bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hot and sick: impacts of warming and oomycete parasite infection on endemic dominant zooplankter of Lake Baikal
Authors: Ozersky Ted , Nakov Teofil , Hampton Stephanie E. , Rodenhouse Nicholas L. , Shchapov Kirill , Woo Kara H. , Wright Katie , Pislegina Helena V. , Izmest’eva Lyubov R. , Silow Eugene A. , Timofeev Maxim A. , Moore Marianne V. 
Published: July 2019

AbstractClimate warming impacts ecosystems through multiple interacting pathways, including via direct thermal responses of individual taxa and the combined responses of closely interacting species. In this study we examined how warming and infection by an oomycete parasite affect the dominant zooplankter of Russia’s Lake Baikal, the endemic cold-adapted stenotherm Epischura baikalensis (Copepoda). We used a combination of laboratory experiments, long-term monitoring data and population modeling. Experiments showed large thermal mismatch between host and parasite, with strong negative effects of warm temperatures on E. baikalensis survival and reproduction and a negative synergistic effect of Saprolegnia infection. However, Saprolegnia infection had an unexpected positive effect on E. baikalensis reproductive output, which may be consistent with fecundity compensation by infected females. Long-term monitoring data showed that Saprolegnia infections were most common during the warmest periods of the year and that infected individuals tended to accumulate in deep water. Population models, parameterized with experimental and literature data, correctly predicted the timing of Saprolegnia epizootics, but overestimated the negative effect of warming on E.baikalensis populations. Models suggest that diel vertical migration may allow E. baikalensis to escape the negative effects of increasing temperatures and parasitism and enable E. baikalensis to persist as Lake Baikal warms. Our results contribute to understanding of how multiple interacting stressors affect warming pelagic ecosystems of cold lakes and oceans and show that the population-level consequences of thermal mismatch between hosts and parasites can vary seasonally, interannual and spatially.
Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes
Authors: Tran Nicholas M. , Shekhar Karthik , Whitney Irene E. , Jacobi Anne , Benhar Inbal , Hong Guosong , Yan Wenjun , Adiconis Xian , Arnold McKinzie E. , Lee Jung Min , Levin Joshua Z. , Lin Dingchang , Wang Chen , Lieber Charles M. , Regev Aviv , He Zhigang , Sanes Joshua R. 
Published: July 2019

SummaryNeuronal types in the central nervous system differ dramatically in their resilience to injury or insults. Here we studied the selective resilience of mouse retinal ganglion cells (RGCs) following optic nerve crush (ONC), which severs their axons and leads to death of ~80% of RGCs within 2 weeks. To identify expression programs associated with differential resilience, we first used single-cell RNA-seq (scRNA-seq) to generate a comprehensive molecular atlas of 46 RGC types in adult retina. We then tracked their survival after ONC, characterized transcriptomic, physiological, and morphological changes that preceded degeneration, and identified genes selectively expressed by each type. Finally, using loss- and gain-of-function assays in vivo, we showed that manipulating some of these genes improved neuronal survival and axon regeneration following ONC. This study provides a systematic framework for parsing type-specific responses to injury, and demonstrates that differential gene expression can be used to reveal molecular targets for intervention.
Sequence alignment using machine learning for accurate template-based protein structure prediction
Authors: Makigaki Shuichiro , Ishida Takashi 
Published: July 2019

