bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accounting for grouped predictor variables or pathways in high-dimensional penalized Cox regression models
Authors: Belhechmi Shaima , Bin Riccardo De , Rotolo Federico , Michiels Stefan 
Published: July 2020

AbstractBackgroundThe standard lasso penalty and its extensions are commonly used to develop a regularized regression model while selecting candidate predictor variables on a time-to-event outcome in high-dimensional data. However, these selection methods focus on a homogeneous set of variables and do not take into account the case of predictors belonging to functional groups; typically, genomic data can be grouped according to biological pathways or to different types of collected data. Another challenge is that the standard lasso penalisation is known to have a high false discovery rate.ResultsWe evaluated different penalizations in a Cox model to select grouped variables in order to further penalize variables that, in addition to having a low effect, belong to a group with a low overall effect; and to favor the selection of variables that, in addition to having a large effect, belong to a group with a large overall effect. We considered the case of prespecified and disjoint groups and proposed diverse weights for the adaptive lasso method. In particular we proposed the product Max Single Wald by Single Wald weighting (MSW*SW) which takes into account the information of the group to which it belongs and of this biomarker. Through simulations, we compared the selection and prediction ability of our approach with the standard lasso, the composite Minimax Concave Penalty (cMCP), the group exponential lasso (gel), the IntegrativeL1-Penalized Regression with Penalty Factors (IPF-Lasso), and the Sparse Group Lasso (SGL) methods. In addition, we illustrated the methods using gene expression data of 614 breast cancer patients.ConclusionsThe adaptive lasso with the MSW*SW weighting method incorporates both the information in the grouping structure and the individual variable. It outperformed the competitors by reducing the false discovery rate without severely increasing the false negative rate.
Prediction of heart disease and classifiers’ sensitivity analysis
Authors: Almustafa Khaled Mohamad 
Published: July 2020

Abstract
Background
Heart disease (HD) is one of the most common diseases nowadays, and an early diagnosis of such a disease is a crucial task for many health care providers to prevent their patients for such a disease and to save lives. In this paper, a comparative analysis of different classifiers was performed for the classification of the Heart Disease dataset in order to correctly classify and or predict HD cases with minimal attributes. The set contains 76 attributes including the class attribute, for 1025 patients collected from Cleveland, Hungary, Switzerland, and Long Beach, but in this paper, only a subset of 14 attributes are used, and each attribute has a given set value. The algorithms used K- Nearest Neighbor (K-NN), Naive Bayes, Decision tree J48, JRip, SVM, Adaboost, Stochastic Gradient Decent (SGD) and Decision Table (DT) classifiers to show the performance of the selected classifications algorithms to best classify, and or predict, the HD cases.

Results
It was shown that using different classification algorithms for the classification of the HD dataset gives very promising results in term of the classification accuracy for the K-NN (K = 1), Decision tree J48 and JRip classifiers with accuracy of classification of 99.7073, 98.0488 and 97.2683% respectively. A feature extraction method was performed using Classifier Subset Evaluator on the HD dataset, and results show enhanced performance in term of the classification accuracy for K-NN (N = 1) and Decision Table classifiers to 100 and 93.8537% respectively after using the selected features by only applying a combination of up to 4 attributes instead of 13 attributes for the predication of the HD cases.

Conclusion
Different classifiers were used and compared to classify the HD dataset, and we concluded the benefit of having a reliable feature selection method for HD disease prediction with using minimal number of attributes instead of having to consider all available ones.
Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus
Authors: Ren Li , Yan Xiaojing , Gao Xin , Cui Jialin , Yan Pengcheng , Wu Chang , Li Wuhui , Liu Shaojun 
Published: July 2020

Abstract
Background
Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animals.

Results
Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. By comparing the expression of BSB- and TC- homoeologous genes between the two reciprocal cross hybrids, we identified 49–348 differentially expressed BSB-homoeologous genes and 54–354 differentially expressed TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonad, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TBF3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BTF3. These results further improve AS prediction at the homoeolog level. The various AS patterns in bmpr2a belonging to the bone morphogenetic protein family were selected as AS models to investigate the expression diversity and its potential effects to body shape traits.

