bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species
Authors: Ren Longhui , Huang Wei , Cannon Steven B.
Published: March 2019

Reconstruction of an ancestral genome for a set of plant species has been a challenging task because of complex histories that may include whole‐genome duplications, segmental duplications, independent gene duplications or losses, diploidization and rearrangement events. Here, we describe the reconstruction a hypothetical ancestral genome for the papilionoid legumes (the largest subfamily within the third largest family in flowering plants), and evaluate the results relative to phylogenetic and chromosomal count data for this group of legumes, spanning 294 diverse papilionoid genera.

To reconstruct the ancestral genomes for nine legume species with sequenced genomes, we used a maximum likelihood approach combined with a novel method for identifying informative markers for this purpose.

Analyzing genomes from four species within the Phaseoleae, two in Dalbergieae, two in the ‘inverted repeat loss’ clade, and one in the Robinieae, we infer a common ancestral genome with nine chromosomes.

The reconstructed genome structural histories are consistent with chromosomal and phylogenetic histories, but we also infer that a common ancestor with nine chromosomes was probably intermediate to an earlier state of 14 chromosomes following a whole‐genome duplication that pre‐dated the radiation of the papilionoid legumes, evidence for which is found in early‐diverging papilionoid lineages.
Theory of Bowstring Disease: Diagnosis and Treatment Bowstring Disease
Authors: Shi Jian‐gang , Xu Xi‐ming , Sun Jing‐chuan , Wang Yuan , Kong Qing‐jie , Shi Guo‐dong
Published: March 2019

Bowstring disease (BSD) is a new classification of spine disease caused by axial stretched lesion on nerve roots and the spinal cord, which is differentiated from disc herniation and canal stenosis in that it is caused by nerve compression lesions. BSD could be caused by mismatched growth rates between the spine and nerve roots (the juvenile type), or by imbalanced degenerative rates between the spine column and nerve roots (degenerative type). Here, we propose that there are several self‐adjust mechanisms to relieve axial nerve tension: (i) nerve growth; (ii) posture adjustment and low back pain; (iii) autogenous degeneration of intervertebral disc; and (iv) idiopathic and degenerative scoliosis. Iatrogenic lesions could also result in BSD, which could be presented as adjacent segment degeneration, leading to adding‐on effects and other neurological symptoms. The diagnosis criteria are proposed based on symptoms, physical examination, and radiological presentations. To remove axial tension on nerve roots, lumbar surgery should aim to restore the coordination of spine and cord units. Capsule surgery, shortening the spine column, could decompress cord and nerve roots 3‐dimensionally.
Recombinant thrombomodulin for acute exacerbation in idiopathic interstitial pneumonias
Authors: Arai Toru , Kida Hiroshi , Ogata Yoshitaka , Marumo Satoshi , Matsuoka Hiroto , Gohma Iwao , Yamamoto Suguru , Mori Masahide , Sugimoto Chikatoshi , Tachibana Kazunobu , Akira Masanori , Edahiro Ryuya , Hamasaki Toshimitsu , Inoue Yoshikazu ,   on behalf of the Osaka Acute Exacerbation of Interstitial Pneumonia Research Group
Published: March 2019

Background and objective

Acute exacerbation (AE) in idiopathic pulmonary fibrosis (IPF) or other idiopathic interstitial pneumonias (IIP) is a poor prognostic event despite conventional therapy with corticosteroids and/or immunosuppressants. We aimed to evaluate the efficacy and safety of recombinant human soluble thrombomodulin (rhTM) for AE‐IIP.

Methods

For this prospective single‐arm open‐label multicentre cohort study, we retrospectively registered 61 cases of AE‐IIP treated with conventional therapy between 2011 and 2013 (control arm), and prospectively enrolled 39 cases of AE‐IIP treated with conventional therapy and rhTM (380 U/kg/day for 6 days) between 2014 and 2016 (rhTM arm). To reduce potential confounding in treatment comparisons, an adjusted mortality analysis for 90‐day survival was conducted with weighted Cox proportional hazards regression models using inverse probability of treatment weighting. Weights were derived from propensity scores estimated using a multivariable logistic regression analysis including potential confounders.

Results

The 90‐day survival rates of AE‐IIP patients treated with/without rhTM were 66.7% (26/39) and 47.5% (29/61), respectively. After adjusting for imbalances, rhTM therapy was significantly associated with reduced mortality (adjusted hazard ratio (HR): 0.453; 95% CI: 0.237–0.864; P = 0.0163). The frequencies of adverse events with/without rhTM were 17.9% (7/39) and 19.7% (12/61), which were similar in both arms (P = 1.0). Two bleeding‐related adverse events occurred in the rhTM arm.

