bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progress of Development and Application of Drag Reduction Agents for Slick-Water Fracturing
Authors: Xu Ke , Lu Yongjun , Chang Jin , Weng Dingwei , Li Yang 
Published: November 2021

Abstract
Fracturing technology is the key technology of shale oil and gas exploitation in the United States. The key of hydraulic fracturing lies in the formulation of fracturing fluid, which can improve the permeability of shale gas layer, reduce pumping resistance, optimize production conditions, reduce strata damage and other purposes. Slick-water is widely used in water-based fracturing for unconventional oil and gas exploitation, which can reduce the friction resistance. As the core of the slickwater fracturing fluid, the friction reducer determine the fluid’s performances. Combining with the related literature at home and abroad, this paper analyzes the mechanism of friction reducer, introduces the research and application progress of natural polysaccharide, surfactant and polyacrylamide. It is considered that both the instant powder polymer and W/W dispersion polymer have great application potential. The friction reducer with high-efficiency sand-carrying and salt resistance is the focus of future research.
Numerical Simulation of Adsorption and Heat Transfer in Porous Media Using Lattice Boltzmann Method
Authors: Wang Jianhu , Duan Zhongdi , Cheng Cheng , Tang Wenyong 
Published: November 2021

Abstract
An adsorption model for fluid flow, heat, and mass transfer of the adsorbent bed was established. Based on the single relaxation time lattice Boltzmann method, a dual-distributed lattice Boltzmann model of density and concentration was established to solve the fluid flow and mass transfer process in the surface area of the adsorbent bed. The adsorption and heat transfer process on the surface of the adsorbent bed was incorporated into the dual-distributed lattice Boltzmann model by the fourth-order Runge-Kutta finite difference method. The multiphysics fields under Poiseuille flow were simulated by the presented model, and the adsorption capacity and temperature distribution during the adsorption process were investigated.
Focusing of Brownian Particles in a Fluid Induced by the Temperature Difference
Authors: Ying Yuxiang , Zheng Kaixuan , Nie Deming 
Published: November 2021

Abstract
In this work the Brownian motion of particles in a two-dimensional channel was numerically studied through a fluctuating-lattice Boltzmann method. The effects of the fluid temperature difference on the biased Brownian motion of particles were examined. It is shown that the particles are likely to move towards and stay at the low temperature zone. More importantly, the focusing of Brownian particles may be realized if the temperature difference is large enough. This paper also provides a quantitative analysis on this issue.
Atmospheric turbulence characterization using a neuromorphic camera-based imaging sensor
Authors: Polnau Ernst , Vorontsov Mikhail A 
Published: November 2021

Abstract
New capabilities for atmospheric turbulence spatio-temporal dynamics characterization and refractive index structure parameter (

C
n

2

) sensing via white light imaging of remotely located non-cooperative targets using an optical system with a neuromorphic (event) based sensor are demonstrated through a set of experimental trials conducted over a 7 km imaging path and proposed event data processing technique.
Occupational Exposure Assessment Tools in Europe: A Comprehensive Inventory Overview
Authors: Peters Susan , Vienneau Danielle , Sampri Alexia , Turner Michelle C , Castaño-Vinyals Gemma , Bugge Merete , Vermeulen Roel 
Published: November 2021

Abstract

Objectives
The Network on the Coordination and Harmonisation of European Occupational Cohorts (OMEGA-NET) was set up to enable optimization of the use of industrial and general population cohorts across Europe to advance aetiological research. High-quality harmonized exposure assessment is crucial to derive comparable results and to enable pooled analyses. To facilitate a harmonized research strategy, a concerted effort is needed to catalogue available occupational exposure information. We here aim to provide a first comprehensive overview of exposure assessment tools that could be used for occupational epidemiological studies.

Methods
An online inventory was set up to collect meta-data on exposure assessment tools. Occupational health researchers were invited via newsletters, editorials, and individual e-mails to provide details of job-exposure matrices (JEMs), exposure databases, and occupational coding systems and their associated crosswalks to translate codes between different systems, with a focus on Europe.

