bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Personalized Survival Prediction of Patients With Diffuse Large B-cell Lymphoma Using Gene Expression Profiling
Authors: Orgueira Adrián Mosquera , Arias José Ángel Díaz , López Miguel Cid , Raindo Andres Peleteiro , Rodriguez Beatriz Antelo , Santos Carlos Aliste , Vence Natalia Alonso , Lopez Angeles Bendaña , Blanco Aitor Abuin , Perez Laura Bao , Perez Marta Sonia Gonzalez , Encinas Manuel Mateo Perez , Rodriguez Maximo Francisco Fraga , Lopez Jose Luis Bello 
Published: July 2020

Abstract
Background30-40% of patients with Diffuse Large B-cell Lymphoma (DLBCL) have an adverse clinical evolution. The increased understanding of DLBCL biology has shed light on the clinical evolution of this pathology, leading to the discovery of prognostic factors based on gene expression data, genomic rearrangements and mutational subgroups. Nevertheless, additional efforts are needed in order to enable survival predictions at the patient level. This study investigated new machine learning models of survival based on transcriptomic and clinical data.MethodsGene expression profiling (GEP) in 2 different publicly available retrospective cohorts were analyzed. Cox regression and unsupervised clustering were performed in order to identify probes associated with overall survival on the largest cohort. Random forests were created to model survival using combinations of GEP data, COO classification and clinical information. Cross-validation was used to compare model results in the training set, and Harrel’s concordance index (c-index) was used to assess model’s predictability. Results were validated in an independent test set. Results233 and 64 patients were included in the training and test set, respectively. Initially we derived and validated a 4-gene expression clusterization that was independently associated with lower survival in 20% of patients. These genes were TNFRSF9, BIRC3, BCL2L1 and G3BP2. Thereafter, we applied machine-learning models to predict survival. A set of 102 genes was highly predictive of disease outcome, outperforming available clinical information and COO classification. The final best model integrated clinical information, COO classification, 4-gene-based clusterization and 50 gene expression data (training set c-index, 0.8404, test set c-index, 0.7942). ConclusionThis study indicates that modelling DLBCL survival with transcriptomic-based machine learning algorithms can largely outperform other important prognostic variables such as disease stage and COO.
A latent class analysis of dietary behaviours associated with metabolic syndrome: a retrospective observational cross-sectional study
Authors: Park Jung Ha , Kim Ju Young , Kim So Hye , Kim Jung Hyun , Park Young Mi , Yeom Hye Seon 
Published: July 2020

Abstract
Background: Obesity defined solely by body mass index may not reflect the true heterogeneity of the obese population. This study aimed to classify the dietary behaviours of obese individuals and to explore the relationship between patterns of dietary behaviour and cardiometabolic risk factors. Methods: A total of 259 patients who visited an outpatient weight management clinic at a tertiary hospital and underwent a dietary behaviour assessment between January 2014 and February 2019 were enrolled in the study. Dietary behaviours were assessed in three domains with nine categories, including choice of food (frequently eating out, instant/fast/takeaway food), eating behaviour (irregular meals; frequent snacking, including eating at night; emotional eating; and overeating/binge eating), and nutrient intake (high-fat/high-calorie foods, salty food, and poorly balanced diet). Latent class analysis (LCA) was used to classify the subjects according to these categories. Associations between latent class and metabolic syndrome were assessed by logistic regression. Results: The subjects were classified into three LCA-driven classes, including a referent class of healthy eaters (n=118), a class of emotional eaters (n=53), and a class of irregular unhealthy eaters (n=88). Compared with the referent class, emotional eaters had a significantly higher body mass index (beta=3.40, P<0.001) accompanied by metabolic syndrome (odds ratio 2.88, 95% confidence interval 1.16–7.13). Conclusions: Our three LCA-driven obesity phenotypes could be useful for assessment and management of obesity and metabolic syndrome. The association between higher BMI and metabolic syndrome was stronger in emotional eaters than in healthy eaters and irregular unhealthy eaters. Emotional eaters might benefit from emotional regulation strategies.
Alcoholic fatty liver disease inhibited the co-expression of Fmo5 and PPARα to activate the NF-κB signaling pathway, thereby reducing liver injury via inducing gut microbiota disturbance
Authors: Kong Ling jian , Chen Jing , Ji Xiao li , Qin Qian , Yang Hui yu , Liu Dan , Li De liang , Sun Mei ling 
Published: July 2020

