bluuebunny/crossref_metadata_2025_split huggingface dataset:
De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria
Authors: Redmond Seth N , MacInnis Bronwyn M , Bopp Selina , Bei Amy K , Ndiaye Daouda , Hartl Daniel L , Wirth Dyann F , Volkman Sarah K , Neafsey Daniel E 
Published: November 2017

AbstractDetecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a larger genome, slower generation times, and a complex life cycle make them difficult to implement. Here we demonstrate the viability of de novo mutation studies in P. falciparum for the first time. Using a set of clinical samples and novel methods of sequencing, library preparation, and genotyping, we have genotyped low-complexity regions of the genome with a high degree of accuracy. Despite its slower evolutionary rate compared to bacterial or viral species, de novo mutation can be detected in P. falciparum across timescales of just 1-2 years and evolutionary rates in low-complexity regions of the genome can be up to twice that detected in the rest of the genome. The increased mutation rate allows the identification of separate clade expansions that cannot be found using previous genomic epidemiology approaches and could be a crucial tool for mapping residual transmission patterns in disease elimination campaigns and reintroduction scenarios.
EditR: A novel base editing quantification software using Sanger sequencing
Authors: Kluesner Mitchell G. , Nedveck Derek A. , Lahr Walker S. , Garbe John R. , Abrahante Juan E. , Webber Beau R. , Moriarity Branden S. 
Published: November 2017

ABSTRACTCRISPR/Cas9-Cytidine deaminase fusion enzymes - termed Base Editors – allow targeted editing of genomic deoxcytidine to deoxthymidine (C→T) without the need for double stranded break induction. Base editors represent a paradigm-shift in gene editing technology, due to their unprecedented efficiency to mediate targeted, single-base conversion; however, current analysis of base editing outcomes rely on methods that are either imprecise or expensive and time consuming. To overcome these limitations, we developed a simple, cost effective, and accurate program to measure base editing efficiency from fluorescence-based Sanger sequencing, termed EditR. We provide EditR as a free online tool or downloadable desktop application requiring a single Sanger sequencing file and guide RNA sequence (baseeditr.com). EditR is more accurate than enzymatic assays, and provides added insight to the position, type and efficiency of base editing. Collectively, we demonstrate that EditR is a robust, inexpensive tool that will facilitate the broad application of base editing technology, thereby fostering further innovation in this burgeoning field.
A theory of multineuronal dimensionality, dynamics and measurement
Authors: Gao Peiran , Trautmann Eric , Yu Byron , Santhanam Gopal , Ryu Stephen , Shenoy Krishna , Ganguli Surya 
Published: November 2017

AbstractIn many experiments, neuroscientists tightly control behavior, record many trials, and obtain trial-averaged firing rates from hundreds of neurons in circuits containing billions of behaviorally relevant neurons. Di-mensionality reduction methods reveal a striking simplicity underlying such multi-neuronal data: they can be reduced to a low-dimensional space, and the resulting neural trajectories in this space yield a remarkably insightful dynamical portrait of circuit computation. This simplicity raises profound and timely conceptual questions. What are its origins and its implications for the complexity of neural dynamics? How would the situation change if we recorded more neurons? When, if at all, can we trust dynamical portraits obtained from measuring an infinitesimal fraction of task relevant neurons? We present a theory that answers these questions, and test it using physiological recordings from reaching monkeys. This theory reveals conceptual insights into how task complexity governs both neural dimensionality and accurate recovery of dynamic portraits, thereby providing quantitative guidelines for future large-scale experimental design.
TCGA-Assembler 2: Software Pipeline for Retrieval and Processing of TCGA/CPTAC Data
Authors: Wei Lin , Jin Zhilin , Yang Shengjie , Xu Yanxun , Zhu Yitan , Ji Yuan 
Published: November 2017