Conclusion

Safety and efficacy were observed for rhTM treatment of AE‐IIP. A future randomized controlled trial is required to draw final conclusions.
Rehabilitation in chronic respiratory diseases: In‐hospital and post‐exacerbation pulmonary rehabilitation
Authors: Ibrahim Wadah , Harvey‐Dunstan Theresa C. , Greening Neil J.
Published: March 2019

Exacerbations of chronic obstructive pulmonary disease (COPD) that require hospitalization are important events for patients. Functional impairment and skeletal muscle dysfunction can increase the risk of hospitalization and readmission, independent of lung function. In addition, once a patient is admitted, multiple factors can lead to worsening outcome including immobility, systemic inflammation and nutritional depletion. These non‐pulmonary factors are potentially amenable to exercise therapy, as part of pulmonary rehabilitation (PR). Peri‐exacerbation PR has an important role in the management of exacerbations of COPD. In this review, we explore how functional limitation and skeletal muscle dysfunction affect patients having a severe exacerbation of COPD, the systemic impact of hospitalization on patients including potential aetiologies and the role of PR around the time of an exacerbation. This includes rehabilitation during the inpatient phase, post‐exacerbation rehabilitation and rehabilitation bridging hospital discharge. We also describe potential future developments in peri‐exacerbation PR.
Indexing Out of Poverty? Fiscal Drag and Benefit Erosion in Cross‐National Perspective
Authors: Paulus Alari , Sutherland Holly , Tasseva Iva
Published: March 2019

We assess how tax‐benefit policy developments in 2001–11 affected the household income distribution in seven EU countries. We use the standard microsimulation‐based decomposition method, separating further the effect of structural policy changes and the uprating of monetary parameters, which allows us to measure the extent of fiscal drag and benefit erosion in practice. The results show that despite different fiscal effects, policies overall mostly reduced poverty and inequality and both types of policy developments had sizeable effects on the income distribution. We also find that the uprating of monetary parameters not only had a positive effect on household incomes, meaning fiscal drag and benefit erosion were avoided, but generally also contributed more to poverty and inequality reduction than structural policy reforms.
Lesbian, Gay, Bisexual, Transgender, and Queer Media: Key Narratives, Future Directions
Authors: Rodriguez Julian A.
Published: March 2019

Lesbian, gay, bisexual, transgender, and queer (LGBTQ) people have become a familiar presence on the media landscape. For more than half a century, scholars have examined the importance of this recognition. In this article, I extend the work of British sociologist Ken Plummer to argue that key narratives have endured in discussions of LGBTQ media. These narratives include the victim, the community, the militant/queer, and the assimilationist. In addition, this paper points toward new directions for analysis and discussion; I argue that future research should take a more nuanced approach by examining overlaps and tensions among these stories.
Phylogenomic analysis of seal lice reveals codivergence with their hosts
Authors: Leonardi María Soledad , Virrueta Herrera Stephany , Sweet Andrew , Negrete Javier , Johnson Kevin P.
Published: March 2019

Lice are considered a model system for studying the process of cospeciation because they are obligate and permanent parasites and are often highly host‐specific. Among lice, species in the family Echinophthiriidae Enderlein (Anoplura) are unique in that they infest mammalian hosts with an amphibious lifestyle, i.e. pinnipeds and the river otter. There is evidence that the ancestor of this group infested the terrestrial ancestor of pinnipeds, which suggests these parasites coevolved with their hosts during the transition to marine environments. However, there has been no previous study investigating the phylogenetic relationships among sucking lice parasitizing seals and sea lions. To uncover the evolutionary history of these parasites, we obtained genomic data for Antarctophthirus microchir Trouessart and Neumann (from two hosts), Antarctophthirus carlinii Leonardi et al., Antarctophthirus lobodontis Enderlein, Antarctophthirus ogmorhini Enderlein, Lepidophthirus macrorhini Enderlein, and Proechinophthirus fluctus Ferris. From genomic sequence reads, we assembled > 1000 nuclear genes and used these data to infer a phylogenetic tree for these lice. We also used the assembled genes in combination with read‐mapping to estimate heterozygosity and effective population size from individual lice. Our analysis supports the monophyly of lice from pinnipeds and uncovers phylogenetic relationships within the group. Surprisingly, we found that A. carlinii, A. lobodontis, and A. ogmorhini have very little genetic divergence among them, whereas the divergence between different geographic representatives of A. microchir indicate that they are possibly different species. Nevertheless, our phylogeny of Echinophthiriidae suggests that these lice have consistently codiverged with their hosts with minimal host switching. Population genomic metrics indicate that louse effective population size is linked to host demographics, which further highlights the close association between pinnipeds and their lice.
Distribution and abundance of invasive Tamarix genotypes in South Africa
Authors: Newete S W , Mayonde S , Byrne M J
Published: March 2019

The exotic Tamarix chinensis and T. ramosissima, believed to have been introduced into South Africa in the early 1900s to control erosion on mine dumps, are invading riparian zones and have been proven to hybridise with T. usneoides, which is native to southern Africa. In this study, we document the abundance of invasive Tamarix genotypes in South Africa. Eleven riparian zones from the Northern, Eastern and Western Cape Provinces were surveyed. Three quadrats of 600 m2 each were selected per site. Plant density, canopy cover and tree height were recorded to quantify invasiveness. Leaf samples were randomly collected from an average of eight individuals per site to record genotypes of the invaders. Tamarix density and canopy cover were significantly greater than those of co‐occurring trees and shrubs in Olifants River in De Rust (Western Cape Province). A linear correlation between percentage Tamarix spp. cover and other co‐occurring tree and shrub species showed a strong negative relationship (R2 = 0.78). Genetic analysis showed that the Western and Eastern Cape Provinces have the highest proportion of the exotic Tamarix species and their hybrids. This suggests that these two provinces require urgent management intervention to contain the spread of the weed. The distinctions made between the native and the exotic Tamarix species and their hybrids should also facilitate the testing and future release of potential biological control agents.
PET-CT in Esophageal Cancer Management: A Cost Effectiveness Analysis Study
Authors: Azmi Nor Aniza , Abdul Razak Hairil Rashmizal , Vinjamuri Sobhan
Published: March 2019