Abstract
Background
Alcohol-induced intestinal dysbiosis disrupts and inflammatory response are essential in the development of alcoholic fatty liver disease (AFLD). Here, we investigate the effects of Fmo5 on changes in enteric microbiome composition in a model of AFLD and dissect the pathogenic role of Fmo5 in AFLD-induced liver pathology.
Materials and methods
The expression profile data of GSE8006 and GSE40334 datasets were downloaded from the GEO database. Weighted gene co-expression network analysis (WGCNA) approach allowed us to investigate the AFLD-correlated module. DEGs were used to perform Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Four PPI networks were constructed using the STRING database and visualized by Cytoscape software. Cytohubba plug-in was used to identify the hub genes. Western blot and immunohistochemistry assays were used to detect protein expressions. ELISA assay was used to detect the level of serum inflammatory cytokines. Lipid droplets in cytoplasm were observed using Oil Red O staining. Cell apoptosis was detected using TUNEL assay and flow cytometry analysis. ROS level were detected using flow cytometry analysis. The nuclear translocation of NF-κB p65 was observed using immunofluorescence staining. Co-immunoprecipitation were used to detect the co-expression of PPARα and Fmo5 in L02 cells. 16S rDNA sequencing defined the bacterial communities in mice with AFLD.
Results
Fmo5 was a key DEG and closely associated with gut microbiota and PPAR signaling pathway. Gut microbiome function in AFLD was significantly related to PPAR signaling pathway. AFLD induced shifts in various bacterial phyla in the cecum, including a reduction in Bacteroidetes and increased Firmicutes. Fmo5 and PPARα co-expression in cell and animal model with AFLD, which decreased significantly. Silencing of Fmo5 and PPARα aggravated the functions of AFLD inducing apoptosis and inflammatory response, promoting liver injury, and activating the NF-κB signaling pathway in vivo and in vitro. NF-κB inhibitor abolished the functions of silencing of Fmo5 and PPARα promoting AFLD-induced apoptosis, inflammatory response, and liver injury.
Conclusions
Our data indicated that the co-expression of Fmo5 and PPARα was involved in AFLD-related gut microbiota composition, alleviated AFLD-induced liver injury, apoptosis and inflammatory response via inhibiting the nuclear translocation of NF-κB p65 to inhibit NF-κB signaling pathway.
Exosomal PD-L1 Derived From Osteosarcoma is Associated With Pulmonary Metastasis for Patients With Osteosarcoma
Authors: Wang Jun , Zhang Hongliang , Sun Xin , Wang Xiaofang , Ren Tingting , Huang Yi , Zhang Ranxin , Zheng Bingxin , Guo Wei 
Published: July 2020

Abstract
Background

Recent studies indicated that exosomal programmed death-ligand 1 (PD-L1) derived from cancers could induce immunosuppression and tumor pathogenesis. However, it is unclear how the exosome influences the osteosarcoma (OS) progression and whether PD-L1 also exists in serum exosomes (Sr-exosomes) of patients with osteosarcoma.
Methods

We examined serum exosomes from 70 patients with osteosarcoma, 9 patients with benign tumors and 22 healthy donors. Osteosarcoma-derived exosomes and exosomal-PD-L1 were functionally evaluated using in vivo and in vitro models.
Results

The characteristics of serum exosomes of OS patients and OS cell line exosomes were confirmed by several methods. Bioinformatic analysis demonstrated that Sr-exosomes isolated from OS patients may involve in the important process of immune function and cancer pathogenesis for OS patients. Meanwhile, exosomes derived from OS cell line and serum of OS patients could induce osteosarcoma migration and invision in vitro. Then, we confirmed PD-L1 existing in Sr-exosomes of patients with osteosarcoma and higher level of Sr-exosomal PD-L1 in OS patients compared to healthy donors and patients with benign tumor. Furthermore, exosomal-PD-L1 derived from osteosarcoma promoted the pulmonary metastasis, which was demonstrated in the osteosarcoma metastatic model.
Conclusion

We confirm that osteosarcoma releases the exosomes carrying PD-L1 on their surface and induces the pathogenesis of pulmonary metastasis for OS patients.
Long noncoding RNA UPK1A-AS1 indicates poor prognosis of hepatocellular carcinoma and promotes cell proliferation through interacting with EZH2
Authors: Zhang Dong-Yan , Sun Qing-Can , Zou Xue-Jing , Song Yang , Li Wen-Wen , Guo Ze-Qin , Liu Shan-Shan , Liu Li , Wu De-Hua 
Published: July 2020

