bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining gender differences of social media use for activity planning and travel choices
Authors: Karatsoli Maria , Nathanail Eftihia 
Published: July 2020

Abstract
Background
The explosive growth of social media has rendered them powerful communication channels. User generated content is an important source of inspiration and influence among web friends, it generates new activities and consequently affects mobility decisions. Whether to visit a place, or how to get to a place of interest are decisions that can be triggered through people’s interactions on social media.

Objective
The main objective of this paper is to investigate the influence of social media use on activity planning and travel arrangements for women and men.

Methods
An online survey was conducted to examine the social media use and the impact of the shared content for women and men, on the phase before any activity in an urban environment. Inferential statistics were applied to detect gender differences in a sample size comprised of 804 respondents.

Result
The significant results showed that the variables gender and social media use for activity planning and travel arrangements are associated with each other. Results have also indicated that the influence of reviews and ratings, photos/ videos and proposed transport mode on activity planning is gender dependent. Photos/ videos influence more often both women (m=3.47) and men (m=3.00) than reviews and ratings (m=3.21 for women and 2.94 for men). Both these contents influence more than proposed transport mode (m=2.62 and 2.37 for women and men).

Conclusion
The analysis of the results indicated that before an activity, both women and men tend to use majorly social media for activity planning and travel arrangements, while photos/videos influence women’s decisions more often than men.Travel arrangements of the majority of respondents would be influenced by a post of a designated account related to transport. Finally, social media use affects travel arrangements of both women and men more before performing an activity rather than during.
Modelling the shape of the pig scapula
Authors: Nordbø Øyvind 
Published: July 2020

Abstract
Background
The shape of pig scapula is complex and is important for sow robustness and health. To better understand the relationship between 3D shape of the scapula and functional traits, it is necessary to build a model that explains most of the morphological variation between animals. This requires point correspondence, i.e. a map that explains which points represent the same piece of tissue among individuals. The objective of this study was to further develop an automated computational pipeline for the segmentation of computed tomography (CT) scans to incorporate 3D modelling of the scapula, and to develop a genetic prediction model for 3D morphology.

Results
The surface voxels of the scapula were identified on 2143 CT-scanned pigs, and point correspondence was established by predicting the coordinates of 1234 semi-landmarks on each animal, using the coherent point drift algorithm. A subsequent principal component analysis showed that the first 10 principal components covered more than 80% of the total variation in 3D shape of the scapula. Using principal component scores as phenotypes in a genetic model, estimates of heritability ranged from 0.4 to 0.8 (with standard errors from 0.07 to 0.08). To validate the entire computational pipeline, a statistical model was trained to predict scapula shape based on marker genotype data. The mean prediction reliability averaged over the whole scapula was equal to 0.18 (standard deviation = 0.05) with a higher reliability in convex than in concave regions.

Conclusions
Estimates of heritability of the principal components were high and indicated that the computational pipeline that processes CT data to principal component phenotypes was associated with little error. Furthermore, we showed that it is possible to predict the 3D shape of scapula based on marker genotype data. Taken together, these results show that the proposed computational pipeline closes the gap between a point cloud representing the shape of an animal and its underlying genetic components.
RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads
Authors: Niebler Stefan , Müller André , Hankeln Thomas , Schmidt Bertil 
Published: July 2020

Abstract
Background
Obtaining data from single-cell transcriptomic sequencing allows for the investigation of cell-specific gene expression patterns, which could not be addressed a few years ago. With the advancement of droplet-based protocols the number of studied cells continues to increase rapidly. This establishes the need for software tools for efficient processing of the produced large-scale datasets. We address this need by presenting RainDrop for fast gene-cell count matrix computation from single-cell RNA-seq data produced by 10x Genomics Chromium technology.

Results
RainDrop can process single-cell transcriptomic datasets consisting of 784 million reads sequenced from around 8.000 cells in less than 40 minutes on a standard workstation. It significantly outperforms the established Cell Ranger pipeline and the recently introduced Alevin tool in terms of runtime by a maximal (average) speedup of 30.4 (22.6) and 3.5 (2.4), respectively, while keeping high agreements of the generated results.