Results
Meta-data on 36 general population JEMs, 11 exposure databases, and 29 occupational coding systems from more than 10 countries have been collected up to August 2021. A wide variety of exposures were covered in the JEMs on which data were entered, with dusts and fibres (in 14 JEMs) being the most common types. Fewer JEMs covered organization of work (5) and biological factors (4). Dusts and fibres were also the most common exposures included in the databases (7 out of 11), followed by solvents and pesticides (both in 6 databases).

Conclusions
This inventory forms the basis for a searchable web-based database of meta-data on existing occupational exposure information, to support researchers in finding the available tools for assessing occupational exposures in their cohorts, and future efforts for harmonization of exposure assessment. This inventory remains open for further additions, to enlarge its coverage and include newly developed tools.
A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape
Authors: Zhang Yongqing , Wang Zixuan , Zeng Yuanqi , Liu Yuhang , Xiong Shuwen , Wang Maocheng , Zhou Jiliu , Zou Quan 
Published: November 2021

AbstractThe discovery of putative transcription factor binding sites (TFBSs) is important for understanding the underlying binding mechanism and cellular functions. Recently, many computational methods have been proposed to jointly account for DNA sequence and shape properties in TFBSs prediction. However, these methods fail to fully utilize the latent features derived from both sequence and shape profiles and have limitation in interpretability and knowledge discovery. To this end, we present a novel Deep Convolution Attention network combining Sequence and Shape, dubbed as D-SSCA, for precisely predicting putative TFBSs. Experiments conducted on 165 ENCODE ChIP-seq datasets reveal that D-SSCA significantly outperforms several state-of-the-art methods in predicting TFBSs, and justify the utility of channel attention module for feature refinements. Besides, the thorough analysis about the contribution of five shapes to TFBSs prediction demonstrates that shape features can improve the predictive power for transcription factors-DNA binding. Furthermore, D-SSCA can realize the cross-cell line prediction of TFBSs, indicating the occupancy of common interplay patterns concerning both sequence and shape across various cell lines. The source code of D-SSCA can be found at https://github.com/MoonLord0525/.
Light attention predicts protein location from the language of life
Authors: Stärk Hannes , Dallago Christian , Heinzinger Michael , Rost Burkhard 
Published: November 2021

AbstractSummaryAlthough knowing where a protein functions in a cell is important to characterize biological processes, this information remains unavailable for most known proteins. Machine learning narrows the gap through predictions from expert-designed input features leveraging information from multiple sequence alignments (MSAs) that is resource expensive to generate. Here, we showcased using embeddings from protein language models for competitive localization prediction without MSAs. Our lightweight deep neural network architecture used a softmax weighted aggregation mechanism with linear complexity in sequence length referred to as light attention. The method significantly outperformed the state-of-the-art (SOTA) for 10 localization classes by about 8 percentage points (Q10). So far, this might be the highest improvement of just embeddings over MSAs. Our new test set highlighted the limits of standard static datasets: while inviting new models, they might not suffice to claim improvements over the SOTA.Availability and implementationThe novel models are available as a web-service at http://embed.protein.properties. Code needed to reproduce results is provided at https://github.com/HannesStark/protein-localization. Predictions for the human proteome are available at https://zenodo.org/record/5047020.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores
Authors: Warmerdam Robert , Lanting Pauline ,   Lifelines Cohort Study, Deelen Patrick , Franke Lude 
Published: November 2021

Abstract

Motivation
Identifying sample mix-ups in biobanks is essential to allow the repurposing of genetic data for clinical pharmacogenetics. Pharmacogenetic advice based on the genetic information of another individual is potentially harmful. Existing methods for identifying mix-ups are limited to datasets in which additional omics data (e.g. gene expression) is available. Cohorts lacking such data can only use sex, which can reveal only half of the mix-ups. Here, we describe Idéfix, a method for the identification of accidental sample mix-ups in biobanks using polygenic scores.

