bluuebunny/crossref_metadata_2025_split huggingface dataset:
scMatch: a single-cell gene expression profile annotation tool using reference datasets
Authors: Hou Rui , Denisenko Elena , Forrest Alistair R R 
Published: April 2019

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) measures gene expression at the resolution of individual cells. Massively multiplexed single-cell profiling has enabled large-scale transcriptional analyses of thousands of cells in complex tissues. In most cases, the true identity of individual cells is unknown and needs to be inferred from the transcriptomic data. Existing methods typically cluster (group) cells based on similarities of their gene expression profiles and assign the same identity to all cells within each cluster using the averaged expression levels. However, scRNA-seq experiments typically produce low-coverage sequencing data for each cell, which hinders the clustering process.

Results
We introduce scMatch, which directly annotates single cells by identifying their closest match in large reference datasets. We used this strategy to annotate various single-cell datasets and evaluated the impacts of sequencing depth, similarity metric and reference datasets. We found that scMatch can rapidly and robustly annotate single cells with comparable accuracy to another recent cell annotation tool (SingleR), but that it is quicker and can handle larger reference datasets. We demonstrate how scMatch can handle large customized reference gene expression profiles that combine data from multiple sources, thus empowering researchers to identify cell populations in any complex tissue with the desired precision.

Availability and implementation
scMatch (Python code) and the FANTOM5 reference dataset are freely available to the research community here https://github.com/forrest-lab/scMatch.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Novel Aspect-based Sentiment Analysis Network Model Based on Multilingual Hierarchy in Online Social Network
Authors: Liu Guangfeng , Huang Xianying , Liu Xiaoyang , Yang Anzhi 
Published: April 2019

AbstractIn recent years, sentiment analysis based on aspects has become one of the research hotspots in the field of natural language processing. Aiming at the fact that the existing network model cannot fully obtain the interrelationship between sentences in the same comment and the long-distance dependence of specific aspects in the whole comment, a multilingual deep hierarchical model combining regional convolutional neural network and bidirectional LSTM network is proposed. The model obtains the time series relationship of different sentences in the comments through the regional CNN, and obtains the local features of the specific aspects in the sentence and the long-distance dependence in the whole comment through the hierarchical attention network. In addition, the model improves the word vector representation based on the gate mechanism to make the model completely independent of the language. Experimental results for different domain datasets in multi-language show that the proposed model achieves better classification results than the traditional deep network model, the network model combining with the attention mechanism and considering the relationship between sentences.
Discriminative Correlation Filter for Long-Time Tracking
Authors: Gong Faming , Yue Hanbing , Yuan Xiangbing , Gong Wenjuan , Song Tao 
Published: April 2019

Abstract
Object tracking is a very important step in building an intelligent video monitoring system that can protect people’s lives and property. In recent years, although visual tracking has made great progress in terms of speed and accuracy, there are still few real-time high-precision tracking algorithms. Although discriminative correlation filters have excellent performance in tracking speed, there are deficiencies in handling fast motion. This leads to the inability to achieve long-term stable tracking results. The long-time tracking with discriminative correlation filter (LT-DCF) was proposed to solve these deficiencies. We use larger size detection image blocks and smaller size filters to increase the proportion of real samples to solve the boundary effects of fast motion. And we combine the histogram of oriented gradient (HOG) feature detection and scale-invariant feature transform (SIFT) key point detection to solve the obstacles caused by scale variations. The detector with deep feature flow is then incorporated into the tracker to detect key frames to improve tracking accuracy. This method has achieved more than 75% of the distance accuracy and 70% of the overlapping success rate on the VOT2015 and VOT2016 datasets, and the stable tracking video length can reach 6895 frames.
Surgical outcome of isolated congenital supravalvular pulmonary stenosis: a case series
Authors: Kumar Vikas , Mahajan Sachin , Jaswal Vivek , Thingnam Shyam Kumar Singh 
Published: April 2019

AbstractBackgroundSupravalvular stenosis of main pulmonary artery is a rare anomaly characterized by the presence of constriction band just above the pulmonary valve. It is mostly acquired after intervention on the pulmonary trunk or less commonly is congenital in origin associated with complex congenital cardiac malformations and very rarely can present as an isolated native congenital supravalvular pulmonary stenosis (SPS).Case summaryWe present a series of four cases of isolated congenital SPS who underwent surgical correction at our tertiary care institute over 8 years. Mean age of the patients was 2.25 ± 0.96 years with all of them being males. Mean peak systolic gradient across the stenosis was 82 ± 21.48 mmHg ranging from 60 mmHg to 110 mmHg. There was no early and medium-term mortality with 100% survival at mean follow-up of 31 months (range 7–85 months).DiscussionSurgical correction of congenital SPS carries excellent early and mid-term results with almost no mortality and very low risk of re-intervention for restenosis.
Eclipsed mitral regurgitation successfully treated with a combination of surgical and pharmacological therapies: a case report
Authors: Ichikawa Keishi , Watanabe Atsuyuki , Ito Hiroshi 
Published: April 2019

Abstract

Background
Eclipsed mitral regurgitation (MR), which is characterized by a transient and reversible massive functional MR, usually causes recurrent episodes of acute pulmonary oedema in patients with a preserved left ventricular ejection fraction. The pathophysiological mechanism and optimal treatment of eclipsed MR are not yet fully understood.