Conclusions
RainDrop is a software tool for highly efficient processing of large-scale droplet-based single-cell RNA-seq datasets on standard workstations written in C++. It is available at https://gitlab.rlp.net/stnieble/raindrop.
Eravacycline susceptibility was impacted by genetic mutation of 30S ribosome subunits, and branched-chain amino acid transport system II carrier protein, Na/Pi cotransporter family protein in Staphylococcus aureus
Authors: Wang Zhanwen , Lin Zhiwei , Bai Bing , Xu Guangjian , Li Peiyu , Yu Zhijian , Deng Qiwen , Shang Yongpeng , Zheng Jinxin 
Published: July 2020

Abstract
Background
Our previous research indicated the excellent in vitro antibacterial activity of Eravacycline (Erava) and its heteroresistance frequency against clinical Staphylococcus aureus isolates. In this study, we further aimed to investigate the mechanisms of Erava resistance and heteroresistance in S. aureus. Eight parental S. aureus isolates were induced under Erava pressure in vitro and the Erava-resistant isolates were selected and identified. Then, the genetic mutations of 30S ribosomal subunits were analyzed by PCR and sequence alignment. RT-qPCR analysis were performed to compare the relative expression of eight candidate genes impacting the susceptibility of tetracycline (Tet) between the resistant or heteroresistant and parental isolates. Furthermore, the in vitro overexpression vectors of three selected candidate genes were constructed to test their impact on the heteroresistance and resistance of Erava in S. aureus.

Results
The MICs elevation in Erava-induced resistant S. aureus isolates were identified and the increasing MICs values of another two Tet class antibiotics, including both omadacycline (Omada) and tigecycline (Tige) were also tested. Genetic mutations in 30S ribosomal protein S10 were found frequently in Erava-derived resistant isolates. RT-qPCR analysis and the in vitro overexpression experiments indicated that USA300HOU_RS00550 (an Na/Pi cotransporter family protein) and USA300HOU_RS01625 (a branched-chain amino acid transport system II carrier protein) contributed to Erava heteroresistance in S. aureus.

Conclusion
Genetic mutation of 30S ribosome subunits contributed to Erava resistance, and the transcriptional overexpression of USA300HOU_RS01625 and USA300HOU_RS00550 also participated in the occurrence of Erava heteroresistance in S. aureus.
Cow manure application effectively regulates the soil bacterial community in tea plantation
Authors: Zhang Shuning , Sun Litao , Wang Yu , Fan Kai , Xu Qingshan , Li Yusheng , Ma Qingping , Wang Jiguo , Ren Wanming , Ding Zhaotang 
Published: July 2020

Abstract
Background
Cow manure is not only an agricultural waste, but also an organic fertilizer resource. The application of organic fertilizer is a feasible practice to mitigate the soil degradation caused by overuse of chemical fertilizers, which can affect the bacterial diversity and community composition in soils. However, to our knowledge, the information about the soil bacterial diversity and composition in tea plantation applied with cow manure fertilization was limited. In this study, we performed one field trial to research the response of the soil bacterial community to cow manure fertilization compared with urea fertilization using the high-throughput sequencing technique of 16S rRNA genes, and analyzed the relationship between the soil bacterial community and soil characteristics during different tea-picking seasons using the Spearman’s rank correlation analysis.

Results
The results showed that the soil bacterial communities were dominated by Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria across all tea-picking seasons. Therein, there were significant differences of bacterial communities in soils with cow manure fertilization (CMF) and urea fertilization (UF) in three seasons: the relative abundance of Bacteroidetes in CMF was significantly higher than that in UF and CK in spring, and the relative abundance of Proteobacteria and Bacteroidetes in CMF was significantly higher than that in UF and CK in autumn. So, the distribution of the dominant phyla was mainly affected by cow manure fertilization. The diversity of bacterial communities in soils with cow manure fertilization was higher than that in soils with urea fertilization, and was the highest in summer. Moreover, soil pH, OM and AK were important environmental properties affecting the soil bacterial community structure in tea plantation.

