bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly
Authors: Roscito Juliana G , Sameith Katrin , Pippel Martin , Francoijs Kees-Jan , Winkler Sylke , Dahl Andreas , Papoutsoglou Georg , Myers Gene , Hiller Michael 
Published: November 2018

Abstract

Background
Reptiles are a species-rich group with great phenotypic and life history diversity but are highly underrepresented among the vertebrate species with sequenced genomes.

Results
Here, we report a high-quality genome assembly of the tegu lizard, Salvator merianae, the first lacertoid with a sequenced genome. We combined 74X Illumina short-read, 29.8X Pacific Biosciences long-read, and optical mapping data to generate a high-quality assembly with a scaffold N50 value of 55.4 Mb. The contig N50 value of this assembly is 521 Kb, making it the most contiguous reptile assembly so far. We show that the tegu assembly has the highest completeness of coding genes and conserved non-exonic elements (CNEs) compared to other reptiles. Furthermore, the tegu assembly has the highest number of evolutionarily conserved CNE pairs, corroborating a high assembly contiguity in intergenic regions. As in other reptiles, long interspersed nuclear elements comprise the most abundant transposon class. We used transcriptomic data, homology- and de novo gene predictions to annotate 22,413 coding genes, of which 16,995 (76%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. CNEs cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being squamate specific. In contrast to placental mammal-specific CNEs, very few of these squamate-specific CNEs (&lt;20 Kb) overlap transposons, highlighting a difference in how lineage-specific CNEs originated in these two clades.

Conclusions
The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provide a valuable resource for comparative genomic studies of reptiles and other amniotes.
What is a scientific instrument, now?
Authors: Taub Liba 
Published: November 2018

Abstract
In 1990, Deborah Jean Warner, a curator at the Smithsonian Institution, published her now-classic article ‘What is a scientific instrument, when did it become one, and why?’. These questions were prompted by practical curatorial considerations: what was she supposed to collect for her museum? Today, we are still considering questions of what we collect for the future, why, and how. These questions have elicited some new and perhaps surprising answers since the publication of Warner’s article, sometimes – but not only – as a reflection of changing technologies and laboratory practices, and also as a result of changes in those disciplines that study science, including history of science and philosophy of science. In focusing attention on meanings associated with scientific instrument collections, and thinking about what objects are identified as scientific instruments, I consider how definitions of instruments influence what is collected and preserved.
Burden of Children Hospitalized With Pertussis in Canada in the Acellular Pertussis Vaccine Era, 1999–2015
Authors: Abu-Raya Bahaa , Bettinger Julie A , Vanderkooi Otto G , Vaudry Wendy , Halperin Scott A , Sadarangani Manish ,   Members of the Canadian Immunization Monitoring Program, Active (IMPACT), Bridger N , Morris R , Top K , Halperin S , Déry P , Thibeault R , Moore D , . Lefebvre M A , Lebel M , Le Saux N , Tran D , Ford-Jones L , Morris S , Embree J , Law B , Tan B , McConnell A , Jadavji T , Chawla R , Vanderkooi O , Kellner J , Vaudry W , Scheifele D , Bettinger J , Sadarangani M , Sauvé L 
Published: November 2018

AbstractBackgroundRecent increases in pertussis morbidity and mortality rates among young infants have led to a recommendation in some countries for vaccination against pertussis during pregnancy. Having data on the burden of pediatric pertussis in a large population over time is important for establishing the true burden of disease in the acellular pertussis (aP) vaccine era. Here, we describe age-specific epidemiology and morbidity and mortality rates in children hospitalized with pertussis over 17 years across Canada in the aP vaccine era.MethodsPatients aged ≤16 years who were admitted to 1 of 12 pediatric tertiary-care hospitals across Canada between 1999 and 2015 with confirmed (laboratory-confirmed or epidemiologically linked) or probable (clinically diagnosed) pertussis were included.ResultsOverall, 1402 patients with pertussis were included. Infants aged &lt;2 months had the highest mean annual incidences of pertussis hospitalization and intensive care unit (ICU) admission (116.40 [95% confidence interval (CI), 85.32–147.49] and 33.48 [95% CI, 26.35–40.62] per 100 000 population, respectively). The overall proportion of children who required ICU admission was 25.46%, and the proportion was highest in infants aged &lt;2 months (37.90%). Over the span of this study, 21 deaths occurred. Age of &lt;16 weeks, prematurity, encephalopathy, and a confirmed pertussis diagnosis were independent risk factors for ICU admission. Age of &lt;4 weeks, prematurity, and female sex were independent risk factors for death.ConclusionsIn the aP vaccine era, endemic pertussis still contributes considerably to childhood morbidity and death, particularly in infants aged &lt;2 months. Vaccination against pertussis during pregnancy has the potential to reduce this disease burden.
Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old
Authors: Belongia Edward A , King Jennifer P , Kieke Burney A , Pluta Joanna , Al-Hilli Ali , Meece Jennifer K , Shinde Vivek 
Published: November 2018

Abstract

Background
The epidemiology and burden of respiratory syncytial virus (RSV) illness are not well defined in older adults.

