bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design powerful predictor for mRNA subcellular location prediction inHomo sapiens
Authors: Zhang Zhao-Yue , Yang Yu-He , Ding Hui , Wang Dong , Chen Wei , Lin Hao 
Published: January 2020

AbstractMessenger RNAs (mRNAs) shoulder special responsibilities that transmit genetic code from DNA to discrete locations in the cytoplasm. The locating process of mRNA might provide spatial and temporal regulation of mRNA and protein functions. The situ hybridization and quantitative transcriptomics analysis could provide detail information about mRNA subcellular localization; however, they are time consuming and expensive. It is highly desired to develop computational tools for timely and effectively predicting mRNA subcellular location. In this work, by using binomial distribution and one-way analysis of variance, the optimal nonamer composition was obtained to represent mRNA sequences. Subsequently, a predictor based on support vector machine was developed to identify the mRNA subcellular localization. In 5-fold cross-validation, results showed that the accuracy is 90.12% for Homo sapiens (H. sapiens). The predictor may provide a reference for the study of mRNA localization mechanisms and mRNA translocation strategies. An online web server was established based on our models, which is available at http://lin-group.cn/server/iLoc-mRNA/.
sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R
Authors: Angelin-Bonnet Olivia , Biggs Patrick J , Baldwin Samantha , Thomson Susan , Vignes Matthieu 
Published: January 2020

Abstract

Summary
We present sismonr, an R package for an integral generation and simulation of in silico biological systems. The package generates gene regulatory networks, which include protein-coding and non-coding genes along with different transcriptional and post-transcriptional regulations. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations but can be defined by the user to higher ploidies. A choice of stochastic simulation algorithms allows us to simulate the expression profiles of the genes in the in silico system. We illustrate the use of sismonr by simulating the anthocyanin biosynthesis regulation pathway for three genetically distinct in silico plants.

Availability and implementation
The sismonr package is implemented in R and Julia and is publicly available on the CRAN repository (https://CRAN.R-project.org/package=sismonr). A detailed tutorial is available from GitHub at https://oliviaab.github.io/sismonr/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Network-based prediction of drug–target interactions using an arbitrary-order proximity embedded deep forest
Authors: Zeng Xiangxiang , Zhu Siyi , Hou Yuan , Zhang Pengyue , Li Lang , Li Jing , Huang L Frank , Lewis Stephen J , Nussinov Ruth , Cheng Feixiong 
Published: January 2020

Abstract

Motivation
Systematic identification of molecular targets among known drugs plays an essential role in drug repurposing and understanding of their unexpected side effects. Computational approaches for prediction of drug–target interactions (DTIs) are highly desired in comparison to traditional experimental assays. Furthermore, recent advances of multiomics technologies and systems biology approaches have generated large-scale heterogeneous, biological networks, which offer unexpected opportunities for network-based identification of new molecular targets among known drugs.

Results
In this study, we present a network-based computational framework, termed AOPEDF, an arbitrary-order proximity embedded deep forest approach, for prediction of DTIs. AOPEDF learns a low-dimensional vector representation of features that preserve arbitrary-order proximity from a highly integrated, heterogeneous biological network connecting drugs, targets (proteins) and diseases. In total, we construct a heterogeneous network by uniquely integrating 15 networks covering chemical, genomic, phenotypic and network profiles among drugs, proteins/targets and diseases. Then, we build a cascade deep forest classifier to infer new DTIs. Via systematic performance evaluation, AOPEDF achieves high accuracy in identifying molecular targets among known drugs on two external validation sets collected from DrugCentral [area under the receiver operating characteristic curve (AUROC) = 0.868] and ChEMBL (AUROC = 0.768) databases, outperforming several state-of-the-art methods. In a case study, we showcase that multiple molecular targets predicted by AOPEDF are associated with mechanism-of-action of substance abuse disorder for several marketed drugs (such as aripiprazole, risperidone and haloperidol).

Availability and implementation
Source code and data can be downloaded from https://github.com/ChengF-Lab/AOPEDF.