Conclusions
Although different fertilizers and seasons affect the diversity and structure of soil microorganisms, the application of cow manure can not only improve the diversity of soil bacteria, but also effectively regulate the structure of soil bacterial community in tea plantation. So, cow manure fertilization is more suitable for tea plantation.
A comparison of residual diagnosis tools for diagnosing regression models for count data
Authors: Feng Cindy , Li Longhai , Sadeghpour Alireza 
Published: July 2020

AbstractBackgroundExamining residuals is a crucial step in statistical analysis to identify the discrepancies between models and data, and assess the overall model goodness-of-fit. In diagnosing normal linear regression models, both Pearson and deviance residuals are often used, which are equivalently and approximately standard normally distributed when the model fits the data adequately. However, when the response vari*able is discrete, these residuals are distributed far from normality and have nearly parallel curves according to the distinct discrete response values, imposing great challenges for visual inspection.MethodsRandomized quantile residuals (RQRs) were proposed in the literature by Dunn and Smyth (1996) to circumvent the problems in traditional residuals. However, this approach has not gained popularity partly due to the lack of investigation of its performance for count regression including zero-inflated models through simulation studies. Therefore, we assessed the normality of the RQRs and compared their performance with traditional residuals for diagnosing count regression models through a series of simulation studies. A real data analysis in health care utilization study for modeling the number of repeated emergency department visits was also presented.ResultsOur results of the simulation studies demonstrated that RQRs have low type I error and great statistical power in comparisons to other residuals for detecting many forms of model misspecification for count regression models (non-linearity in covariate effect, over-dispersion, and zero inflation). Our real data analysis also showed that RQRs are effective in detecting misspecified distributional assumptions for count regression models.ConclusionsOur results for evaluating RQRs in comparison with traditional residuals provide further evidence on its advantages for diagnosing count regression models.
The Strengths and Difficulties Questionnaire is a usable way to address mental health at well-child visits in general practice - a qualitative study of feasibility
Authors: Stokholm Julie Ravneberg , Lykke Kirsten 
Published: July 2020

Abstract
Background
Mental health problems is frequent among children and psychopathology in early childhood seems to predict mental disorders in adulthood. All Danish children are offered seven free well-child visits at their General Practitioner (GP) during their first 5 years of life. GPs have a unique position to address mental health problems at the well-child visits, but they lack a systematic approach when assessing children’s mental health. The purpose of this study was to investigate if the Strengths and Difficulties Questionnaire (SDQ) is a usable way to address preschool children’s mental health in general practice.

Methods
A qualitative study of feasibility. Parents completed an online version of the SDQ at home. At the well-child visit, the GP used the SDQ results as a basis for a talk about the child’s mental health. Afterwards the author JS conducted semistructured interviews with both the parent and the GP over the phone. The interviews were descriptively analyzed using the Framework Approach.

Results
Five primary care centres with 22 general practitioners in both Copenhagen and Region Zealand participated. Twenty four parents completed the SDQ and were interviewed. Participating parents and GPs agreed, that the SDQ introduced mental health as a natural and important part of the well-child visit. Online access had clear advantages: time for reflection at home and preparation, plus a clear result summary for the GP. Some of the GPs were worried that the questionnaire would be too time consuming, and might compromise the individualistic style of general practice. Some parents were worried if children with minor problems would be diagnosed.

Conclusions
The online SDQ was well-accepted and feasible in daily practice. Implementing the SDQ into the well-child visit could strengthen the focus on the child’s mental health. However, before the SDQ can be generally implemented a guideline on how to utilize it in the well-child visit is needed, as well as studies of efficacy in this setting.

Trial registration
Not relevant.
Interrelationships between symptom burden and health functioning and health care utilization among veterans with persistent physical symptoms
Authors: Fried Dennis , McAndrew Lisa M. , Helmer Drew A. , Markowitz Sarah , Quigley Karen S. 
Published: July 2020

Abstract
Background
Between 10 and 50% of primary care patients present with persistent physical symptoms (PPS). Patients with PPS tend to utilize excessive or inappropriate health care services, while being stuck in a deleterious cycle of inactivity, deconditioning, and further worsening of symptoms and disability. Since military deployment (relative to non-deployment) is associated with greater likelihood of PPS, we examined the interrelationships of health care utilization, symptom burden and functioning among a sample of recently deployed Veterans with new onset persistent physical symptoms.

