bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling a composite assembly for repair of trunk pipelines
Authors: Mukhametzyanov Z R , Kulakov P A , Rubtsov A V , Churakov Yu A 
Published: July 2020

Abstract
The article considers the issue of the efficiency of the use of composite materials in the repair of trunk pipelines. During the study, simulation experiments were carried out using the Solidworks program for the main product pipeline under excess pressure P = 4 MPa. Altogether, eight situations were studied that differed in the amount of composite material applied to the defect. The criterion for determining the number of situations was determined by the number of layers of the composite material at which a favorable situation for the operation of the pipeline occurs. As a result of the experiments, the dependence of the stress-deformed state on the number of layers of the composite material deposited at the defect site is obtained. This dependence allows us to recommend a certain composition of the composite unit for repair of trunk pipelines. The research results obtained have the prospect of their further application in the development of a standard program for the repair of trunk pipelines using composite materials.
The influence of the rocks material composition on the reservoir properties of the reservoir
Authors: Malyarenko A M , Kotenev Yu A , Mukhametshin V Sh , Bogdan V A , Kotenev A Yu , Blinov S A , Umetbaev V G 
Published: July 2020

Abstract
High oil reserves characterize most fields in Western Siberia. However, along with this, zones of the productive formation that are poorly involved in development and production wells, in which products with a high proportion of water are produced, are distinguished within limits. For understanding the causes of this problem, it is important to consider the material composition of the reservoirs. In particular, it is necessary to consider the clay content, which is associated with the reservoir properties of rocks, hydrophilicity, hydrophobicity and, accordingly, with wettability. The article examined and analyzed a representative sample of core study of two wells in the Gubkinsky oil and gas region, which suggested the possible reasons for the lack of oil reserves.
To the study of the dynamics of layered structures with plane inclusions
Authors: Pavlova A V , Telyatnikov I S 
Published: July 2020

Abstract
We consider the problem of vibration for a layered package with defects such as hard inclusions on interlayer interfaces. Using the factorization approach, we obtain recurrence relations for the construction of functional-matrix equation systems for problems of elastic vibrations of a multilayer structure with a finite number of planar defects. When studying the resonance properties of the structures under consideration, the obtained representations of matrix kernel symbols of the integral equation systems allow us to implement numerical algorithms and construct the root and polar sets of their elements and determinants for a wide range of problems. The approach presented in this work makes it possible to efficiently study vibrational regimes for multilayer structures taking into account non-ideal interlayer contact. The developed scheme can also be applied to the case of an arbitrary number and alternation of parallel cracks and inclusions. Theoretical results can find applications in engineering practice when studying the strength properties of designed materials, when assessing the operational characteristics of composite structural elements, etc.
Software for tracking aquatic environment geographic information systems for further integration with advanced search capabilities
Authors: Volkov D A , Gorodov A A , Goncharov A E , Shepeta N A , Bashmur K A 
Published: July 2020

Abstract
A close inspection of existing software for relatively accessible underwater imaging and data-gathering systems reveals its inadequacy for conducting search operations and subsequent map making. In order to broaden the application of existing recreational and low-cost echo sounders and side scan sonar (SSS), the authors of this paper propose a program, which is part of a specialized software and hardware complex under implementation. Being the initial stage of the project, the proposed program is capable of visualizing routes on a graph and displaying the resulting trajectory using a GNSS receiver, further synchronizing it with hydrographic data from a sonar device.
Breast Reconstruction in the Social Media Age
Authors: Nguyen Jonathan , Thompson Peter , Losken Albert 
Published: July 2020

Abstract

Background
The internet and social media are sources of information regarding breast reconstruction, which can educate and influence patients.

Objectives
This study aimed to evaluate internet and social media usage by breast reconstruction patients and its impact on patients.

Methods
Eighty-six breast reconstruction patients over a 7-month period answered an anonymous survey, which queried demographics, reconstruction type, internet usage, social media usage, expectations, and impact on decisions. Fisher’s exact test was performed to evaluate the use of social media.

Results
Overall, 95% of patients used the internet for breast reconstruction information. The information was found to be easy to understand by 70% of patients, helpful by 76%, and trustworthy by 60%. The information influenced decisions regarding procedure by 23% of patients, regarding surgeon by 23%, and regarding hospital by 22%. Social media was used by 71% of the patients; 62% of patients found it easy to understand, 57% found it helpful, and 48% found it trustworthy. The information influenced decisions regarding procedure by 16% of patients, regarding surgeon by 11%, and regarding hospital by 10%. Twenty-six percent of women expected their final breast reconstruction to look better than their premastectomy breasts, 55% as good or similar, and 12% reported appearance to be unimportant. Women found social media information to be less helpful than internet information. There was no significant association between expectations and social media vs no social media usage.

