bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid attentional memory network for computational drug repositioning
Authors: He Jieyue , Yang Xinxing , Gong Zhuo , Zamit lbrahim 
Published: December 2020

AbstractBackgroundDrug repositioning has been an important and efficient method for discovering new uses of known drugs. Researchers have been limited to one certain type of collaborative filtering (CF) models for drug repositioning, like the neighborhood based approaches which are good at mining the local information contained in few strong drug–disease associations, or the latent factor based models which are effectively capture the global information shared by a majority of drug–disease associations. Few researchers have combined these two types of CF models to derive a hybrid model which can offer the advantages of both. Besides, the cold start problem has always been a major challenge in the field of computational drug repositioning, which restricts the inference ability of relevant models.ResultsInspired by the memory network, we propose the hybrid attentional memory network (HAMN) model, a deep architecture combining two classes of CF models in a nonlinear manner. First, the memory unit and the attention mechanism are combined to generate a neighborhood contribution representation to capture the local structure of few strong drug–disease associations. Then a variant version of the autoencoder is used to extract the latent factor of drugs and diseases to capture the overall information shared by a majority of drug–disease associations. During this process, ancillary information of drugs and diseases can help alleviate the cold start problem. Finally, in the prediction stage, the neighborhood contribution representation is coupled with the drug latent factor and disease latent factor to produce predicted values. Comprehensive experimental results on two data sets demonstrate that our proposed HAMN model outperforms other comparison models based on the AUC, AUPR and HR indicators.ConclusionsThrough the performance on two drug repositioning data sets, we believe that the HAMN model proposes a new solution to improve the prediction accuracy of drug–disease associations and give pharmaceutical personnel a new perspective to develop new drugs.
ped_draw: pedigree drawing with ease
Authors: Velinder Matt , Lee Dillon , Marth Gabor 
Published: December 2020

Abstract
Background
Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples. While the text based format of ped files is efficient for computational methods, it is not immediately intuitive to a bioinformatician or geneticist trying to understand family structures, many of which encode the affected status of individuals across multiple generations. The visualization of pedigrees into connected nodes with descriptive shapes and shading provides a far more interpretable format to recognize visual patterns and intuit family structures. Despite these advantages of a visual pedigree, it remains difficult to quickly and accurately visualize a pedigree given a pedigree text file.

Results
Here we describe ped_draw a command line and web tool as a simple and easy solution to pedigree visualization. Ped_draw is capable of drawing complex multi-generational pedigrees and conforms to the accepted standards for depicting pedigrees visually. The command line tool can be used as a simple one liner command, utilizing graphviz to generate an image file. The web tool, https://peddraw.github.io, allows the user to either: paste a pedigree file, type to construct a pedigree file in the text box or upload a pedigree file. Users can save the generated image file in various formats.

Conclusions
We believe ped_draw is a useful pedigree drawing tool that improves on current methods due to its ease of use and approachability. Ped_draw allows users with various levels of expertise to quickly and easily visualize pedigrees.
Decoy selection for protein structure prediction via extreme gradient boosting and ranking
Authors: Akhter Nasrin , Chennupati Gopinath , Djidjev Hristo , Shehu Amarda 
Published: December 2020

AbstractBackgroundIdentifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and negative samples (native and non-native decoys) in a decoy set makes the problem even more complicated. Consensus methods show varied success in handling the challenge of decoy selection despite some issues associated with clustering large decoy sets and decoy sets that do not show much structural similarity. Recent investigations into energy landscape-based decoy selection approaches show promises. However, lack of generalization over varied test cases remains a bottleneck for these methods.ResultsWe propose a novel decoy selection method, ML-Select, a machine learning framework that exploits the energy landscape associated with the structure space probed through a template-free decoy generation. The proposed method outperforms both clustering and energy ranking-based methods, all the while consistently offering better performance on varied test-cases. Moreover, ML-Select shows promising results even for the decoy sets consisting of mostly low-quality decoys.ConclusionsML-Select is a useful method for decoy selection. This work suggests further research in finding more effective ways to adopt machine learning frameworks in achieving robust performance for decoy selection in template-free protein structure prediction.
Expression patterns of ciliopathy genes ARL3 and CEP120 reveal roles in multisystem development
Authors: Powell L. , Barroso-Gil M. , Clowry G. J. , Devlin L. A. , Molinari E. , Ramsbottom S. A. , Miles C. G. , Sayer J. A. 
Published: December 2020