Methods
This study analyzed a cohort of 790 U.S. soldiers who recently returned from deployment to Iraq or Afghanistan. Data for this analysis were obtained at pre- and post-deployment. We used moderation analyses to evaluate interactions between physical symptom burden and physical and mental health functioning and four types of health care utilization one-year after deployment, after adjusting for key baseline measures.

Results
Moderation analyses revealed significant triple interactions between physical symptom burden and health functioning and: primary care (F = 3.63 [2, 303], R2Δ = .02, p = 0.03), specialty care (F = 6.81 [2, 303] R2Δ =0.03, p < .001), allied therapy care (F = 3.76 [2, 302], R2Δ = .02, p = 0.02), but not mental health care (F = 1.82 [1, 303], R2Δ = .01, p = .16), one-year after deployment.

Conclusions
Among U.S. Veterans with newly emerging persistent physical symptoms one-year after deployment, increased physical symptom burden coupled with decreased physical and increased mental health functioning was associated with increased medical care use in the year after deployment. These findings support whole health initiatives aimed at improving health function/well-being, rather than merely symptom alleviation.
Management and treatment of HIV: are primary care clinicians prepared for their new role?
Authors: Wijesinghe Sampath , Alexander Jeffrey L. 
Published: July 2020

Abstract
Background
Current literature suggests the number of HIV clinicians in the United States is diminishing. There are 294,834 primary care providers (PCP) in the United States, and, of these, 3101 provide care to HIV-positive patients. More PCPs to treat and manage HIV patients may be the solution to alleviate the HIV provider shortage. However, PCPs also face challenges, including workforce shortages. We surveyed PCPs to determine perceived barriers, beliefs, and attitudes about their readiness to manage and treat HIV patients.

Methods
Following a quantitative, descriptive, cross-sectional survey design, currently practicing clinicians in primary care (physicians, residents, physician assistants, family nurse practitioners) were emailed a link to the study survey. Three hundred forty-seven family medicine clinicians from 47 states met the study inclusion criteria.

Results
Most (245/347, 70.6%) of the PCPs agreed that PCPs should take care of HIV patients. PCPs practicing HIV medicine (n = 171) were more likely than those not practicing HIV medicine (n = 176) to agree that PCPs should help with the HIV provider shortage (U = 10,384, p < 0.001) and that PCPs are the best solution to the HIV provider shortage (U = 10,294, p < 0.001). The majority (206, 59.4%) believed PCPs are the best solution for the HIV provider shortage. Of 133 physician assistants (PAs) and family nurse practitioners (NPs), seventy (52.6%) believed they could be ready to manage HIV patients with some training.

Conclusion
The HIV provider shortage in the United States is likely to continue. To alleviate the provider shortage, PCPs should be offered additional training, decreased workload, and increased compensation when treating and managing HIV patients. Also, encouraging PAs and family NPs to be involved with HIV medicine may be a solution.
Incidence and factors associated with geographical relocation in patients receiving renal replacement therapy
Authors: Cheikh Hassan Hicham I , Chen Jenny HC , Murali Karumathil 
Published: July 2020

Abstract
Background
Renal replacement therapy (RRT) places a burden on patients, and geographical relocation for easier access to healthcare facilities is a necessity for some. Incidence and factors associated with relocation has not been comprehensively examined at a national level. We aimed to determine proportion, incidence, characteristics of RRT patients who relocate and relocation rate by remoteness of residence and dialysis modality.

Methods
Retrospective cohort analysis using Australian and New Zealand Dialysis and Transplant Registry to examine RRT patients in Australia from January 2005 to December 2015. Relocation incidence was calculated for remoteness of residence and RRT modality as rate per 100 patient years. Factors associated with relocation were examined using competing risk regression models with death as a competing event.

