bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study on sedimentation stability of magnetorheological fluids based on different lubricant formulations
Authors: Zhibin Su , Yiping Luo , Ying Wang , Jiao Luo , Dongsheng Ji 
Published: August 2020

Abstract
Magnetorheological Fluids (MRFs) is rapidly emerging as a type of new fluid intelligence material that is controllable and low-energy consuming with high output and fast response. It has already received widespread attention from many international scholars. In this paper, the orthogonal test of MRFs configuration with six different types of lubricating additives (oleic acid, hydrogenated castor oil, teflon, boron nitride, molybdenum disulfide, graphite) is conducted to study the wettability, zero-field viscosity and yield stress of MRFs under different solid lubricants. According to the size of contact angle, the ability of anti-sedimentation stability of MRFs under different lubricants is compared. The zero-field viscosity of MRFs is tested by viscometer, and the strength of viscosity under the zero-field condition is compared. The yield stress is measured by a self-made yield stress device, and then the sedimentation stability characteristics of MRFs are analyzed. Finally, through the analysis and evaluation of experimental data, it is concluded that molybdenum disulfide as a lubricating additive can effectively improve the anti-sedimentation stability of MRFs, and the general rules of lubricating additives used in MRFs formulations with excellent performance are summarized.
High performance photodetectors using porous silicon-TiO2 heterostructure
Authors: Banerjee Debika , Asuo Ivy M , Pignolet Alain , Nechache Riad , Cloutier Sylvain G 
Published: August 2020

Abstract
In this study, a feasible approach for UV–vis photodetection using hybrid heterojunction by integrating porous silicon and TiO2 thin film is demonstrated. The photodetector demonstrates excellent photoresponse by three orders of magnitude enhancement and fast rise/decay time constants of 0.16/0.14 ms. Under small bias (1 V), the photodetector exhibits very high responsivity up to 40 A W−1 at 532 nm irradiation over a broadband wavelength range from 300–700 nm. The heterostructure geometry yields high-performance devices useful for many optoelectronic and biomedical applications.
The heat is on: towards the realization of non-cryogenic photonic quantum technologies
Authors: Holmes Mark J , Arakawa Yasuhiko 
Published: August 2020

Abstract
Solid-state devices capable of emitting single photons on demand are poised to allow the development of several photonic quantum technologies. Although high-performance devices have been reported in laboratory settings, the vast majority of experimental demonstrations performed to date have required the assistance of cryogenic cooling. In this perspective article we discuss the general progress and future challenges for the development of single photon emitters capable of operation at higher temperatures: negating the need for costly and cumbersome cryogenic cooling systems and their related vacuum requirements.
A review of digital cytometry methods: estimating the relative abundance of cell types in a bulk of cells
Authors: Le Trang , Aronow Rachel A , Kirshtein Arkadz , Shahriyari Leili 
Published: August 2020

AbstractDue to the high cost of flow and mass cytometry, there has been a recent surge in the development of computational methods for estimating the relative distributions of cell types from the gene expression profile of a bulk of cells. Here, we review the five common ‘digital cytometry’ methods: deconvolution of RNA-Seq, cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), CIBERSORTx, single sample gene set enrichment analysis and single-sample scoring of molecular phenotypes deconvolution method. The results show that CIBERSORTx B-mode, which uses batch correction to adjust the gene expression profile of the bulk of cells (‘mixture data’) to eliminate possible cross-platform variations between the mixture data and the gene expression data of single cells (‘signature matrix’), outperforms other methods, especially when signature matrix and mixture data come from different platforms. However, in our tests, CIBERSORTx S-mode, which uses batch correction for adjusting the signature matrix instead of mixture data, did not perform better than the original CIBERSORT method, which does not use any batch correction method. This result suggests the need for further investigations into how to utilize batch correction in deconvolution methods.
DataRemix: a universal data transformation for optimal inference from gene expression datasets
Authors: Mao Weiguang , Rahimikollu Javad , Hausler Ryan , Chikina Maria 
Published: August 2020

Abstract

Motivation
RNA-seq technology provides unprecedented power in the assessment of the transcription abundance and can be used to perform a variety of downstream tasks such as inference of gene-correlation network and eQTL discovery. However, raw gene expression values have to be normalized for nuisance biological variation and technical covariates, and different normalization strategies can lead to dramatically different results in the downstream study.

