bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osmotic Swelling Responses are Conserved Across Cartilaginous Tissues with Varied Sulfated-Glycosaminoglycan Contents
Authors: Baylon Eva G. , Levenston Marc E. 
Published: November 2018

AbstractThe interactions between the negatively charged sulfated glycosaminoglycan (sGAG) chains and the ionic interstitial fluid in articular cartilage and meniscal fibrocartilage give rise to an osmotic swelling stress that is critical for the load-bearing capability of both tissues. This osmotic swelling stress is altered when the sGAG content is changed, as during progression of degenerative joint disease; understanding the influence of sGAG concentration on the osmotic swelling stress of cartilage and meniscus is important to enhance our understanding of physiology and disease. This study compared the effect of altered osmotic environments on the confined compression swelling behavior of bovine tissues spanning a range of sGAG concentrations: juvenile articular cartilage, juvenile and adult meniscus, and juvenile cartilage degraded to reduce sGAG content. The transient response to changes in bath conditions was evaluated for explants assigned to one of three compressive offsets (5%, 10%, or 15% strain) and one of three bath conditions (0.1X, 1X, or 10X Phosphate Buffered Saline). Our results show that relative responses to alterations to the osmotic environment are consistent across tissue types, demonstrating that the role of sGAG in the swelling properties of the tissues tested is conserved, even when sGAG is present at low concentrations. Additionally, this study found unexpected correlations across tissue types between sGAG and collagen contents and between the aggregate modulus and both sGAG and collagen contents. These results suggest some conservation of composition-function relationships across a range of tissue types.
Chimpanzee SIV Envelope trimer: structure and deployment as an HIV vaccine template
Authors: Andrabi Raiees , Pallesen Jesper , Allen Joel , Song Ge , Zhang Jinsong , de Val Natalia , Gegg Gavin , Porter Katelyn , Su Ching-Yao , Pauthner Matthias , Newman Amanda , Bouton-Vervelle Hilary , Garces Fernando , Wilson Ian A. , Crispin Max , Hahn Beatrice H. , Haynes Barton F. , Verkoczy Laurent , Ward Andrew B. , Burton Dennis R. 
Published: November 2018

SummaryEpitope-targeted HIV vaccine design seeks to focus antibody responses to broadly neutralizing antibody (bnAb) sites by sequential immunization. Chimpanzee SIV Envelope (Env) shares a single bnAb site, the V2-apex, with HIV, suggesting its possible utility in an HIV immunization strategy. Accordingly, we generated a chimpanzee SIV Env trimer, MT145K, which displays selective binding to HIV V2-apex bnAbs and precursor versions, but no binding to other HIV specificities. We determined the structure of the MT145K trimer by cryo-EM and showed its architecture was remarkably similar to HIV Env. Immunization of an HIV V2-apex bnAb precursor Ab-expressing knock-in mouse with chimpanzee MT145K trimer induced HIV V2-specific neutralizing responses. Subsequent boosting with an HIV trimer cocktail induced responses exhibiting some virus cross-neutralization. Overall, the chimpanzee MT145K trimer behaves as expected from design both in vitro and in vivo and is an attractive potential component of a sequential immunization regimen to induce V2-apex bnAbs.
Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding
Authors: Li Jianlong , Lawson Handley Lori-Jayne , Harper Lynsey R. , Brys Rein , Watson Hayley V. , Hänfling Bernd 
Published: November 2018

AbstractEnvironmental DNA (eDNA) metabarcoding is a promising tool for rapid, non-invasive biodiversity monitoring. In this study, eDNA metabarcoding is applied to explore the spatial and temporal distribution of eDNA in two ponds following the introduction and removal of two rare fish species. When two rare species were introduced and kept at a fixed location in the ponds, eDNA concentration (i.e., proportional read counts abundance) of the introduced species typically peaked after two days. Thereafter, it gradually declined and stabilised after six days. These findings are supported by the highest community dissimilarity of different sampling positions being observed on the second day after introduction, which then gradually decreased over time. On the sixth day, there was no longer a significant difference in community dissimilarity between sampling days. The introduced species were no longer detected at any sampling positions 48 hrs after removal from the ponds. The eDNA signal and detection probability of the introduced species were strongest near the keepnets, resulting in the highest community variance of different sampling events at this position. Thereafter, the eDNA signal significantly decreased with increasing distance, although the signal increased slightly again at 85 m position away from the keepnets. Collectively, these findings reveal that eDNA distribution in lentic ecosystems is highly localised in space and time, which adds to the growing weight of evidence that eDNA signal provides a good approximation of the presence and distribution of species in ponds. Moreover, eDNA metabarcoding is a powerful tool for detection of rare species alongside more abundant species due to the use of generic PCR primers, and can enable monitoring of spatial and temporal community variance.
White Matter Microstructure Correlates of General and Specific Second-Order Factors of Psychopathology
Authors: Hinton Kendra E. , Lahey Benjamin B. , Villalta-Gil Victoria , Meyer Francisco A. C. , Burgess Leah L. , Chodes Laura K. , Applegate Brooks , Van Hulle Carol A. , Landman Bennett A. , Zald David H. 
Published: November 2018