AbstractBackgroundJoubert syndrome and related disorders (JSRD) and Jeune syndrome are multisystem ciliopathy disorders with overlapping phenotypes. There are a growing number of genetic causes for these rare syndromes, including the recently described genesARL3andCEP120.MethodsWe sought to explore the developmental expression patterns ofARL3andCEP120in humans to gain additional understanding of these genetic conditions. We used an RNA in situ detection technique called RNAscope to characteriseARL3andCEP120expression patterns in human embryos and foetuses in collaboration with the MRC-Wellcome Trust Human Developmental Biology Resource.ResultsBothARL3andCEP120are expressed in early human brain development, including the cerebellum and in the developing retina and kidney, consistent with the clinical phenotypes seen with pathogenic variants in these genes.ConclusionsThis study provides insights into the potential pathogenesis of JSRD by uncovering the spatial expression of two JSRD-causative genes during normal human development.
Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control
Authors: Zhang Hanbang , Ehrenkaufer Gretchen M. , Hall Neil , Singh Upinder 
Published: December 2020

Abstract
Background
The RNA interference (RNAi) pathway is a gene regulation mechanism that utilizes small RNA (sRNA) and Argonaute (Ago) proteins to silence target genes. Our previous work identified a functional RNAi pathway in the protozoan parasite Entamoeba histolytica, including abundant 27 nt antisense sRNA populations which associate with EhAgo2–2 protein. However, there is lack of understanding about the sRNAs that are bound to two other EhAgos (EhAgo2–1 and 2–3), and the mechanism of sRNA regulation itself is unclear in this parasite. Therefore, identification of the entire pool of sRNA species and their sub-populations that associate with each individual EhAgo protein would be a major step forward.

Results
In the present study, we sequenced sRNA libraries from both total RNAs and EhAgo bound RNAs. We identified a new population of 31 nt sRNAs that results from the addition of a non-templated 3–4 adenosine nucleotides at the 3′-end of the 27 nt sRNAs, indicating a non-templated RNA-tailing event in the parasite. The relative abundance of these two sRNA populations is linked to the efficacy of gene silencing for the target gene when parasites are transfected with an RNAi-trigger construct, indicating that non-templated sRNA-tailing likely play a role in sRNA regulation in this parasite. We found that both sRNA populations (27 nt and 31 nt) are present in the related parasite Entamoeba invadens, and are unchanged during the development. In sequencing the sRNAs associating with the three EhAgo proteins, we observed that despite distinct cellular localization, all three EhAgo sRNA libraries contain 27 nt sRNAs with 5′-polyphosphate (5′-polyP) structure and share a largely overlapping sRNA repertoire. In addition, our data showed that a fraction of 31 nt sRNAs associate with EhAgo2–2 but not with its mutant protein (C-terminal deletion), nor other two EhAgos, indicating a specific EhAgo site may be required for sRNA modification process in the parasite.

Conclusion
We identified a new population of sRNA with non-templated oligo-adenylation modification, which is the first such observation amongst single celled protozoan parasites. Our sRNA sequencing libraries provide the first comprehensive sRNA dataset for all three Entamoeba Ago proteins, which can serve as a useful database for the amoeba community.
Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease
Authors: Xiao Chunfang , Huang Mengling , Gao Jianhua , Wang Zhen , Zhang Denghong , Zhang Yuanxue , Yan Lei , Yu Xiao , Li Bo , Shen Yanfen 
Published: December 2020