The present investigation deals with the assessment of clinicians perceived views on the impact of PET-CT in esophageal cancer management from practicality, clinical efficacy and cost –effectiveness point of views. Review of publication and retrospective data to develop and carry out a decision making model-based economic evaluation to investigate the relative cost-effectiveness of PET/CT in esophageal cancer management staging compared with conventional pathway. Clinicians identified from patient medical records included in the survey. Retrospective analysis of patient data from 2001-2008 taken from esophageal cancer patient medical records and North West Cancer Intelligence Services (NWCIS) database. A decision tree was developed using TREEAGE software. The results of the cost-effectiveness analysis are presented in terms of the incremental cost-effectiveness ratios (ICERs). PET compared with conventional work-up results for ICER for the strategy estimated at £28,460 per QALY; PET/CT compared with PET for ICER was £ 32,590 per QALY; and the ICER for PET/CT combined with conventional work-up versus PET/CT was £ 44,118. The package become more expensive with each additional diagnostic test added to PET and more effective in terms of QALYs gained. The conventional work-up is the preferred options as probabilistic sensitivity analysis shows at a willingness-to-pay threshold of £ 20,000 per QALY. Result of the current analysis suggests that the use of PET/CT in the diagnosis of esophageal cancer is unlikely to be cost-effective given the current willingness-to-pay thresholds that are accepted in the United Kingdom by decision-making bodies such as the National Institute for Health and Clinical Excellence.
Measurement of trabecular bone parameters with different bone thickness and voxel size in mice using micro CT
Authors: Abu Bakar Nurin Nadzlah , Saidi Basri , Mohamad Yamin Lyana Shahirah
Published: March 2019

Micro-CT is one of the best modalities in assessing bone morphology and microarchitecture in small animal models. Voxel size is directly related to the image resolution as it influences the bone morphology results. The purpose of this study was to assess the effects of t different thicknesses of structures on the trabecular bone qualitative parameters. It was also to find out the most appropriate voxel size when scanning a certain or specific body part with different thicknesses. Five BALB-C breed mice carcasses were scanned using two different voxel sizes of 18 and 35 µm. The scanning acquisition times were recorded to be compared and the trabecular bone parameters measurements were taken. Both trabecular number and trabecular separation were increased in thicker structures meanwhile bone volume fraction and trabecular thickness values were inconsistent with the increment of the structure thickness. The bone volume fraction, trabecular thickness and trabecular separation were higher in larger voxel size and vice versa for trabecular number. The scanning acquisition time has no apparent correlation with the trabecular bone parameters. The thickness of the bone structure did affect trabecular number and trabecular separation significantly but less affecting bone volume fraction and trabecular thickness. All trabecular bone parameters were found affected by the size of scanning voxel size used. The usage of 35 µm voxel was more recommended than 18 µm to save time and give out less radiation dose to specimen unless the detailed features of the trabecular pattern was very important.
Preparation and characterization of polysulfone membrane coated with poly(ether block amid) for oxygen enrichment process
Authors: Chung Chong Kok , Chan Yin Yin , Lau Woei Jye , Lai Soon Onn , Ismail Ahmad Fauzi , Thiam Hui Shan
Published: March 2019

Oxygen enriched air (OEA) is widely applied in various areas such as chemical and medical applications. Currently, cryogenic distillation and pressure swing adsorption are the two common technologies that being commercially used for i the production of OEA. However, these two techniques are not economically favorable due to required intensive energy and large built-up area. With the advancement of membrane technology in separation process, it garners the interest from both industrial and academic to explore the feasibility of membrane in gas separation. In this study, polysulfone (PSF) hollow fiber membranes with poly(ether block amide) (PEBAX) coating were used for the separation of O2/N2 gas. The hollow fiber membranes used in this work were fabricated by phase inversion spinning process using PSF pellet, along with N,N-dimetyhlacetamide (DMAc) and ethanol (EtOH) as solvent and co-solvent, whereas tetrahydrofuran (THF) as additive. The fabricated membrane exhibited dense structure in the inner layer whereas finger like layer at the outer surface. The formation of this structure was attributed by rapid phase inversion of the solution arose from strong solvent used. The EDX surface mapping analysis confirmed the formation of PEBAX coating on the membrane surface. Gas permeation study in this work illustrated that the pristine PSF membrane exhibited better gas separation performance relative to the PEBAX coated membrane with 20% higher in terms of permeance. The results obtained from this work suggested that the PEBAX coating enhanced the membrane surface but not certain to improve the gas separation performance. Further study on the PEBAX materials for the membrane coating is essential to polish its potential in gas separation.
Valoración del servicio de enfermería por parte de adolescentes gestantes antes de una intervención en atención prenatal y después de esta
Authors: Reyes Bravo Diana María , Muñoz de Rodriguez Lucy
Published: March 2019