Conclusions
The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects were the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.
Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.
Authors: Tian Haiying , Guo Feng , Zhang Zhimeng , Ding Hong , Meng Jingjing , Li Xinguo , Peng Zhenying , Wan Shubo 
Published: July 2020

Abstract
Background
Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown.

Results
A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners.

Conclusions
This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.
Group testing performance evaluation for SARS-CoV-2 massive scale screening and testing
Authors: Nalbantoglu Ozkan Ufuk 
Published: July 2020

Abstract
Background
The capacity of the current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in the current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important as the symptomatic cases in the spread of the disease. Group testing is a feasible and promising approach when the resources are scarce and when a relatively low prevalence regime is observed on the population.

Methods
We employed group testing with a sparse random pooling scheme and conventional group test decoding algorithms both for exact and inexact recovery.

Results
Our simulations showed that significant reduction in per case test numbers (or expansion in total test numbers preserving the number of actual tests conducted) for very sparse prevalence regimes is available. Currently proposed COVID-19 group testing schemes offer a gain up to 15X-20X scale-up. There is a good probability that the required scale up to achieve massive scale testing might be greater in certain scenarios. We investigated if further improvement is available, especially in sparse prevalence occurrence where outbreaks are needed to be avoided by population scans.

Conclusion
Our simulations show that sparse random pooling can provide improved efficiency gains compared to conventional group testing or Reed-Solomon error correcting codes. Therefore, we propose that special designs for different scenarios could be available and it is possible to scale up testing capabilities significantly.
Management of work-related common mental disorders in general practice: a cross-sectional study
Authors: Rivière M. , Toullic Y. , Lerouge P. , Blanchon T. , Leroyer A. , Plancke L. , Prazuck T. , Melchior M. , Younès N. 
Published: July 2020

Abstract
Background
General practitioners (GPs) often manage individuals with work-related common mental disorders (CMD: depressive disorders, anxiety and alcohol abuse). However, little is known about the ways in which they proceed. The aim of this study is to analyze GPs’ management and patterns of referral to other health professionals of patients with work-related CMD and associated factors.

Method
We used data from a cross-sectional study of 2027 working patients of 121 GPs in the Nord – Pas-de-Calais region in France (April – August 2014). Statistical analyses focused on patients with work-related CMD detected by the GP and examined the ways in which GPs managed these patients’ symptoms. Associations between patient, work, GP and contextual characteristics and GPs’ management were explored using modified Poisson regression models with robust variance.

Results
Among the 533 patients with work-related CMD in the study, GPs provided psychosocial support to 88.0%, prescribed psychotropic treatment to 82.4% and put 50.7% on sick leave. Referral rates to mental health specialists and occupational physicians were respectively 39.8 and 26.1%. Several factors including patients’ characteristics (occupational and sociodemographic), GPs’ characteristics and environmental data were associated with the type of management used by the GP.

Conclusion
Our study emphasizes the major and often lonesome role of the GP in the management of patients with work-related CMDs. Better knowledge of the way GPs manage those patients could help GPs in their practice, improve patients care and be a starting point to implement a more collaborative care approach.
Use of resuscitation promoting factors to screen for tuberculosis infection in household-exposed children in The Gambia
Authors: van Loon W. , Gomez M. P. , Jobe D. , Franken K. L. M. C. , Ottenhoff T. H. M. , Coninx M. , Kestens L. , Sutherland J. S. , Kampmann B. , Tientcheu L. D. 
Published: July 2020

Abstract
Background
Interferon-γ release assays (IGRA) with Resuscitation promoting factor (Rpf) proteins enhanced tuberculosis (TB) screening and diagnosis in adults but have not been evaluated in children. Children often develop paucibacillary TB and their immune response differs from that of adults, which together affect TB disease diagnostics and immunodiagnostics. We assessed the ability of Rpf to identify infection among household TB-exposed children in The Gambia and investigated their ability to discriminate Mycobacterium tuberculosis complex (MTBC) infection from active TB disease in children.

