bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic model based on autophagy-related lncRNAs in gastric cancer
Authors: Cheng Mengqiu , Cao Wei , Chen Bo 
Published: May 2020

Abstract
Background: Gastric cancer (GC) is one of the most pravelent cancer in the world. Although increasing studies have indicated that autophagy-related long non-coding RNA (lncRNA) plays an essential role in the occurrence of GC, the prognosis of GC based on autophagy is still deficient.Method: Autophagy-related lncRNAs were obtained by using the correlation test with the autophagy-related gene. Data was downloaded from The Cancer Genome of Atlas stomach adenocarcinoma (TCGA-STAD) dataset. The prognostic autophagy-related lncRNAs significantly correlated with survival of TCGA-STAD dataset were obtained by using Kaplan-Meier and univariate Cox regression analysis. TCGA-STAD dataset was separated into a training set and a testing set randomly. The model was constructed based on the training set through the least absolute shrinkage and selection operator (LASSO) regression. The testing set and TCGA-STAD were used to validate the accuracy of the model. Every patient got a risk score (RS) and patients were separate into high-risk group and low-risk group due to the median RS. The prognostic network was built and the mRNAs in the system were analyzed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The signaling pathways that the differentially expressed genes (DEGs) between two types of risk group mainly participated in were distinguished through Gene Set Enrichment Analysis (GSEA). The individual’s survival rate was predicted through the nomogram.Results: 24 autophagy-related lncRNAs were found strongly associated with the survival of the TCGA-STAD dataset. Among them, 11 lncRNAs were selected to build the risk score model through LASSO regression. The multivariate Cox analysis showed that the RS could be an independent prognosis predictor. The Kaplan-Meier survival analysis and the Receiver Operating Characteristic (ROC) curve indicated the model had an excellent prediction effect. GO, and KEGG analysis revealed that the mRNAs in the prognostic network were mainly involved in the autophagy and ubiquitin-like protein ligase binding. GSEA analysis uncovered that the DEGs in high-risk group partially participated in the ECM receptor interaction and other signaling pathways.Conclusions: Our results indicated that the risk score model based on the autophagy-related lncRNAs performed well in the prediction of prognosis for patients with GC.
Identifying Research Priorities for Health Professions Education Research in Sub-Saharan Africa using a Modified Delphi Method
Authors: Schalkwyk Susan C van , Kiguli-Malwadde Elsie , Budak Jehan Z , Reid Michael JA , De Villiers Marietjie Rene 
Published: May 2020

Abstract
Background: Recent increases in health professions education (HPE) research in sub-Saharan Africa (SSA), though substantial, have predominantly originated from single institutions and remained uncoordinated. A shared research agenda can guide the implementation of HPE practices to ultimately influence the recruitment and retention of the health workforce. Thus, the authors aimed to generate and prioritise a list of research topics for HPE research (HPER) in SSA.Methods: A modified Delphi process was designed to prioritise a shared agenda. Members of the African Forum for Research and Education in Health (AFREhealth) technical working group (TWG) were asked to first list potential research topics. Then, members of the same TWG and attendees at the annual AFREhealth academic symposium held in Lagos, Nigeria in August 2019 rated the importance of including each topic on a 3-point Likert scale, through two rounds of consensus seeking. Consensus for inclusion was predefined as ≥ 70% of respondents rating the topic as “must be included.”Results: Health professions educators representing a variety of professions and 13 countries responded to the survey rounds. Twenty-three TWG members suggested 26 initial HPER topics; subsequently 90 respondents completed round one, and 51 completed round 2 of the modified Delphi. The final list of 12 research topics which met predetermined consensus criteria were grouped into three categories: (1) creating an enabling environment with sufficient resources and relevant training; (2) enhancing student learning; and (3) identifying and evaluating strategies to improve pedagogical practice.Conclusions: Establishing research priorities for HPE is important to ensure efficient and appropriate allocation of resources. This study serves as a reminder of how the prevailing context within which HPE, and by implication research in the field, is undertaken will inevitably influence choices about research foci. It further points to a potential advocacy role for research that generates regionally relevant evidence.
Aspartate transaminase/alanine transaminase ratio as a significant prognostic factor in patients with sepsis: a retrospective analysis
Authors: Zhao Pengyue , Yao Renqi , Ren Chao , Li Songyan , Li Yuxuan , Zhu Shengyu , Yao Yongming , Du Xiaohui 
Published: May 2020