Introducción: Investigaciones sobre gestación en mujeres adolescentes han detectado ciertas necesidades, como sentirse escuchadas o apoyadas y recibir trato humanizado. Objetivo: Determinar cómo adolescentes gestantes valoraron el cuidado proporcionado por el servicio de enfermería antes de una intervención y después de esta, en una institución de salud de Bucaramanga, en 2015. Método: Estudio cuasi experimental pretest y postest en 39 adolescentes asistentes a atención prenatal. Para la valoración del cuidado se utilizó la Escala Profesional de Cuidado, organizada en las subescalas: sanador compasivo y competente. La valoración pretest se realizó después del control prenatal convencional, por enfermería, y la postest, después de la intervención de cuidado, fundamentada en la teoría de Swanson. Resultados: Aunque las valoraciones del cuidado fueron excelentes antes de la intervención, mejoraron posteriormente, lo que muestra un aumento de puntajes mínimos de 48 antes, a 57 después de la intervención, y en disminución de las desviaciones estándar 2,6704 y 0,6863, respectivamente. Estos cambios son notorios en el sanador compasivo referido a la relación afectuosa y de confianza que establece el enfermero(a) en la interacción de cuidado. Conclusiones: La teoría de Swanson permitió abordar a la adolescente en la atención prenatal, supliendo necesidades de escucha, trato humanizado y apoyo. Ello se evidencia en la valoración posterior.
Relative Nucleus Pulposus Area and Position Alter Disk Joint Mechanics
Authors: Yang Bo , Lu Yintong , Um Colin , O'Connell Grace D.
Published: March 2019

Aging and degeneration of the intervertebral disk are noted by changes in tissue composition and geometry, including a decrease in nucleus pulposus (NP) area. The NP centroid is positioned slightly posterior of the disk's centroid, but the effect of NP size and location on disk joint mechanics is not well understood. We evaluated the effect of NP size and centroid location on disk joint mechanics under dual-loading modalities (i.e., compression in combination with axial rotation or bending). A finite element model (FEM) was developed to vary the relative NP area (NP:Disk area ratio range = 0.21–0.60). We also evaluated the effect of NP position by shifting the NP centroid anteriorly and posteriorly. Our results showed that compressive stiffness and average first principal strains increased with NP size. Under axial compression, stresses are distributed from the NP to the annulus, and stresses were redistributed toward the NP with axial rotation. Moreover, peak stresses were greater for disks with a smaller NP area. NP centroid location had a greater impact on intradiscal pressure during flexion and extension, where peak pressures in the posterior annulus under extension was greater for disks with a more posteriorly situated NP. In conclusion, the findings from this study highlight the importance of closely mimicking NP size and location in computational models that aim to understand stress/strain distribution during complex loading and for developing repair strategies that aim to recapitulate the mechanical behavior of healthy disks.
Numerical Simulation of Re-Entrant Bowl Effects on Natural-Gas Spark-Ignition Operation
Authors: Liu Jinlong , Dumitrescu Cosmin Emil
Published: March 2019

Heavy-duty compression–ignition (CI) engines converted to natural gas (NG) spark ignition (SI) operation have the potential to increase the use of NG in the transportation sector. A three-dimensional (3D) numerical simulation was used to predict how the conventional CI combustion chamber geometry (i.e., re-entrant bowl and flat head) affects the combustion stability, performance, and emissions of a single-cylinder CI engine that was converted to SI operation by adding a low-pressure gas injector in the intake manifold and a spark plug in place of the diesel injector. The G-equation based 3D computational fluid dynamics (CFD) simulation investigated three different combustion chamber configurations that change the size of the squish region at a constant compression ratio (CR) and a clearance height. The results show that the different flame propagation speeds inside and outside the re-entrant bowl can create a two-zone combustion phenomenon. Moreover, a larger squish region increased the flame burning speed, which decreased late-combustion duration (DOC). All these findings support the need for further investigations of the combustion chamber shape design for optimum engine performance and emissions in CI engines converted to NG SI operation.
The Phan-Thien and Tanner Model Applied to the Lubrication of Knee Prostheses
Authors: Weiss Brenda A. , Bou-Saïd Benyebka , Ubal Sebastián , Di Paolo José
Published: March 2019

This work aims to provide a contribution to determine a proper model for the study of fluid film lubrication for the reduction of knee prostheses failure due to polyethylene wear. The Phan-Thien and Tanner (PTT) rheological law and the elastic deformation of the articular surfaces were considered in this modeling. The governing equations were solved numerically for different geometries and different Weissenberg numbers. The lubrication approximation applied to the PTT rheological law leads to an expression for the apparent viscosity similar to the Cross model. The results attest the importance of considering the non-Newtonian behavior of the synovial fluid, the elastic deformation, and the geometrical features of the prostheses to obtain quantitative information.
Power Scaling of Radial Outflow: Bernoulli Pads in Equilibrium
Authors: Kamensky Kristina M. , Hellum Aren M. , Mukherjee Ranjan
Published: March 2019