AbstractMotivationTemplate-based modeling, the process of predicting the tertiary structure of a protein by using homologous protein structures, is useful if good templates can be found. Although modern homology detection methods can find remote homologs with high sensitivity, the accuracy of template-based models generated from homology-detection-based alignments is often lower than that from ideal alignments.ResultIn this study, we propose a new method that generates pairwise sequence alignments for more accurate template-based modeling. The proposed method trains a machine learning model using the structural alignment of known homologs. It is difficult to directly predict sequence alignments using machine learning. Thus, when calculating sequence alignments, instead of a fixed substitution matrix, this method dynamically predicts a substitution score from the trained model. We evaluate our method by carefully splitting the training and test datasets and comparing the predicted structure’s accuracy with that of state-of-the-art methods. Our method generates more accurate tertiary structure models than those produced from alignments obtained by other methods.Availability and Implementationhttps://github.com/shuichiro-makigaki/exmachinaContactishida@c.titech.ac.jp or makigaki@cb.cs.titech.ac.jp
Yellow fever virus spread in Rio de Janeiro and Espírito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies
Authors: Giovanetti Marta , de Mendonça Marcos Cesar Lima , Fonseca Vagner , Mares-Guia Maria Angélica , Fabri Allison , Xavier Joilson , de Jesus Jaqueline Goes , Gräf Tiago , dos Santos Rodrigues Cintia Damasceno , dos Santos Carolina Cardoso , Sampaio Simone Alves , Chalhoub Flavia Lowen Levy , de Bruycker Nogueira Fernanda , Theze Julien , Romano Alessandro Pecego Martins , Ramos Daniel Garkauskas , de Abreu Andre Luiz , Oliveira Wanderson Kleber , do Carmo Said Rodrigo Fabiano , de Alburque Carlos F. Campelo , de Oliveira Tulio , Fernandes Carlos Augusto , Aguiar Shirlei Ferreira , Chieppe Alexandre , Sequeira Patrícia Carvalho , Faria Nuno Rodrigues , Cunha Rivaldo Venâncio , Alcantara Luiz Carlos Junior , de Filippis Ana Maria Bispo 
Published: July 2019

ABSTRACTThe recent re-emergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the virus’ rapid dissemination in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil we generated 18 complete and near-complete genomes from the peak of the epidemic curve from non-human primates (NHPs) and human infected cases across Espírito Santo and Rio de Janeiro states. Genomic sequencing of 18 YFV genomes revealed the timing, source and likely routes of yellow fever virus transmission and dispersion during the one of the largest outbreaks ever registered in Brazil. We showed that the recent YFV epidemic spillover southwards several times from Minas Gerais to Espírito Santo and Rio de Janeiro states in 2016 to 2019. The quick production and analysis of data from portable sequencing could identify the corridor of spread of YFV. These findings reinforce that real-time and continued genomic surveillance strategies can assist in the monitoring and public health responses of arbovirus epidemics.IMPORTANCEArbovirus infections in Brazil including Yellow Fever, Dengue, Zika and Chikungunya result in considerable morbidity and mortality and are pressing public health concerns. However, our understanding of these outbreaks is hampered by limited availability of real time genomic data. In this study, we investigated the genetic diversity and spatial distribution of YFV during the current outbreak in southeastern Brazil. To gain insights into the routes of YFV introduction and dispersion, we tracked the virus by sequencing YFV genomes sampled from non-human primates and infected patients from the southeastern region. Our study provides an understanding of how YFV initiates transmission in new Brazilian regions and illustrates that near-real time genomics in the field can augment traditional approaches to infectious disease surveillance and control.
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genusEscherichiarevealed by a genome-wide association study
Authors: Galardini Marco , Clermont Olivier , Baron Alexandra , Busby Bede , Dion Sara , Schubert Sören , Beltrao Pedro , Denamur Erick 
Published: July 2019