Abstract
Background: The study was performed to investigate the relationship between aspartate transaminase/alanine transaminase ratio (DRR) and long-term mortality among patients diagnosed with sepsis or septic shock. Methods: We conducted a retrospective study among adult septic patients who were admitted to surgical intensive care unit (ICU) of the Chinese People's Liberation Army (PLA) General Hospital from January 2014 to December 2018. Baseline characteristics were compared between survivors and non-survivors. We applied univariate as well as multivariate Cox regression analyses to evaluate DRR in relation to 180-day mortality. The potential prognostic value of DRR in predicting mortality rate was assessed by receiver operating curve (ROC) analysis. Besides, we conducted subgroup analysis by stratifying patients via optimal DRR cut-off value. Results: We included a total number of 183 patients in the current study, 44 (24%) patients died within 180-day hospitalization. Univariate and multivariate Cox analysis revealed that DRR was an independent predictor of 180-day mortality (hazard ratio [HR] 1.421, 95% confidence interval [CI] 1.073-1.883, P = 0.014). The predicting accuracy of 180-day mortality for DRR was presented as ROC with an area under the curve (AUC) of 0.708 (95% CI 0.629–0.786, P < 0.001). As we stratified all enrolled patients into two groups by using the optimal cut-off value of 1.29, we observed a significantly higher mortality in patients with relatively high DRR. Conclusions: An elevated DRR was associated with higher 180-day mortality among septic patients, and DRR might be an optimal marker for predicting the long-term mortality of sepsis. More prospective and randomized trials are needed to confirm the prognostic value of DRR.
Validation of the Palliative Prognostic Index, Performance Status–based Palliative Prognostic Index and Chinese Prognostic Scale in a Home Palliative Care Setting for Patients With Advanced Cancer in China
Authors: Zhou Jun , Xu Sitao , Cao Ziye , Tang Jing , Qin Ling , Zhou Fangping , He Yuzhen , Zhong Xueren , Hu Mingcai , Wang Yan , Lu Fengjuan , Bao Yongzheng , Dai Xiangheng , Wu Qiang 
Published: May 2020

Abstract
Background:Thepredictive value of theprognostic tool for patients with advanced cancer isuncertainin mainland China, especially in the home-based palliative care (HPC) setting. This study aimed to compare the accuracy of the Palliative Prognostic Index (PPI), the Performance Status–Based Palliative Prognostic Index (PS-PPI), and the Chinese Prognosis Scale (ChPS) for patients with advanced cancer in the HPC setting in mainland China.Methods:Patients with advanced cancer admitted to the hospice center of Yuebei People’s Hospital between January 2014 and December 2018 were retrospectively calculated the scores according to the three prognostic tools. The Kaplan-Meier method was used to compare survival times among different risk groups. Receiver operating characteristic curve analysis was used to assess the predictive value. The accuracy of 21-, 42- and 90-day survival was compared among the three prognostic tools.Results: A total of 1863 patients were included. Survival time among the risk groups of all prognostic tools was significantly different from each other except for the PPI. The AUROC of the ChPS was significantly higher than that of the PPI and PS-PPI for 7-, 14, 21-, 42-, 90-, 120-, 150- and 180-day survival (P <0.05). The AUROC of the PPI and PS-PPI were not significantly different from each other (P >0.05).Conclusions: The ChPS is more suitable than the PPI and PS-PPI for advanced cancer patients in the HPC setting. More researches are needed to verify the predictive value of the ChPS, PPI, and PS-PPI in the HPC setting in the future.
Impact on place of death in cancer patients: a causal exploration in southern Switzerland
Authors: Kern Heidi , Corani Giorgio , Huber David , Vermes Nicola , Zaffalon Marco , Varini Marco , Wenzel Claudia , Fringer André 
Published: May 2020