A Bernoulli pad uses an axial jet to produce radial outflow between the pad and a proximally located parallel surface. The flow field produces a force between the surfaces, which depends upon their spacing h. The direction of this force is repulsive as h approaches zero and becomes attractive as h increases. This yields a stable equilibrium point heq, where the force is equal to zero. The present computational work indicates that a power-law relationship exists between heq and the inlet fluid power required to sustain this equilibrium spacing when each is appropriately scaled. This scaling is derived principally from the wall shear; an additional term incorporating the inlet Reynolds number is used to account for the force applied to the system. The relationship is valid over a range of forces acting on the system, geometric, and material properties.
Knowledge Translation Practices, Enablers, and Constraints: Bridging the Research–Practice Divide in Sport Management
Authors: Schaillée Hebe , Spaaij Ramón , Jeanes Ruth , Theeboom Marc
Published: March 2019

Funding bodies seek to promote scientific research that has a social or economic impact beyond academia, including in sport management. Knowledge translation in sport management remains largely implicit and is yet to be fully understood. This study examines how knowledge translation in sport management can be conceptualized and fostered. The authors draw on a comparative analysis of coproduced research projects in Belgium and Australia to identify the strategic, cognitive, and logistic translation practices that researchers adopt, as well as enablers and constraints that affect knowledge translation. The findings show ways in which knowledge translation may be facilitated and supported, such as codesign, boundary spanning, adaptation of research products, and linkage and exchange activities. The findings reveal individual, organizational, and external constraints that need to be recognized and, where possible, managed.
A Highly Unusual V1 Region of Env in an Elite Controller of HIV Infection
Authors: Silver Zachary A. , Dickinson Gordon M. , Seaman Michael S. , Desrosiers Ronald C.
Published: March 2019

Elite controllers have long provided an avenue for researchers to reveal mechanisms underlying control of HIV-1. While the role of host genetic factors in facilitating elite control is well known, the possibility of infection by attenuated strains of HIV-1 has been much less studied. Here we describe an unusual viral feature found in an elite controller of HIV-1 infection and demonstrate its role in conferring escape from monoclonal antibodies of the V3-glycan class. Our results suggest that extreme variation may be needed by HIV-1 to escape neutralization by some antibody specificities.
Fifteen-minute consultation: A guide to managing a child with a new finding of neutropenia
Authors: James Rebecca M , Phillips Bob
Published: March 2019

Objective

To describe a structured approach for managing a child with a new finding of neutropenia.

Method

Literature review and consensus practice of clinicians in our regional centre.

Conclusion

Neutropenia may arise in a variety of situations from a well child with a physiological neutropenia to a sick infant with life-threatening infection. In most cases a thoughtful history and directed examination will help to identify the severity in order to determine an appropriate care pathway.

Scenario

A 6-year-old boy presented earlier in the day to the acute assessment unit with lethargy and a sore throat. At handover time his blood results are phoned through and show that he is neutropenic.
New approach in prophylactic treatment of a challenged HAE patient
Authors: Jordal Oda , Bygum Anette
Published: March 2019

Hereditary angioedema (HAE) is a relapsing swelling disorder which can cause severe pain, affect quality of life and potentially be life threatening with involvement of the airways. We present a 34-year-old immigrant who suffered from very frequent and severe HAE attacks. The attacks often involved the face, mouth and the airways. She often went to the hospital for treatment, where the language barrier made the situation complicated. The traditional therapy for HAE was not successful treating this patient. In June 2017, off-label treatment with prophylactic subcutaneous complement C1-inhibitor concentrate was initiated. The treatment was very successful and the patient has not been hospitalised since. Treatment for HAE is nowadays under investigation, and many drugs are under development. Especially, medication which works prophylactically and is administered orally or subcutaneously is in the horizon.
Reporting guidelines for health research: protocol for a cross-sectional analysis of the EQUATOR Network Library
Authors: Catalá-López Ferrán , Alonso-Arroyo Adolfo , Page Matthew J , Hutton Brian , Ridao Manuel , Tabarés-Seisdedos Rafael , Aleixandre-Benavent Rafael , Moher David
Published: March 2019

Introduction

Transparency and completeness of health research is highly variable, with important deficiencies in the reporting of methods and results of studies. Reporting guidelines aim to improve transparency and quality of research reports, and are often developed by consortia of journal editors, peer reviewers, authors, consumers and other key stakeholders. The objective of this study will be to investigate the characteristics of scientific collaboration among developers and the citation metrics of reporting guidelines of health research.

Methods and analysis

This is the study protocol for a cross-sectional analysis of completed reporting guidelines indexed in the Enhancing the QUAlity and Transparency Of health Research Network Library. We will search PubMed/MEDLINE and the Web of Science. Screening, selection and data abstraction will be conducted by one researcher and verified by a second researcher. Potential discrepancies will be resolved via discussion. We will include published papers of reporting guidelines written in English. Published papers will have to meet the definition of a reporting guideline related to health research (eg, a checklist, flow diagram or explicit text), with no restrictions by study design, medical specialty, disease or condition. Raw data from each included paper (including title, publication year, journal, subject category, keywords, citations, and the authors’ names, author’s affiliated institution and country) will be exported from the Web of Science. Descriptive analyses will be conducted (including the number of papers, citations, authors, countries, journals, keywords and main collaboration metrics). We will identify the most prolific authors, institutions, countries, journals and the most cited papers. Network analyses will be carried out to study the structure of collaborations.

