bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of Clinical Identifications With Deep Transferrable Imaging Feature Representations Can Help Predict Prostate Cancer Aggressiveness and Outcome
Authors: Bao Jie , Hou Ying , Zhi Rui , Wang Xi-ming , Hu Chun-hong , Zhang Yu-Dong 
Published: January 2021

Abstract
Background: A pretreatment risk stratification of prostate cancer (PCa) is important for determining appropriate treatment option and prognostic prediction. Although numerous quantifiable approaches can provide fundamental insights in PCa, a clinical tool should leverage the integration of all data representations to enables detailed assessment. We developed a generalizable machine learning platform, designated PI-Risk, which incorporates clinicians’ prior identifications with deep transferrable imaging feature representations into predictive models for PCa Gleason grade. Methods: A retrospective study included 1442 biopsy-naïve patients from two tertiary care medical centers between January 2014 and December 2019. Model performance was typically evaluated against a “ground truth” with imaging-histopathologic annotations using receiver operating characteristic (ROC). Detection rates such as true positive, true negative, false positive and false negative rate were reported using a confusion matrix analysis. The Cox model’s performance was evaluated based on Harrell’s concordance index (C-index), calibration curves and Kaplan–Meier survival analysis. Results: In multinomial regression analyzing model, predicted IntraT-Rad G0 (odds ratio [OR], 3.01; 95% confidence intervals [CIs], 2.74–3.34, p < 0.001) and PI-RADS score 2 (OR, 2.88; 95% CIs, 2.47–3.17, p = 0.002) were two independent predictors of G0 stage. Predicted IntraT-Rad G1 (OR, 2.42; 95% CIs, 2.13–2.86, p < 0.001) and PSA 4-10 ng/ml (OR, 1.29; 95% CIs, 1.06–1.43, p = 0.037) were two independent predictors of G1 stage. PSA 10-20 ng/ml (OR, 1.52; 95% CIs, 1.32–1.67, p = 0.005), Predicted PeriT-DLR-SqueezeNet G1 (OR, 1.31; 95% CIs, 1.14–1.52, p = 0.009) and Predicted IntraT-Rad G3 (OR, 1.29; 95% CIs, 1.07–1.44, p = 0.011) were three independent predictors of G2 stage. PI-RADS score 5 (OR, 1.84; 95% CIs, 1.74–2.31, p < 0.001) were the independent predictor of G3 stage. PI-RADS score 5 (OR, 2.84; 95% CIs, 2.62–3.17, p < 0.001) and PSA > 100 ng/ml (OR, 1.69; 95% CIs, 1.36–1.83, p = 0.007) were two independent predictors of G4 stage. And the multivariate Cox analysis model shows that, among the 5 pretreatment risk factors (age, PSA, PCa location, PI-RADS score and PI-Risk score), PSA ≥ 20 ng/ml (OR, 1.58; 95% CI, 1.20-2.08; p = 0.001) and PI-Risk ≥ G3 (OR, 1.45; 95% CI, 1.12-1.88; p = 0.005) were the independent predictors of BCR.Conclusions: We concluded that the PI-Risk can offer a noninvasive alternative tool to stratify PCa aggressiveness. This enables a step towards PCa risk stratification.
Genome-Wide Perturbations of Alu Expression and Alu-Associated Post-Transcriptional Regulations Find a Uniqueness in Oligodendroglioma
Authors: Hwang Taeyoung , Kim Sojin , Chowdhury Tamrin , Yu Hyeon Jong , Kim Kyung-Min , Kang Ho , Won Jae Kyung , Park Sung-Hye , Shin Joo Heon , Park Chul-Kee 
Published: January 2021