Results
In the Lifelines population-based biobank, we calculated polygenic scores (PGSs) for 25 traits for 32 786 participants. We then applied Idéfix to compare the actual phenotypes to PGSs, and to use the relative discordance that is expected for mix-ups, compared to correct samples. In a simulation, using induced mix-ups, Idéfix reaches an AUC of 0.90 using 25 polygenic scores and sex. This is a substantial improvement over using only sex, which has an AUC of 0.75. Subsequent simulations present Idéfix’s potential in varying datasets with more powerful PGSs. This suggests its performance will likely improve when more highly powered GWASs for commonly measured traits will become available. Idéfix can be used to identify a set of high-quality participants for whom it is very unlikely that they reflect sample mix-ups, and for these participants we can use genetic data for clinical purposes, such as pharmacogenetic profiles. For instance, in Lifelines, we can select 34.4% of participants, reducing the sample mix-up rate from 0.15% to 0.01%.

Availabilityand implementation
Idéfix is freely available at https://github.com/molgenis/systemsgenetics/wiki/Idefix. The individual-level data that support the findings were obtained from the Lifelines biobank under project application number ov16_0365. Data is made available upon reasonable request submitted to the LifeLines Research office (research@lifelines.nl, https://www.lifelines.nl/researcher/how-to-apply/apply-here).

Supplementary information
Supplementary data are available at Bioinformatics online.
GNN-based embedding for clustering scRNA-seq data
Authors: Ciortan Madalina , Defrance Matthieu 
Published: November 2021

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) provides transcriptomic profiling for individual cells, allowing researchers to study the heterogeneity of tissues, recognize rare cell identities and discover new cellular subtypes. Clustering analysis is usually used to predict cell class assignments and infer cell identities. However, the high sparsity of scRNA-seq data, accentuated by dropout events generates challenges that have motivated the development of numerous dedicated clustering methods. Nevertheless, there is still no consensus on the best performing method.

Results
graph-sc is a new method leveraging a graph autoencoder network to create embeddings for scRNA-seq cell data. While this work analyzes the performance of clustering the embeddings with various clustering algorithms, other downstream tasks can also be performed. A broad experimental study has been performed on both simulated and scRNA-seq datasets. The results indicate that although there is no consistently best method across all the analyzed datasets, graph-sc compares favorably to competing techniques across all types of datasets. Furthermore, the proposed method is stable across consecutive runs, robust to input down-sampling, generally insensitive to changes in the network architecture or training parameters and more computationally efficient than other competing methods based on neural networks. Modeling the data as a graph provides increased flexibility to define custom features characterizing the genes, the cells and their interactions. Moreover, external data (e.g. gene network) can easily be integrated into the graph and used seamlessly under the same optimization task.

Availability and implementation
https://github.com/ciortanmadalina/graph-sc.

Supplementary information
Supplementary data are available at Bioinformatics online.
Induction of mismatch repair deficiency, compromised DNA damage signaling and compound hypermutagenesis by a dietary mutagen in a cell-based model for Lynch syndrome
Authors: Ijsselsteijn Robbert , van Hees Sandrine , Drost Mark , Jansen Jacob G , de Wind Niels 
Published: November 2021

Abstract
The prevalent cancer predisposition Lynch syndrome (LS, OMIM #120435) is caused by an inherited heterozygous defect in any of the four core DNA mismatch repair (MMR) genes MSH2, MSH6, MLH1 or PMS2. MMR repairs errors by the replicative DNA polymerases in all proliferating tissues. Its deficiency, following somatic loss of the wild-type copy, results in a spontaneous mutator phenotype that underlies the rapid development of, predominantly, colorectal cancer (CRC) in LS. Here, we have addressed the hypothesis that aberrant responses of intestinal stem cells to diet-derived mutagens may be causally involved in the restricted cancer tropism of LS. To test this we have generated a panel of isogenic mouse embryonic stem (mES) cells with heterozygous or homozygous disruption of multiple MMR genes and investigated their responses to the common dietary mutagen and carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Our data reveal that PhIP can inactivate the wild-type allele of heterozygous mES cells via the induction of either loss of heterozygosity (LOH) or intragenic mutations. Moreover, while protective DNA damage signaling (DDS) is compromised, PhIP induces more mutations in Msh2, Mlh1, Msh6 or Pms2-deficient mES cells than in wild-type cells. Combined with their spontaneous mutator phenotypes, this results in a compound hypermutator phenotype. Together, these results indicate that dietary mutagens may promote CRC development in LS at multiple levels, providing a rationale for dietary modifications in the management of LS.
Prenatal gyrification pattern affects age at onset in frontotemporal dementia
Authors: Harper Luke , Lindberg Olof , Bocchetta Martina , Todd Emily G , Strandberg Olof , van Westen Danielle , Stomrud Erik , Landqvist Waldö Maria , Wahlund Lars-Olof , Hansson Oskar , Rohrer Jonathan D , Santillo Alexander 
Published: November 2021