Abstract
Background
Dysregulations of lncRNA are responsible for cancer initiation and development, positioning lncRNAs as not only biomarkers but also promising therapeutic targets for cancer treatment. Growing number of lncRNAs have been reported in HCC but their functional and mechanistic roles remain unclear.
Methods
Gene Set Enrichment Analysis was used to investigate the molecular mechanism of lncRNA UPK1A antisense RNA 1 (UPK1A-AS1). CCK-8 assay, EdU assay, flow cytometry, western blot, and xenograft assay were used to confirm the role of UPK1A-AS1 in proliferation of HCC cells both in vitro and in vivo. Bioinformatics analysis and qRT-PCR were performed to explore the interplay between UPK1A-AS1 and Enhancer of Zeste Homologue 2 (EZH2). RNA immunoprecipitation, RNA-pull down assay, western blot, qRT-PCR, and were conducted to confirm the interaction between UPK1A-AS1 and EZH2. Finally, the expression level and prognosis value of UPK1A-AS1 in HCC were analyzed using RNA-seq data from TCGA datasets.
Results
We showed that UPK1A-AS1, a newly identified lncRNA, promoted cellular proliferation and tumor growth by accelerating cell cycle progression. Cell cycle related genes including CyclinD1, CDK2, CDK4, CCNB1 and CCNB2 were significantly upregulated in HCC cells with UPK1A-AS1 overexpression. Furthermore, overexpression of UPK1A-AS1 could protect HCC cells from cis-platinum toxicity. Mechanistically, UPK1A-AS1 interacted with EZH2 to mediate its nuclear translocation and reinforce its binding to SUZ12, leading to the increasing trimethylation of H27K3. Targeting EZH2 with specific siRNA impaired UPK1A-AS1-mediated upregulation of proliferation and cell cycle progression related genes. Moreover, UPK1A-AS1 was significantly upregulated in HCC, and upregulation of UPK1A-AS1 predicted poor prognosis for patients with HCC.
Conclusions
Our study reveals that UPK1A-AS1 promotes HCC development by accelerating cell cycle progression in an EZH2-dependent manner, suggesting that UPK1A-AS1 possesses substantial potential as a novel biomarker for HCC prognosis and therapy.
The Shape of Incident Shock Wave in Steady Axisymmetric Conical Mach Reflection
Authors: Ren Yu-Xin , Tan Lianhua , Wu zi-niu 
Published: July 2020

Abstract
For internal flow with supersonic inflow boundary conditions, a complicated oblique shock reflection may occur. Different from the planar shock reflection problem, where the shape of the incident shock can be a straight line, the shape of the incident shock wave in the inward-facing axisymmetric shock reflection in steady flow is an unknown curve. In this paper, a simple theoretical approach is proposed to determine the shape of this incident shock wave. The present theory is base on the steady Euler equations. When the assumption that the steam-lines are straight lines at locations just behind the incident shock is adopted, an ordinary differential equation can be derived, and the shape of the incident shock wave is given by the solution of this ordinary differential equation. The predicted curves of the incident shock wave at several inlet conditions agree very well with the results of the numerical simulations.
Learning from the emergency remote teaching-learning in China when primary and secondary schools were disrupted by COVID-19 pandemic
Authors: ZHANG TIANHONG 
Published: July 2020

Abstract
China educational system launched the emergency remote teaching-learning (ERT) as the response to the COVID-19 pandemic with the mission of “suspending schools without stopping teaching-learning”. When schools moved to temporary remote instruction, teachers, students and parents encountered challenges in terms of deep remote teaching and learning. In the current study, parent (N=741) and teacher (N=145) from 16 provinces in China gave responses to four open-ended questions in the web-based questionnaires released on wjx.cn. The themes arose from the thematic analysis. The participants emphasized that online teaching-learning can’t replace face-to-face one in the brick-and-mortar classrooms in terms of the glitchy technology, engaging students into learning, enhancing students learning and leaning atmosphere. Teachers felt unprepared for teaching online. Teachers and parents also argued that remote teaching-learning only benefit those students with good self-discipline and high autonomy in learning. The current study suggests the provincial governments equipping schools with a standardized online teaching-learning management system (LMS), followed by the instructional technology professional development for ensuring online teaching quality at timely manner. This might make ERT teaching evaluation possible. Schools can develop a checklist of prioritized perspectives and actionable strategies for preparing students and their parents for online learning success.
Docking and in silico toxicity assessment of Arthrospira compounds as potential antiviral agents against SARS-CoV-2
Authors: PETIT Lena , VERNES Lea , CADORET Jean-Paul 
Published: July 2020