Abstract
BackgroundAlu is a primate-specific repeat element in the human genome and has been increasingly appreciated as a regulatory element in many biological processes. But the role of Alu has not been studied comprehensively in brain tumor because an evolutionary perspective has been the subject of little research in brain tumor. We aim to investigate the relevance of Alu to the gliomagenesis.MethodsUsing a total of 41 pairs of neurotypicial brain tissue samples and samples of diverse gliomas, we performed strand-specific RNA-seq and analyzed two Alu-associated post-transcriptional regulations, A-to-I editing and circular RNAs, and Alu expression in a genome-wide way. ResultsWe found that while both A-to-I editing and circular RNA are decreased overall in gliomas, grade 2 oligodendrogliomas do not show this same pattern of global changes. Instead, in comparison with other gliomas, oligodendrogliomas showed a higher proportion of perturbed Alu RNA. Adenosine deaminase acting on RNA 2 (ADAR2) was down-regulated in gliomas other than grade 2 oligodendrogliomas, contributing to the observed Alu-associated perturbation. ConclusionsOur results demonstrate that Alu is associated with glioma development and grade 2 oligodendroglioma exhibits a unique pattern of Alu-associated post-transcriptional regulations, which provides an insight to gliomagenesis from the perspective of an evolutionary genetic element.
Raising Employment and Mental Well-being Among People With Disadvantages – Results of a Hungarian Project
Authors: Kuklek Noemi Meisznerne , Cséplő Máté , Pozsonyi Eszter , Pusztafalvi Henriette 
Published: January 2021

Abstract
Background: People with disadvantages are a high-risk group of unemployment or underemployment. Disadvantages include disability, under-education, being a single parent or a member of a minority, etc. Effective labor market programs could be a key in raising employment and quality of life among this high-risk group of the society. The TOP 6.8.2.-15-NA1 project is one of the main Hungarian labor market programs. Methods: The project’s primary aims are increasing the employability of disadvantaged unemployed and supporting the efficiency of job-seeking. The sample of our study contains participants of the project (n=300), based in Zala County, Hungary. Results: We could identify low educated participants and older participants as higher risk groups of long-term unemployment. Conclusions: We emphasize the role of these services in the long-term individual success of participants. Improving the employment rate for people with disadvantages is a critical factor for enhancing the quality of life for individuals with disadvantages.
Feasibility study of a 3D-printed personalized immobilization device integrating a patient-specific probe holder for prostate radiotherapy combined with adjuvant MR-guided transperineal ultrasound hyperthermia
Authors: Dipasquale Giovanna , Guillemin Pauline Coralie , Jaccard Maud , Uiterwijk Johannes W.E. , Lorton Orane , Tsoutsou Pelagia , Poletti Pierre-Alexandre , Gariani Joanna , Salomir Rares Vincent , Zilli Thomas 
Published: January 2021

Abstract
The authors have requested that this preprint be removed from Research Square.
Research on Job Satisfaction and Influencing Factors of Scientific Researchers in S Hospital of Guizhou Province
Authors: Fu Shanyong , Nie Yujie , Chen Hui , Nie Yingjie 
Published: January 2021

Abstract
Objective: To analyze the job satisfaction of hospital researchers and its influencing factors. Methods: A questionnaire survey was conducted to investigate the job satisfaction of 276 researchers in S Hospital of Guizhou Province from May to July of 2020. Independent sample T test and one-way variance were used to analyze the satisfaction of researchers with demographic characteristics. Multiple linear regression analysis was used to analyze the factors affecting the satisfaction of researchers. Results: The average score of the hospital researchers' overall job satisfaction was 3.64±0.42, which was at the satisfaction level. The six dimensions, including self-efficacy, scientific research system and salary and welfare, were significantly positively correlated with overall satisfaction (r>0.4).The differences in overall satisfaction of different ages were statistically significant (P=0.013<0.05).The linear regression analysis found that all the six dimensions had a significant positive impact on the overall job satisfaction, of which the scientific research system had the most significant impact. Conclusion: We can improve the hospital scientific research level by improving the salary and welfare level of scientific research staff, changing the scientific research management concept, establishing and perfecting the scientific research management system, and taking targeted measures for the researchers with low satisfaction.
Neuropathic&nbsp;pain: a principal component of pain that should not be neglected in ankylosing spondylitis
Authors: zhou Ling , li ting , wu xin , Lu Hongjuan , Lin Li , Ye Lingying , yin jian , zhao juan , wang xiuwen , bian jianye , Xu Huji 
Published: January 2021

Abstract
Background

Pain in AS is currently considered an inflammatory pain (IP). However, it was found that some patients still had the sensation of pain even without inflammation. Our study was to investigate whether ankylosing spondylitis (AS) pain has a neuropathic pain (NeP) component.
Methods