Methods
Detailed clinical investigations were done on 93 household TB-exposed Gambian children and a tuberculin skin test (TST) was administered to asymptomatic children. Venous blood was collected for overnight stimulation with ESAT-6/CFP-10-fusion protein (EC), purified protein derivative and RpfA, B, C, D and E. Interferon gamma (IFN-γ) production was measured by ELISA in supernatants and corrected for the background level. Infection status was defined by IGRA with EC and TB disease by mycobacterial confirmation and/or clinical diagnosis. We compared IFN-γ levels between infected and uninfected children and between infected and TB diseased children using a binomial logistic regression model while correcting for age and sex. A Receiver Operating Characteristics analysis was done to find the best cut-off for IFN-γ level and calculate sensitivity and specificity.

Results
Interferon gamma production was significantly higher in infected (IGRA+, n = 45) than in uninfected (IGRA-, n = 20) children after stimulation with RpfA, B, C, and D (P = 0.03; 0.007; 0.03 and 0.003, respectively). Using RpfB and D-specific IFN-γ cut-offs (33.9 pg/mL and 67.0 pg/mL), infection was classified with a sensitivity-specificity combination of 73–92% and 77–72% respectively, which was similar to and better than 65–75% for TST. Moreover, IFN-γ production was higher in infected than in TB diseased children (n = 28, 5 bacteriologically confirmed, 23 clinically diagnosed), following RpfB and D stimulation (P = 0.02 and 0.03, respectively).

Conclusion
RpfB and RpfD show promising results for childhood MTBC infection screening, and both performed similar to and better than the TST in our study population. Additionally, both antigens appear to discriminate between infection and disease in children and thus warrant further investigation as screening and diagnostic antigens for childhood TB.
Induced neuroprotection by remote ischemic perconditioning as a new paradigm in ischemic stroke at the acute phase, a systematic review
Authors: Purroy Francisco , García Cristina , Mauri Gerard , Pereira Cristina , Torres Coral , Vazquez-Justes Daniel , Vicente-Pascual Mikel , Vena Ana , Arque Gloria 
Published: July 2020

Abstract
Background
Remote ischemic conditioning during cerebral ischemia (remote ischemic perconditioning, RIPerC) refers to the application of several cycles of brief ischemia and reperfusion (I/R) commonly to a limb, and it represents a new paradigm in neuroprotection with multiple mechanisms of action in ischemic stroke (IS) patients during acute phase. Some clinical trials just finished, and a few others are still ongoing; gather the current knowledge and pull it down to influence the present and future studies was the goal of this paper.

Methods
A systematic review of published research papers and/or registered clinical trials since 2000 was performed.

Results
Nineteen studies were identified and only four studies were completed. All of them have demonstrated that RIPerC is safe, feasible and well tolerated in IS patients. However, a high heterogeneity of clinical trial characteristics was observed: five (26.3%) randomized clinical trials (RCTs) included only thrombolytic-treated patients, three (15.8%) RCTs only thrombectomy-treated patients, and five (26.3%) RCTs required radiological confirmation of IS. Temporal inclusion criteria vary from 4 h to 48 h. Most of the clinical trials used 4 cycles of RIPerC in the upper non-affected limb. Interestingly, only three (16.7%) RCTs applied RIPerC during the transportation in the ambulance. Neuroimaging outputs were the main endpoints when endovascular therapy was applied; functional outcome is also the main endpoint in large-medium size studies.

Conclusions
This review summarizes the completed and ongoing clinical trials on RIPerC in IS patients, where RIPerC has been used alone or in combination with recanalization therapies. Ongoing clinical trials will provide new information on the best RIPerC intervention strategy and potentially improve the functional outcome of IS patients; definition of new RIPerC strategies would ideally aim at enhancing tissue preservation, promoting neurological recovery, and stratify patients to improve treatment feasibility.
Pregnant women’s clinical characteristics, intrapartum interventions, and duration of labour in urban China: a multi-center cross-sectional study
Authors: Gu Chunyi , Wang Xiaojiao , Zhang Zhijie , Schwank Simone , Zhu Chunxiang , Zhang Zheng , Qian Xu 
Published: July 2020

Abstract
Background
There is an increasing global trend towards the widespread over-medicalisation of labour and childbirth. The present study aimed to investigate pregnant women’s clinical characteristics, intrapartum interventions, duration of labour and its associated factors; and to compare the differences of these variables between nulliparas and multiparas in China.