Results
We describe a generalization of singular value decomposition-based reconstruction for which the common techniques of whitening, rank-k approximation and removing the top k principal components are special cases. Our simple three-parameter transformation, DataRemix, can be tuned to reweigh the contribution of hidden factors and reveal otherwise hidden biological signals. In particular, we demonstrate that the method can effectively prioritize biological signals over noise without leveraging external dataset-specific knowledge, and can outperform normalization methods that make explicit use of known technical factors. We also show that DataRemix can be efficiently optimized via Thompson sampling approach, which makes it feasible for computationally expensive objectives such as eQTL analysis. Finally, we apply our method to the Religious Orders Study and Memory and Aging Project dataset, and we report what to our knowledge is the first replicable trans-eQTL effect in human brain.

Availabilityand implementation
DataRemix is an R package which is freely available at GitHub (https://github.com/wgmao/DataRemix).

Supplementary information
Supplementary data are available at Bioinformatics online.
KORP-PL: a coarse-grained knowledge-based scoring function for protein–ligand interactions
Authors: Kadukova Maria , Machado Karina dos Santos , Chacón Pablo , Grudinin Sergei 
Published: August 2020

AbstractMotivationDespite the progress made in studying protein–ligand interactions and the widespread application of docking and affinity prediction tools, improving their precision and efficiency still remains a challenge. Computational approaches based on the scoring of docking conformations with statistical potentials constitute a popular alternative to more accurate but costly physics-based thermodynamic sampling methods. In this context, a minimalist and fast sidechain-free knowledge-based potential with a high docking and screening power can be very useful when screening a big number of putative docking conformations.ResultsHere, we present a novel coarse-grained potential defined by a 3D joint probability distribution function that only depends on the pairwise orientation and position between protein backbone and ligand atoms. Despite its extreme simplicity, our approach yields very competitive results with the state-of-the-art scoring functions, especially in docking and screening tasks. For example, we observed a twofold improvement in the median 5% enrichment factor on the DUD-E benchmark compared to Autodock Vina results. Moreover, our results prove that a coarse sidechain-free potential is sufficient for a very successful docking pose prediction.Availabilityand implementationThe standalone version of KORP-PL with the corresponding tests and benchmarks are available at https://team.inria.fr/nano-d/korp-pl/ and https://chaconlab.org/modeling/korp-pl.Supplementary informationSupplementary data are available at Bioinformatics online.
Interim recruitment prediction for multi-center clinical trials
Authors: Urbas Szymon , Sherlock Chris , Metcalfe Paul 
Published: August 2020

SummaryWe introduce a general framework for monitoring, modeling, and predicting the recruitment to multi-center clinical trials. The work is motivated by overly optimistic and narrow prediction intervals produced by existing time-homogeneous recruitment models for multi-center recruitment. We first present two tests for detection of decay in recruitment rates, together with a power study. We then introduce a model based on the inhomogeneous Poisson process with monotonically decaying intensity, motivated by recruitment trends observed in oncology trials. The general form of the model permits adaptation to any parametric curve-shape. A general method for constructing sensible parameter priors is provided and Bayesian model averaging is used for making predictions which account for the uncertainty in both the parameters and the model. The validity of the method and its robustness to misspecification are tested using simulated datasets. The new methodology is then applied to oncology trial data, where we make interim accrual predictions, comparing them to those obtained by existing methods, and indicate where unexpected changes in the accrual pattern occur.
Interactions Between Odorants and Glutathione Transferases in the Human Olfactory Cleft
Authors: Schwartz Mathieu , Menetrier Franck , Heydel Jean-Marie , Chavanne Evelyne , Faure Philippe , Labrousse Marc , Lirussi Frédéric , Canon Francis , Mannervik Bengt , Briand Loïc , Neiers Fabrice 
Published: August 2020