Case summary
A 72-year-old woman was hospitalized with cardiogenic shock and takotsubo cardiomyopathy. After hospitalization worsening dyspnoea again appeared, and urgent transthoracic echocardiography revealed severe MR, which spontaneously resolved in a few minutes. At this point, eclipsed MR was detected for the first time. Diagnostic examination revealed that the eclipsed MR was caused by a left ventricular afterload increase. Ultimately, the patient began medical therapy and underwent mitral valve replacement. The subsequent clinical course was favourable.

Discussion
This case illustrates the importance of early intervention for eclipsed MR. A combination of surgical and pharmacological therapies can serve as one treatment option for an eclipsed MR.
Minimally invasive aortic valve replacement with a catheter-based cerebral protection system: transferring percutaneous technologies into a surgical intervention
Authors: Di Eusanio Marco , Cefarelli Mariano , Berretta Paolo , Capestro Filippo 
Published: April 2019

Abstract
Patients with severe aortic valve stenosis are currently treated with 2 different interventional techniques: surgical aortic valve replacement or transcatheter aortic valve implantation (TAVI). Both have strengths and limitations. On the one hand, TAVI represents a valuable option in high- and intermediate-risk patients and is commonly preferred over surgical aortic valve replacement in subjects with porcelain or severely calcified aorta, on the other, the lack of data on valve durability raises concerns on its use in young, low-risk patients. We present herein the case of a low-risk 71-year-old patient with a severely calcified ascending aorta. We successfully combined our minimally invasive surgical approach with the use of a percutaneous cerebral protection system commonly employed during TAVI procedures. We believe that cardiac surgeons could adopt transcatheter technology to improve operative results.
Pichia pastoris-expressed Zika virus envelope domain III on a virus-like particle platform: design, production and immunological evaluation
Authors: Shanmugam Rajgokul K , Ramasamy Viswanathan , Shukla Rahul , Arora Upasana , Swaminathan Sathyamangalam , Khanna Navin 
Published: April 2019

ABSTRACT
Zika virus (ZIKV) is an arbovirus which shares antigenic similarity and the mosquito vector with dengue viruses (DENVs). ZIKV is a neurotropic virus capable of causing congenital neurodevelopmental birth defects. As ZIKV antibodies (Abs) can potentially enhance infection by DENVs, a preventive ZIKV vaccine must be designed to eliminate antibody dependent enhancement of infection. We developed a Zika Subunit Vaccine (ZSV) consisting of two proteins, ZS and S, in a genetically pre-determined ratio of 1:4, using the methylotrophic yeast Pichia pastoris. ZS is an in-frame fusion of ZIKV envelope domain III with the Hepatitis B virus (HBV) surface antigen, and S is the un-fused HBV surface antigen. Using specific monoclonal Abs we showed the presence of ZS and S in the co-purified material which were found to co-assemble into virus-like particles (VLPs), based on dynamic light scattering and electron microscopic analyses. These VLPs were immunogenic in BALB/c mice, eliciting Abs capable of neutralizing ZIKV reporter virus particles. Further, the VLP-induced Abs did not enhance a sub-lethal DENV-2 challenge in AG129 mice. This important safety feature, coupled to the well-documented advantage of P. pastoris expression system, warrants further exploration of ZSV VLP as a possible vaccine candidate.
Social Relationships and Risk of Type 2 Diabetes Among Postmenopausal Women
Authors: Hendryx Michael , Nicholson Wanda , Manson JoAnn E , Kroenke Candyce H , Lee Jennifer , Weitlauf Julie C , Garcia Lorena , Jonasson Junmei M , Wactawski-Wende Jean , Luo Juhua 
Published: April 2019

Abstract

Objectives
We examined whether social relationship variables (social support, social strain, social network size, and stressful life events) were associated with risk of developing type 2 diabetes among postmenopausal women.

Method
139,924 postmenopausal women aged 50–79 years without prevalent diabetes at baseline were followed for a mean of 14 years. 19,240 women developed diabetes. Multivariable Cox proportional hazard models tested associations between social relationship variables and diabetes incidence after consideration of demographics, depressive symptoms, and lifestyle behaviors. We also examined moderating effects of obesity and race/ethnicity, and we tested whether social variable associations were mediated by lifestyle or depressive symptoms.