Abstract
A course is currently being launched as a result of the international health situation. This race aims to find, by various means, weapons to counter the Covid-19 pandemic now widespread on all continents. The aquatic world and in particular that of photosynthetic organisms is regularly highlighted but paradoxically little exploited in view of the tremendous possibilities it offers. Computational tools allow not only to clear the existence and activity of many molecules, but also to model their relationships with receptors identified in potential hosts. On a routine basis, our laboratory carries out a research activity on functionalities of molecules derived from algae, using in silico tools. We have implemented our skills, in algae biology and in modeling, as tests in order to identify molecules expressed by the genus Arthrospira showing an antiviral potential and more particularly anti SARS-CoV-2. Using Autodock Vina, we were able to identify 3 molecules: phycocyanobilin, phycoerythrobilin and folic acid. These 3 compounds showed binding energies able to compete with the SARS-CoV-2/ACE2 complex. Toxicity prediction as well as current regulations support their use as potential candidates for the fight against Covid-19.
Pseudomonas Aeruginosa Bloodstream Infection at A Tertiary Referral Hospital For Children
Authors: Dame Joycelyn Assimeng , Beylis Natalie , Nuttall James , Eley Brian 
Published: July 2020

Abstract
Background: This study describes the disease burden, clinical characteristics, antibiotic management, impact of multidrug resistance and outcome of Pseudomonas aeruginosa bloodstream infection (PABSI) among children admitted to a tertiary referral hospital for children in Cape Town, South Africa.Methods: A retrospective descriptive cohort study was conducted at a paediatric referral hospital in Cape Town, South Africa. Demographic and clinical details, antibiotic management and patient outcome information were extracted from medical and laboratory records. Antibiotic susceptibility results of identified organisms were obtained from the National Health Laboratory Service database.Results: The overall incidence risk of PABSI was 5.4 PABSI episodes / 10,000 hospital admissions and the most common presenting feature was respiratory distress, 34/91 (37.4%). Overall, 69/91 (75.8%) of the PA isolates were susceptible to all antipseudomonal antibiotic classes evaluated. Fifty (54.9%) of the PABSI episodes were treated with appropriate empiric antibiotic therapy. The mortality rate was 24.2% and in multivariable analysis, empiric antibiotic therapy to which PA isolates were not susceptible, infections present on admission, and not being in the intensive care unit at the time that PABSI was diagnosed were significantly associated with 14-day mortality.Conclusions: The study provided insight into factors associated with PABSI in a tertiary hospital in Sub-Saharan Africa. Empiric antipseudomonal antibiotic therapy was associated with a decrease in 14-day mortality.
Clinical signs of tuberculosis relapses in HIV patients
Authors: Zorkаltsevа E. Yu. , Egorovа Yu. O. 
Published: July 2020

The objective: to study clinical manifestations of tuberculosis relapses and their treatment outcomes in patients with HIV infection.Subjects and Methods. 132 medical records of patients with tuberculosis relapses were analyzed; 69 of them were HIV-positive and 63 were HIV-negative. All of them were admitted to Irkutsk Regional Clinical Tuberculosis Hospital from 2016 to 2019, and then continued treatment of tuberculosis on the out-patient basis. Treatment efficacy was assessed in February 2020.Results. More severe clinical forms of tuberculosis relapses were typical of HIV patients including generalized forms affecting the central nervous system. Therefore, among these patients, the mortality rate is significantly higher (24.6%) than in tuberculosis relapses with no concurrent HIV infection (6.3%), p ≤ 0.05.
Prediction of lethal outcomes in COVID-19 cases based on the results chest computed tomography
Authors: Morozov S. P. , Gombolevskiy V. A. , Cherninа V. Yu. , Blokhin I. A. , Mokienko O. A. , Vlаdzimirskiy A. V. , Belevskiy A. S. , Protsenko D. N. , Lysenko M. A. , Zayrаtyants O. V. , Nikonov E. L. 
Published: July 2020