Results
Of 24,676 incident patients on RRT, 5888 (23.9%) relocated with a median time of 1.6 years [IQR 0.7–3.4] years. Relocation incidence was 7.9 per 100 patient years and increased from major cities to very remote regions (7.2 to 48.8 per 100 patient years respectively, p < 0.001). Remoteness of residence was associated with geographical relocation in competing risk analysis especially in remote (SHR 1.20, 95%CI 1.01, 1.41 p = 0.034) and very remote regions (SHR 3.51 95% 3.05, 4.04 p < 0.001). Aboriginal or Torres Strait Islander ethnicity, compared to Caucasian, was independently associated with relocation (SHR 1.18, 95% CI 1.06,1.31, p = 0.002) while transplant patients were less likely to relocate compared to haemodialysis patients (HR 0.37, 95%CI 0.34, 0.39, p < 0.001).

Conclusions
Relocation in patients receiving RRT is associated with remoteness of residence, RRT modality and ethnicity. Reasons for relocation and its impact on patient wellbeing and outcome should be further explored.
The correlation analysis between the Oxford classification of Chinese IgA nephropathy children and renal outcome - a retrospective cohort study
Authors: Wu Heyan , Xia Zhengkun , Gao Chunlin , Zhang Pei , Yang Xiao , Wang Ren , Wang Meiqiu , Peng Yingchao 
Published: July 2020

Abstract
Background
The 2016 Oxford Classification’s MEST-C scoring system predicts outcomes in adults with IgA nephropathy (IgAN), but it lacks tremendous cohort validation in children with IgAN in China. We sought to verify whether the Oxford classification could be used to predict the renal outcome of children with IgAN.

Methods
In this retrospective cohort study, 1243 Chinese IgAN children who underwent renal biopsy in Jinling Hospital were enregistered from 2000 to 2017. The combined endpoint was defined as either a ≥ 50% reduction in estimated glomerular filtration rate (eGFR) or end-stage renal disease (ESRD). We probed into the relevance betwixt the Oxford classification and renal prognosis.

Results
There were 29% of children with mesangial proliferation(M1), 35% with endocapillary proliferation (E1), 37% with segmental sclerosis/adhesion lesion (S1), 23% with moderate tubular atrophy/interstitial fibrosis (T1 25–50% of cortical area involved), 4.3% with severe tubular atrophy/interstitial fibrosis (T2 > 50% of cortical area involved), 44% with crescent in< 25% of glomeruli(C1), and 4.6% with crescent in> 25% of glomeruli (C2). All children were followed for a medial of 7.2 (4.6–11.7) years, 171 children (14%) arrived at the combined endpoint. The multivariate COX regression model revealed that the presence of lesions S (HR2.7,95%CI 1.8 ~ 4.2, P<0.001) and T (HR6.6,95%CI 3.9 ~ 11.3, P<0.001) may be the reason for poorer prognosis in the whole cohort. In contrast, C lesion showed a significant association with the outcome only in children received no immunosuppressive treatment.

Conclusions
This study revealed that S and T lesions were useful as the long-term renal prognostic factors among Chinese IgAN children.
Bilateral thalamic lesions in a patient with probable acute disseminating encephalomyelitis: a case report
Authors: Zheng Yiming , Zhang Wei , Hao Hongjun , Gao Feng 
Published: July 2020

Abstract
Background
Bilateral thalamic lesions are rare. Here, we describe a case of probable acute disseminating encephalomyelitis (ADEM) with symmetrical bilateral thalamic lesions.

Case presentation
An 85-year-old man presented with weakness of the lower limbs and urinary retention for 1 day, soon followed by coma. He had an H1N1 influenza vaccination 3 months ago. A lumbar puncture showed positive oligoclonal bands and negative results for anti-AQP4 antibodies. A head MRI demonstrated focal symmetrical bilateral thalamic lesions. An MRI of the thoracic spinal cord showed longitudinally extensive lesions in the spinal cord. He was diagnosed with probable ADEM. Despite being treated with IVIG, the patient remained unconscious and died a month later from pneumonia.

Conclusions
In cases with bilateral thalamic lesions, the possibility of ADEM should be considered. The characteristics of the thalamic lesions and imaging findings in other parts of the brain or spinal cord should be taken into account in association with the clinical and laboratory information in making a correct diagnosis.