AbstractIncreasing data indicate that prevalent forms of psychopathology can be organized into second-order dimensions based on their correlations, including a general factor of psychopathology that explains the common variance among all disorders and specific second-order externalizing and internalizing factors. Despite this organization, and high levels of comorbidity between diagnoses, most existing studies on the neural correlates of psychopathology employ case-control designs that treat diagnoses as independent categories. Thus, for instance, although perturbations in white matter microstructure have been identified across a range of disorders, the majority of such studies have used case-control designs, leaving it unclear whether observed relations reflect disorder specific characteristics, or transdiagnostic patterns. Using a representative community twin sample of 410 young adults, we tested the hypothesis that some relations between white matter microstructure properties in major tracts are related to second-order factors of psychopathology. We examined fractional anisotropy (FA), radial diffusivity (RD), and axial diffusivity (AD). White matter correlates of all second-order factors were identified after controlling for multiple tests, including the general factor (FA in the body of the corpus callosum), specific internalizing (AD in the fornix), and specific externalizing (AD in the splenium of the corpus callosum, sagittal stratum, anterior corona radiata, and internal capsule). These findings suggest that features of white matter within specific tracts are associated with broad transdiagnostic dimensions of psychopathology rather than being restricted to individual diagnostic categories.
GenPipes: an open-source framework for distributed and scalable genomic analyses
Authors: Bourgey Mathieu , Dali Rola , Eveleigh Robert , Chen Kuang Chung , Letourneau Louis , Fillon Joel , Michaud Marc , Caron Maxime , Sandoval Johanna , Lefebvre Francois , Leveque Gary , Mercier Eloi , Bujold David , Marquis Pascale , Van Patrick Tran , Morais David , Tremblay Julien , Shao Xiaojian , Henrion Edouard , Gonzalez Emmanuel , Quirion Pierre-Olivier , Caron Bryan , Bourque Guillaume 
Published: November 2018

ABSTRACTWith the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High Performance Computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq, Hi-C, capture Hi-C, metagenomics and PacBio long read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has been already configured on several servers and a docker image is also available to facilitate additional installations. In summary, GenPipes offers genomic researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
Atypical Functional Connectivity in Tourette Syndrome Differs Between Children and Adults
Authors: Nielsen Ashley N. , Gratton Caterina , Church Jessica A. , Dosenbach Nico U.F. , Black Kevin J. , Petersen Steven E. , Schlaggar Bradley L. , Greene Deanna J. 
Published: November 2018

ABSTRACTBackgroundTourette syndrome (TS) is a neuropsychiatric disorder characterized by motor and vocal tics that typically change over development. Whether and how brain function in TS also differs across development has been largely understudied. Here, we used functional connectivity MRI to examine whole brain functional networks in children and adults with TS.MethodsMultivariate classification methods were used to find patterns among functional connections that distinguish TS from controls separately for children and adults (total N = 202). We tested whether the patterns of connections that classify diagnosis in one age group (e.g., children) could classify diagnosis in another age group (e.g., adults). We also tested whether the developmental trajectory of these connections were altered in TS.ResultsPatterns of functional connections that distinguished TS from controls were generalizable to an age-matched independent test set, but not to other age groups. While diagnostic classification was successful in children and adults separately, the connections that best distinguished TS from controls were age-specific. When contextualized with typical development, some functional connections exhibited accelerated maturation in childhood TS, while others exhibited delayed maturation in adulthood TS.ConclusionsOur results demonstrate that brain networks are differentially altered in children and adults with TS, and that the developmental trajectory of affected connections is disrupted. These findings further our understanding of neurodevelopmental trajectories in TS and carry implications for future applications aimed at predicting the clinical course of TS in individuals over development.
TLR3 deficiency exacerbates the loss of epithelial barrier function during genital tractChlamydia muridaruminfection
Authors: Kumar Ramesh , Gong Haoli , Liu Luyao , Ramos-Solis Nicole , Seye Cheikh I. , Derbigny Wilbert A. 
Published: November 2018