Ethics and dissemination

No ethical approval will be required. Findings from this study will be published in peer-reviewed journals. All data will be deposited in a cross-disciplinary public repository. It is anticipated the study findings could be relevant to a variety of audiences.
Children and Teens in Charge of their Health (CATCH): A protocol for a feasibility randomised controlled trial of solution-focused coaching to foster healthy lifestyles in childhood disability
Authors: McPherson Amy C , Biddiss Elaine , Chen Lorry , Church Paige Terrien , de Groot Janke F , Keenan Sarah , King Gillian , Lui Toni , Maltais Desiree B , Mérette Chantal , Moffet Hélène , Moola Fiona , Schwellnus Heidi
Published: March 2019

Introduction

Children with physical disabilities are rarely included in interventions to promote healthy lifestyles, despite being at higher risk for suboptimal dietary and physical activity behaviours. The Children and Teens in Charge of their Health study explores the feasibility and acceptability of conducting a randomised controlled trial (RCT) of a strengths-based, solution-focused coaching intervention for improving and sustaining physical activity and healthy dietary habits in children and young people with physical disabilities.

Methods and analysis

Thirty children aged 10–18 years with a diagnosis of spina bifida or cerebral palsy who are able to set healthy lifestyle goals will be recruited from two children’s rehabilitation hospitals in Ontario, Canada. Participants will be enrolled in the study for twelve months. All participants will receive standard care and printed information about healthy lifestyles. Of the 30 participants, 15 will be randomised to receive a coaching intervention for the first 6 months. Health indicators and psychosocial outcomes will be assessed by blinded assessors four times: at the start of the trial, immediately postintervention (6 months after randomisation), and at 3 and 6 months postintervention (9 and 12 months after randomisation, respectively). Predefined success criteria will be used to assess the feasibility of trial processes such as recruitment, attrition, stratification and intervention fidelity. Acceptability and perceived impact of the intervention will be explored qualitatively.

Ethics and dissemination

The study has been approved by Holland Bloorview Kids Rehabilitation Hospital’s Research Ethics Board (Ref: 17–752). A knowledge translation planning template will be used to ensure our findings have maximum reach.

Trial registration number

NCT03523806.
Occurrence of Salmonella, Campylobacter, Clostridium and Enterobacteriaceae in raw meat‐based diets for dogs
Authors: Hellgren Josefin , Hästö Lovisa Staaf , Wikström Camilla , Fernström Lise‐Lotte , Hansson Ingrid
Published: March 2019

The practice of feeding raw meat‐based diets (RMBD) to dogs has increased in popularity in recent years. However, RMBD are based on offal that has not undergone any type of treatment to reduce the microbial content, so there is a risk of potential pathogenic microorganisms being present. Frozen samples from 60 RMBD packs produced by 10 different manufacturers were analysed for their content of bacteria belonging to the family Enterobacteriaceae, for Clostridium perfringens and for the presence of Salmonella and Campylobacter. Enterobacteriaceae were detected in all 60 samples and in 31 samples exceeded a level of 5000 bacteria/g, which is the threshold for satisfactory microbial hygiene according to EU regulations. In two samples, the amount of C. perfringens exceeded 5000 bacteria/g, which is the maximum level of anaerobic bacteria permitted by Swedish national guidelines. Salmonella species were found in four (7 per cent) and Campylobacter species in three (5 per cent) samples. These results show that it is critical to maintain good hygiene when storing, handling and feeding RMBD, in order to limit the potential health risks to animals and humans, especially young and immunocompromised individuals.
Efficacy of HPPD-inhibiting herbicides applied preemergence or postemergence for control of multiple herbicide resistant waterhemp [Amaranthus tuberculatus (Moq.) Sauer]
Authors: Benoit Lauren , Soltani Nader , Hooker David C. , Robinson Darren E. , Sikkema Peter H.
Published: March 2019

Research was conducted in 2017 and 2018 to determine the relative efficacy of five HPPD-inhibitors, tank-mixed with atrazine, for the control of multiple herbicide resistant waterhemp. At 12 wk after application (WAA), isoxaflutole + atrazine, mesotrione + atrazine, and tembotrione + atrazine, applied preemergence (PRE), controlled waterhemp 90%, 87%, and 81%, respectively. None of the HPPD-inhibiting herbicides applied PRE controlled waterhemp similar to the weed-free control 12 WAA. Applied postemergence, topramezone + atrazine, mesotrione + atrazine, tolpyralate + atrazine, and tembotrione + atrazine controlled waterhemp 87%, 94%, 97%, and 98% 12 WAA, respectively, and were all similar to the weed-free control.
Characterization of Infinite LSP Words and Endomorphisms Preserving the LSP Property
Authors: Richomme Gwenaël
Published: March 2019