Abstract
Background Most terminally ill cancer patients prefer to die at home, but a majority die in institutional settings. Research questions about this discrepancy have not been fully answered. This study applies artificial intelligence and machine learning techniques to explore the complex network of factors and the cause-effect relationships affecting the place of death, with the ultimate aim of developing policies favouring home-based end-of-life care. Methods A data mining algorithm (a classifier) and a causal probabilistic model (a credal network) for data analysis were developed with information derived from expert knowledge that was merged with data from 116 deceased cancer patients in southern Switzerland. This data set was obtained via a retrospective clinical chart review. Results Dependencies of disease and treatment-related decisions demonstrate an influence on the place of death of 13%. Anticancer treatment in advanced disease prevents or delays communication about the end of life between oncologists, patients and families. Unknown preferences for the place of death represent a great barrier to a home death. A further barrier is the limited availability of family caregivers for terminal home care. The family’s preference for the last place of care has a high impact on the place of death of 51%, while the influence of the patient’s preference is low, at 14%. Approximately one-third of family systems can be empowered by health care professionals to provide home care through open end-of-life communication and good symptom management. Such intervention has an influence on the place of death of 17%. If families express a convincing preference for home care, the involvement of a specialist palliative home care service can increase the probability of home deaths by 24%. Conclusion Concerning death at home, open communication about dying is essential. Furthermore, for the patient preference for home care to be respected, the family’s decision for the last place of care seems key. Early initiation of family-centred palliative care and provision of specialist palliative home care for patients who wish to die at home are suggested. Keywords Cancer; End-of-life care; Palliative Home care; Place of death; Communication; Family caregivers; Patient preference; Bayesian networks; Credal networks; Bayesian classifiers
Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women with Alzheimer's Disease
Authors: Paranjpe Manish , Belonwu Stella , Wang Jason K , Oskotsky Tomiko , Gupta Aarzu , Taubes Alice , Zalokusky Kelly , Paranjpe Ishan , Glicksberg Benjamin S , Huang Yadong , Sirota Marina 
Published: May 2020

Abstract
Background: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the United States. In spite of evidence of females having a greater lifetime risk of developing Alzheimer’s Disease (AD) and greater apolipoprotein E4-related (apoE4) AD risk compared to males, molecular signatures underlying these findings remain elusive. Methods: We took a meta-analysis approach to study gene expression in the brains of 1,084 AD patients and age-matched controls and whole blood from 645 AD patients and age-matched controls in seven independent datasets. Sex-specific gene expression patterns were investigated through use of gene-based, pathway-based and network-based approaches. The ability of a sex-specific AD gene expression signature to distinguish Alzheimer’s disease from healthy controls was assessed using a linear support vector machine model. Cell type deconvolution from whole blood gene expression data was performed to identify differentially regulated cells in males and females with AD.Results: Strikingly gene-expression, network-based analysis and cell type deconvolution approaches revealed a consistent immune signature in the brain and blood of female AD patients that was absent in males. In females, network-based analysis revealed a coordinated program of gene expression involving several zinc finger nuclease genes related to Herpes simplex viral infection whose expression was modulated by the presence of the apolipoprotein ε4 allele. Interestingly, this gene expression program was missing in the brains of male AD signature. Cell type deconvolution identified an increase in neutrophils and naïve B cells and a decrease in M2 macrophages, memory B cells, and CD8+ T cells in AD samples compared to controls in females. Interestingly, among males with AD, no significant differences in immune cell proportions compared to controls were observed. Machine learning-based classification of AD using gene expression from whole blood in addition to clinical features produced an improvement in classification accuracy upon stratifying by sex, achieving an AUROC of 0.91 for females and 0.80 for males. Conclusions: These results help identify sex and apoE4 genotype-specific transcriptomic signatures of AD and underscore the importance of considering sex in the development of biomarkers and therapeutic strategies for AD.
Tolerability of duloxetine in the elderly and in adults: a protocol and preliminary results of a systematic review and individual participant data meta-analysis of randomized placebo-controlled trials
Authors: ROY Jean-Charles , Rousseau Chloé , Jutel Alexis , Naudet Florian , Robert Gabriel 
Published: May 2020