Conclusions
Patients who undergo breast reconstruction use the internet and social media as sources of information. Although the information is generally trusted, it does not seem to heavily influence patient decision-making. Providers remain patients’ main source of information, and need to direct patients to high-quality and accessible resources.
Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response
Authors: Hu Fei-Fei , Liu Chun-Jie , Liu Lan-Lan , Zhang Qiong , Guo An-Yuan 
Published: July 2020

Abstract
Immune checkpoint genes (ICGs) play critical roles in circumventing self-reactivity and represent a novel target to develop treatments for cancers. However, a comprehensive analysis for the expression profile of ICGs at a pan-cancer level and their correlation with patient response to immune checkpoint blockade (ICB) based therapy is still lacking. In this study, we defined three expression patterns of ICGs using a comprehensive survey of RNA-seq data of tumor and immune cells from the functional annotation of the mammalian genome (FANTOM5) project. The correlation between the expression patterns of ICGs and patients survival and response to ICB therapy was investigated. The expression patterns of ICGs were robust across cancers, and upregulation of ICGs was positively correlated with high lymphocyte infiltration and good prognosis. Furthermore, we built a model (ICGe) to predict the response of patients to ICB therapy using five features of ICG expression. A validation scenario of six independent datasets containing data of 261 patients with CTLA-4 and PD-1 blockade immunotherapies demonstrated that ICGe achieved area under the curves of 0.64–0.82 and showed a robust performance and outperformed other mRNA-based predictors. In conclusion, this work revealed expression patterns of ICGs and underlying correlations between ICGs and response to ICB, which helps to understand the mechanisms of ICGs in ICB signal pathways and other anticancer treatments.
The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge
Authors: Pham Vu V H , Li Xiaomei , Truong Buu , Nguyen Thin , Liu Lin , Li Jiuyong , Le Thuc D 
Published: July 2020

Abstract

Motivation
Predicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM challenge on single-cell transcriptomics required participants to predict the locations of single cells in the Drosophila embryo using single-cell transcriptomic data.

Results
We have developed over 50 pipelines by combining different ways of preprocessing the RNA-seq data, selecting the genes, predicting the cell locations and validating predicted cell locations, resulting in the winning methods which were ranked second in sub-challenge 1, first in sub-challenge 2 and third in sub-challenge 3. In this paper, we present an R package, SCTCwhatateam, which includes all the methods we developed and the Shiny web application to facilitate the research on single-cell spatial reconstruction. All the data and the example use cases are available in the Supplementary data.
Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae
Authors: Wang Dan , Lai Fei-Liao , Gao Feng 
Published: July 2020

Abstract
DNA replication is a fundamental process in all organisms; this event initiates at sites termed origins of replication. The characteristics of eukaryotic replication origins are best understood in Saccharomyces cerevisiae. For this species, origin prediction algorithms or web servers have been developed based on the sequence features of autonomously replicating sequences (ARSs). However, their performances are far from satisfactory. By utilizing the Z-curve methodology, we present a novel pipeline, Ori-Finder 3, for the computational prediction of replication origins in S. cerevisiae at the genome-wide level based solely on DNA sequences. The ARS exhibiting both an AT-rich stretch and ARS consensus sequence element can be predicted at the single-nucleotide level. For the identified ARSs in the S. cerevisiae reference genome, 83 and 60% of the top 100 and top 300 predictions matched the known ARS records, respectively. Based on Ori-Finder 3, we subsequently built a database of the predicted ARSs identified in more than a hundred S. cerevisiae genomes. Consequently, we developed a user-friendly web server including the ARS prediction pipeline and the predicted ARSs database, which can be freely accessed at http://tubic.tju.edu.cn/Ori-Finder3.
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity
Authors: Pan Xiaoyong , Zuallaert Jasper , Wang Xi , Shen Hong-Bin , Campos Elda Posada , Marushchak Denys O , De Neve Wesley 
Published: July 2020

Abstract

Motivation
Genetically engineering food crops involves introducing proteins from other species into crop plant species or modifying already existing proteins with gene editing techniques. In addition, newly synthesized proteins can be used as therapeutic protein drugs against diseases. For both research and safety regulation purposes, being able to assess the potential toxicity of newly introduced/synthesized proteins is of high importance.

