bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population structure of theBrachypodiumspecies complex and genome wide association of agronomic traits in response to climate
Authors: Wilson Pip , Streich Jared , Murray Kevin , Eichten Steve , Cheng Riyan , Aitkin Niccy , Spokas Kurt , Warthmann Norman ,   Accession Contributors, Borevitz Justin 
Published: January 2018

AbstractThe development of model systems requires a detailed assessment of standing genetic variation across natural populations. TheBrachypodiumspecies complex has been promoted as a plant model for grass genomics with translational to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands ofBrachypodiumaccessions from around the globe were collected and sequenced using genotyping by sequencing (GBS). Overall, 1,897 samples were classified into two diploid or allopolyploid species and then further grouped into distinct inbred genotypes. A core set of diverseB. distachyondiploid lines were selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22 and 47 QTLs were identified for flowering time, early vigour and energy traits, respectively. Overall, the results highlight the genomic structure of theBrachypodiumspecies complex and allow powerful complex trait dissection within this new grass model species.
Widespread and targeted gene expression by systemic AAV vectors: Production, purification, and administration
Authors: Challis Rosemary C , Kumar Sripriya Ravindra , Chan Ken Y , Challis Collin , Jang Min J , Rajendran Pradeep S , Tompkins John D , Shivkumar Kalyanam , Deverman Benjamin E , Gradinaru Viviana 
Published: January 2018

ABSTRACTWe recently developed novel AAV capsids for efficient and noninvasive gene transfer across the central and peripheral nervous systems. In this protocol, we describe how to produce and systemically administer AAV-PHP viruses to label and/or genetically manipulate cells in the mouse nervous system and organs including the heart. The procedure comprises three separate stages: AAV production, intravenous delivery, and evaluation of transgene expression. The protocol spans eight days, excluding the time required to assess gene expression, and can be readily adopted by laboratories with standard molecular and cell culture capabilities. We provide guidelines for experimental design and choosing the capsid, cargo, and viral dose appropriate for the experimental aims. The procedures outlined here are adaptable to diverse biomedical applications, from anatomical and functional mapping to gene expression, silencing, and editing.
Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians
Authors: Fisher Matthew C. , Ghosh Pria , Shelton Jennifer M. G. , Bates Kieran , Brookes Lola , Wierzbicki Claudia , Rosa Gonçalo M. , Farrer Rhys A. , Aanensen David M. , Alvarado-Rybak Mario , Bataille Arnaud , Berger Lee , Böll Susanne , Bosch Jaime , Clare France C. , Courtois Elodie , Crottini Angelica , Cunningham Andrew A. , Doherty-Bone Thomas M. , Gebresenbet Fikirte , Gower David J. , Höglund Jacob , James Timothy Y. , Jenkinson Thomas S. , Kosch Tiffany A. , Lambertini Carolina , Laurila Anssi , Lin Chun-Fu , Loyau Adeline , Martel An , Meurling Sara , Miaud Claude , Minting Pete , Ndriantsoa Serge , Pasmans Frank , Rakotonanahary Tsanta , Rabemananjara Falitiana C. E. , Ribeiro Luisa P. , Schmeller Dirk S. , Schmidt Benedikt R. , Skerratt Lee , Smith Freya , Soto-Azat Claudio , Tessa Giulia , Toledo Luís Felipe , Valenzuela-Sánchez Andrés , Verster Ruhan , Vörös Judit , Waldman Bruce , Webb Rebecca J. , Weldon Che , Wombwell Emma , Zamudio Kelly R. , Longcore Joyce E. , Garner Trenton W.J. 
Published: January 2018

ABSTRACTParasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into sterile culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to interested researchers worldwide as part of the BiodivERsA project RACE – here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been widely applied across at least 5 continents, 23 countries and in 62 amphibian species, and have been successfully used to isolate chytrids in remote field locations. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this important group of emerging fungal pathogens.
Task-Related EEG Source Localization via Graph Regularized Low-Rank Representation Model
Authors: Liu Feng , Rosenberger Jay , Qin Jing , Lou Yifei , Wang Shouyi 
Published: January 2018