The study consisted of three parts. The first included 182 AS patients to assess neuropathic pain in AS patients. The second included63 patients to evaluate pain improvement after etanercept therapy. The third included 20 AS patients and 10 healthy controls (HCs) to detect serum neurotransmitters.
Results

We found out that 55 paitents (30.21%) had possible NeP, and 14 (7.70%) had definite NeP. There were significant differences between the groups with respect to nocturnal pain (NP), peripheral pain (PP), total back pain (TBP), BASDAI, ASDAS-CRP, HAD-A, HAD-D and BASDAI-fatigue but not CRP concentrations. Principal component analysis (PCA) of AS pain revealed that the weight of NeP was greater than PP in the first principal component (0.703 vs 0.639). Structural equation modelling (SEM) revealed that NeP altered disease activity (β = 0.62, P < 0.001), which influenced psychological status (β = 0.42, P < 0.001). Of 63 patients who used etanercept for 3 months, significant improvement was found in NP, TBP and PP (all P < 0.0001) but not in PDQ (10.60 ± 6.85vs 9.98 ± 6.40, P = 0.067). Serum norepinephrine concentrations in patients with positive PDQ were greater than those in patients with negative PDQ and HC.
Conclusions

We conclude that NeP contributes to pain in AS patients.
Genetic Characterization of Plasmodium vivax Isolates from Pakistan Using Circumsporozoite Protein (pvcsp) and Merozoite Surface Protein-1 (pvmsp-1) genes as genetic markers
Authors: Bibi Zainab , Fatima Anam , Rani Rehana , Maqbool Ayesha , Khan Samea , Naz Shumaila , Waseem Shahid 
Published: January 2021

Abstract
Background: Plasmodium vivax contributes to over 70% malaria burden in Pakistan, but limited data exists on various aspects including genetic diversity of the parasite as compared to other parts of the world. Since the information about the genetic diversity of P. vivax assists to understand the population dynamics of the parasite, the current study was designed to understand population divergence of Plasmodium vivax in Pakistan using circumsporozoite protein (pvcsp) and merozoite surface protein-1 (pvmsp-1) genes as molecular markers. Methods: The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates followed by DNA sequencing of only 35 and 30 respective amplified PCR products for both pvcsp and pvmsp-1 genes. Genetic diversity and polymorphism were analyzed using ChromasPro, ClustalW, MEGA7, DnaSP v.5 and WebLogo programs. Results: The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates and resulting the PCR products ranging from 900 to 1100 bp for pvcsp and ~400bp for pvmsp-1 genes, respectively. In the central-repeat region (CRR) of pvcsp gene, sequences comprised of four variable repeats of PRMs, out of which GDRADGQPA (PRM1), GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~400bp) of block 2 of pvmsp-1 gene depicted high level of diversity.Conclusion: The results revealed the polymorphism and genetic diversity especially at the CRR of pvcsp and block 2 of pvmsp-1 genes respectively. The base-line data presented here warrants future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of population dynamics of P. vivax that will help to control malaria at individual and community level.
Development of Integration Indexes to Determine the Extent of Family Planning and Child Immunization Services Integration in Health Facilities in Urban Areas of Nigeria
Authors: Sheahan Kate L. , Orgill-Meyer Jennifer , Speizer Ilene , Curtis Siân , Paul John , Weinberger Morris , Bennett Antonia V. 
Published: January 2021