Supplementary information
Supplementary data are available at Bioinformatics online.
Antioxidant supplementation partially rescues accelerated ovarian follicle loss, but not oocyte quality, of glutathione-deficient mice†
Authors: Lim Jinhwan , Ali Samiha , Liao Lisa S , Nguyen Emily S , Ortiz Laura , Reshel Samantha , Luderer Ulrike 
Published: January 2020

Abstract
The tripeptide thiol antioxidant glutathione (GSH) has multiple physiological functions. Female mice lacking the modifier subunit of glutamate cysteine ligase (GCLM), the rate-limiting enzyme in GSH synthesis, have decreased GSH concentrations, ovarian oxidative stress, preimplantation embryonic mortality, and accelerated age-related decline in ovarian follicles. We hypothesized that supplementation with thiol antioxidants, N-acetyl cysteine (NAC), or α-lipoic acid (ALA) will rescue this phenotype. Gclm−/− and Gclm+/+ females received 0 or 80 mM NAC in drinking water from postnatal day (PND) 21–30; follicle growth was induced with equine chorionic gonadotropin (eCG) on PND 27, followed by an ovulatory dose of human CG and mating with a wild type male on PND 29 and zygote harvest 20 h after hCG. N-acetyl cysteine supplementation failed to rescue the low rate of second pronucleus formation in zygotes from Gclm−/− versus Gclm+/+ females. In the second study, Gclm−/− and Gclm+/+ females received diet containing 0, 150, or 600 mg/kg ALA beginning at weaning and were mated with wild type males from 8 to 20 weeks of age. α-Lipoic acid failed to rescue the decreased offspring production of Gclm−/− females. However, 150 mg/kg diet ALA partially rescued the accelerated decline in primordial follicles, as well as the increased recruitment of follicles into the growing pool and the increased percentages of follicles with γH2AX positive oocytes or granulosa cells of Gclm−/− females. We conclude that ovarian oxidative stress is the cause of accelerated primordial follicle decline, while GSH deficiency per se may be responsible for preimplantation embryonic mortality in Gclm−/− females.
Niclosamide suppresses macrophage-induced inflammation in endometriosis†
Authors: Sekulovski Nikola , Whorton Allison E , Tanaka Tomoki , Hirota Yasushi , Shi Mingxin , MacLean James A , de Mola Julio Ricardo Loret , Groesch Kathleen , Diaz-Sylvester Paula , Wilson Teresa , Hayashi Kanako 
Published: January 2020

Abstract
Endometriosis is a common gynecological disease, which causes chronic pelvic pain and infertility in women of reproductive age. Due to limited efficacy of current treatment options, a critical need exists to develop new and effective treatments for endometriosis. Niclosamide is an efficacious and FDA-approved drug for the treatment of helminthosis in humans that has been used for decades. We have reported that niclosamide reduces growth and progression of endometriosis-like lesions via targeting STAT3 and NFĸB signaling in a mouse model of endometriosis. To examine the effects of niclosamide on macrophage-induced inflammation in endometriosis, a total of 29 stage III–IV endometrioma samples were used to isolate human endometriotic stromal cells (hESCs). M1 or M2 macrophages were isolated and differentiated from fresh human peripheral blood samples. Then, hESCs were cultured in conditioned media (CM) from macrophages with/without niclosamide. Niclosamide dose dependently reduced cell viability and the activity of STAT3 and NFκB signaling in hESCs. While macrophage CM stimulated cell viability in hESCs, niclosamide inhibited this stimulation. Macrophage CM stimulated the secretion of proinflammatory cytokines and chemokines from hESCs. Most of these secreted factors were inhibited by niclosamide. These results indicate that niclosamide is able to reduce macrophage-induced cell viability and cytokine/chemokine secretion in hESCs by inhibiting inflammatory mechanisms via STAT3 and/or NFκB signaling.
Consensus on the reporting and experimental design of clinical and cognitive-behavioural neurofeedback studies (CRED-nf checklist)
Authors: Ros Tomas , Enriquez-Geppert Stefanie , Zotev Vadim , Young Kymberly D , Wood Guilherme , Whitfield-Gabrieli Susan , Wan Feng , Vuilleumier Patrik , Vialatte François , Van De Ville Dimitri , Todder Doron , Surmeli Tanju , Sulzer James S , Strehl Ute , Sterman Maurice Barry , Steiner Naomi J , Sorger Bettina , Soekadar Surjo R , Sitaram Ranganatha , Sherlin Leslie H , Schönenberg Michael , Scharnowski Frank , Schabus Manuel , Rubia Katya , Rosa Agostinho , Reiner Miriam , Pineda Jaime A , Paret Christian , Ossadtchi Alexei , Nicholson Andrew A , Nan Wenya , Minguez Javier , Micoulaud-Franchi Jean-Arthur , Mehler David M A , Lührs Michael , Lubar Joel , Lotte Fabien , Linden David E J , Lewis-Peacock Jarrod A , Lebedev Mikhail A , Lanius Ruth A , Kübler Andrea , Kranczioch Cornelia , Koush Yury , Konicar Lilian , Kohl Simon H , Kober Silivia E , Klados Manousos A , Jeunet Camille , Janssen T W P , Huster Rene J , Hoedlmoser Kerstin , Hirshberg Laurence M , Heunis Stephan , Hendler Talma , Hampson Michelle , Guggisberg Adrian G , Guggenberger Robert , Gruzelier John H , Göbel Rainer W , Gninenko Nicolas , Gharabaghi Alireza , Frewen Paul , Fovet Thomas , Fernández Thalía , Escolano Carlos , Ehlis Ann-Christine , Drechsler Renate , Christopher deCharms R , Debener Stefan , De Ridder Dirk , Davelaar Eddy J , Congedo Marco , Cavazza Marc , Breteler Marinus H M , Brandeis Daniel , Bodurka Jerzy , Birbaumer Niels , Bazanova Olga M , Barth Beatrix , Bamidis Panagiotis D , Auer Tibor , Arns Martijn , Thibault Robert T 
Published: January 2020