AbstractThe genusEscherichiais composed of several species and cryptic clades, includingE. coli, which behave as a vertebrate gut commensal, but also as an opportunistic pathogen involved in both diarrheic and extra-intestinal diseases. To characterize the genetic determinants of extra-intestinal virulence within the genus, we carried out an unbiased genome-wide association study (GWAS) on 370 commensal, pathogenic and environmental strains representative of theEscherichiagenus phylogenetic diversity and includingE. albertii(n=7),E. fergusonii(n=5),Escherichiaclades (n=32) andE. coli(n=326), tested in a mouse model of sepsis. We found that the high-pathogenicity island (HPI), a ∼35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors also related to iron uptake, such as the aerobactin and thesitABCDoperons. We validated the associationin vivoby deleting key components of the HPI inE. colistrains in two phylogenetic backgrounds, and found that virulence is correlated inE. coliwith growth in the presence of various stressors including several antimicrobials, which hints at collateral sensitivities associated with intrinsic virulence. This study points to the major role of iron capture systems in the extra-intestinal virulence of the genusEscherichiaand the collateral effects on cell growth of such systems.
Development and Characterization of a New Endoscopic Drug Eluting Platform with Proven Efficacy in Acute and Chronic Experimental Colitis
Authors: Bon I , Cano-Sarabia M , de la Ossa N , Bartolí R , Lorenzo-Zúñiga V 
Published: July 2019

ABSTRACTBackground&AimsMucosal lesions refractory to biological treatments represent unmet needs in patients with inflammatory bowel disease (IBD) that require new treatment modalities. We developed and characterized a new endoscopic drug-eluting hydrogel (CoverGel) with proven efficacy in acute and chronic experimental colitis (EC) in ratsMethodsCoverGel was developed based on appropriate rheological, drug release, gelation, structural and degradation properties capacities to allow endoscopic application. Experimental colitis (EC) was induced by TNBS application in rats. In acute EC 40 rats were randomized in 5 groups (8 each): sham, control, CoverGel, CoverGel+Infliximab (IFX) and CoverGel+Vedolizumab (VDZ). In chronic EC 12 rats were randomized in 2 groups (6 each): IFX s.c and CoverGel+IFX. Endoscopic, histological and blood test were performed during follow-up to evaluate clinical success. Antibodies to IFX (ATIs) were evaluated in chronic EC animal studyResultsCoverGel is a biocompatible and bioadhesive reverse thermo sensitive gelation hydrogel with macroporous structure and drug release capacity. In acute EC animals treated with CoverGel+IFX or CoverGel+VDZ showed significantly clinical success (weight recovery, mucosal restoration and bacterial translocation) as compare with controls and animals without bioactive drug. In chronic EC animal study, clinical efficacy was comparable in both groups. Levels of ATIs were significantly lower in animals treated with CoverGel+IFX vs. IFX s.c (0.90 ± 0.06 μg/mL-c vs. 1.97 ± 0.66 μg/mL-c, p=0.0025).ConclusionsCoverGel is an endoscopic vehicle to locally deliver biological drugs with proven efficacy in acute and chronic EC in rats and inducing less immunogenicity reaction.
What does mitogenomics tell us about the evolutionary history of theDrosophila buzzatiicluster (repletagroup)
Authors: Moreyra Nicolás N. , Mensch Julián , Hurtado Juan , Almeida Francisca , Laprida Cecilia , Hasson Esteban 
Published: July 2019

AbstractTheDrosophila repletagroup is an array of more than 100 cactophilic species endemic to the “New World”. The acquisition of the ability to utilize decaying cactus tissues as breeding and feeding sites is a key aspect that allowed the successful diversification of therepletagroup in the American deserts. Within this group, theDrosophila buzzatiicluster is a South American clade of seven cactophilic closely related species in different stages of divergence, a feature that makes it a valuable model system for evolutionary research. However, even though substantial effort has been devoted to elucidating the phylogenetic relationships among members of theD. buzzatiicluster, the issue is still controversial. In effect, molecular phylogenetic studies performed to date generated ambiguous results since tree topologies depend on the kind of molecular marker employed. Curiously, even though mitochondrial DNA has become a popular marker in evolutionary biology and population genetics, none of the more than twentyDrosophilamitogenomes assembled so far belongs to this cluster. In this work we report the assembly of six complete mitogenomes of five species:D. antonietae,D. borborema, D. buzzatii,D. seriemaand two strains ofD. koepferae, with the aim to revisit the phylogenetic relationships and divergence times by means of a mitogenomic approach. The recovered topology using complete mitogenomes gives support to the hypothesis of the monophyly of that theD. buzzatiicluster and shows two main clades, one includingD. buzzatiiandD. koepferae(both strains) and the other the remaining species. These results are in agreement with previous reports based on a few mitochondrial and/or nuclear genes but in conflict with the results of a recent large-scale nuclear phylogeny, suggesting that nuclear and mitochondrial genomes depict different evolutionary histories.
Corporate social responsibility employment narratives: a linguistic analysis
Authors: Li Zhongtian , Haque Shamima 
Published: July 2019