AbstractMotivationThe Cancer Genome Atlas (TCGA) program has produced huge amounts of cancer genomics data providing unprecedented opportunities for research. In 2014, we developed TCGA-Assembler (Zhu et al, 2014), a software pipeline for retrieval and processing of public TCGA data. In 2016, TCGA data were transferred from the TCGA data portal to the Genomic Data Commons (GDC), which is supported by a different set of data storage and retrieval mechanisms. In addition, new proteomics data of TCGA samples have been generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, which were not available for downloading through TCGA-Assembler. It is desirable to acquire and integrate data from both GDC and CPTAC.ResultsWe develop TCGA-Assembler 2 (TA2) to automatically download and integrate data from GDC and CPTAC. We make substantial improvement on the functionality of TA2 to enhance user experience and software performance. TA2 together with its previous version have helped more than 2,000 researchers from 64 countries to access and utilize TCGA and CPTAC data in their research. Availability of TA2 will continue to allow existing and new users to conduct reproducible research based on TCGA and CPTAC data.Availabilityhttp://www.compgenome.org/TCGA-Assembler/Contactkoaeraser@gmail.com or zhuyitan@gmail.com
TNER: A Novel Background Error Suppression Method for Mutation Detection in Circulating Tumor DNA
Authors: Deng Shibing , Lira Maruja , Huang Stephen , Wang Kai , Valdez Crystal , Kinong Jennifer , Rejto Paul A , Bienkowska Jadwiga , Hardwick James , Xie Tao 
Published: November 2017

AbstractThe use of ultra-deep, next generation sequencing of circulating tumor DNA (ctDNA) holds great promise for early detection of cancer as well as a tool for monitoring disease progression and therapeutic responses. However, the low abundance of ctDNA in the bloodstream coupled with technical errors introduced during library construction and sequencing complicates mutation detection. To achieve high accuracy of variant calling via better distinguishing low frequency ctDNA mutations from background errors, we introduce TNER (Tri-Nucleotide Error Reducer), a novel background error suppression method that provides a robust estimation of background noise to reduce sequencing errors. It significantly enhances the specificity for downstream ctDNA mutation detection without sacrificing sensitivity. Results on both simulated and real healthy subjects’ data demonstrate that the proposed algorithm consistently outperforms a current, state of the art, position-specific error polishing model, particularly when the sample size of healthy subjects is small. TNER is publicly available at https://github.com/ctDNA/TNER.
Participation and Chinese non-government organization accountability
Authors: Zhong Ling , Fisher Karen R. 
Published: November 2017

Purpose
As transition countries shift to a mixed welfare system, the accountability of non-government organizations (NGOs) becomes critical to quality services. Yet, poor financial and managerial practices of some NGOs in China have led to distrust from citizens. The purpose of this paper is to use a democratic accountability framework to examine citizen participation in NGOs as an approach to understand an angle of this distrust. Does the Chinese language academic literature about NGO accountability engage with concepts of participation in NGO governance, management and service use?

Design/methodology/approach
The method was content analysis of a search of words and concepts relating to NGOs, participation and accountability in the available Chinese language literature on NGO accountability through the newly developed search engine Wenjin Search of the National Library of China.

Findings
The analysis found that most Chinese literature only emphasizes problems of accountability, causes and regulatory solutions. When the literature includes participation, it refers to it as a platform for civil society, rather than a process of accountability within an NGO.

Research limitations/implications
Searching by keywords in one search engine may not be exhaustive. The results probably reflect most of the current research of Chinese scholars, considering the depth of the search engine.

Practical implications
Formal NGOs are relatively new in the Chinese political landscape; and government regulations are largely administrative and unenforced. At conceptual and political levels, the absence of discussion about other forms of accountability ignores questions about public dissatisfaction with NGO performance and the public’s willingness to contribute to NGO effectiveness, and civic engagement.