AbstractTo infer brain source activation patterns under different cognitive tasks is an integral step to understand how our brain works. Traditional electroencephalogram (EEG) Source Imaging (ESI) methods usually do not distinguish task-related and spurious non-task-related sources that jointly generate EEG signals, which inevitably yield misleading reconstructed activation patterns. In this research, we argue that the task-related source signal intrinsically has a low-rank property, which is exploited to to infer the true task-related EEG sources location. Although the true task-related source signal is sparse and low-rank, the contribution of spurious sources scattering over the source space with intermittent activation patterns makes the actual source space lose the low-rank property. To reconstruct a low-rank true source, we propose a novel ESI model that involves a spatial low-rank representation and a temporal Laplacian graph regularization, the latter of which guarantees the temporal smoothness of the source signal and eliminate the spurious ones. To solve the proposed model, an augmented Lagrangian objective function is formulated and an algorithm in the framework of alternating direction method of multipliers is proposed. Numerical results illustrate the effectiveness of the proposed method in terms of reconstruction accuracy with high effciency.
Reducing False Positives in CRISPR/Cas9 Screens from Copy Number Variations
Authors: Wu Alexander , Xiao Tengfei , Fei Teng , Shirley Liu X. , Li Wei 
Published: January 2018

AbstractCRISPR/Cas9 knockout screens have been widely used to interrogate gene functions across a wide range of cell systems. However, the screening outcome is biased in amplified genomic regions, due to the ability of the Cas9 nuclease to induce multiple double-stranded breaks and strong DNA damage responses at these regions. We developed algorithms to correct biases associated with copy number variations (CNV), even when the CNV profiles are unknown. We demonstrated that our methods effectively reduced false positives in amplified regions while preserving signals of true positives. In addition, we developed a sliding window approach to estimate regions of high copy numbers for cases in which CNV information is not available. These copy number estimations can subsequently be used to effectively correct CNV-related biases in CRISPR screening experiments. Our approach is integrated into the existing MAGeCK/MAGeCK-VISPR analysis pipelines and provides a convenient framework to improve the precision of CRISPR screening results.
Warfare, atrocities, and political participation: eastern Africa
Authors: Ember Carol R. , Jones Eric C. , Skoggard Ian , Adem Teferi Abate 
Published: January 2018

Purpose
Ember et al. (1992) addressed whether the “democracies rarely fight each other” hypothesis held true in the anthropological record of societies of various sizes and scales around the world. They indeed found that more participatory polities had less internal warfare – or warfare between one society’s territorial units (e.g. bands, villages, districts). The purpose of this paper is to examine when political participation would have similar effects in eastern Africa, and whether more participatory polities commit fewer atrocities against each other.

Design/methodology/approach
A cross-cultural sample of 46 societies from eastern Africa was used to retest the original Ember et al. (1992) multiple regression model and revised post-hoc models. The team read ethnographies to code for levels of political participation at the local and multilocal levels. Other variables came from previous research including warfare and atrocity variables (Ember et al., 2013).

Findings
The Ember et al. (1992) model did not replicate in eastern Africa, but analysis with additional variables (degree of formal leadership, presence of state-level organization, and threat of natural disasters that destroy food supplies) suggested that greater local political participation does predict less internal warfare. Also, more participatory polities were less likely to commit atrocities in the course of internal warfare.

Originality/value
This study demonstrates regional comparisons are important because they help us evaluate the generalizability of worldwide findings. Additionally, adding atrocities to the study of democracy and warfare is new and suggests reduced atrocities as an additional benefit of political participation.
Co-production in integrated health and social care programmes: a pragmatic model
Authors: Kaehne Axel , Beacham Andrea , Feather Julie 
Published: January 2018

Purpose
The purpose of this paper is to outline the current thinking on co-production in health and social care, examine the challenges in implementing genuine co-production and argue for a pragmatic version of co-production that may assist programme managers in deciding which type of co-production is most suitable for which programme.

Design/methodology/approach
A discussion paper based on the professional and academic knowledge and insights of the authors. A focus group interview schedule was used to guide discussions between authors.

Findings
The authors argue for a pragmatic approach to co-production within integrated care programmes. The authors set out the basic parameters of such an approach containing procedural rather than substantive standards for co-production activities leaving sufficient room for specific manifestations of the practice in particular contexts.

Practical implications
The authors put forward a pragmatic model of co-production that defines the essential elements of a process for ensuring services are designed to meet with the needs of patients yet allowing the process itself to be adapted to different circumstances.

Originality/value
The paper summarises the discussion on co-production in relation to integration programmes. It formulates a pragmatic model of co-production that may assist programme managers in establishing good practice co-production frameworks when designing or implementing integrated health and social care services.
Adult attachment and perceived parental style may shape leadership behaviors
Authors: Eldad Rom , Benatov Joy 
Published: January 2018