PurposeThe purpose of this paper is twofold: first, it investigates whether and to what extent “linguistic hedging”, an impression management form of linguistic expression that conveys an ambiguous level of commitment, is used in corporate social responsibility (CSR) employment narratives; and second, it explores whether there is any difference in the use of linguistic hedging between written and spoken corporate forms of language. It mobilises these objectives by examining employee-related narratives made by electronic manufacturing services (EMS) providers domiciled in Taiwan, in the context of labour malpractice incidents.Design/methodology/approachTwo groups of data are examined: corporate responsibility reports (written language) and interviews and speeches of corporate founders and senior executives (spoken language). The research sample is ten Taiwanese EMS firms, all of which attracted public criticism and scrutiny due to a series of employee-related incidents. The sample period is between 2009 and 2013. Linguistic hedging is measured quantitatively by the relative word frequency of hedges, using the concordance software ANTCONC, with findings interpreted through the lens of legitimacy theory and impression management.FindingsThe study found that hedging was evident in CSR narratives. The EMS providers in Taiwan appeared to use hedging in employee-related disclosures to manage legitimacy challenges due to employee-related incidents that had happened in their assembly plants. The adjustments in employee-related disclosures made by the EMS firms as a legitimation strategy can be seen as a rhetoric device of impression management or a form of symbolic legitimation to persuade society to restore their legitimacy status. Further, overall hedging was more frequently used in spoken than written language, which suggests that rhetorical hedging in written narratives is more likely to be a deliberate choice of tactics to influence stakeholder perceptions and thereby manage corporate legitimacy.Originality/valueThe study introduces a new analytical technique, linguistic hedging, into the CSR literature. This enriches research methods used in this field, providing more compelling insights into the relationship between the use of language and CSR narratives in the process of corporate legitimation of employee-related practices. This study thus provides a platform for future computational-linguistics studies in the field of CSR.
An investigation of the knowledge of intimate partner violence among clinical staff working with male substance misusers
Authors: Falcone M. Aurora , Meynen Tim 
Published: July 2019

Purpose
The purpose of this paper is to describe a Service Improvement Project aimed at assessing the level of knowledge of intimate partner violence (IPV) of clinical staff working in Community Drug and Alcohol Services (CDAS) in four boroughs of South London.

Design/methodology/approach
Clinical staff (n=90) completed a survey which was based on the Capability Framework (Hughes et al., 2015), developed to describe the key capabilities required to work with men who misuse drug and alcohol and perpetrate IPV. Two separate surveys were prepared for clinical (core) staff (n=76) and for manager (senior) staff (n=14).

Findings
The Capability Framework provided a useful structure for identifying key strengths and gaps in knowledge and skills related to substance use and IPV treatment in frontline CDAS staff. Significant strengths which emerged in the “core staff” survey related to the importance of assessing IPV and being empathic. Gaps related to the confidence in working with these issues and receiving support. Significant strengths which emerged in the “senior staff” survey related to the availability of supervision, information and training on IPV. Gaps related to using the Capability Framework and discussing IPV in supervision.