AbstractXenobiotic metabolizing enzymes and other proteins, including odorant-binding proteins located in the nasal epithelium and mucus, participate in a series of processes modulating the concentration of odorants in the environment of olfactory receptors (ORs) and finely impact odor perception. These enzymes and transporters are thought to participate in odorant degradation or transport. Odorant biotransformation results in 1) changes in the odorant quantity up to their clearance and the termination of signaling and 2) the formation of new odorant stimuli (metabolites). Enzymes, such as cytochrome P450 and glutathione transferases (GSTs), have been proposed to participate in odorant clearance in insects and mammals as odorant metabolizing enzymes. This study aims to explore the function of GSTs in human olfaction. Using immunohistochemical methods, GSTs were found to be localized in human tissues surrounding the olfactory epithelium. Then, the activity of 2 members of the GST family toward odorants was measured using heterologously expressed enzymes. The interactions/reactions with odorants were further characterized using a combination of enzymatic techniques. Furthermore, the structure of the complex between human GSTA1 and the glutathione conjugate of an odorant was determined by X-ray crystallography. Our results strongly suggest the role of human GSTs in the modulation of odorant availability to ORs in the peripheral olfactory process.
Clinical Practice Guidelines by the Infectious Diseases Society of America (IDSA): 2020 Guideline on Diagnosis and Management of Babesiosis
Authors: Krause Peter J , Auwaerter Paul G , Bannuru Raveendhara R , Branda John A , Falck-Ytter Yngve T , Lantos Paul M , Lavergne Valéry , Meissner H Cody , Osani Mikala C , Rips Jane Glazer , Sood Sunil K , Vannier Edouard , Vaysbrot Elizaveta E , Wormser Gary P 
Published: August 2020

AbstractThe purpose of this guideline is to provide evidence-based guidance for the most effective strategies for the diagnosis and management of babesiosis. The diagnosis and treatment of co-infection with babesiosis and Lyme disease will be addressed in a separate Infectious Diseases Society of America (IDSA), American Academy of Neurology (AAN), and American College of Rheumatology (ACR) guideline [1]. Recommendations for the diagnosis and treatment of human granulocytic anaplasmosis can be found in the recent rickettsial disease guideline developed by the Centers for Disease Control and Prevention [2]. The target audience for the babesiosis guideline includes primary care physicians and specialists caring for this condition, such as infectious diseases specialists, emergency physicians, intensivists, internists, pediatricians, hematologists, and transfusion medicine specialists.
A Genome-wide Association Study Identifies SERPINB10, CRLF3, STX7, LAMP3, IFNG-AS1, and KRT80 As Risk Loci Contributing to Cutaneous Leishmaniasis in Brazil
Authors: Castellucci Léa C , Almeida Lucas , Cherlin Svetlana , Fakiola Michaela , Francis Richard W , Carvalho Edgar M , Santos da Hora Anadílton , do Lago Tainã Souza , Figueiredo Amanda B , Cavalcanti Clara M , Alves Natalia S , Morais Katia L P , Teixeira-Carvalho Andréa , Dutra Walderez O , Gollob Kenneth J , Cordell Heather J , Blackwell Jenefer M 
Published: August 2020

Abstract

Background
Our goal was to identify genetic risk factors for cutaneous leishmaniasis (CL) caused by Leishmania braziliensis.

Methods
Genotyping 2066 CL cases and 2046 controls using Illumina HumanCoreExomeBeadChips provided data for 4 498 586 imputed single-nucleotide variants (SNVs). A genome-wide association study (GWAS) using linear mixed models took account of genetic diversity/ethnicity/admixture. Post-GWAS positional, expression quantitative trait locus (eQTL) and chromatin interaction mapping was performed in Functional Mapping and Annotation (FUMA). Transcriptional data were compared between lesions and normal skin, and cytokines measured using flow cytometry and Bioplex assay.