Methods
A multi-center cross-sectional study was carried out in three tertiary hospitals of Fudan University in Shanghai, China. A total of 1523 participants were approched and assessed for eligibility. Data on women’s sociodemographic characteristics, intrapartum interventions, and duration of labour were measured and collected. Kaplan-Meier survival analysis was performed to present the curves of total duration of labour by parity. After z-transformation of labour duration, multivariable linear regression was used to control for confounding and to identify independent associations between potential associated factors and the primary outcome of labour duration.

Results
Overall, 1209 eligible women agreed to participate and were investigated. Rates of different intrapartum interventions were 27.4% in use of amniotomy, 37.9% in use of oxytocin, 53.0% in continuous electronic fetal monitoring, and 52.9% in epidural use, respectively. The curve of total duration of labour was significantly different between nulliparas and multiparas (P < .001). Of the 1209 participants, 983 (81.3%) women eventually achieved successful vaginal birth while 226 (18.7%) women ended in intrapartum caesarean section. The median duration of total stage of labour was significantly longer in the nulliparous group [9.38 (6.33,14.10) hours] than that in the multiparous group [5.08 (3.00,7.83) hours] (P < .001). The following factors were independently associated with longer duration of total stage of labour: epidural analgesia (P < .001), primiparity (P < .001), continuous electronic fetal monitoring (P = .035), and increased birth weight (P = .005).

Conclusions
Intrapartum medical interventions become common obstetric practices in urban China. Multifactorial variables independently associated with longer duration of labour were identified, including epidural analgesia, primiparity, continuous electronic fetal monitoring, and increased birth weight. Further research is required to validate these variables and to determine the modifiable factors for labour management. And models of care with lower intervention rates such as midwife-led models of care should be developed and implemented in China.
PODXL might be a new prognostic biomarker in various cancers: a meta-analysis and sequential verification with TCGA datasets
Authors: He Siying , Du Wenjie , Li Menglan , Yan Ming , Zheng Fang 
Published: July 2020

ABSRACT
Background
Several studies have investigated the associations between the podocalyxin-like protein (PODXL) expression quantity or locations and cancers survival, but the results were far from conclusive. Therefore, we proceeded a meta-analysis on PODXL in various human cancers to find its prognostic value and followed confirmation using the TCGA datasets.

Methods
We performed a systematic search, and 18 citations, including 5705 patients were pooled in meta-analysis. The results were verified with TCGA datasets.

Results
Total eligible studies comprised 5705 patients with 10 types of cancer. And the result indicated that PODXL high-expression or membrane-expression were significantly related to poor overall survival (OS). However, subgroup analysis showed a significant association between high expressed PODXL and poor OS in the colorectal cancer, pancreatic cancer, urothelial bladder cancer, renal cell carcinoma and glioblastoma multiforme. Then, we validated the inference using TCGA datasets, and the consistent results were demonstrated in patients with pancreatic cancer, glioblastoma multiforme, gastric cancer, esophageal cancer and lung adenocarcinoma.

Conclusion
The result of meta-analysis showed that high expressed PODXL was significantly linked with poor OS in pancreatic cancer and glioblastoma multiforme, but not in gastric cancer, esophageal cancer or lung adenocarcinoma. And the membrane expression of PODXL might also associate with poor OS. PODXL may act as tumor promotor and may serve as a potential target for antitumor therapy.
Case report-immune recovery posterior scleritis in a HIV positive patient
Authors: Che Xin , Jiang Jing , Qian Yiwen , Li Qingjian , Zhang Yu , Wang Zhiliang 
Published: July 2020

AbstractBackgroundPosterior scleritis is an uncommon vision-threatening disorder that is often recurrent and difficult to cure due to its complex etiology. In HIV patients, posterior scleritis may develop several months after significant rise in CD4+ T-lymphocyte, even after several years, which may be diagnosed as late-onset immune recovery scleritis.Case presentationHere we report a case of posterior scleritis in a HIV positive patient who presented with severe periocular pain and decreased vision in the left eye, with exudative retinal detachment and optic nerve involvement.ConclusionsEarly differential diagnosis of immune recovery posterior scleritis and intensive corticosteroids treatment, can prevent vision loss effectively in HIV patients.