Originality/value
Findings have important implications for the development of training addressing gaps in current knowledge and skills required when working with IPV in the context of drug and alcohol misuse.
Drug and alcohol workers’ view of positive psychology in the treatment of coexisting problems
Authors: Ujhelyi Gomez Katalin , Carson Jerome , Brown Gill , Holland Mark 
Published: July 2019

PurposePositive psychology (PP) interventions have been suggested to be beneficial in the treatment of dual diagnosis (DD). The purpose of this paper is to investigate the perspective of psychosocial intervention (PSI) workers to explore the potential of a positive strengths-based approach in DD recovery.Design/methodology/approachA qualitative approach was employed with PSI workers who attended and observed a positive intervention delivered to DD clients. A focus group explored what these practitioners are already doing that resembles PP and their opinion regarding the utility of such interventions in recovery.FindingsFindings revealed that practitioners were already engaging in positive practice, however, randomly and infrequently with limited impact. Although this new approach was found valuable, potential challenges were identified and a possible discrepancy between staff views of clients and clients’ views of themselves in terms of their potential was detected.Research limitations/implicationsThe study involved a small and homogeneous sample. Further research is necessary to investigate staff views and ways of integrating PP with traditional treatment.Practical implicationsRather than merely attending to the psychological problems and dealing with symptoms, it is also necessary to directly target well-being to enable people to flourish with consideration of their readiness to change.Originality/valueAddressing a gap in the literature, the present study explored positive themes in current practice and forms part of the evaluation of a newly developed strengths-based approach for individuals with coexisting problems.
Chasing the golden fleece
Authors: MacVane Phipps Fiona 
Published: July 2019

Purpose
The purpose of this paper is to develop a common theme between the six research articles submitted for IJHG 24.3.

Design/methodology/approach
All articles are read and themes extracted which are used to write a review summarising the key points in each while developing an overarching theme for the issue of IJHG. Other literature supporting the development of this theme is also reviewed and used to contribute insights.

Findings
The findings consist of the common themes developed. In this issue, the common theme was improving care while saving costs in healthcare and the theme was explored in each article in relation to a lean healthcare management/governance philosophy.

Practical implications
The review section of IJHG allows readers to gain a quick overview of the content and then select the articles they wish to read in full.

Originality/value
IJHG is the only journal in the Emerald portfolio with a review section of this kind. Thus it provides added value.
Mechanisms enabling knowledge production in learning study
Authors: Kullberg Angelika , Vikström Anna , Runesson Ulla 
Published: July 2019

PurposeThe purpose of this paper is to add to the discussion about practitioner research in schools – by addressing mechanisms and systematic strategies based on theory in a research model, which enables the creation of knowledge products that enhance student learning and are sharable between teachers.Design/methodology/approachThe research question is the following: Can a specific form of teachers’ research produce practice-based knowledge relevant beyond the borders of the local school context? This question is addressed through empirical examples from previously published papers on learning studies in natural sciences, mathematics and language.FindingsThis paper promotes the view that teachers in learning studies can create practical public knowledge relevant beyond their local context. The authors suggest that learning studies and variation theory can offer teachers mechanisms to create such public knowledge.Originality/valueThe paper proposes that teachers’ collaboration in professional learning communities, as in a learning study, not only has the capacity to increase students’ and teachers’ learning, but it can also be used to create practical public knowledge.
Leadership and the rule of law in conflict and post-conflict societies
Authors: Jean Stéphane 
Published: July 2019

Purpose
The purpose of this paper is to explore the leadership dimensions in developing the rule of law. The paper considers the perspective from the United Nations, with the leadership tension is primarily seen from the prism of the rule of law.

Design/methodology/approach
This paper explores the leadership challenges in specific recent case studies.

Findings
The paper concludes that the most difficult challenge is a culture shift toward respect for the rule of law is required. The paper notes the importance of political leadership in developing consensus.

Originality/value
The challenge is that the implementation of rule of law reform is primarily a political endeavor that affects the balance of powers within the State. This need for leaders to develop the space for institutions advancing the rule of law is most certainly the case in, and exacerbated by, conflict and post-conflict situations.