Results
Positional mapping identified 32 genomic loci associated with CL, none achieving genome-wide significance (P &lt; 5 × 10−8). Lead SNVs at 23 loci occurred at protein coding or noncoding RNA genes, 15 with eQTLs for functionally relevant cells/tissues and/or showing differential expression in lesions. Of these, the 6 most plausible genetic risk loci were SERPINB10 (Pimputed_1000G = 2.67 × 10−6), CRLF3 (Pimputed_1000G = 5.12 × 10−6), STX7 (Pimputed_1000G = 6.06 × 10−6), KRT80 (Pimputed_1000G = 6.58 × 10−6), LAMP3 (Pimputed_1000G = 6.54 × 10−6), and IFNG-AS1 (Pimputed_1000G = 1.32 × 10−5). LAMP3 (Padjusted = 9.25 × 10−12; +6-fold), STX7 (Padjusted = 7.62 × 10−3; +1.3-fold), and CRLF3 (Padjusted = 9.19 × 10−9; +1.97-fold) were expressed more highly in CL biopsies compared to normal skin; KRT80 (Padjusted = 3.07 × 10−8; −3-fold) was lower. Multiple cis-eQTLs across SERPINB10 mapped to chromatin interaction regions of transcriptional/enhancer activity in neutrophils, monocytes, B cells, and hematopoietic stem cells. Those at IFNG-AS1 mapped to transcriptional/enhancer regions in T, natural killer, and B cells. The percentage of peripheral blood CD3+ T cells making antigen-specific interferon-γ differed significantly by IFNG-AS1 genotype.

Conclusions
This first GWAS for CL identified multiple genetic risk loci including a novel lead to understanding CL pathogenesis through regulation of interferon-γ by IFNG antisense RNA 1.
Droplets and Aerosols Generated by Singing and the Risk of Coronavirus Disease 2019 for Choirs
Authors: Bahl Prateek , de Silva Charitha , Bhattacharjee Shovon , Stone Haley , Doolan Con , Chughtai Abrar Ahmad , MacIntyre C Raina 
Published: August 2020

Abstract
Choral singing has become a major risk during the coronavirus disease 2019 (COVID-19) pandemic due to high infection rates. Our visualization and velocimetry results reveal that the majority of droplets expelled during singing follow the ambient airflow pattern. These results point toward the possibility of COVID-19 spread by small airborne droplets during singing.
Non-invasive detection of exercise-induced cardiac conduction abnormalities in sudden cardiac death survivors in the inherited cardiac conditions
Authors: Leong Kevin Ming Wei , Ng Fu Siong , Shun-Shin Matthew J , Koa-Wing Michael , Qureshi Norman , Whinnett Zachary I , Linton Nick F , Lefroy David , Francis Darrel P , Harding Sian E , Davies D Wyn , Peter Nicholas S , Lim Phang Boon , Behr Elijah , Lambiase Pier D , Varnava Amanda , Kanagaratnam Prapa 
Published: August 2020

Abstract

Aims
Rate adaptation of the action potential ensures spatial heterogeneities in conduction across the myocardium are minimized at different heart rates providing a protective mechanism against ventricular fibrillation (VF) and sudden cardiac death (SCD), which can be quantified by the ventricular conduction stability (V-CoS) test previously described. We tested the hypothesis that patients with a history of aborted SCD due to an underlying channelopathy or cardiomyopathy have a reduced capacity to maintain uniform activation following exercise.

Methods and results
Sixty individuals, with (n = 28) and without (n = 32) previous aborted-SCD event underwent electro-cardiographic imaging recordings following exercise treadmill test. These included 25 Brugada syndrome, 13 hypertrophic cardiomyopathy, 12 idiopathic VF, and 10 healthy controls. Data were inputted into the V-CoS programme to calculate a V-CoS score that indicate the percentage of ventricle that showed no significant change in ventricular activation, with a lower score indicating the development of greater conduction heterogeneity. The SCD group, compared to those without, had a lower median (interquartile range) V-CoS score at peak exertion [92.8% (89.8–96.3%) vs. 97.3% (94.9–99.1%); P &lt; 0.01] and 2 min into recovery [95.2% (91.1–97.2%) vs. 98.9% (96.9–99.5%); P &lt; 0.01]. No significant difference was observable later into recovery at 5 or 10 min. Using the lowest median V-CoS scores obtained during the entire recovery period post-exertion, SCD survivors had a significantly lower score than those without for each of the different underlying aetiologies.