AbstractBackgroundLate blight disease (LBD) caused by the pathogenPhytophthora infestans(PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emerging and appearing in new areas at a very high intensity. A better understanding of the natural defense mechanisms against PI in different potato cultivars especially at the protein level is still lacking. Therefore, to elucidate potato proteome response to PI, we investigated changes in the proteome and leaf morphology of three potato cultivars, namely; Favorita (FA), Mira (MA), and E-malingshu N0.14 (E14) infected with PI by using the iTRAQ-based quantitative proteomics analysis.ResultsA total of 3306 proteins were found in the three potato genotypes, and 2044 proteins were quantified. Cluster analysis revealed MA and E14 clustered together separately from FA. The protein profile and related functions revealed that the cultivars shared a typical hypersensitive response to PI, including induction of elicitors, oxidative burst, and suppression of photosynthesis in the potato leaves. Meanwhile, MA and E14 deployed additional specific response mechanism different from FA, involving high induction of protease inhibitors, serine/threonine kinases, terpenoid, hormone signaling, and transport, which contributed to MA tolerance of LBD. Furthermore, inductions of pathogenesis-related proteins, LRR receptor-like kinases, mitogen-activated protein kinase, WRKY transcription factors, jasmonic acid, and phenolic compounds mediate E14 resistance against LBD. These proteins were confirmed at the transcription level by a quantitative polymerase chain reaction and at the translation level by western-blot.ConclusionsWe found several proteins that were differentially abundant among the cultivars, that includes common and cultivar specific proteins which highlighted similarities and significant differences between FA, MA, and E14 in terms of their defense response to PI. Here the specific accumulation of mitogen-activated protein kinase, Serine/threonine kinases, WRKY transcription played a positive role in E14 immunity against PI. The candidate proteins identified reported in this study will form the basis of future studies and may improve our understanding of the molecular mechanisms of late blight disease resistance in potato.
Transcriptome profiling revealed early vascular smooth muscle cell gene activation following focal ischemic stroke in female rats – comparisons with males
Authors: Rehnström Mimmi , Frederiksen Simona Denise , Ansar Saema , Edvinsson Lars 
Published: December 2020

AbstractBackgroundWomen account for 60% of all stroke deaths and are more often permanently disabled than men, despite their higher observed stroke incidence. Considering the clinical population affected by stroke, an obvious drawback is that many pre-clinical and clinical studies only investigate young males. To improve therapeutic translation from bench to bedside, we believe that it is advantageous to include both sexes in experimental models of stroke. The aims of this study were to identify early cerebral vascular responses to ischemic stroke in females, compare the differential gene expression patterns with those seen in males, and identify potential new therapeutic targets.ResultsTransient middle cerebral artery occlusion (tMCAO) was used to induce stroke in both female and male rats, the middle cerebral arteries (MCAs) were isolated 3 h post reperfusion and RNA was extracted. Affymetrix whole transcriptome expression profiling was performed on female (n = 12) MCAs to reveal differentially expressed genes. In total, 1076 genes had an increased expression and 879 genes a decreased expression in the occluded MCAs as compared with the control MCAs from female rats. An enrichment of genes related to apoptosis, regulation of transcription, protein autophosphorylation, inflammation, oxidative stress, and tissue repair and recovery were seen in the occluded MCA.The high expression genes chosen for qPCR verification (Adamts4,Olr1,JunB,Fosl1,Serpine1,S1pr3,Ccl2andSocs3) were all shown to be upregulated in the same manner in both females and males after tMCAO (p < 0.05;n = 23). When comparing the differentially expressed genes in female MCAs (occluded and non-occluded) with our previous findings in males after tMCAO, a total of 297 genes overlapped (all groups had 32 genes in common).ConclusionsThe cascades of processes initiated in the vasculature following reperfusion are complex. Dynamic gene expression alterations were observed in the occluded MCAs, and to a less pronounced degree in the non-occluded MCAs. Dysregulation of inflammation and blood-brain barrier breakdown are possible pharmacological targets. The sample of genes (< 1% of the differentially expressed genes) validated for this microarray did not reveal any sex differences. However, sex differences might be observed for other gene targets.
Two-weeks repeated-dose oral toxicity study of Pediococcus acidilactici J9 in a mice model
Authors: Lee Mijung , Chung Jin-Young , Kim Ka Yeun , Im Wooseok , Kim Manho 
Published: December 2020