Abstract
The paracingulate sulcus is a tertiary sulcus formed during the third trimester. In healthy individuals paracingulate sulcation is more prevalent in the left hemisphere. The anterior cingulate and paracingulate gyri are focal points of neurodegeneration in behavioral variant frontotemporal dementia (bvFTD). This study aims to determine the prevalence and impact of paracingulate sulcation in bvFTD. Structural magnetic resonance images of individuals with bvFTD (n = 105, mean age 66.9 years), Alzheimer’s disease (n = 92, 73.3), and healthy controls (n = 110, 62.4) were evaluated using standard protocol for hemispheric paracingulate sulcal presence. No difference in left hemisphere paracingulate sulcal frequency was observed between groups; 0.72, 0.79, and 0.70, respectively, in the bvFTD, Alzheimer’s disease, and healthy control groups, (P = 0.3). A significant impact of right (but not left) hemispheric paracingulate sulcation on age at disease onset was identified in bvFTD (mean 60.4 years where absent vs. 63.8 where present [P = 0.04, Cohen’s d = 0.42]). This relationship was not observed in Alzheimer’s disease. These findings demonstrate a relationship between prenatal neuronal development and the expression of a neurodegenerative disease providing a gross morphological example of brain reserve.
Modes of the bioprosthetic valve failure of the porcine and pericardial valves in the mitral position
Authors: Uchino Gaku , Murakami Hirohisa , Mukohara Nobuhiko , Tanaka Hiroshi , Nomura Yoshikatsu , Miyahara Syunsuke , Kawashima Motoharu , Fujisue Jun , Tonoki Shuto 
Published: November 2021

Abstract

OBJECTIVES
This study was conducted to examine the incidence and modes of the bioprosthetic valve failure of the porcine valve in the mitral position and compare them with those of the pericardial valve.

METHODS
This study included 240 patients (116 men [48.3%]; mean age, 74.87 ± 6.61 years) who underwent mitral valve replacement using the St. Jude Medical Epic bioprosthesis (Epic) (N = 125) or Carpentier–Edwards Perimount (CEP) pericardial valve (N = 115) from January 2000 to December 2020.

RESULTS
The median clinical follow-up durations in the Epic and CEP groups were 54.5 months (range, 0–111 months) and 81.5 months (range, 0–194 months), respectively. Structural valve degeneration (SVD) was observed in 9 patients (7.2%) in the Epic group and 11 patients (9.6%) in the CEP group. The rates of freedom from SVD at 3, 5 and 7 years were 97.7%, 90.5% and 75.5% in the Epic group and 100.0%, 96.1% and 90.0% in the CEP group, respectively. SVD reoperation was performed for 7 patients (5.6%) in the Epic group and 6 patients (5.2%) in the CEP group. The rates of freedom from SVD reoperation at 3, 5 and 7 years were 97.7%, 90.5% and 75.5% in the Epic group and 100%, 96.1% and 90.0% in the CEP group, respectively. Epic SVD was predominantly due to leaflet tearing, whereas CEP SVD was predominantly due to leaflet calcification and adhesion to the subvalvular apparatus.

CONCLUSIONS
SVD of the porcine valve was predominantly due to leaflet tearing. The rate of reoperation for SVD was slightly higher for the porcine valve in the mitral position than for the pericardial valve at adjusted survival analysis.
Predictors of mortality in patients with acute small-bowel perforation transferred to ICU after emergency surgery: a single-centre retrospective cohort study
Authors: Wu Jianzhang , Shu Ping , He Hongyong , Li Haojie , Tang Zhaoqing , Sun Yihong , Liu Fenglin 
Published: November 2021

Abstract

Background
Although small-bowel perforation is a life-threatening emergency even after immediate surgical intervention, studies have rarely investigated surgical outcomes due to its relatively low incidence. This study aimed to investigate the outcomes of emergency surgery for patients with small-bowel perforation transferred to the intensive care unit (ICU) and the risk factors for mortality.