Answering a question of G. Fici, we give an [Formula: see text]-adic characterization of the family of infinite LSP words, that is, the family of infinite words having all their left special factors as prefixes. More precisely we provide a finite set of morphisms [Formula: see text] and an automaton [Formula: see text] such that an infinite word is LSP if and only if it is [Formula: see text]-adic and one of its directive words is recognizable by [Formula: see text]. Then we characterize the endomorphisms that preserve the property of being LSP for infinite words. This allows us to prove that there exists no set [Formula: see text] of endomorphisms for which the set of infinite LSP words corresponds to the set of [Formula: see text]-adic words. This implies that an automaton is required no matter which set of morphisms is used.
Sageretia thea Inhibits Inflammation through Suppression of NF-κB and MAPK and Activation of Nrf2/HO-1 Signaling Pathways in RAW264.7 Cells
Authors: Kim Ha Na , Park Gwang Hun , Park Su Bin , Kim Jeong Dong , Eo Hyun Ji , Son Ho-Jun , Song Jeong Ho , Jeong Jin Boo
Published: March 2019

Sageretia thea (S. thea) commonly known as Chinese sweet plum or Chinese bird plum has been used for treating hepatitis and fevers in Korea and China. S. thea has been reported to exert anti-oxidant, anticancer and anti-human immunodeficiency virus activity. However, there is little study on the anti-inflammatory activity of S. thea. Thus, we evaluated the anti-inflammatory effect of extracts of leaves (ST-L) and branches (ST-B) from Sageretia thea in LPS-stimulated RAW264.7 cells. ST-L and ST-B significantly inhibited the production of the pro-inflammatory mediators such as NO, iNOS, COX-2, IL-1[Formula: see text] and IL-6 in LPS-stimulated RAW264.7 cells. ST-L and ST-B blocked LPS-induced degradation of I[Formula: see text]B-[Formula: see text] and nuclear accumulation of p65, which resulted in the inhibition of NF-[Formula: see text]B activation in RAW264.7 cells. ST-L and ST-B also attenuated the phosphorylation of ERK1/2, p38 and JNK in LPS-stimulated RAW264.7 cells. In addition, ST-L and ST-B increased HO-1 expression in RAW264.7 cells, and the inhibition of HO-1 by ZnPP reduced the inhibitory effect of ST-L and ST-B against LPS-induced NO production in RAW264.7 cells. Inhibition of p38 activation and ROS elimination attenuated HO-1 expression by ST-L and ST-B, and ROS elimination inhibited p38 activation induced by ST-L and ST-B. ST-L and ST-B dramatically induced nuclear accumulation of Nrf2, but this was significantly reversed by the inhibition of p38 activation and ROS elimination. Collectively, our results suggest that ST-L and ST-B exerts potential anti-inflammatory activity by suppressing NF-[Formula: see text]B and MAPK signaling activation, and activating HO-1 expression through the nuclear accumulation of Nrf2 via ROS-dependent p38 activation. These findings suggest that ST-L and ST-B may have great potential for the development of anti-inflammatory drug to treat acute and chronic inflammatory disorders.
Pre-saddle and pre-scission neutron emission rates in heavy-ion induced fission of 16O +208Pb and 16O +209Bi systems
Authors: Soheyli Saeed , Khalili Morteza Khalil , Ashrafi Ghazaaleh
Published: March 2019

Whereas there is a slight information on the pre-saddle neutron emission rate and neutron multiplicity, as well as it is impossible to separate the pre-saddle and saddle to scission neutron contributions experimentally, the theoretical studies of pre-saddle neutron emission rate and neutron multiplicity are of great importance. In the present work, the calculations of pre-saddle neutron multiplicity are performed using the analysis of fission fragment angular anisotropy data for [Formula: see text] and [Formula: see text] reaction systems. The obtained results show that the pre-saddle neutron multiplicity decreases by increasing the initial excitation energy and it has found to be characterized by a nonlinear behavior. Through the analysis of pre-saddle neutron multiplicity and pre-saddle transition time by means of the neutron clock method, the pre-saddle neutron emission rate is calculated for the first time. The findings of this study show that the pre-scission neutron emission rate is lower than the pre-saddle neutron emission rate.
Harnessing epoch-based reclamation for efficient range queries
Authors: Arbel-Raviv Maya , Brown Trevor
Published: March 2019

Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system.
A persistent lock-free queue for non-volatile memory
Authors: Friedman Michal , Herlihy Maurice , Marathe Virendra , Petrank Erez
Published: March 2019

Non-volatile memory is expected to coexist with (or even displace) volatile DRAM for main memory in upcoming architectures. This has led to increasing interest in the problem of designing and specifying
durable
data structures that can recover from system crashes. Data structures may be designed to satisfy stricter or weaker durability guarantees to provide a balance between the strength of the provided guarantees and performance overhead. This paper proposes three novel implementations of a concurrent lock-free queue. These implementations illustrate algorithmic challenges in building persistent lock-free data structures with different levels of durability guarantees. In presenting these challenges, the proposed algorithmic designs, and the different durability guarantees, we hope to shed light on ways to build a wide variety of durable data structures. We implemented the various designs and compared their performance overhead to a simple queue design for standard (volatile) memory.
Hierarchical memory management for mutable state
Authors: Guatto Adrien , Westrick Sam , Raghunathan Ram , Acar Umut , Fluet Matthew
Published: March 2019

It is well known that modern functional programming languages are naturally amenable to parallel programming. Achieving efficient parallelism using functional languages, however, remains difficult. Perhaps the most important reason for this is their lack of support for efficient in-place updates, i.e., mutation, which is important for the implementation of both parallel algorithms and the run-time system services (e.g., schedulers and synchronization primitives) used to execute them.