AbstractBackgroundHelicobacter pylori (H. pylori) is an important pathogen that causes chronic gastritis and peptic ulcer, and is related to the development of gastric carcinoma. Several chemicals, including antibiotics, have been used to eradicateH.pylori. However, more studies are yet requred to accomplish a sufficient therapy.Pediococcus acidilactici(P. acidilactici) J9 were studied for inhibition of binding ofH.pyloribinding to human gastric cell lines. This study was performed in order to investigate the repeated-dose toxicity ofP. acidilacticiJ9 in male and female mice.ResultsC57BL/6 male and femaleMus musculuswere divided into four groups (n = 10 in each group).P. acidilacticiJ9 was administered daily by oral injection of vehicle control at dosage levels to a low-dose group (500 mg/kg/day), middle-dose group (1000 mg/kg/day), and high-dose group (2000 mg/kg/day) for 2 weeks. After 14 days of exposure, the blood biochemistry and hematology were investigated, along with a histopathology exam. There were no bacterial-related deaths or abnormal clinical signs in either gender of mouse. The data was observed during the period in terms of body weight, food intake, and water consumption. Also, no alterations in organ weights upon administration ofP. acidilacticiJ9 alone were observed. The adhesion and growth ofH. pyloriwere inhibited by a 24 h treatment ofH. pyloriandP. acidilacticiJ9 on adenocarcinoma gastric (AGS) cells, which are gastric cancer cells. Compared to the control group (AGS cell andH. pylori), the number ofH. pylorianalyzed by FACS significantly (p < 0.01) decreased after incubation of AGS cell withP. acidilacticiJ9 for 24 h.ConclusionsThese results suggest that the oral application ofP. acidilacticiJ9, up to a dosage level of 2000 mg/kg/day, causes no adverse effects in both male and female mice.P. acidilacticiJ9 inhibits the adhesion ofH.pylorito AGS cancer cells. When used as probiotics,P. acidilacticiJ9 may help decrease the occurrence of gastritis and reduce the risk ofH.pyloriinfection with promising safety issues.
Physical functional performance and prognosis in patients with heart failure: a systematic review and meta-analysis
Authors: Fuentes-Abolafio Iván José , Stubbs Brendon , Pérez-Belmonte Luis Miguel , Bernal-López María Rosa , Gómez-Huelgas Ricardo , Cuesta-Vargas Antonio Ignacio 
Published: December 2020

Abstract
Background
Patients with Heart Failure (HF) show impaired functional capacities which have been related to their prognosis. Moreover, physical functional performance in functional tests has also been related to the prognosis in patients with HF. Thus, it would be useful to investigate how physical functional performance in functional tests could determine the prognosis in patients with HF, because HF is the leading cause of hospital admissions for people older than 65 years old. This systematic review and meta-analysis aims to summarise and synthesise the evidence published about the relationship between physical functional performance and prognosis in patients with HF, as well as assess the risk of bias of included studies and the level of evidence per outcome.

Methods
Major electronic databases, such as PubMed, AMED, CINAHL, EMBASE, PEDro, Web of Science, were searched from inception to March 2020 for observational longitudinal cohort studies (prospective or retrospective) examining the relationship between physical functional performance and prognosis in patients with HF.

Results
44 observational longitudinal cohort studies with a total of 22,598 patients with HF were included. 26 included studies reported a low risk of bias, and 17 included studies showed a moderate risk of bias. Patients with poor physical functional performance in the Six Minute Walking Test (6MWT), in the Short Physical Performance Battery (SPPB) and in the Gait Speed Test showed worse prognosis in terms of larger risk of hospitalisation or mortality than patients with good physical functional performance. However, there was a lack of homogeneity regarding which cut-off points should be used to stratify patients with poor physical functional performance from patients with good physical functional performance.