Abstract
Neurofeedback has begun to attract the attention and scrutiny of the scientific and medical mainstream. Here, neurofeedback researchers present a consensus-derived checklist that aims to improve the reporting and experimental design standards in the field.
Pharmacoepidemiology of Ceftazidime-Avibactam Use: A Retrospective Cohort Analysis of 210 US Hospitals
Authors: Strich Jeffrey R , Ricotta Emily , Warner Sarah , Lai Yi Ling , Demirkale Cumhur Y , Hohmann Samuel F , Rhee Chanu , Klompas Michael , Palmore Tara , Powers John H , Dekker John P , Adjemian Jennifer , Matsouaka Roland , Woods Christopher W , Danner Robert L , Kadri Sameer S 
Published: January 2020

Abstract

Background
Ceftazidime-avibactam has in vitro activity against some carbapenem-resistant gram-negative infections (GNIs), and therefore may be a useful alternative to more toxic antibiotics such as colistin. Understanding ceftazidime-avibactam uptake and usage patterns would inform hospital formularies, stewardship, and antibiotic development.

Methods
A retrospective cohort study assessed inpatient encounters in the Vizient database. Ceftazidime-avibactam and colistin administrations were categorized into presumed empiric (3 consecutive days of therapy or less with qualifying exclusions) versus targeted therapy (≥4 consecutive days of therapy) for presumed carbapenem-resistant GNIs. Quarterly percentage change (QPC) using modified Poisson regression and relative change in frequency of targeted ceftazidime-avibactam to colistin encounters was calculated. Factors associated with preferentially receiving targeted ceftazidime-avibactam versus colistin were identified using generalized estimating equations.

Results
Between 2015 quarter (q) 1 and 2017q4, ceftazidime-avibactam was administered 21 215 times across 1901 encounters. Inpatient prescriptions for ceftazidime-avibactam increased from 0.44/10 000 hospitalizations in 2015q1 to 7.7/10 000 in 2017q4 (QPC, +11%; 95% CI, 10–13%; P &lt; .01), while conversely colistin prescriptions decreased quarterly by 5% (95% CI, 4–6%; P &lt; .01). Ceftazidime-avibactam therapy was categorized as empiric 25% of the time, targeted 65% of the time, and indeterminate 10% of the time. Patients with chronic kidney disease were twice as likely to receive targeted ceftazidime-avibactam versus colistin (RR, 2.02; 95% CI, 1.82–2.25), whereas those on dialysis were less likely to receive ceftazidime-avibactam than colistin (RR, 0.71; 95% CI, .61–.83).