PurposeThe purpose of this paper is to examine the role of both attachment and parental styles in shaping leadership behavioral patterns. Research predictions were that childhood perceived parental experiences will be associated with attachment style, and that both perceived parental and attachment styles will fulfill a significant role in shaping the individual’s leadership orientation in adulthood.Design/methodology/approachThe authors tested the research hypotheses with a field survey data from 90 supervisors belonging to diverse industrial and service organizations. During their attendance in a leadership seminar, the managers’ attachment style was assessed using the Experiences in Close Relationship Inventory. They were also asked to report on their childhood experiences using the Parenting Style Index, and to answer questions regarding their leadership behavior, using a short version of the Multifactor Leadership Questionnaire.FindingsResults indicated associations between parental style, attachment style, and leadership. Specifically, parental autonomy granting was negatively associated with both attachment anxiety and avoidance. Both transformational and transactional leadership styles were positively associated with parental autonomy, but only transformational leadership was also positively associated with parental involvement. In addition, transactional leadership was positively associated with attachment avoidance in close relationships.Research limitations/implicationsTesting the contributions of perceived parental style in childhood and attachment style in adulthood to the manager’s manifested leadership style helps to advance our theoretical understanding of important leadership antecedents. The findings may also help practitioners in developing leadership skills and assisting managers in finding ways to moderate their natural tendencies and better depend on, delegate, and empower subordinates.Originality/valueThis empirical study provides evidence of the important role of perceived parental style in the development of adult attachment and leadership styles. The effects found in the study also extend the existing findings by showing that not only the attachment style but also parental style play a significant role in shaping the individual’s leadership behaviors.
Genetic Basis of Emerging Vancomycin, Linezolid, and Daptomycin Heteroresistance in a Case of Persistent Enterococcus faecium Bacteremia
Authors: Chacko Kieran I. , Sullivan Mitchell J. , Beckford Colleen , Altman Deena R. , Ciferri Brianne , Pak Theodore R. , Sebra Robert , Kasarskis Andrew , Hamula Camille L. , van Bakel Harm 
Published: January 2018

ABSTRACT

Whole-genome sequencing was used to examine a persistent
Enterococcus faecium
bacteremia that acquired heteroresistance to three antibiotics in response to prolonged multidrug therapy. A comparison of the complete genomes before and after each change revealed the emergence of known resistance determinants for vancomycin and linezolid and suggested that a novel mutation in
fabF
, encoding a fatty acid synthase, was responsible for daptomycin nonsusceptibility. Plasmid recombination contributed to the progressive loss of vancomycin resistance after withdrawal of the drug.
A systematic review of network meta-analyses for pharmacological treatment of common mental disorders
Authors: Williams Taryn , Stein Dan J , Ipser Jonathan 
Published: January 2018

QuestionNetwork meta-analyses (NMAs) of treatment efficacy across different pharmacological treatments help inform clinical decision-making, but their methodological quality may vary a lot depending also on the quality of the included primary studies. We therefore conducted a systematic review of NMAs of pharmacological treatment for common mental disorders in order to assess the methodological quality of these NMAs, and to relate study characteristics to the rankings of efficacy and tolerability.Study selection and analysisWe searched three databases for NMAs of pharmacological treatment used in major depression, generalised anxiety disorder (GAD), social anxiety disorder (SAD), post-traumatic stress disorder (PTSD), obsessive-compulsive disorder (OCD) and specific phobia.Studies were appraised using the International Society for Pharmacoeconomics and Outcomes Research checklist of good research practices for indirect-treatment-comparison and network-meta-analysis studies.FindingsTwenty NMAs were eligible for inclusion. The number of randomised controlled trials per NMA ranged from 11 to 234, and included between 801 to more than 26 000 participants. Overall, antidepressants were found to be efficacious and tolerable agents for several disorders based on rankings (45%) or statistical significance (55%). The majority of NMAs in this review adhered to guidelines by including a network diagram (70%), assessing consistency (75%), making use of a random effects model (75%), providing information on the model used to fit the data (75%) and adjusting for covariates (75%).ConclusionsThe 20 NMAs of depression and anxiety disorders, PTSD and/or OCD included in this review demonstrate some methodological strengths in comparison with the larger body of published NMAs for medical disorders, support current treatment guidelines and help inform clinical decision-making.
Hazardous alcohol consumption among spouses or partners of military service personnel: a systematic review of the literature
Authors: Gribble Rachael , Thandi G K , Goodwin L , Fear N T 
Published: January 2018