Conclusion
The review includes a large number of studies which show a strong relationship between physical functional performance and prognosis in patients with HF. Most of the included studies reported a low risk of bias, and GRADE criteria showed a low and a moderate level of evidence per outcome.
Establishment and validation of a risk model for prediction of in-hospital mortality in patients with acute ST-elevation myocardial infarction after primary PCI
Authors: Gao Nan , Qi Xiaoyong , Dang Yi , Li Yingxiao , Wang Gang , Liu Xiao , Zhu Ning , Fu Jinguo 
Published: December 2020

AbstractBackgroundCurrently, how to accurately determine the patient prognosis after a percutaneous coronary intervention (PCI) remains unclear and may vary among populations, hospitals, and datasets. The aim of this study was to establish a prediction model of in-hospital mortality risk after primary PCI in patients with acute ST-elevated myocardial infarction (STEMI).MethodsThis was a multicenter, observational study of patients with acute STEMI who underwent primary PCI. The outcome was in-hospital mortality. The least absolute shrinkage and selection operator (LASSO) method was used to select the features that were the most significantly associated with the outcome. A regression model was built using the selected variables to select the significant predictors of mortality. Receiver operating characteristic (ROC) curve and decision curve analysis (DCA) were used to evaluate the performance of the nomogram.ResultsTotally, 1169 and 316 patients were enrolled in the training and validation sets, respectively. Fourteen predictors were identified by the LASSO analysis: sex, Killip classification, left main coronary artery disease (LMCAD), grading of thrombus, TIMI classification, slow flow, application of IABP, administration of β-blocker, ACEI/ARB, symptom-to-door time (SDT), symptom-to-balloon time (SBT), syntax score, left ventricular ejection fraction (LVEF), and CK-MB peak. The mortality risk prediction nomogram achieved good discrimination for in-hospital mortality (training set: C-statistic = 0.987; model calibration:P = 0.722; validation set: C-statistic = 0.984, model calibration:P = 0.669). Area under the curve (AUC) values for the training and validation sets are 0.987 (95% CI: 0.981–0.994,P = 0.003) and 0.990 (95% CI: 0.987–0.998,P = 0.007), respectively. DCA shows that the nomogram can achieve good net benefit.ConclusionsA novel nomogram was developed and is a simple and accurate tool for predicting the risk of in-hospital mortality in patients with acute STEMI who underwent primary PCI.
Inverse association of diabetes and dialysis with the severity of femoropopliteal lesions and chronic total occlusion: a cross-sectional study of 2056 cases
Authors: Takahara Mitsuyoshi , Soga Yoshimitsu , Fujihara Masahiko , Kawasaki Daizo , Kozuki Amane , Iida Osamu 
Published: December 2020

Abstract
Background
This study aimed to reveal the association of diabetes mellitus and dialysis-dependent renal failure with the lesion severity and chronic total occlusion (CTO) in patients undergoing femoropopliteal endovascular therapy for intermittent claudication.

Methods
This multicenter retrospective study analyzed the data of 2056 consecutive patients with moderate to severe intermittent claudication, who underwent endovascular therapy for de novo lesions in the superficial femoral artery to the proximal popliteal artery between 2010 and 2018 at five cardiovascular centers in Japan. The association of the clinical characteristics with severity of the lesions, as assessed by the Trans-Atlantic Inter-Society Consensus (TASC) II classification, was investigated using the ordinal logistic regression model. Their association with CTO, lesion length, and severity of calcifications was additionally analyzed using the binomial logistic regression model.

Results
The prevalence of diabetes mellitus and dialysis-dependent renal failure was 54.7% and 21.4%, respectively; 12.5% of the patients had lesions corresponding to TASC II class D, and 39.3% of the patients had CTO. Current smoking and severe claudication were associated with more severe lesions assessed according to the TASC II classification; diabetes mellitus and dialysis dependence were inversely associated with disease severity. The adjusted odds ratios of diabetes mellitus and dialysis dependence were 0.82 (95% confidence interval 0.70–0.97; p = 0.018) and 0.76 (0.62–0.94; p = 0.009), respectively. Diabetes mellitus and dialysis dependence were also inversely associated with CTO (both p < 0.05). Furthermore, diabetes mellitus was inversely associated with a long lesion (p < 0.05). Diabetes mellitus and dialysis dependence were positively associated with severe calcification (both p < 0.05).

Conclusions
Diabetes mellitus and dialysis-dependent renal failure were inversely associated with the lesion severity, as assessed by the TASC II classification, and CTO in patients undergoing femoropopliteal endovascular therapy for intermittent claudication.