Conclusions
Since approval in 2015, ceftazidime-avibactam use has grown for presumed carbapenem-resistant GNIs, while colistin has correspondingly declined. Renal function drove the choice between ceftazidime-avibactam and colistin as targeted therapy.
Appraisal of Two Arabic Opinion Summarization Methods: Statistical Versus Machine Learning
Authors: Touati Imen , Ellouze Mariem , Graja Marwa , Hadrich Belguith Lamia 
Published: January 2020

Abstract
In this paper, we propose to overcome the challenge of digesting opinions in a news article. Our objective is to provide a summary of opinions delivered by many sources about a main topic in an Arabic news article. In literature, several studies addressed issues related to opinion summarization. However, we noticed a lack of studies that address this problem in Arabic language. So, we have proposed two different methods: multi-criteria and machine learning-based methods. We proceed by comparing the results provided by the proposed methods for opinionated sentence extraction. The proposed methods were evaluated using two feature types: text-based features and opinion-specific features. Experimental results show the robustness of machine learning method to extract opinionated sentences with consideration of two sets of features.
Effects of ultraviolet-B radiation on physiology, immune function and survival is dependent on temperature: implications for amphibian declines
Authors: Lundsgaard Niclas U , Cramp Rebecca L , Franklin Craig E 
Published: January 2020

AbstractMultiple environmental changes are thought to be contributing to the widespread decline of amphibians in montane regions, but interactions between drivers of decline are not well understood. It has been proposed previously that elevated ultraviolet-B radiation (UBVR) and low temperatures may interact in their negative effects on health, immune function and disease susceptibility in exposed amphibians. In the present study, we chronically exposed larvae of the striped-marsh frog (Limnodynastes peronii) to a factorial combination of high and low UVBR and high and low temperature to assess interactive effects on growth, survival and indices of immune function. The high UVBR treatment reduced growth and survival of larvae compared to the low UVBR treatment at both temperatures, but the effects were significantly enhanced at low temperature. High UVBR exposure also induced a chronic inflammatory response as evidenced by an increase in the leucocyte proportion of total cells and altered the ratio of neutrophils to lymphocytes in the blood, highlighting a potential mechanistic basis for increased disease susceptibility in amphibians living at high altitudes. Our findings stress the importance of investigating environmental factors in combination when assessing their effects and highlight the mechanistic basis for how key environmental drivers in montane regions affect amphibian health. Continuation of this work is necessary for the development of targeted conservation strategies that tackle the root causes of montane amphibian declines.
Perioperative immunonutrition in esophageal cancer patients undergoing esophagectomy: the first meta-analysis of randomized clinical trials
Authors: Mingliang Wang , Zhangyan Ke , Fangfang Fan , Huizhen Wang , Yongxiang Li 
Published: January 2020

Summary
Although several randomized controlled trials have been published in recent years, the effect of perioperative immunonutrition in esophageal cancer (EC) patients remains unclear. This initial meta-analysis was conducted to assess whether perioperative enteral immunonutrition reduces postoperative complications in patients undergoing esophagectomy for EC. Relevant randomized controlled trials published before 1st September 2019 were retrieved from the Cochrane Library, PubMed, and EMBASE databases. After the literature was screened, two researchers extracted the information and data from eligible studies according to predefined selection criteria. Obtained data were pooled and analyzed by RevMan 5.3 software. The results were presented as risk ratios (RRs) with 95% confidence intervals (CIs). The heterogeneity among studies was tested by I2 test. Seven high-quality randomized controlled trials were included, with a total of 606 patients, 311 of whom received immunonutrition before and after surgery, while 295 received perioperative standard nutrition. No significant difference was observed between the two groups in the incidence of postoperative infection complications, including total infection complications (RR = 0.97, CI: 0.78–1.20, P = 0.76), pneumonia (RR = 0.97, CI: 0.71–1.33, P = 0.84), wound infection (RR = 0.80, CI: 0.46–1.40, P = 0.44), sepsis (RR = 1.35, CI: 0.67–2.71, P = 0.40), and urinary tract infection (RR = 0.87, CI: 0.54–1.40, P = 0.56). The prevalence of anastomotic leakage in the two groups was 9.4 and 5.4%, but the difference was not statistically significant (RR = 0.59, CI: 0.33–1.04, P = 0.07). Perioperative enteral immunonutrition provided no benefit in terms of the incidence of infection complications and anastomotic leakage in EC patients undergoing esophagectomy. Further large-scale randomized controlled trials are needed to confirm this conclusion.
Long-term oncological outcomes following completely minimally invasive esophagectomy versus open esophagectomy
Authors: Patel K , Askari A , Moorthy K 
Published: January 2020