Originality/value
An implication is that until Chinese NGO research also incorporates democratic accountability concepts, it will continue to ignore the internal and external drivers from citizens for NGO change. Transition country NGOs that encourage participation have the potential to engender greater accountability in the organization, community and in state relations.
GoodYarn: building mental health literacy in New Zealand’s rural workforce
Authors: Morgaine Kate , Thompson Louise , Jahnke Katie , Llewellyn Rebecca 
Published: November 2017

Purpose
“GoodYarn” is a skills-based workshop that focusses on building mental health literacy in rural communities, members of which are known to experience geographic, attitudinal and service configuration barriers to accessing mental health services. The purpose of this paper is to evaluate the impact of the GoodYarn project on raising mental health literacy in the rural community.

Design/methodology/approach
GoodYarn is primarily for farmers, their families and farm workers, as well as the “farmer facing” workforce. The focus on mental health literacy aligns with the mental health promotion approach of using methods that foster supportive environments. By raising the mental health literacy of those not directly needing help, but in positions to help those that do – such as employers, rural professionals and rural support industries who are well placed to perceive stressors in farmers – GoodYarn builds a community with the knowledge and skills to identify and approach those experiencing mental distress or illness, and direct them to appropriate support and services. All participants in the GoodYarn workshops (n=430) were invited to complete a questionnaire at the end of the workshop. All participants answered the questionnaire, with over 80 per cent answering all questions.

Findings
Participant feedback affirmed the utility of GoodYarn as an effective vehicle to facilitate the discussion of mental illness in rural farming communities of New Zealand. GoodYarn had a significant positive impact on the three immediate workshop indicators of awareness, confidence and knowledge (p<0.001 for all three indicators). Further, the high level of concordance in workshop outcomes across various organisations’ delivery indicates programme consistency and quality has been maintained throughout the upscaling of the programme.

Originality/value
The uptake of the GoodYarn programme by rural organisations and communities at a national level, and the positive evaluation results, provide encouragement that building mental health literacy in the rural workforce is a promising mental health promotion strategy.
Social entrepreneurship: the role of national leadership culture
Authors: Coker Kesha K. , Flight Richard L. , Valle Kelly N. 
Published: November 2017

Purpose
Social entrepreneurship has emerged as an important realm of entrepreneurship during the last decade. Research on what motivates social entrepreneurial activity continues to be of interest in the field. Given the integral role of the social entrepreneur, one area identified as deserving more attention is the leadership traits of the social entrepreneur. This paper addresses this gap by presenting a conceptual model on the role of national leadership culture on social entrepreneurship.

Design/methodology/approach
As part of the social fabric of a country, national leadership culture is viewed as a social contextual factor that can either enhance or hinder social entrepreneurial activity. As its broader conceptual base, this paper relies on institutional theory, marketing systems and leadership theory. At the heart of the proposed conceptual model are six leadership dimensions from the Global Leadership and Organizational Behavior Effectiveness (GLOBE) theoretical model: charismatic/value-based, team-oriented, participative, self-protective, humane-oriented and autonomous. These leadership dimensions are central to the propositions that accompany the proposed conceptual model.

Findings
Implications of this research for entrepreneurial marketing and public policy are presented. Since this research is conjectural, future directions for empirical research on national leadership culture in social entrepreneurship are discussed.

Originality/value
The conceptual model is the first to examine the role of national leadership culture on social entrepreneurship. The research adds value to the growing body of research on social entrepreneurship in its social context. It answers the call in the literature to examine leadership as it pertains to the individual entrepreneur’s pre-disposition to engage in social entrepreneurial activity.
Dynamic capabilities in aged care service innovation: the role of social assistive technologies and consumer-directed care strategy
Authors: Khaksar Seyed Mohammad Sadegh , Shahmehr Fatemeh S. , Khosla Rajiv , Chu Mei Tai 
Published: November 2017

Purpose
By developing a conceptual model, the purpose of this paper is to improve the understanding of the role of social assistive technologies in facilitating the process of service innovation in care providing organisations to adopt the principles of the consumer-directed care strategy and reduce perceived consumer vulnerability.