Abstract
Background Integrating family planning into child immunization services may address unmet need for contraception by offering family planning information and services to postpartum women during routine child immunization visits. However, policies and programs promoting integration are often based on insubstantial or conflicting evidence about its effects on service delivery and health outcomes. While integration models vary, many studies measure integration as binary (a facility is integrated or not) rather than a multidimensional and varying continuum. It is thus challenging to ascertain the determinants and effects of integrated service delivery. This study creates Facility and Provider Integration Indexes, which measure capacity to support integrated family planning and child immunization services and applies them to analyze the extent of integration across 400 health facilities. Methods This study utilizes cross-sectional health facility (N= 400; 58% hospitals, 42% primary healthcare centers) and healthcare provider (N= 1,479) survey data that were collected in six urban areas of Nigeria for the impact evaluation of the Nigerian Urban Reproductive Health Initiative. Principal Component Analysis was used to develop Provider and Facility Integration Indexes that estimate the extent of integration in these health facilities. The Provider Integration Index measures provider skills and practices that support integrated service delivery while the Facility Integration Index measures facility norms that support integrated service delivery. Index scores range from zero (low) to ten (high). Results Mean Provider Integration Index score is 5.42 (SD 3.10), and mean Facility Integration Index score is 6.22 (SD 2.72). Twenty-three percent of facilities were classified as having low Provider Integration scores, 32% as medium, and 45% as high. Fourteen percent of facilities were classified as having low Facility Integration scores, 38% as medium, and 48% as high. Conclusion Many facilities in our sample have achieved high levels of integration, while many others have not. Results suggest that using more nuanced measures of integration may (a) more accurately reflect true variation in integration within and across health facilities, (b) enable more precise measurement of the determinants or effects of integration, and (c) provide more tailored, actionable information about how best to improve integration. Overall, results reinforce the importance of utilizing more nuanced measures of facility-level integration.
Gemini surfactant assisted synthesis of mesoporous Mn/Mg bimetal doped TiO2 nanomaterial: Characterization and photocatalytic activity studies under visible light irradiation
Authors: Miditana Sankara Rao , Tirukkovalluri Siva Rao , Raju Imandi Manga , Alim Shaik Abdul , Jaishree Genji , Chippada M.L.V. Prasanna 
Published: January 2021

Abstract
The present work mainly aimed to synthesize different weight percentages (0.25-1.00 wt%) of Manganese (Mn2+) and Magnesium (Mg2+) bimetal ions doped TiO2 nanomaterial assisted with different weight percentages (5-15 wt%) of Gemini surfactant (GS) using sol-gel method. The bimetal doped and undoped TiO2 photocatalysts were characterized by X-ray Diffraction, Scanning Electron Microscopy, Energy Dispersive X-ray Spectroscopy, Fourier Transform Infrared Spectroscopy (FT-IR), UV-Visible Diffused Reflectance Spectroscopy, Transmission Electron Microscopy, Brunauer-Emmett-Teller surface area analyzer, and Photoluminescence Spectroscopy. Characterization results revealed that mesoporous multi-particle anatase TiO2 nanoparticles with a narrowed band gap, small particle size, and high surface area were formed due to the combined effect of Mn2+/Mg2+ bimetal ions doping and effective encapsulation of GS over the initially formed TiO2 nanoparticles. The surface elemental composition of the 0.25 wt% Mn2+ and 1.00 wt% Mg2+ bimetal doped TiO2 in the presence of 10 wt% of GS (after calcination) revealed the presence of both the metal dopants Mn2+ and Mg2+ along with the Ti and O and their chemical interactions were further confirmed by FT-IR results. The photocatalytic activity of these catalysts was assessed by the degradation of Methyl Red using visible light irradiation. To understand the effect of different reaction parameters on the photocatalytic activity of the nanocatalysts such as the dopant concentration, surfactant concentration, catalyst dosage, solution pH, and initial dye concentrations were investigated and optimized to achieve the best performance. The photoluminescence results conclude that OH radicals are the crucial reactive species responsible for oxidative photocatalytic degradation of Methyl Red.
RASMA: A Reverse Search Algorithm for Mining Maximal Frequent Subgraphs
Authors: Salem Saeed , Alokshiya Mohammed , Hasan Mohammad Al 
Published: January 2021