The objective: to predict lethal outcomes in patients with COVID-19 based on the result of chest computed tomography (chest CT) using a semi-quantitative visual scale of the pulmonary parenchyma lesion.Subjects and methods. Inclusion criteria: patients who underwent chest CT from March 2 to May 1, 2020, inclusively, upon referral of a general practitioner due to suspected community-acquired pneumonia caused by COVID-19. Chest CT was performed in 48 medical organizations providing primary medical care to the adult population in Moscow. Exclusion criteria: patients whose chest CT was not assessed by CT 0-4 score; patients who were not confirmed as COVID-19 positive.In the Russian Federation, CT 0-4 score is recommended to be used for assessment of the extent of lung parenchyma lesion in cases with suspected COVID-19.Data on fatal outcomes were received on May 4, 2020 inclusive.Results: data of 13,003 patients from the Unified Radiological Information Service were retrospectively included in the study according to inclusion and exclusion criteria. The test aimed to detect a trend of directional changes in the proportion of deceased patients among various categories using CT 0-4 score demonstrated a statistically significant result (p < 0.0001). The chance of a lethal outcome increases directionally from CT-0 to CT-4. The test for deviations from the linear trend also provided p < 0.0001, i.e. when moving to higher scores (CT-3 and CT-4), there was an accelerated increase in the risk of death. Analysis of overall survival using the Cox regression model showed that the assessed factors (age and CT 0-4 score) were statistically significantly associated with the time to death from COVID-19 (p < 0.05). The risk of death increased with age, on average, 8.6% for every 5 years (95% CI 0.8-17.0%). When transferring from one category of CT to the next one, the risk increased by 38% on the average (95% CI 17.1-62.6%). There was no statistically significant association of gender factor with overall survival (p = 0.408).The visual score of CT 0-4 recommended for use in the Russian Federation to assess lung parenchyma lesions according to chest CT data, is a predictor of a lethal outcome in patients with COVID-19. CT 0-4 score is convenient for practical use.
A review of sanitation technologies for flood-prone areas
Authors: Borges Pedro João Paulo , Oliveira Cássio Augusto da Silva , de Lima Sonaly Cristina Rezende Borges , von Sperling Marcos 
Published: July 2020

Abstract
Despite the formal acknowledgment of sanitation as a fundamental human right, more than 600 million people still practice open defecation, most of them in poor countries. A part of this challenge is related to the type of natural environment such as floodable areas where flooding affects thousands of people every year and has a direct impact on their access to sanitation. Although there is a wide range of technological sanitation options for vulnerable communities, few publications explore their applicability to areas prone to constant natural floods, thereby hampering the possibilities for improving sanitation conditions in such areas. This review aims at compiling and consolidating current information on sanitation options for floodable areas with a focus on their technological, environmental, and managerial peculiarities. A systematic review identified 28 relevant publications presenting sanitation solutions for those environments. They were grouped into dry solutions and wet solutions. Our analysis showed that there is no single universal technology capable of solving the problem but instead, a set of different technological arrangements that could be implemented bearing in mind the environmental and social contexts in which they are inserted.
This article has been made Open Access thanks to the generous support of a global network of libraries as part of the Knowledge Unlatched Select initiative.
Sensitivity of physical parameterization schemes in WRF model for dynamic downscaling of climatic variables over the MRB
Authors: Pervin Lia , Gan Thian Yew 
Published: July 2020

Abstract
The Weather Research and Forecasting (WRF) model was tested through 18 different combinations of physics parameters to simulate the regional climate over the Mackenzie River Basin (MRB). The objective was to investigate the response to the physics parameters for dynamic downscaling of climatic variables. The rainfall, temperature, albedo, and surface pressure from the 18 different WRF setups were compared with the reference data and were found sensitive to land surface physics and microphysics and to the radiation physics. The combination of Noah Land Surface Physics with the WRF Single-moment 6-class microphysics and CAM shortwave and longwave schemes produced comparable results for summer 2009. This WRF setup was further tested for summers 1979–1991 and it was found that WRF could simulate air temperature more accurately than the rainfall, since the rainfall over the mountainous regions was over-simulated. Then the selected combinations of WRF parameterizations were used to downscale the CanESM2 historical temperature and rainfall for summers 1979–2005, which showed good agreement with the reference data. The suggested WRF parameters from this study could be utilized for regional climate modeling of MRB.