Summary
Open esophagectomy (OE) for esophageal and gastroesophageal junctional cancers is associated with high morbidity. Completely minimally invasive esophagectomy (CMIE) techniques have evolved over the last two decades and significantly reduce surgical trauma compared to open surgery. Despite this, long-term oncological outcomes following CMIE compared to OE remain unclear. This systematic review and meta-analysis aimed to compare overall 5-year survival (OFS) and disease-free 5-year survival (DFFS) between CMIE and OE. It was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A comprehensive electronic literature search from MEDLINE, EMBASE, Web of Science, Scopus and the Cochrane Central Register of Controlled Trials was conducted. The PROSPERO database was also searched for studies comparing OFS and DFFS between CMIE and OE. The Newcastle Ottawa Scale was used to assess study quality for included studies. Overall, seven studies (containing 949 patients: 527 OE and 422 CMIE) were identified from screening. On pooled meta-analysis, there was no significant difference in OFS or DFFS between CMIE and OE cohorts ([odds ratio 1.12; 95% CI: 0.85 to 1.48; P = 0.41] and [odds ratio 1.34; 95% CI: 0.81–2.22; P = 0.25] respectively). Sensitivity and subgroup analysis with high-quality studies, three highest sample sized studies, and three most recent studies also revealed no difference in long-term oncological outcomes between the two operative groups. This review demonstrates long-term oncological outcomes following CMIE appear equivalent to OE based on amalgamation of existing published literature. Limited high-level evidence comparing OFS and DFFS between CMIE and OE exists. Further research with a randomized controlled trial is required to clinically validate these findings.
OP06 Comparison between Crohn and coeliac diseases small intestine transcriptomics and microbial data define similarities and divergent pathways linked to pathogenesis
Authors: Haberman Ziv Y , Loberman-Nachum N , Katya S , Di Segni A , Efroni G , Braun T , BenShoshan M , Shouval D , Denson L A , Amir A , Unger R , Weiss B 
Published: January 2020

Abstract

Background
Crohn disease and coeliac disease are two inflammatory conditions known to cause small intestine inflammation. Using high throughput transcriptomics, microbial, and bioinformatics approaches we aimed to capture differences and similarities linked to the pathogenesis and to future potential interventions for those chronic manifestations.

Methods
We performed high throughput transcriptomics and 16S microbial characterisation of 55 paediatric new-onset coeliac patients and controls using clinical pathology specimens, and compared those signatures to our previously reported 248 RISK Crohn’s disease newly diagnosed cohort. ToppGene/ToppCluster and ClueGO platforms were used for functional annotation enrichment analyses, and MaAsLin for microbial differential abundance.

Results
A substantial number (&gt;90%) of genes passed the expression filtering criteria in both studies enabling the comparison. Of the 354 coeliac down-regulated genes, 59% (209/354) overlapped with the reduced Crohn signature. Shared reduced signatures and functions included a decrease in epithelial lipid metabolism, oxidoreductase activity, and brush border transport signatures. In contrast, a significantly smaller proportion [19% (97/427, Chi-squares p &lt; 0.001] of the coeliac disease 524 up-regulated genes overlapped with the induced Crohn disease signature. We noted shared enriched signatures for adaptive immune-related pathways and interferon-γ in both coeliac and Crohn diseases. However, the Crohn disease signature exhibited more specific enrichments for signatures associated with innate immune pathways and with a strong signal for granulocytes, an extracellular matrix signature, and CXCR chemokines signalling, while the coeliac up-regulated signature showed unique enrichment for cell cycle and mitosis. As opposed to the robust dysbiosis previously characterised in Crohn disease, we were only able to identify significant enrichment for Bacteroidetes taxa in coeliac patients in comparison to controls.

Conclusion
We highlight important biologic differences between Crohn and coeliac diseases emphasising an intensified innate granulocytes activation signature in Crohn disease and a specific epithelial proliferative signal in coeliac disease. Unlike the robust dysbiosis linked to Crohn disease, the coeliac patient showed only modest enrichment for several Bacteroidetes taxa in comparison to controls. It is possible that microbial alteration in Crohn disease triggers granulocytes activation, and that this signal inhibits epithelial proliferation/renewal, eventually leading the epithelial damage seen in Crohn but not coeliac disease. Inhibiting innate immune activation or reverting Crohn dysbiosis may be a beneficial future therapy for Crohn disease.