Abstract
Background. Duloxetine is an antidepressant which benefits from a wide range of approval in elderly population while its safety of use in elderly population, compared to younger adults, is not clearly assessed. A comparison of tolerability of duloxetine between elderly and younger adults would help to rule on this issue. Methods and Design. This protocol outlines a systematic review and meta-analysis of individual participant data (IPD) of all double-blind randomized controlled trials comparing the number of serious adverse events among individuals taking duloxetine in comparison to placebo between participants at least 65 years and younger adults in conditions approved by the European Medical Agency (EMA) and the Food Drug Administration (FDA). Secondarily, will be compared the number of any adverse events, clinical efficacy and quality of life between elderly and younger adults under duloxetine, in comparison to placebo. Relevant studies were selected on ClinicalTrials.gov, Clinicaltrialsregister.eu, data sharing platforms, FDA and EMA websites, and from systematic reviews and meta-analyses of duloxetine on PubMed, following Cochrane’s recommendations. Sponsors and authors from eligible studies were invited to share IPD on data sharing platform or directly with our research team. As data cannot be aggregate into a unique database, a two step-approach meta-analysis will be undertaken. Qualitative results from available data. 77 eligible randomized controlled trials were identified, representing 25303 participants. From online available data, 35 trials were assessed as being at an overall low risk of bias, 31 trials at an unclear risk of bias and 1 at high risk of bias. Evaluation of risk of bias was not feasible for 10 studies. Conclusion. This study would represent the first meta-analysis investigating the safety of duloxetine in elderly population across all conditions approved by European and American regulatory authorities with an overall low risk of bias. Registration. PROSPERO: 2019 CRD42019130488.
Analysis of HIV-1 Molecular Transmission Network in Sexually Transmitted Population in Liaoning, China
Authors: Ma Ning , Chen Xing-hua , Zhao Yan , Kang Xu , Pan Shan , Yao Wen-qing 
Published: May 2020

Abstract
Background In recent years, with the development of molecular epidemiology, molecular transmission networks based on evolutionary theory and sequence analysis have been widely used in the study of HIV-1 transmission kinetics and precision intervention in high-risk populations ,especially HIV − 1 Long-term monitoring of drug resistance and real-time prevention interventions. To analyze the characteristics of HIV-1 molecular transmission network in Liaoning, China .Methods A study on HIV infected persons with STIs in Liaoning Province from 2003 to 2019. HIV-1 RNA was extracted, amplified and sequenced, and a phylogenetic tree was constructed to determine the subtype using the well matched pol gene region sequence. The gene distance between sequences was calculated, the threshold was determined, and the propagation network was constructed.Results 109 samples of pol gene region were obtained, The main subtype of HIV-1 was CRF01, followed by B, CRF07, BC, etc.12.8% of them were resistant to HIV.At the threshold of 0.55% gene distance, 60.6% of them entered the HIV-1 molecular transmission network. Workers, sample source VCT, other testing, subtype B and drug resistance are the factors influencing the access to HIV-1 molecular transmission network.The subtype of CRF01 _ AE propagated in the molecular network to form six clusters. In the network, the difference of connection degree between different subtypes was statistically significant .Conclusion Liaoning Province should build a molecular transmission network and carry out long-term monitoring, so as to take targeted measures to block the spread of HIV and achieve accurate prevention and control.
Modification of transcriptional factor ACE3 enhances protein production in Trichoderma reesei in the absence of cellulase gene inducer.
Authors: Luo Yun , Valkonen Mari , Jackson Raymond E. , Palmer Jonathan M. , Bhalla Aditya , Nikolaev Igor , Saloheimo Markku , Ward Michael 
Published: May 2020