Methods
Adults ≥60 years old seeking outpatient care for acute respiratory illness were recruited from 2004–2005 through 2015–2016 during the winter seasons. RSV was identified from respiratory swabs by multiplex polymerase chain reaction. Clinical characteristics and outcomes were ascertained by interview and medical record abstraction. The incidence of medically attended RSV was estimated for each seasonal cohort.

Results
RSV was identified in 243 (11%) of 2257 enrollments (241 of 1832 individuals), including 121 RSV type A and 122 RSV type B. The RSV clinical outcome was serious in 47 (19%), moderate in 155 (64%), and mild in 41 (17%). Serious outcomes included hospital admission (n = 29), emergency department visit (n = 13), and pneumonia (n = 23) and were associated with lower respiratory tract symptoms during the enrollment visit. Moderate outcomes included receipt of a new antibiotic prescription (n = 144; 59%), bronchodilator/nebulizer (n = 45; 19%), or systemic corticosteroids (n = 28; 12%). The relative risk of a serious outcome was significantly increased in persons aged ≥75 years (vs 60–64 years) and in those with chronic obstructive pulmonary disease or congestive heart failure. The average seasonal incidence was 139 cases/10 000, and it was significantly higher in persons with cardiopulmonary disease compared with others (rate ratio, 1.89; 95% confidence interval, 1.44–2.48).

Conclusions
RSV causes substantial outpatient illness with lower respiratory tract involvement. Serious outcomes are common in older patients and those with cardiopulmonary disease.
The Synthetic Genome Summer Course
Authors: Blount Benjamin A , Ellis Tom 
Published: November 2018

Abstract
The Synthetic Genome Summer Course was convened with the aim of teaching a wide range of researchers the theory and practical skills behind recent advances in synthetic biology and synthetic genome science, with a focus on Sc2.0, the synthetic yeast genome project. Through software workshops, tutorials and research talks from leading members of the field, the 30 attendees learnt about relevant principles and techniques that they were then able to implement first-hand in laboratory-based practical sessions. Participants SCRaMbLEd semi-synthetic yeast strains to diversify heterologous pathways, used automation to build combinatorial pathway libraries and used CRISPR to debug fitness defects caused by synthetic chromosome design changes. Societal implications of synthetic chromosomes were explored and industrial stakeholders discussed synthetic biology from a commercial standpoint. Over the 5 days, participants gained valuable insight and acquired skills to aid them in future synthetic genome research.
When Rebels Attack: Quantifying the Impacts of Capturing Territory from the Government in Yemen
Authors: Tandon Sharad 
Published: November 2018

Abstract
Households were adversely affected by the mostly nonviolent capture of Yemen’s capital in 2014. Although socioeconomically advantaged households were initially better able to cope with the shock than other households, the capture resulted in a decline in expenditure for the entire population within three months. Struggling households turned to several coping strategies—they increasingly made purchases on credit, increased their reliance on self-employment to deal with a decline in the economic climate, and reduced both the quantity and quality of foods consumed. Furthermore, there was evidence of a loss of autonomy for women, where women were less likely to oversee food purchases and more likely to be in the household during the survey interview. These results demonstrate that the capture of territory without widespread violence can result in a decline in standards of living and further illustrate the manners in which households were able to cope with the shock.
Climate or disturbance: temperate forest structural change and carbon sink potential
Authors: Andrewsa Travis , Dietzeb Michael , Boothc Robert 
Published: November 2018

