bluuebunny/crossref_metadata_2025_split 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

Summary

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.
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

ABSTRACTBackground and objectiveAcute 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.MethodsFor 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.ConclusionSafety 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

ABSTRACTExacerbations 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.
Lesbian, Gay, Bisexual, Transgender, and Queer Media: Key Narratives, Future Directions
Authors: Rodriguez Julian A. 
Published: March 2019

AbstractLesbian, 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

AbstractLice 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

SummaryThe 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.
Fifteen-minute consultation: A guide to managing a child with a new finding of neutropenia
Authors: James Rebecca M , Phillips Bob 
Published: March 2019

ObjectiveTo describe a structured approach for managing a child with a new finding of neutropenia.MethodLiterature review and consensus practice of clinicians in our regional centre.ConclusionNeutropenia 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.ScenarioA 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.
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

IntroductionTransparency 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 analysisThis 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 disseminationNo 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

IntroductionChildren 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 analysisThirty 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 disseminationThe 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 numberNCT03523806.
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.
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.
Griffin
Authors: Liu Yang , Wang Jianguo , Swanson Steven 
Published: March 2019

Interactive information retrieval services, such as enterprise search and document search, must provide relevant results with consistent, low response times in the face of rapidly growing data sets and query loads. These growing demands have led researchers to consider a wide range of optimizations to reduce response latency, including query processing parallelization and acceleration with co-processors such as GPUs. However, previous work runs queries either on GPU or CPU, ignoring the fact that the best processor for a given query depends on the query's characteristics, which may change as the processing proceeds.
We present Griffin, an IR systems that dynamically combines GPU- and CPU-based algorithms to process individual queries according to their characteristics. Griffin uses state-of-the-art CPU-based query processing techniques and incorporates a novel approach to GPU-based query evaluation. Our GPU-based approach, as far as we know, achieves the best available GPU search performance by leveraging a new compression scheme and exploiting an advanced merge-based intersection algorithm. We evaluate Griffin with real world queries and datasets, and show that it improves query performance by 10x compared to a highly optimized CPU-only implementation, and 1.5x compared to our GPU-approach running alone. We also find that Griffin helps reduce the 95th-, 99th-, and 99.9th-percentile query response time by 10.4x, 16.1x, and 26.8x, respectively.
swSpTRSV
Authors: Wang Xinliang , Liu Weifeng , Xue Wei , Wu Li 
Published: March 2019

Sparse triangular solve (SpTRSV) is one of the most important kernels in many real-world applications. Currently, much research on parallel SpTRSV focuses on level-set construction for reducing the number of inter-level synchronizations. However, the out-of-control data reuse and high cost for global memory or shared cache access in inter-level synchronization have been largely neglected in existing work.
In this paper, we propose a novel data layout called Sparse Level Tile to make all data reuse under control, and design a Producer-Consumer pairing method to make any inter-level synchronization only happen in very fast register communication. We implement our data layout and algorithms on an SW26010 many-core processor, which is the main building-block of the current world fastest supercomputer Sunway Taihulight. The experimental results of testing all 2057 square matrices from the Florida Matrix Collection show that our method achieves an average speedup of 6.9 and the best speedup of 38.5 over parallel level-set method. Our method also outperforms the latest methods on a KNC many-core processor in 1856 matrices and the latest methods on a K80 GPU in 1672 matrices, respectively.
Graph partitioning applied to DAG scheduling to reduce NUMA effects
Authors: Sánchez Barrera Isaac , Casas Marc , Moretó Miquel , Ayguadé Eduard , Labarta Jesús , Valero Mateo 
Published: March 2019

The complexity of shared memory systems is becoming more relevant as the number of memory domains increases, with different access latencies and bandwidth rates depending on the proximity between the cores and the devices containing the data. In this context, techniques to manage and mitigate non-uniform memory access (NUMA) effects consist in migrating threads, memory pages or both and are typically applied by the system software.
We propose techniques at the runtime system level to reduce NUMA effects on parallel applications. We leverage runtime system metadata in terms of a task dependency graph. Our approach, based on graph partitioning methods, is able to provide parallel performance improvements of 1.12X on average with respect to the state-of-the-art.
Retrodifferentiation of Human Tumor Hepatocytes to Stem Cells Leads to Metabolic Reprogramming and Chemoresistance
Authors: Fekir Karim , Dubois-Pot-Schneider Hélène , Désert Romain , Daniel Yoann , Glaise Denise , Rauch Claudine , Morel Fabrice , Fromenty Bernard , Musso Orlando , Cabillic Florian , Corlu Anne 
Published: March 2019

Abstract

Human hepatocellular carcinoma (HCC) heterogeneity promotes recurrence and therapeutic resistance. We recently demonstrated that inflammation favors hepatocyte retrodifferentiation into progenitor cells. Here, we identify the molecular effectors that induce metabolic reprogramming, chemoresistance, and invasiveness of retrodifferentiated HCC stem cells. Spheroid cultures of human HepaRG progenitors (HepaRG-Spheres), HBG-BC2, HepG2, and HuH7 cells and isolation of side population (SP) from HepaRG cells (HepaRG-SP) were analyzed by transcriptomics, signaling pathway analysis, and evaluation of chemotherapies. Gene expression profiling of HepaRG-SP and HepaRG-Spheres revealed enriched signatures related to cancer stem cells, metastasis, and recurrence and showed that HepaRG progenitors could retrodifferentiate into an immature state. The transcriptome from these stem cells matched that of proliferative bad outcome HCCs in a cohort of 457 patients. These HCC stem cells expressed high levels of cytokines triggering retrodifferentiation and displayed high migration and invasion potential. They also showed changes in mitochondrial activity with reduced membrane potential, low ATP production, and high lactate production. These changes were, in part, related to angiopoietin-like 4 (ANGPTL4)–induced upregulation of pyruvate dehydrogenase kinase 4 (PDK4), an inhibitor of mitochondrial pyruvate dehydrogenase. Upregulation of ANGPTL4 and PDK4 paralleled that of stem cells markers in human HCC specimens. Moreover, the PDK4 inhibitor dichloroacetate reversed chemoresistance to sorafenib or cisplatin in HCC stem cells derived from four HCC cell lines. In conclusion, retrodifferentiated cancer cells develop enhanced invasion and therapeutic resistance through ANGPTL4 and PDK4. Therefore, restoration of mitochondrial activity in combination with chemotherapy represents an attractive therapeutic approach in HCC.

Significance:
Restoring mitochondrial function in human hepatocellular carcinomas overcomes cancer resistance.