Results
In this study, we present ToxDL, a deep learning-based approach for in silico prediction of protein toxicity from sequence alone. ToxDL consists of (i) a module encompassing a convolutional neural network that has been designed to handle variable-length input sequences, (ii) a domain2vec module for generating protein domain embeddings and (iii) an output module that classifies proteins as toxic or non-toxic, using the outputs of the two aforementioned modules. Independent test results obtained for animal proteins and cross-species transferability results obtained for bacteria proteins indicate that ToxDL outperforms traditional homology-based approaches and state-of-the-art machine-learning techniques. Furthermore, through visualizations based on saliency maps, we are able to verify that the proposed network learns known toxic motifs. Moreover, the saliency maps allow for directed in silico modification of a sequence, thus making it possible to alter its predicted protein toxicity.

Availability and implementation
ToxDL is freely available at http://www.csbio.sjtu.edu.cn/bioinf/ToxDL/. The source code can be found at https://github.com/xypan1232/ToxDL.

Supplementary information
Supplementary data are available at Bioinformatics online.
Geographical differences in competitive hierarchy in a native–invasive system
Authors: Pujol-Buxó Eudald , Kaliontzopoulou Antigoni , Unanue-Goikoetxea Gerezti , Ambrós Bàrbara , Llorente Gustavo A 
Published: July 2020

AbstractBiological invasions can create novel competitive interactions and force ecological shifts in both native and invasive species. Anuran tadpoles are able to modify their behaviour, morphology, growth and development to cope with competitive pressure. This plasticity is a good target for natural selection and can drive rapid evolutionary changes in response to novel interactions. Here, we explore changes in plastic responses and fitness of competing invasive and native tadpoles by exposing tadpoles from different locations with contrasting evolutionary histories to the same set of varied competitive conditions. Eggs were collected from one site near the first introduction of the invasive frog (~110 years of coexistence) and from a second site that was invaded recently. We hypothesized less favourable outcomes for the invasive species in long-coexisting populations, where the native competitor might have developed adaptive responses. Most results support the hypothesis. Where the invasion was older, invasive tadpoles exposed to native competitors grew less, developed more slowly and displayed morphologies linked to competitive stress, whereas the developmental stability and canalization of native tadpoles increased. On the whole, the asymmetric competitive relationship thus appeared to approach symmetry after ~35 generations, highlighting a noteworthy example of rapid adaptation after an invasion.
Potentially functional variants in nucleotide excision repair pathway genes predict platinum treatment response of Chinese ovarian cancer patients
Authors: Li Haoran , Dai Hongji , Shi Tingyan , Cheng Xi , Sun Menghong , Chen Kexin , Wang Mengyun , Wei Qingyi 
Published: July 2020

Abstract
Acquired platinum resistance impedes successful treatment of epithelial ovarian cancer (EOC), and this resistance may be associated with inherited DNA damage–repair response. In the present study, we performed a two-phase analysis to assess associations between 8191 single-nucleotide polymorphisms within 127 genes of nucleotide excision repair pathway from a genome-wide association study dataset and platinum treatment response in 803 Han Chinese EOC patients. As a result, we identified that platinum-based chemotherapeutic response was associated with two potentially functional variants MNAT1 rs2284704 T&gt;C [TC + CC versus TT, adjusted odds ratio (OR) = 0.89, 95% confidence interval (CI) = 0.83–0.95 and P = 0.0005] and HUS1B rs61748571 A&gt;G (AG + GG versus AA, OR = 1.10, 95% CI = 1.03–1.18 and P = 0.005). Compared with the prediction model for clinical factors only, models incorporating HUS1B rs61748571 [area under the curve (AUC) 0.652 versus 0.672, P = 0.026] and the number of unfavorable genotypes (AUC 0.652 versus 0.668, P = 0.040) demonstrated a significant increase in the AUC. Further expression quantitative trait loci analysis suggested that MNAT1 rs2284704 T&gt;C significantly influenced mRNA expression levels of MNAT1 (P = 0.003). These results indicated that MNAT1 rs2284704 T&gt;C and HUS1B rs61748571 A&gt;G may serve as potential biomarkers for predicting platinum treatment response of Chinese EOC patients, once validated by further functional studies.
Response System for and Epidemiological Features of COVID-19 in Gyeongsangnam-do Province in South Korea
Authors: Wi Yu Mi , Lim Su Jin , Kim Si-Ho , Lim Seungjin , Lee Su Jin , Ryu Byung-Han , Hong Sun In , Cho Oh-Hyun , Moon Kyunglan , Hong Kyung-Wook , Kim Sunjoo , Bae In-Gyu 
Published: July 2020

Abstract

Background
The South Korean government has been combating the coronavirus disease 2019 (COVID-19) outbreak using public information and extensive viral screening. We describe the application of the Korean response system in Gyeongsangnam-do province and outline the epidemiological features of COVID-19 in the cohort.

Methods
A Rapid Response Team tracked the patients’ activities and identified close contacts. A Patient Management Team made decisions regarding the severity of illness, hospital allocation depending on severity, and time of discharge. A national medical center with 155 beds and 4 university-affiliated hospitals with 48 negative-pressure isolation rooms were dedicated for patients with COVID-19.