Results
Compared with the lowest quartile, women in the highest social support quartile had lower risk of diabetes after adjusting for demographic factors, health behaviors, and depressive symptoms (hazard ratio [HR] = 0.93, 95% confidence interval [CI] = 0.89–0.97). Social strain (HR = 1.09, 95% CI = 1.04–1.13) and stressful life events (HR = 1.10, 95% CI = 1.05–1.15) were associated with higher diabetes risks. The association between diabetes and social strain was stronger among African American women. Social relationship variables had direct relationships to diabetes, as well as indirect effects partially mediated by lifestyle and depressive symptoms.

Discussion
Social support, social strain, and stressful life events were associated with diabetes risk among postmenopausal women independently of demographic factors and health behaviors. In addition to healthy behaviors such as diet and physical activity, healthy social relationships among older women may be important in the prevention of diabetes.
Credit Constraints and the Composition of Housing Sales. Farewell to First-Time Buyers?
Authors: Carozzi Felipe 
Published: April 2019

AbstractDuring the housing bust of 2008–2009, housing prices and transaction volumes fell across the United Kingdom. Although the drop in prices was similar across housing types, transaction volumes fell more for units at the lower end of the market. I document this fact and provide panel and instrumental variable estimates showing its link with tightening credit conditions in England and Wales during 2008. I then use an overlapping-generation framework to relate the change in the composition of sales with the reduction in loan-to-value ratios by British banks and to derive additional predictions. As down-payment requirements increase, young households with scarce financial resources are priced out by older owners who retain their previous houses as rental properties when trading up. Recent changes in aggregate housing tenure, disaggregated changes in renting, and sales in areas with different age compositions, are consistent with these predictions. The results presented here show how the composition of sales changes over the housing cycle and may inform ongoing policy discussions about reduced access to home-ownership by the young.
ANCHOR surgeon views of patient selection and expectations for periacetabular osteotomy
Authors: Edelstein Adam I , Kaiser Tegel Karen , Shaunfield Sara ,   ANCHOR Group, Beaulé Paul E , Clohisy John C , Millis Michael , Novais Eduardo , Peters Christopher L , Sankar Wudbhav N , Sierra Rafael J , Sink Ernest L , Stover Michael D , Zaltz Ira , Clohisy John C , Stover Michael D 
Published: April 2019

AbstractPreoperative expectations impact shared decision making and patient satisfaction. Surgeon views of patient selection, expected outcomes and patient expectations after periacetabular osteotomy (PAO) for treatment of acetabular dysplasia have not been defined. We assessed surgeon views of patient selection and expected outcomes after PAO. A sample of experienced PAO surgeons participated in semi-structured phone interviews assessing: (i) factors that determine patient candidacy for PAO; (ii) surgeon expectations for PAO outcomes; (iii) surgeon perceptions of patient expectations for PAO outcomes and (iv) surgeon perceptions of discrepancies in surgeon and patient expectations and approaches for reconciling these discrepancies. Twelve surgeons (77% of PAO-performing ANCHOR surgeons) participated. The factors most commonly mentioned in determining patient candidacy for PAO were: symptoms, radiographic findings, absence of arthritis and age. Only one-quarter of the sample mentioned patient expectations as a factor in determining patient candidacy for PAO. The most common surgeon expectations were: pain reduction, joint preservation, function with activities of daily living and return to desired activities. 58% of surgeons felt that surgeon and patient expectations align most of the time. Common expectation discrepancies included return to unrestricted activities and complete pain relief. Detailed discussion was the most commonly employed strategy to resolve expectation discrepancies. PAO surgeons felt that patient expectations of complete pain relief and return to unrestricted activities were misaligned with their own expectations. Development of an expectations survey may facilitate shared decision making.
Mass loss via solar wind and coronal mass ejections during solar cycles 23 and 24
Authors: Mishra Wageesh , Srivastava Nandita , Wang Yuming , Mirtoshev Zavkiddin , Zhang Jie , Liu Rui 
Published: April 2019

ABSTRACT
Similar to the Sun, other stars shed mass and magnetic flux via ubiquitous quasi-steady wind and episodic stellar coronal mass ejections (CMEs). We investigate the mass loss rate via solar wind and CMEs as a function of solar magnetic variability represented in terms of sunspot number and solar X-ray background luminosity. We estimate the contribution of CMEs to the total solar wind mass flux in the ecliptic and beyond, and its variation over different phases of the solar activity cycles. The study exploits the number of sunspots observed, coronagraphic observations of CMEs near the Sun by SOHO/LASCO, in situ observations of the solar wind at 1 AU by WIND, and GOES X-ray flux during solar cycles 23 and 24. We note that the X-ray background luminosity, occurrence rate of CMEs and ICMEs, solar wind mass flux, and associated mass loss rates from the Sun do not decrease as strongly as the sunspot number from the maximum of solar cycle 23 to the next maximum. Our study confirms a true physical increase in CME activity relative to the sunspot number in cycle 24. We show that the CME occurrence rate and associated mass loss rate can be better predicted by X-ray background luminosity than the sunspot number. The solar wind mass loss rate which is an order of magnitude more than the CME mass loss rate shows no obvious dependency on cyclic variation in sunspot number and solar X-ray background luminosity. These results have implications for the study of solar-type stars.
Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility
Authors: Kuriata Aleksander , Iglesias Valentin , Pujols Jordi , Kurcinski Mateusz , Kmiecik Sebastian , Ventura Salvador 
Published: April 2019