Conclusion
Data from this pilot study demonstrate the potential use of this technique in risk stratification for the inherited cardiac conditions.
Drug-related medical hospital admissions during and after a period of head shop expansion
Authors: Smyth Bobby P , O’Farrell Anne , Cullen Walter 
Published: August 2020

Abstract

Background
New psychoactive substance (NPS) use can negatively impact health and may result in drug-related hospital admissions (DRHAs). Irish youth reported very high rates of NPS use by international standards, the most common being synthetic cannabinoids and cathinones. There was a rapid expansion in specialist shops, called head shops, selling NPS in 2010. Government responded to public protests about head shops by enacting legislation in May and August 2010 to end this trade. Many academics argued that such actions would prove futile. We sought to determine if changes in head shop activity coincided with changes in DRHA.

Methods
The national database on admissions to general hospitals hospital in-patient enquiry was examined focusing on young adults admitted from 2008 to 2012, and all emergency admissions with an International Classification of Diseases-10 diagnosis of mental disorder related to any drug (F11–F19) were identified. Joinpoint regression analysis was utilized to explore for the presence of trend changes in DRHA.

Results
Joinpoint regression analysis identified a significant downward trend change which occurred in June 2010 (95% CI February 2010 to January 2011). DRHA increased by 0.5% (95% CI 0.1–0.9) per month prior to this and then fell by 2.6% (95% CI −1.4 to −3.8) per month over the next 16 months.

Conclusions
Cessation of NPS sale by head shops coincided with a reversal in the upward trend of emergency hospital admissions related to drugs. Although correlation does not confirm causation, legislation which successfully curtails the commercial sale of NPS may result in reduced hospitalizations.
Couple relationship problems—a task for the general practitioner? A cross-sectional survey from Norway
Authors: Berge Siri Dalsmo , Meland Eivind , Brekke Mette , Bondevik Gunnar Tschudi , Thuen Frode , Mildestvedt Thomas 
Published: August 2020

Abstract

Background
A healthy couple relationship is a predictor of good health. There is a lack of knowledge about what role family and couples counselling should have in general practice.

Objectives
To identify the prevalence of patients who have talked, or want to talk, with their general practitioner (GP) about their couple relationship, to investigate what characterizes these patients and to explore whether they believe that couple relationship problems should be dealt with in general practice.

Methods
We conducted a cross-sectional survey in 70 general practices in Norway during spring 2019. A questionnaire was answered by 2178 consecutive patients (response rate 75%) in GP waiting rooms. Data were examined using frequencies and linear and logistic regression models.

Results
We included 2097 responses. Mean age was 49.0 years and 61.3% were women. One in four (25.0%) had already talked with their GP about couple relationship problems, while one in three (33.5%) wanted to talk with their GP about their couple relationship problems. These patients more frequently had experience of divorce, poor self-rated health, an opinion that their couple relationship had a significant impact on their health and lower couple relationship quality when adjusted for age, sex, present marital status and children living at home. We found that 46.4% of patients believed that GPs should be interested in their couple relationship problems.

Conclusion
Relationship problems are frequently addressed in general practice. GPs should be prepared to discuss this issue to facilitate help for couples earlier than they might otherwise expect.
Glacier retreat in the High Arctic: opportunity or threat for ectomycorrhizal diversity?
Authors: Botnen S S , Mundra S , Kauserud H , Eidesen P B 
Published: August 2020

ABSTRACTClimate change causes Arctic glaciers to retreat faster, exposing new areas for colonization. Several pioneer plants likely to colonize recent deglaciated, nutrient-poor areas depend on fungal partners for successful establishment. Little is known about general patterns or characteristics of facilitating fungal pioneers and how they vary with regional climate in the Arctic. The High Arctic Archipelago Svalbard represents an excellent study system to address these questions, as glaciers cover ∼60% of the land surface and recent estimations suggest at least 7% reduction of glacier area since 1960s. Roots of two ectomycorrhizal (ECM) plants (Salix polaris and Bistorta vivipara) were sampled in eight glacier forelands. Associated ECM fungi were assessed using DNA metabarcoding. About 25% of the diversity was unknown at family level, indicating presence of undescribed species. Seven genera dominated based on richness and abundance, but their relative importance varied with local factors. The genus Geopora showed surprisingly high richness and abundance, particularly in dry, nutrient-poor forelands. Such forelands will diminish along with increasing temperature and precipitation, and faster succession. Our results support a taxonomical shift in pioneer ECM diversity with climate change, and we are likely to lose unknown fungal diversity, without knowing their identity or ecological importance.