In this paper, we propose techniques for efficient mutation in parallel functional languages. To this end, we couple the memory manager with the thread scheduler to make reading and updating data allocated by nested threads efficient. We describe the key algorithms behind our technique, implement them in the MLton Standard ML compiler, and present an empirical evaluation. Our experiments show that the approach performs well, significantly improving efficiency over existing functional language implementations.
Bridging the gap between deep learning and sparse matrix format selection
Authors: Zhao Yue , Li Jiajia , Liao Chunhua , Shen Xipeng
Published: March 2019

This work presents a systematic exploration on the promise and special challenges of deep learning for sparse matrix format selection---a problem of determining the best storage format for a matrix to maximize the performance of Sparse Matrix Vector Multiplication (SpMV). It describes how to effectively bridge the gap between deep learning and the special needs of the pillar HPC problem through a set of techniques on matrix representations, deep learning structure, and cross-architecture model migrations. The new solution cuts format selection errors by two thirds, and improves SpMV performance by 1.73X on average over the state of the art.
Cache-tries
Authors: Prokopec Aleksandar
Published: March 2019

Concurrent non-blocking hash tries have good cache locality, and horizontally scalable operations. However, operations on most existing concurrent hash tries run in
O
(log
n
) time.

In this paper, we show that the concurrent hash trie operations can run in expected constant time. We present a novel lock-free concurrent hash trie design that exerts less pressure on the memory allocator. This hash trie is augmented with a quiescently consistent cache, which permits the basic operations to run in expected
O
(1) time. We show a statistical analysis for the constant-time bound, which, to the best of our knowledge, is the first such proof for hash tries. We also prove the safety, lock-freedom and linearizability properties. On typical workloads, our implementation demonstrates up to 5X performance improvements with respect to the previous hash trie variants.
FlashR
Authors: Zheng Da , Mhembere Disa , Vogelstein Joshua T. , Priebe Carey E. , Burns Randal
Published: March 2019

R is one of the most popular programming languages for statistics and machine learning, but it is slow and unable to scale to large datasets. The general approach for having an efficient algorithm in R is to implement it in C or FORTRAN and provide an R wrapper. FlashR accelerates and scales existing R code by parallelizing a large number of matrix functions in the R
base
package and scaling them beyond memory capacity with solid-state drives (SSDs). FlashR performs memory hierarchy aware execution to speed up parallelized R code by
(i)
evaluating matrix operations lazily,
(ii)
performing all operations in a DAG in a single execution and with only one pass over data to increase the ratio of computation to I/O,
(iii)
performing two levels of matrix partitioning and reordering computation on matrix partitions to reduce data movement in the memory hierarchy. We evaluate FlashR on various machine learning and statistics algorithms on inputs of up to four billion data points. Despite the huge performance gap between SSDs and RAM, FlashR on SSDs closely tracks the performance of FlashR in memory for many algorithms. The R implementations in FlashR outperforms H
2
O and Spark MLlib by a factor of 3 -- 20.
D
is
CV
ar
Authors: Menon Harshitha , Mohror Kathryn
Published: March 2019

Aggressive technology scaling trends have made the hardware of high performance computing (HPC) systems more susceptible to faults. Some of these faults can lead to silent data corruption (SDC), and represent a serious problem because they alter the HPC simulation results. In this paper, we present a full-coverage, systematic methodology called D
is
CV
ar
to identify critical variables in HPC applications for protection against SDC. D
is
CV
ar
uses automatic differentiation (AD) to determine the sensitivity of the simulation output to errors in program variables. We empirically validate our approach in identifying vulnerable variables by comparing the results against a full-coverage code-level fault injection campaign. We find that our D
is
CV
ar
correctly identifies the variables that are critical to ensure application SDC resilience with a high degree of accuracy compared to the results of the fault injection campaign. Additionally, D
is
CV
ar
requires only two executions of the target program to generate results, whereas in our experiments we needed to perform millions of executions to get the same information from a fault injection campaign.
Practical concurrent traversals in search trees
Authors: Drachsler-Cohen Dana , Vechev Martin , Yahav Eran
Published: March 2019

Operations of concurrent objects often employ optimistic concurrency-control schemes that consist of a traversal followed by a validation step. The validation checks if concurrent mutations interfered with the traversal to determine if the operation should proceed or restart. A fundamental challenge is to discover a
necessary
and sufficient validation check that has to be performed to guarantee correctness.

In this paper, we show a necessary and sufficient condition for validating traversals in search trees. The condition relies on a new concept of
succinct path snapshots
, which are derived from and embedded in the structure of the tree. We leverage the condition to design a general lock-free membership test suitable for any search tree. We then show how to integrate the validation condition in update operations of (non-rebalancing) binary search trees, internal and external, and AVL trees. We experimentally show that our new algorithms outperform existing ones.