Abstract
Background: Given a collection of coexpression networks over a set of genes, identifying subnetworks that appear frequently is an important research problem known as mining frequent subgraphs. Maximal frequent subgraphs is a representative set of frequent subgraphs; A frequent subgraph is maximal if it does have a super-graph that is frequent. In the bioinformatics discipline, methodologies for mining frequent and/or maximal frequent subgraphs can be used to discover interesting network motifs that elucidate complex interactions among genes, reflected through the edges of the frequent subnetworks. Further study of frequent coexpression subnetworks enhances the discovery of biological modules and biological signatures for gene expression and disease classification.Results: We propose a reverse search algorithm, called RASMA, for mining frequent and maximal frequent subgraphs in a given collection of graphs. A key innovation in RASMA is a connected subgraph enumerator that uses a reverse-search strategy to enumerate connected subgraphs of an undirected graph. Using this enumeration strategy, RASMA obtains all maximal frequent subgraphs very efficiently. To overcome the computationally prohibitive task of enumerating all frequent subgraphs while mining for the maximal frequent subgraphs, RASMA employs several pruning strategies that substantially improve its overall runtime performance. Experimental results show that on large gene coexpression networks, the proposed algorithm efficiently mines biologically relevant maximal frequent subgraphs.Conclusion: Extracting recurrent gene coexpression subnetworks from multiple gene expression experiments enables the discovery of functional modules and subnetwork biomarkers. We have proposed a reverse search algorithm for mining maximal frequent subnetworks. Enrichment analysis of the extracted maximal frequent subnetworks reveals that subnetworks that are frequent are highly enriched with known biological ontologies.
Overexpression of CCNE1 confers a poorer prognostic in triple negative breast cancer identified by bioinformatic analysis
Authors: Yuan Qianqian , Zheng Lewei , Liao Yiqin , Wu Gaosong 
Published: January 2021

Abstract
Background. Triple-negative breast cancer (TNBC) is a major subtype of breast cancer. Due to the lack of effective therapeutic targets, the prognosis is poor. In order to find an effective target, despite many efforts, the molecular mechanisms of TNBC are still not well understood which remain to be a profound clinical challenge.Methods. To identify the candidate genes in the carcinogenesis and progression of TNBC, microarray datasets GSE36693 and GSE65216 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and functional and pathway enrichment analyses were performed using the Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) databases via DAVID. We constructed the protein-protein interaction network (PPI) and the performed the module analysis using STRING and Cytoscape. Then we reanalyzed the selected DEGs genes and the survival analysis was performed using cBioportal.Results. A total of 140 DEGs were identified, consisting of 69 upregulated genes and 71 downregulated genes. Three hub genes were up-regulated among the selected genes from PPI and biological process analysis uncovered the fact that these genes were mainly enriched in p53 pathway and the pathways in cancer. Survival analysis showed that only CCNE1 may be involved in the carcinogenesis, invasion or recurrence of TNBC. Conclusion. CCNE1 could confer a poorer prognostic in TNBC identified by bioinformatic analysis and play key roles in the progression of TNBC which may contribute potential targets for the diagnosis, treatment and prognosis assessment of TNBC.
Epidemiological and Clinical Characteristics of Patients with COVID-19 in Arak, Iran
Authors: Mousavi-Hasanzadeh Morteza , Sarmadian Hossein , Safi Fatemeh , Jamalian Mohammad , Almasi-Hashiani Amir 
Published: January 2021

Background:
The number of confirmed cases of COVID-19 is increasing. Here we present the clinical characteristics and outcomes of COVID-19 in Arak, Iran.

Methods:
In this study, 139 COVID-19 confirmed cases from 15 February to 15 March 2020 in Arak, Iran, were investigated. The clinical signs, symptoms, laboratory and radiological findings and outcomes were analyzed.

Results:
The mean age of the patients was 55.41 years (S.D.: 17.11) and 55.40% of them were males. 26.81% of patients had recently traveled to other epidemic cities. The most common clinical manifestations were fever (71.64%), cough (67.16%), shortness of breath (55.22%), muscle ache (50.00%) and the most prevalent complications were taste and smell disruption (29.5%), weakness (22.3%), anorexia (20.1%) and acute respiratory distress syndrome (ARDS) (15.8%). Almost half of the patients had lymphopenia, an elevated level of erythrocyte sedimentation rate (ESR) and C - reactive protein (CRP). In terms of outcome, 9.3% of patients needed an ICU admission as a result of ARDS in which 15.32% were directly admitted to the ICU. 43.2% of patients have been discharged and the case fatality rate (CFR) was estimated as 11.5%.

Conclusion:
COVID-19 pneumonia usually occurred at an age older than 50 years and in the male gender. The most common initial clinical laboratories and radiological presentations are fever, cough, lymphopenia with elevated CRP and ESR and Bilateral mixed ground-glass opacities with consolidation.