ABSTRACTAnticipating forest responses to changing climate and disturbance regimes requires understanding long-term successional processes and aggregating these local processes into global relevance. Estimates of existing forest structure and biomass are improving globally; however, vegetation models continue to show substantial spread in predictions of future land carbon uptake and the roles of forest structural change and demography are increasingly being recognized as important. To identify mechanisms that drive change in tree size, density, and carbon, we need a better understanding of forest structural trajectories and the factors that affect those trajectories. Here we reveal a coherent, cyclic pattern of structural change in temperate forests, as predicted by successional theory, and identify significant sensitivity to climatic precipitation and temperature anomalies using large datasets and empirical modeling. For example, in the eastern US above average temperature (+1°C) was associated with a 27% (−0.4±0.1 Mg C ha-1yr-1) reduction in productivity attributed to higher rates of disease (+23%), weather disturbance (+57%), and sapling mortality. Projections of future vegetative carbon sink potential suggests biomass would be lowest on managed lands (72±2 Mg C ha-1) and highest when larger trees survive in undisturbed conditions (153±21 Mg C ha-1). Overall, the indirect effects of disturbance and mortality were considerably larger than the direct effects of climate on productivity when predicting future vegetative carbon sinks. Results provide robust comparisons for global vegetation models, and valuable projections for management and carbon mitigation efforts.
Differential requirement for centriolar satellites in cilium formation among different vertebrate cells
Authors: Odabasi Ezgi , Ohlsen Signe K. , Gul Seref , Kavakli Ibrahim H. , Andersen Jens S. , Firat-Karalar Elif N. 
Published: November 2018

AbstractCentriolar satellites are ubiquitous in vertebrate cells. They have recently emerged as key regulators of centrosome/cilium biogenesis, and their mutations are linked to ciliopathies. However, their precise functions and mechanisms of action, which potentially differ between cell types, remain poorly understood. Here, we generated retinal pigmental and kidney epithelial cells lacking satellites by genetically ablating PCM1 to investigate their functions. While satellites were essential for cilium assembly in retinal epithelial cells, kidney epithelial cells lacking satellites still formed full-length cilia but at significantly lower levels, with reduced centrosomal levels of key ciliogenesis factors. Using these cells, we identified the first satellite-specific functions at cilia, specifically in regulating ciliary content, Hedgehog signalling, and epithelial cell organization. However, other satellite-linked functions, namely proliferation, cell cycle progression and centriole duplication, were unaffected in these cells. Quantitative transcriptomic and proteomic profiling revealed that loss of satellites scarcely affects transcription, but significantly alters the proteome, particularly actin cytoskeleton pathways and neuronal functions. Together, our findings identify cell type-specific roles for satellites and provide insight into the phenotypic heterogeneity of ciliopathies.
Decoration of the enterococcal polysaccharide antigen EPA is essential for virulence, cell surface charge and resistance to innate immunity
Authors: Smith Robert E. , Salamaga Bartłomiej , Szkuta Piotr , Hajdamowicz Natalia , Prajsnar Tomasz K. , Bulmer Gregory , Fontaine Thierry , Kołodziejczyk Justyna , Herry Jean-Marie , Hounslow Andrea , Williamson Mike P. , Serror Pascale , Mesnage Stéphane 
Published: November 2018

AbstractEnterococcus faecalisis an opportunistic pathogen with an intrinsically high resistance to lysozyme, a key effector of the innate immune system. This high level of resistance requires several genes (oatA, pgdA, dltAandsigV) acting synergistically to inhibit both the enzymatic and cationic antimicrobial peptide activities of lysozyme. We sought to identify novel genes modulatingE. faecalisresistance to lysozyme. Random transposon mutagenesis carried out in the quadrupleoatA/pgdA/dltA/sigVmutant led to the identification of several independent insertions clustered on the chromosome. These mutations were located in a locus referred to as the enterococcal polysaccharide antigen (EPA) variable region located downstream of the highly conservedepaA-epaRgenes proposed to encode a core synthetic machinery. Theepavariable region was previously proposed to be responsible for EPA decorations, but the role of this locus remains largely unknown. Here, we show that EPA decoration contributes to resistance towards charged antimicrobials and underpins virulence in the zebrafish model of infection by conferring resistance to phagocytosis. Collectively, our results indicate that the production of the EPA rhamnopolysaccharide backbone is not sufficient to promoteE. faecalisinfections and reveal an essential role of the modification of this surface polymer for enterococcal pathogenesis.
Effects of post-training novelty exposure on contextual fear memory: An attempt to translate behavioral tagging to humans
Authors: McClay Mason , Dunsmoor Joseph E. 
Published: November 2018

AbstractIn rodents, poorly formed hippocampal memories can be improved by novelty exploration within a critical time window, in line with the “behavioral tagging” hypothesis. Here, we sought to establish an analogue protocol to investigate if novelty exploration similarly operates to rescue weak hippocampal-dependent memories in humans. Adult humans underwent suboptimal contextual fear conditioning, followed 10 minutes later by open field novelty exploration in immersive 3D virtual reality. Novelty exploration did not improve long-term contextual fear memory, contrary to a behavioral tagging hypothesis. Despite this null result, we suggest further attempts to translate behavioral tagging from rodents to humans is warranted.
Glycolytic inhibitor 2-deoxyglucose prevents cortical hyperexcitability after traumatic brain injury
Authors: Koenig Jenny B. , Cantu David , Low Cho , Noubary Farzad , Croker Danielle , Whalen Michael , Kong Dong , Dulla Chris G. 
Published: November 2018