Design/methodology/approach
Using a cross-sectional survey method, the authors collected data through a survey questionnaire distributed among 335 aged caregivers and specialists. The conceptual model and its 11 research hypotheses were examined using confirmatory factor analysis in structural equation modelling. The rival and mediation models were also estimated.

Findings
The conceptual model was validated and eight of eleven hypotheses were supported. It was found that dynamic capabilities are crucial to developing service innovation concept in care providing organisations. In this way, social assistive technologies play a facilitating role to promote the consumer-directed care strategy throughout care providing organisations and allow care providers to enhance wellbeing of vulnerable older people based on their socio-economic status. From the lens of aged care providers, it was also found that the consumer-directed care strategy implemented in aged care facilities may help reduce consumer vulnerability among older people especially when they use social assistive technologies in their service settings.

Practical implications
This study suggests aged care service providers should boost dynamic service innovation capabilities to improve the need for social assistive technologies in aged care facilities with respect to the importance of the consumer-directed care strategy.

Originality/value
This study contributes to the development and validation of a conceptual model for the use of social assistive technologies to sustain service innovation in aged care business models and enhance the consumer-directed care strategy’s performance to better understand consumer vulnerability among older people.
Helpless helpers: primary care therapist self-efficacy working with intimate partner violence and ageing women
Authors: Watson Carlie , Carthy Nikki , Becker Sue 
Published: November 2017

Purpose
The purpose of this paper is to explore primary care psychological therapists’ experiences of working with mid-life and older women presenting with intimate partner violence (IPV) and develop a theoretical framework using a grounded theory approach to identify the experiences of those practitioners working with this phenomenon.

Design/methodology/approach
Interviews with 17 practitioners were conducted. The data analysis was informed by a grounded theory approach, which requires three states of data coding: open, axial and selective. Data codes were thematically sorted into causal, contextual, strategic, intervening, interactional and consequential conditions.

Findings
A core state of therapist helplessness was uncovered. The framework demonstrates that psychological therapists can doubt their ability to work meaningfully with women over 45 years of age experiencing IPV. To avoid the core state of helplessness, therapists use strategies such as avoiding asking questions about partner violence, making assumptions of how patients interpret their own experiences, addressing symptoms rather than the root cause and going above and beyond in attempts to rescue patients. The consequence of therapists’ helplessness often results in burnout.

Research limitations/implications
The framework identifies barriers in working effectively with IPV and women in the mid-to older-aged populations.

Originality/value
This study is the first to suggest a framework that is grounded in practitioner experience with capability to transfer to a range of professionals working with mid-to older-aged women such as forensic, medical and specialist psychologists.
Multidisciplinary attitudes to people with dementia; training and environmental factors play a role in caring for people with dementia in a Cardiac Catheterisation Laboratory
Authors: Ainsworth Karen , Richardson Cliff 
Published: November 2017

Purpose
The purpose of this paper is to explore multidisciplinary attitudes and environmental factors affecting dementia care in the Cardiac Catheter Laboratory (CCL).

Design/methodology/approach
Questionnaires (n=87) were distributed in a hospital CCL in the North of England. The authors utilised the Dementia Attitudes Scale which incorporates two subscales: Social Comfort and Dementia Knowledge. In addition, a newly devised questionnaire asking about perceptions of how the CCL environment affected care of patients with dementia was added.

Findings
The response rate was 71 per cent (n=62). Years’ experience in the CCL was associated with lower Social Comfort scores (p=0.026). Dementia training was associated with higher mean Dementia Attitudes Scale and Social Comfort scores (p=0.021, p=0.007). Participants who had undertaken “Professional studies” had higher Dementia Attitudes Scale and Dementia Knowledge mean scores (p=0.038, p=0.046) but “On-the-job” training was perceived as most beneficial (32 per cent, n=20). Unit co-ordinators and nurses felt the CCL was an unfavourable environment for patients with dementia. Care was perceived to be impaired by environmental functionality, equipment and the presence of ionising radiation.