BackgroundAlcohol misuse is particularly high among both the UK and US Armed Forces. As alcohol use among couples is associated, military spouses or partners may therefore be at a higher risk of acquiring hazardous drinking behaviours than people in relationships with other occupational groups.MethodA literature review using a systematic approach was undertaken in four medical databases and supplemented with hand searches of specialist publications and reference lists. The prevalence of hazardous alcohol consumption among military spouses or partners was estimated and potential sociodemographic and military factors associated with this outcome were identified.ResultsNine papers met inclusion criteria, of which eight focused on female spouses or partners only. The limited evidence suggests hazardous alcohol consumption was not a common outcome among spouses or partners. None of the papers statistically compared the prevalence among spouses or partners to estimates from the general population and few reported associations with sociodemographic or military factors. Deployment abroad did not appear to be significantly associated with hazardous consumption, although increasing periods of separation from Service personnel may be associated with increased hazardous consumption among spouses or partners.ConclusionLimited evidence was found concerning the prevalence of hazardous alcohol consumption among military spouses or partners or which sociodemographic and military factors might be associated with this outcome. The a dominance of US studies means applying the estimates of these outcomes to other nations must be undertaken with care due to differences in cultural attitudes to alcohol as well as differences between military structure and operations between the US and other nations.
Blood pressure levels post mechanical thrombectomy and outcomes in non-recanalized large vessel occlusion patients
Authors: Goyal Nitin , Tsivgoulis Georgios , Pandhi Abhi , Dillard Kira , Alsbrook Diana , Chang Jason J , Krishnaiah Balaji , Nickele Christopher , Hoit Daniel , Alsherbini Khalid , Alexandrov Andrei V , Arthur Adam S , Elijovich Lucas 
Published: January 2018

ObjectivePermissive hypertension may benefit patients with non-recanalized large vessel occlusion (nrLVO) post mechanical thrombectomy (MT) by maintaining brain perfusion. Data evaluating the impact of post-MT blood pressure (BP) levels on outcomes in nrLVO patients are scarce. We investigated the association of the post-MT BP course with safety and efficacy outcomes in nrLVO.MethodsHourly systolic BP (SBP) and diastolic BP (DBP) values were prospectively recorded for 24 hours following MT in consecutive nrLVO patients. Maximum, minimum, and mean BP levels were documented. Three-month functional independence (FI) was defined as modified Rankin Scale (mRS) scores of 0–2.ResultsA total of 88 nrLVO patients were evaluated post MT. Patients with FI had lower maximum SBP (160±19 mmHg vs 179±23 mmHg; P=0.001) and higher minimum SBP levels (119±12 mmHg vs 108±25 mmHg; P=0.008). Maximum SBP (183±20 mmHg vs 169±23 mmHg; P=0.008) and DBP levels (105±20 mmHg vs 89±18 mmHg; P=0.001) were higher in patients who died at 3 months while minimum SBP values were lower (102±28 mmHg vs 115±16 mmHg; P=0.007). On multivariable analyses, both maximum SBP (OR per 10 mmHg increase: 0.55, 95% CI 0.39 to 0.79; P=0.001) and minimum SBP (OR per 10 mmHg increase: 1.64, 95% CI 1.04 to 2.60; P=0.033) levels were independently associated with the odds of FI. Maximum DBP (OR per 10 mmHg increase: 1.61; 95% CI 1.10 to 2.36; P=0.014) and minimum SBP (OR per 10 mmHg increase: 0.65, 95% CI 0.47 to 0.90; P=0.009) values were independent predictors of 3-month mortality.ConclusionsOur study demonstrates that wide BP excursions from the mean during the first 24 hours post MT are associated with worse outcomes in patients with nrLVO.
Effect of mechanical preconditioning on the electrical properties of knitted conductive textiles during cyclic loading
Authors: Isaia Cristina , McNally Donal S , McMaster Simon A , Branson David T 
Published: January 2018

This paper presents, for the first time, the electrical response of knitted conductive fabrics to a considerable number of cycles of deformation in view of their use as wearable sensors. The changes in the electrical properties of four knitted conductive textiles, made of 20% stainless steel and 80% polyester fibers, were studied during unidirectional elongation in an Instron machine. Two tests sessions of 250 stretch–recovery cycles were conducted for each sample at two elongation rates (9.6 and 12 mm/s) and at three constant currents (1, 3 and 6 mA). The first session assessed the effects of an extended cyclic mechanical loading (preconditioning) on the electrical properties, especially on the electrical stabilization. The second session, which followed after a 5 minute interval under identical conditions, investigated whether the stabilization and repeatability of the electrical features were maintained after rest. The influence of current and elongation rate on the resistance measurements was also analyzed. In particular, the presence of a semiconducting behavior of the stainless steel fibers was proved by means of different test currents. Lastly, the article shows the time-dependence of the fabrics by means of hysteresis graphs and their non-linear behavior thanks to a time–frequency analysis. All knit patterns exhibited interesting changes in electrical properties as a result of mechanical preconditioning and extended use. For instance, the gauge factor, which indicates the sensitivity of the fabric sensor, varied considerably with the number of cycles, being up to 20 times smaller than that measured using low cycle number protocols.