarker which makes overall survival lower in patients with colorectal cancer undergoing pulmonary metastasis surgery. Certainly, this interesting evidence represents the first step towards a deeper understanding of the molecular mechanisms underlying tumor behavior and patient outcomes in a subgroup of clinically selected colorectal cancer patients. By considering tumor molecular characteristics and other clinical-pathological factors, our results confirm the use of new therapeutic models to predict outcomes of patients undergoing colorectal lung metastasis surgery and to isolate both systemic and loco-regional treatment strategies.
Comparing VBM and ROI Analyses for Detection of Gray Matter Abnormalities in Patients with Bipolar Disorder using MRI
Authors: Seyedi Seyedehsomayyeh , Jafari Raheleh , Talaei Ali , Naseri Shahrokh , Momennezhad Mahdi , Moghaddam Maliheh Dadgar , Akbari-Lalimi Hossein 
Published: January 2020

Abstract
Background: With the increasing efforts to a better understanding of psychiatric diseases, detection of brain morphological alterations are necessary. This study compared two methods-voxel based morphometry (VBM) and region of interest (ROI) analyses- to identify significant gray matter changes of patients with bipolar disorder type I (BP I).
Methods: The structural MRI were obtained in a total of 50 subjects (25 healthy subjects with a mean age of 34.48±8.32 years as a control group and 25 patients with a mean age of 37.68±10.88 years). We compared the gray matter alteration results obtained by VBM analysis using the DARTEL approach with those obtained using ROI analysis which applies three probabilistic brain atlases namely, hammers, lpba40, and neuromorphometrics atlases. All analyses were conducted via the Computational Anatomy Toolbox (CAT12) implemented in Statistical Parametric Mapping (SPM12) software package.
Results: The VBM findings suggested that gray matter reductions in left precentral and right precuneus of the patients compared to healthy subjects(α=0.0005, uncorrected). However, No regions reached the level of significance in ROI analysis using the three atlases (α=0.0005).
Conclusion: It can be concluded that VBM analysis seems to be more sensitive to partial changes in this study. If ROI analysis is employed in studies to detect structural brain alterations between groups, it is highly recommended to use VBM analysis besides.
Keywords: Voxel-Based Morphometry; ROI Analysis; bipolar disorder; MRI; brain.
MiR-103a-3p antagonism attenuates pneumonia via inactivating the PI3K/AKT/NF-κB signaling pathway by targeting PTEN
Authors: Xu Lin , Song Qingying , Ouyang Zhanghong , Zhang Xiangyan , Zhang Cheng 
Published: January 2020

Abstract
Pneumonia accounts for approximately 15% mortalities in adolescents worldwide. MicroRNAs (miRNAs) regulate numerous diseases including pneumonia. miRNA and mRNA expression levels were detected by real time polymerase chain reaction (RT-qPCR). Protein expression levels were determined by enzyme-linked immunosorbent assay (ELISA) and western blot. The interaction between phosphatase and tensin homolog on chromosome ten (PTEN) and miR-103a-3p was explored by dual luciferase reporter assay. Cell viability and cell apoptosis were detected by cell Counting Kit-8 (CCK-8) and flow cytometry. Herein, we discovered that PTEN was decreased and miR-103a-3p was overexpressed in Ana-1 cells of in vitro pneumonia model. miR-103a-3p downregulated the expression levels of PTEN. AntagomiR-103a-3p reversed the increased cell apoptosis and decreased cell viability and inflammatory cytokine expression levels (tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and IL-6) induced by LPS in Ana-1 cells by PTEN. AntagomiR-103a-3p inhibited the activation of PTEN/PI3K/AKT/NF-κB signaling pathway induced by LPS in Ana-1 cells. Taken together, our findings exhibited that miR-103a-3p attenuated LPS induced pneumonia by blocking the activation of PTEN/PI3K/AKT/NF-κB signaling pathway and the following cell apoptosis as well as release of proinflammatory cytokines, suggesting that miR-103a-3p might serve as a novel therapeutic target for the treatment of pneumonia.
A clinical study of musculoskeletal dysfunction in targets of workplace bullying
Authors: Buhaug Kristin , Magerøy Nils , Einarsen Ståle , Assmus Jörg , Kvåle Alice 
Published: January 2020

Abstract
Background – The study was designed to examine whether patients exposed to workplace bullying have clinically evident dysfunction in their musculoskeletal system. Furthermore, we wanted to explore the relationship between clinical findings and self-reported data on mental and musculoskeletal symptoms in the included patients. Methods – Targets of workplace bullying referred to an occupational outpatient clinic in Norway in the period August 2011 to February 2017 were invited to participate in the study. The included patients had a high degree of post-traumatic stress symptoms; mean score on the IES-R was 42.9, well above the suggested cut-off at 33 points for Posttraumatic stress disorder (PTSD). The patients underwent a clinical program, and a physiotherapist used the Global Physiotherapy Examination 52 (GPE-52), a standardized test battery with 13 sub-domains, and five main domains examining posture, respiration, movement, muscle and skin. Self–report questionnaires were used to assess subjective musculoskeletal (MSI) and psychological symptoms (PI), as well as anxiety and depression (HADS) and post-traumatic stress symptoms (IES-R). Results – Altogether 144 patients were included in the study, whereof 65 (45%) had an ongoing musculoskeletal disorder (MSD). Mean scores on the physiotherapy examination showed dysfunction in nine of 13 subdomains. The total GPE-52 sum-score was comparable to patients sick-listed with long-lasting MSD, and significantly higher (worse) than in healthy persons. The physical examination indicated that the bullied patients had reduced flexibility and ability to relax, as well as restricted respiration and tense and painful muscles. The total GPE-52 sum-score as well as the main domains Movement and Muscle had significant correlations with all self-reported health variables. The strongest correlations were found between Movement and Muscle, and PI and HADS (r ≥ 0.32). Conclusions – Patients exposed to workplace bullying had a high degree of clinically evident dysfunction in the musculoskeletal system, comparable to patients with MSD. These findings confirm previous questionnaire studies on physical health in workers exposed to workplace bullying. The extent of the musculoskeletal problems revealed in our study clearly indicates that future health services to these patients should be multi-dimensional and include bodily assessment.
An interpretable machine learning method for detecting novel pathogens
Authors: Zhao Xiaoyong , Wang Ningning 
Published: January 2020

Abstract
Background: According to the World Health Organization (WHO), infectious diseases continue to one of the leading causes of death worldwide. Since the core microbiota flora of humans is largely diverse and horizontal gene transfer (HGT), it is very challenging to determine whether a particular bacterial strain is commensal or pathogenic to humans. With the latest advances in next-generation sequencing (NGS) technology, bioinformatics tools and techniques using NGS data have increasingly been used for the diagnosis and monitoring of infectious diseases. Even if the biological background is not available, the machine learning method can still infer the pathogenic phenotype from the NGS readings, independent of the database of known organisms, and being studied intensively.However, previous methods have not considered opportunistic pathogenic and interpretability of black box model, are not well suited for clinical requirements. Results:In this study, we proposed a novel interpretable machine learning approach (IMLA) to identify the pathogenicity of bacterial genomes: human pathogens (HP), opportunistic pathogenicity (OHP) or non-pathogenicity(NHP), then use the following model-agnostic interpretation methods to interpret model: feature importance, accumulated local effects and Shapley values, due to the model interpretability is essential for healthcare applications. To our knowledge, our paper is the first attempt to infer opportunistic pathogenicity and explain the model. Conclusions: According to the simulation results, our approach IMLA can be a great addition to detect novel pathogens. Keywords: interpretable; machine learning; bacterial pathogen;