Abstract
Protein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and assist the engineering of soluble protein-based drugs. A few years ago, we developed a method for structure-based prediction of aggregation properties that takes into account the dynamic fluctuations of proteins. The method has been made available as the Aggrescan3D (A3D) web server and applied in numerous studies of protein structure-aggregation relationship. Here, we present a major update of the A3D web server to version 2.0. The new features include: extension of dynamic calculations to significantly larger and multimeric proteins, simultaneous prediction of changes in protein solubility and stability upon mutation, rapid screening for functional protein variants with improved solubility, a REST-ful service to incorporate A3D calculations in automatic pipelines, and a new, enhanced web server interface. A3D 2.0 is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/
Distance Control and Virtual Drilling Improves Anatomical Orientation During Anterior Petrosectomy
Authors: Voormolen Eduard H , Diederen Sander , Cebula Helene , Woerdeman Peter A , Noordmans Herke Jan , Viergever Max A , Robe Pierre A , Froelich Sebastien , Regli Luca , Berkelbach van der Sprenkel Jan Willem 
Published: April 2019

Abstract

BACKGROUND
A combined drill distance control and virtual drilling image guidance feedback method was developed.

OBJECTIVE
To investigate whether first-time usage of the proposed method, during anterior petrosectomy (AP), improves surgical orientation and surgical performance. The accuracy of virtual drilling and the clinical practicability of the method were also investigated.

METHODS
In a simulated surgical setting using human cadavers, a trial was conducted with 5 expert skull base surgeons from 3 different hospitals. They performed 10 AP approaches, using either the feedback method or standard image guidance. Damage to critical structures was assessed. Operating time, drill cavity sizes, and proximity of postoperative drill cavities to the cochlea and the acoustic meatus, were measured. Questionnaires were obtained postoperatively. Errors in the virtual drill cavities as compared with actual postoperative cavities were calculated. In a clinical setup, the method was used during AP.

RESULTS
Surgeons rated their intraoperative orientation significantly better with the feedback method compared with standard image guidance. During the cadaver trial, the cochlea was harmed on 1 occasion in the control group, while surgeons drilled closer to the cochlea and meatus without injuring them in the group using feedback. Virtual drilling under- and overestimation errors were 2.2 ± 0.2 and −3.0 ± 0.6 mm on average. The method functioned properly during the clinical setup.

CONCLUSION
The proposed feedback method improves orientation and surgical performance in an experimental setting. Errors in virtual drilling reflect spatial errors of the image guidance system. The feedback method is clinically practicable during AP.
The Perceptual Present
Authors: Connor Abigail , Smith Joel 
Published: April 2019

AbstractPhenomenologically speaking, we perceive the present, recall the past, and anticipate the future. We offer an account of the temporal content of the perceptual present that distinguishes it from the recalled past and the anticipated future. We distinguish two views: the Token-Reflexive Account and the Minimal Account. We offer reasons to reject the Token-Reflexive Account, and defend the Minimal Account, according to which the temporal content of the perceptual present is exhausted by its direct reference to the interval of time over which it occurs.
Aiming for impact: Differential effect of motivational drivers on effort and performance in knowledge valorisation
Authors: van de Burgwal Linda H M , Hendrikse Rana , Claassen Eric 
Published: April 2019

Abstract
Societal engagement of scientists critically depends on their intrinsic motivation. Nevertheless, it remains unclear how motivational drivers influence effort and performance in engaging with four distinct stakeholder domains: academic, civil society, state-governmental, and economic. This article tests motivational drivers in a survey among 706 Dutch Life Scientists to study direct and indirect effects on effort and performance and finds that drivers differentially influence effort and performance in the four domains. Analysis supported the identification of a fourth category of drivers: ‘moral’—next to the well-recognised gold, ribbon, and puzzle drivers—and demonstrated their importance for performance in the civil society and state-governmental domains, two domains that have been underserved in previous studies. Pecuniary drivers influenced engagement with academic, as well as economic domains. In line with these findings, spreading responsibilities for engagement with different domains in line with the interests and motivations of individual scientists is recommended.