Results
As of 15 April, 17 400 residents were tested, of whom 111 were confirmed positive cases. Of the 111 patients, 78 were cured and discharged, 2 recovered after mechanical ventilation, and none died. One healthcare worker at the national center tested positive for SARS-CoV-2. All 412 staff members at the center were tested, but there were no additional infections. Cough (30.0%) was the most common initial symptom, whereas anosmia and ageusia were the first symptoms in 14.7% and 15.7% of the patients, respectively. Overall, 25 patients (22.5%) reported having no symptoms at admission and 7 (6.3%) remained asymptomatic at discharge.

Conclusions
A response system that enabled the early detection of COVID-19 cases, including asymptomatic and presymptomatic cases, and timely quarantine of these patients and their contacts, along with efficient allocation of medical resources, was the key to curbing the COVID-19 outbreak in Gyeongsangnam-do Province.
Measuring disturbance at swift breeding colonies due to the visual aspects of a drone: a quasi-experiment study
Authors: Mesquita Geison P , Rodríguez-Teijeiro José D , Wich Serge A , Mulero-Pázmány Margarita 
Published: July 2020

Abstract
There is a growing body of research indicating that drones can disturb animals. However, it is usually unclear whether the disturbance is due to visual or auditory cues. Here, we examined the effect of drone flights on the behavior of great dusky swifts Cypseloides senex and white-collared swifts Streptoprocne zonaris in 2 breeding sites where drone noise was obscured by environmental noise from waterfalls and any disturbance must be largely visual. We performed 12 experimental flights with a multirotor drone at different vertical, horizontal, and diagonal distances from the colonies. From all flights, 17% caused &lt;1% of birds to temporarily abandon the breeding site, 50% caused half to abandon, and 33% caused more than half to abandon. We found that the diagonal distance explained 98.9% of the variability of the disturbance percentage and while at distances &gt;50 m the disturbance percentage does not exceed 20%, at &lt;40 m the disturbance percentage increase to &gt; 60%. We recommend that flights with a multirotor drone during the breeding period should be conducted at a distance of &gt;50 m and that recreational flights should be discouraged or conducted at larger distances (e.g. 100 m) in nesting birds areas such as waterfalls, canyons, and caves.
SPDB: a specialized database and web-based analysis platform for swine pathogens
Authors: Wang Xiaoru , Liu Zongbao , Li Xiaoying , Li Danwei , Cai Jiayu , Yan He 
Published: July 2020

Abstract
The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research.
Database URL: http://spdatabase.com:2080/
Evaluating the diagnostic and prognostic value of biomarkers for heart disease and major adverse cardiac events in patients with muscular dystrophy
Authors: Nikhanj Anish , Miskew Nichols Bailey , Wang Kaiming , Siddiqi Zaeem A , Oudit Gavin Y 
Published: July 2020

Abstract

Aims
Heart disease is recognized as the leading cause of morbidity and mortality in patients with muscular dystrophy (MD). Our study demonstrates the clinical utility of cardiac biomarkers to improve the diagnosis of cardiomyopathy and prognostication of major adverse cardiac events (MACE) in these vulnerable patients.

Methods and results
We prospectively followed 117 patients [median age, 42 [interquartile range (IQR), 26–50) years; 49 (41.9%) women] at the Neuromuscular Multidisciplinary clinic diagnosed with a dystrophinopathy, limb-girdle MD, type 1 myotonic dystrophy, or facioscapulohumeral MD. We determined that B-type natriuretic peptide (BNP) and high-sensitive troponin I (hsTnI) were effective diagnostic markers of cardiomyopathy [area under the curve (AUC), 0.64; P = 0.017; and AUC, 0.69; P = 0.001, respectively]. Patient risk stratification for MACE was based on cut-off values of BNP and hsTnI defined a priori as 30.5000 pg/mL and 7.6050 ng/L, respectively. Over a median follow-up period of 2.09 (IQR, 1.17–2.81) years there were 36 confirmed MACE. Multivariate regression analyses showed that patients with BNP and hsTnI levels above the respective cut-off values had a 3.70-fold (P = 0.001) and 3.24-fold (P = 0.002) greater risk of MACE, respectively, compared with patients with biomarker levels below. Furthermore, patients with biomarker levels above both cut-off values had a 4.08-fold (P = 0.001) greater risk of MACE. Inflammatory biomarkers did not show clinical utility for heart disease in these patients.

Conclusion
Our study demonstrates important diagnostic and prognostic value of BNP and hsTnI as part of a comprehensive cardiac assessment to augment the management and treatment of heart disease in patients with MD.