AbstractProblemChlamydia trachomatisinfections are often associated with acute syndromes including cervicitis, urethritis, and endometritis, which can lead to chronic sequalae such as pelvic inflammatory disease (PID), chronic pelvic pain, ectopic pregnancy, and tubal infertility. As epithelial cells are the major cell type productively infected during genital tractChlamydiainfections, we investigated whetherChlamydiahas any impact on the integrity of the host epithelial barrier as a possible mechanism to facilitate the dissemination of infection, and examined whether TLR3 function modulates its impact.Method of StudyWe used wild-type and TLR3-deficient murine oviduct epithelial (OE) cells to ascertain whetherC. muridaruminfection had any effect on the epithelial barrier integrity of these cells as measured by transepithelial resistance (TER) and cell permeability assays. We next assessed whether infection impacted the transcription and protein function of the cellular tight-junction (TJ) genes for claudins1-4, ZO-1, JAM1 and occludin via quantitative real-time PCR (qPCR) and western blot.ResultsqPCR, immunoblotting, transwell permeability assays, and TER studies show thatChlamydiacompromises cellular TJ function throughout the course of infection in murine OE cells, and that TLR3 deficiency significantly exacerbates this effect.ConclusionOur data show that TLR3 plays a role in modulating epithelial barrier function duringChlamydiainfection of epithelial cells lining the genital tract. This proposes a role for TLR3 signaling in maintaining the integrity of epithelial barrier function during genital tractChlamydiainfection, a function that we hypothesize is important in helping limit the chlamydial spread and subsequent genital tract pathology.
Single-molecule imaging of DNA gyrase activity in livingEscherichia coli
Authors: Stracy Mathew , Wollman Adam J.M. , Kaja Elzbieta , Gapinski Jacek , Lee Ji-Eun , Leek Victoria A. , McKie Shannon J. , Mitchenall Lesley A. , Maxwell Anthony , Sherratt David J. , Leake Mark C. , Zawadzki Pawel 
Published: November 2018

ABSTRACTBacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by transcription. Removal of these positive supercoils is essential for replication fork progression and for the overall unlinking of the two duplex DNA strands, as well as for ongoing transcription. To address how gyrase copes with these topological challenges, we used high-speed single-molecule fluorescence imaging in liveEscherichia colicells. We demonstrate that at least 300 gyrase molecules are stably bound to the chromosome at any time, with ∼12 enzymes enriched near each replication fork. Trapping of reaction intermediates with ciprofloxacin revealed complexes undergoing catalysis. Dwell times of ∼2 s were observed for the dispersed gyrase molecules, which we propose maintain steady-state levels of negative supercoiling of the chromosome. In contrast, the dwell time of replisome-proximal molecules was ∼8 s, consistent with these catalyzing processive positive supercoil relaxation in front of the progressing replisome.
Collaboration between housing, health and social care
Authors: Brown Tim 
Published: November 2018

Purpose
Comment on the contribution that housing can make to delivering better health and wellbeing outcomes. More specifically, the purpose of this paper is threefold: summarise recent evidence that makes the case for housing in helping to address health and social care issues; comment on the challenges and opportunities of partnership working; and describe examples of interesting and innovative local joint provision.

Design/methodology/approach
Draws on the author’s briefing papers on housing, health and social care for housing quality network, which is a national housing consultancy organisation as well as the author’s role as Chairperson of East Midlands Housing Care and Support, which is a regional housing association.

Findings
Collaboration between housing, health and social care is making slow progress at the national level in England. This is despite an ever-increasing evidence base highlighting that good housing can help to address issues, such as delayed discharges. Nevertheless, there are an increasing number of interesting examples of successful local initiatives on housing, health and adult social care. The way forward is to facilitate joint working at a local level.

Originality/value
Focusses on the success of examples of local joint working between housing, health and social care to achieve better outcomes for vulnerable people.
Hospital discharge planning for Canadians experiencing homelessness
Authors: Buccieri Kristy , Oudshoorn Abram , Frederick Tyler , Schiff Rebecca , Abramovich Alex , Gaetz Stephen , Forchuk Cheryl 
Published: November 2018

Purpose
People experiencing homelessness are high-users of hospital care in Canada. To better understand the scope of the issue, and how these patients are discharged from hospital, a national survey of key stakeholders was conducted in 2017. The paper aims to discuss this issue.