Abstract
The authors have removed this preprint from Research Square.
Consolidated bioprocessing of lignocellulose for production of glucaric acid by an artificial microbial consortium
Authors: Li Chaofeng , Lin Xiaofeng , Ling Xing , Li Shuo , Fang Hao 
Published: May 2020

Abstract
Background

The biomanufacturing of D-glucaric acid has been attracted increasing interest and the industrial yeast Saccharomyces cerevisiae is regarded as an excellent host for D-glucaric acid production.

Results

Here we constructed the biosynthetic pathway of D-glucaric acid in S. cerevisiae INVSc1 whose opi1 was knocked out and obtained two engineered strains, LGA-1 and LGA-C, producing record breaking titers of D-glucaric acid, 9.53 ± 0.46 g/L and 11.21 ± 0.63 g/L D-glucaric acid from 30 g/L glucose and 10.8 g/L myo -inositol in the mode of fed-batch fermentation, respectively. Due to the genetic stability and the outperformance in subsequent applications, however, LGA-1 was a preferable strain. As one of the top chemicals from biomass, there have been no reports on D-glucaric acid production from lignocellulose, which is the most abundant renewable on earth. Therefore, the biorefinery processes of lignocellulose for D-glucaric acid production including separated hydrolysis and fermentation (SHF), simultaneous saccharification and fermentation (SSF) and consolidated bioprocessing (CBP) were investigated in this work and CBP by an artificial microbial consortium composed of Trichoderma reesei Rut-C30 and S. cerevisiae LGA-1 was found to have relatively high D-glucaric acid titers and yields after 7 d fermentation, 0.54 ± 0.12 g/L D-glucaric acid from 15 g/L Avicel, and 0.45 ± 0.06 g/L D-glucaric acid from 15 g/L steam exploded corn stover (SECS), respectively.

Conclusions

In attempts to design the microbial consortium for more efficient CBP the team consisted of the two members, T. reesei Rut-C30 and S. cerevisiae LGA-1, was found to be the best with excellent work distribution and collaboration. This desirable and promising approach for direction production of D-glucaric acid from lignocellulose deserves extensive and in-depth research.
Age-related Changes of Microbiota in Midlife Associated with Reduced Saccharolytic Potential: An In Vitro Study
Authors: Zhu Liying , Chen Junkui , Pi Xionge , Li Jinjun , Liu Wei , Ding Qunfang , Wang Xin , Jia Weiguo 
Published: May 2020

Abstract
Background: Gut microbiota diversity and abundance are critical in maintaining human health, and subject to significantly reduce in seniors. Gut microbiota are reported to be stable across the long adulthood in general, but lack of careful examination, especially for the midlife people.Results: To characterize the gut microbiota in midlife, we investigated the faecal microbiota between two groups of healthy people, young, 20-39 years old, n=15; and midlife, 40-60 years old, n=15. Metabolic responses of the microbiota were studied through in vitro batch fermentation model. Despite no difference was observed in the diversity indies between the two age groups, a wide range taxonomic changes were found in the faecal microbiota. Furthermore, substantial Bifidobacterium reduction was also found in both faecal and fermented samples. The level of SCFAs in both faecal and starch fermented samples is similar in both groups. However, when fermentation was performed with inulin as the sole carbon source, the acetate concentration and inulin degradation rate decreased while the gas production increased in midlife group, suggesting a deficiency of saccharolytic potential in midlife, especially for non-digestible carbohydrate. Conclusions: Our data demonstrate that gut microbiota begin to change as early as in midlife. The reduction in Bifidobacterium dominates the change of the microbiota composition in midlife resulting in attenuated saccharolytic capability of inulin, leading to insufficient acetate production which might be associated with healthy problems in this transition period from young to elderly.