Research limitations/implications
The small sample limits generalisability. Although the Dementia Attitudes Scale is a validated questionnaire it has not been widely used so reliability of these results is unclear.

Practical implications
Caring for patients with dementia has unique challenges especially in areas like the CCL. These results suggest that practical experience and training can affect the perception of staff to patients with dementia hence there may be a need to assess what would be the most appropriate training to give health professionals in the future.

Originality/value
The authors believe this to be the first multi-professional research study into care of patients with dementia in a specialised acute unit. This was the most diverse sample known to have attitudes to dementia measured quantitatively in an acute hospital department and the results need to be replicated before practice should be changed.
External validation of the traumatic aortic injury score
Authors: Bade‐Boon Jordan , Mathew Joseph K. , Fitzgerald Mark C. , Mitra Biswadev 
Published: November 2017

AimTraumatic aortic injury (TAI) is a serious complication of blunt chest trauma. The traumatic aortic injury score (TRAINS) is a clinical tool for risk determination, with patients scoring <4 considered low risk. The aim of the present study was to determine the sensitivity of TRAINS on a population of blunt trauma patients with TAI at an Australian major trauma centre.Patients and MethodsPatients diagnosed with thoracic TAI between 2006 and 2014 were identified from an institutional registry. Radiological studies (chest X‐ray) were reviewed, while blood pressure on arrival to hospital was extracted from the registry. Using abbreviated injury scale codes, the presence of the five associated injuries included in the TRAINS model was determined.ResultsA TRAINS ≥4 was observed in 28 out of 63 cases, with complete data available (sensitivity = 44.4 per cent; 95 per cent confidence interval: 32.8–56.7), with minimum and maximum possible sensitivities of 42.4 per cent and 47 per cent, respectively, as determined by two‐way sensitivity analysis.ConclusionsThis independent external validation of the TRAINS concluded a poor sensitivity for excluding TAI in the blunt chest trauma population. In the absence of reliable predictive tools, a low threshold for thoracic computed tomography imaging and clinical gestalt remain essential tools for the early diagnosis of TAI.
Increased levels of neutrophil extracellular trap remnants in the serum of patients with rheumatoid arthritis
Authors: Wang Wei , Peng Wanchan , Ning Xingwang 
Published: November 2017

AbstractAimsNeutrophil extracellular traps (NETs) comprise a unique form of non‐apoptotic cell death exhibited by neutrophils, which occurs in a stepwise process termed NETosis. It has been postulated that NETosis plays an important role in the pathogenesis of autoimmune disorders. The aim of this study was to evaluate serum levels of NET remnants in patients with rheumatoid arthritis (RA), as well as potential associations between NET remnants and indicators of RA.MethodsSerum levels of myeloperoxidase (MPO)‐DNA complexes (NET remnants) were examined in 74 RA patients and 50 healthy controls using a modified enzyme‐linked immunosorbent assay. Associations between the levels of these complexes and indicators of RA were then statistically evaluated.ResultsRA patients exhibited significantly higher levels of MPO‐DNA complexes than the healthy controls, and these levels were associated with increased neutrophil counts and positivity for rheumatoid factor (RF) and anti‐citrullinated protein/peptide antibodies (ACPA). Among the 63 ACPA‐positive RA patients examined, those with ACPA titers > 1600 U/mL showed significantly increased MPO‐DNA levels. Receiver operating characteristic analysis determined that the area under the curve for all 74 RA patients was 0.798, with a sensitivity of 91.9% and a specificity of 56.0%, while that for the ACPA‐negative patients was 0.891, with a sensitivity and specificity of 81.8% and 84.0%, respectively.ConclusionsThe results of this study suggest that the disease status of RA is associated with increased NETosis. In particular, evaluation of serum MPO‐DNA levels may comprise a useful complementary tool for discriminating RA patients from healthy individuals.