Design/methodology/approach
The Canadian Observatory on Homelessness distributed an online survey to their network of members through e-mail and social media. A sample of 660 stakeholders completed the mixed-methods survey, including those in health care, non-profit, government, law enforcement and academia.

Findings
Results indicate that hospitals and homelessness sector agencies often struggle to coordinate care. The result is that these patients are usually discharged to the streets or shelters and not into housing or housing with supports. The health care and homelessness sectors in Canada are currently structured in a way that hinders collaborative transfers of patient care. The three primary and inter-related gaps raised by survey participants were: communication, privacy and systems pressures.

Research limitations/implications
The findings are limited to those who voluntarily completed the survey and may indicate self-selection bias. Results are limited to professional stakeholders and do not reflect patient views.

Practical implications
Identifying systems gaps from the perspective of those who work within health care and homelessness sectors is important for supporting system reforms.

Originality/value
This survey was the first to collect nationwide stakeholder data on homelessness and hospital discharge in Canada. The findings help inform policy recommendations for more effective systems alignment within Canada and internationally.
The GP role in improving outcomes for homeless inpatients
Authors: Khan Zana , Haine Philip , Dorney-Smith Samantha 
Published: November 2018

Purpose
Homeless people experience extreme health inequalities and high rates of morbidity and mortality (Aldridge et al., 2017). Use of primary care services are low, while emergency healthcare use is high (Mathie, 2012; Homeless Link, 2014). Duration of admission has been estimated to be three times longer for homeless patients who often experience poor hospital discharge arrangements (Mathie, 2012; Homeless Link, 2014). This reflects ongoing and unaddressed care and housing needs (Blackburn et al., 2017). The paper aims to discuss these issues.

Design/methodology/approach
This paper reveals how GPs employed in secondary care, as part of Pathway teams, support improved health and housing outcomes and safe transfer of care into community services. It draws on published literature on role of GPs in working with excluded groups, personal experience of working as a GP in secondary care, structured interviews with Pathway GPs and routine data collected by the team to highlight key outcomes.

Findings
The expertise of GPs is highlighted and includes holistic assessment, management of multimorbidity or “tri-morbidity” – the combination of addictions problems, mental illness and physical health (Homeless Link, 2014; Stringfellow et al., 2015) and research and teaching.

Originality/value
The role of the GP in the care of patients with complex needs is more visible in primary care. This paper demonstrates some of the ways in which in-reach GPs play an important role in the care of multiply excluded groups attending and admitted to secondary care settings.
Sharīʿah-compliance ratings of the Islamic financial services industry: a quantitative approach
Authors: Hanif Muhammad 
Published: November 2018

Purpose
This study aims to develop a Sharīʿah-compliance rating mechanism for the Islamic financial services industry (IFSI), with a special focus on banking. The banking sector is taken as the area of focus due to its leadership role in the volume of global Sharīʿah-compliant assets.

Design/methodology/approach
The objectives of the Islamic financial system (IFS) are selected as the basis for ratings. A range of performance indicators (leading to achievement of the objectives) is grouped into four broader categories and used in the study to allocate scores with a sum total of 100. Special considerations – including the amount of resources required in performing an activity, suitability of prevailing business conditions, the degree of compulsion/discretion in performing a task and linkage with the essence of the IFS – were taken into account in the allocation of scores.

Findings
This study groups multiple performance measures into four categories, including portfolio construction (deposits mechanism, participatory and asset-based modes of financing), access to finance (service to the less-privileged and sector screening), reputation (disclosures and stakeholders’ survey) and Sharīʿah governance (Sharīʿah supervision and controls, charitable operations, human resources, product development and organization). The Portfolio, Audit, Reputation and System (PARS) rating system is then developed.

Practical implications
A Sharīʿah-compliance rating system is helpful in measuring the progress towards goal achievement of the IFS and in gaining stakeholders’ trust. It is also important for Sharīʿah boards and regulators in policy formulation, for management in addressing weaknesses and taking corrective measures and potentially for standard-setting bodies.

Originality/value
This study presents a comprehensive quantitative Sharīʿah-compliance rating mechanism, taking into consideration the objectives of the IFS – equitable distribution of wealth and financial stability, in addition to Sharīʿah-compliance in operations. Development of Sharīʿah-compliance quality ratings for Islamic banking is essential to gain customers’ trust; the suggested methodology is thus a contribution to the literature on Islamic finance.