Methods
Consecutive patients with small-bowel perforation who were confirmed via emergency surgery and transferred to the ICU in Zhongshan Hospital, Fudan University (Shanghai, China) between February 2011 and May 2020 were retrospectively analysed. Medical records were reviewed to determine clinical features, laboratory indicators, surgical findings, and pathology.

Results
A total of 104 patients were included in this study, among whom 18 (17.3%), 59 (56.7%), and 27 (26.0%) underwent perforation repair, segmental resection with primary anastomosis, and small-bowel ostomy, respectively. Malignant tumours were the leading cause of perforation in these patients (40.4%, 42/104). The overall post-operative complication rate and mortality rates were 74.0% (77/104) and 19.2% (20/104), respectively. Malignant tumour-related perforation (odds ratio [OR], 4.659; 95% confidence interval [CI], 1.269–17.105; P = 0.020) and high post-operative arterial blood-lactate level (OR, 1.479; 95% CI, 1.027–2.131; P = 0.036) were identified as independent risk factors for post-operative mortality in patients with small-bowel perforation transferred to the ICU.

Conclusions
Patients with small-bowel perforation who are transferred to the ICU after emergency surgery face a high risk of post-operative complications and mortality. Moreover, those patients with malignant tumour-related perforation and higher post-operative blood-lactate levels have poor prognosis.
The Association Between Leisure Activity Engagement and Health-Related Quality of Life in Middle-Aged and Older People With HIV
Authors: Wion Rachel K , Fazeli Pariya L , Vance David E 
Published: November 2021

Abstract

Background and Objectives
Middle-aged and older adults with human immunodeficiency virus (HIV) are at risk for decreased health-related quality of life (HRQoL), which may be improved by engaging in leisure activities. We examined associations between HRQoL and participation in cognitive, physical, social, and passive leisure activities, and whether depressive symptoms mediated these relationships. Wilson and Cleary’s conceptual model of HRQoL guided this study.

Research Design and Methods
In this cross-sectional observational study, we enrolled 174 adults living with HIV aged 40 and older (M = 51.3, SD = 7.03). Participants completed assessments of leisure activities, depressive symptoms, and HRQoL. Data were analyzed using Spearman’s rho correlations, hierarchal multiple regression, and mediation analyses.

Results
Greater engagement in physical activities was associated with higher physical HRQoL (b = 2.02, p &lt; .05). Greater engagement in social activities was associated with both higher physical (b = 1.44, p &lt; .05) and mental HRQoL (b = 1.95, p &lt; .01). However, all associations between leisure activities and HRQoL were fully attenuated by depressive symptoms. Cognitive and passive leisure activities were not significantly correlated with HRQoL. Mediation analyses confirmed that depressive symptoms were the mediator mechanism by which social activities affected mental and physical HRQoL.

Discussion and Implications
More frequent engagement in physical and social leisure activities is associated with better HRQoL, and social leisure activities improve HRQoL via their impact on mood. Interventions to increase leisure activities, especially among people living with HIV who have poorer affective functioning, may be the most effective approach to improving HRQoL.
Does Corruption Corrupt? The Behavioral Effects of Mediated Exposure to Corruption
Authors: Waismel-Manor Israel , Moy Patricia , Neumann Rico , Shechnick Moran 
Published: November 2021

Abstract
Corruption is a complex, widespread phenomenon with harmful economic and societal effects. Drawing upon theories in social psychology, political science, and communication, this study examines the direct and joint effects of mediated exposure to grand corruption and the presence of monetary incentives on people’s likelihood to engage in dishonest behavior. In a 2 × 2 factorial design (N = 404), half of all participants were exposed to a newscast about political corruption and one half was offered a reward for correctly answering questions about the newscast. Findings suggest that incentivizing was highly effective in predicting chances of cheating while news exposure to corruption was not. The data also indicate cheating is more common among certain sociodemographic groups.