AbstractTraumatic brain injury (TBI) causes cortical dysfunction and can lead to post-traumatic epilepsy. Multiple studies demonstrate that GABAergic inhibitory network function is compromised following TBI, which may contribute to hyperexcitability and motor, behavioral, and cognitive deficits. Preserving the function of GABAergic interneurons, therefore, is a rational therapeutic strategy to preserve cortical function after TBI and prevent long-term clinical complications. Here, we explored an approach based on the ketogenic diet, a neuroprotective and anticonvulsant dietary therapy which results in reduced glycolysis and increased ketosis. Utilizing a pharmacologic inhibitor of glycolysis (2-deoxyglucose, or 2-DG), we found that acute in vitro glycolytic inhibition decreased the excitability of excitatory neurons, but not inhibitory interneurons, in cortical slices from naïve mice. Employing the controlled cortical impact (CCI) model of TBI in mice, we found that in vitro 2-DG treatment rapidly attenuated epileptiform activity seen in acute cortical slices 3-5 weeks after TBI. One week of in vivo 2-DG treatment immediately after TBI prevented the development of epileptiform activity, restored excitatory and inhibitory synaptic activity, and attenuated loss of parvalbumin-positive inhibitory interneurons. In summary, inhibition of glycolysis with 2-DG may have therapeutic potential to restore network function following TBI.One Sentence SummaryFollowing traumatic brain injury in mice, in vivo treatment with the glycolytic inhibitor 2-deoxyglucose prevented cortical network pathology including cortical hyperexcitability, changes in synaptic activity, and loss of parvalbumin-expressing GABAergic interneurons.
Biochat: a database for natural language processing of Gene Expression Omnibus data
Authors: Khomtchouk Bohdan B. , Dyomkin Vsevolod , Vand Kasra A. , Assimes Themistocles , Gozani Or 
Published: November 2018

AbstractA biological dataset’s metadata profile (e.g., study description, organism name, sequencing type, etc.) typically contains terse but descriptive textual information that can be used to link it with other similar biological datasets for the purpose of integrating omics data of different types to inform hypotheses and biological questions. Here we present Biochat, a database containing a multi-omics data integration support system to aid in cross-linking Gene Expression Omnibus (GEO) records to each other by metadata similarity through a user-friendly web application. Biochat is publicly available at: http://www.biochat.ai. Biochat source code is hosted at: https://github.com/Bohdan-Khomtchouk/Bio-chat.Database URLhttps://github.com/Bohdan-Khomtchouk/Bio-chat
Fool’s gold? A critical assessment of sources of data on heritage crime
Authors: Grove Louise , Thomas Suzie , Daubney Adam 
Published: November 2018

Purpose
The purpose of this paper is to explore critically various sources of data available on heritage crime, and consider how these may be utilised and improved.

Design/methodology/approach
This study is primarily a scoping review of the current heritage crime data climate, embedding examples from a range of existing and potential information sources. It highlights opportunities to improve data resources.

Findings
A lack of consistency in reporting and recording practices means there is little meaningful evidence about heritage crime trends and patterns. This needs to change in order to develop and evaluate appropriate strategies to reduce the problem of heritage crime nationally and internationally.

Research limitations/implications
It is hoped that urging improvement of data resources in the heritage crime sector will inspire a greater number of researchers to analyse and address key problems within heritage crime.

Practical implications
This paper encourages the development of new and improved data collection methods to foster effective assessment of existing heritage crime reduction schemes and better support victims of heritage crime.

Social implications
Increasing availability and accessibility of high-quality data on heritage crime would allow for developing better protections and resource allocation for vulnerable heritage.

Originality/value
This paper has drawn together, for the first time, evidence of the existing state of affairs of data availability within heritage crime. It is a position paper which encourages the development of improved recording and reporting practices both formally and informally across heritage and criminal justice sectors in order to support further research and understanding of the heritage crime problem.
Exploring the integration between Lean and the Theory of Constraints in Operations Management
Authors: Pacheco Diego Augusto de Jesus , Pergher Isaac , Antunes Junior José Antônio Valle , Roehe Vaccaro Guilherme Luís 
Published: November 2018

PurposeThe purpose of this study is to compare different models integrating the TOC and Lean approaches.Design/methodology/approachThe models of reference were identified through a comprehensive literature review. A qualitative and comparative analysis was carried out by pointing out the strengths, weaknesses and gaps of models integrating the TOC and Lean based on the production system requirements.FindingsThe findings indicate that these models can be improved by introducing aspects related to the system structure such as main key performance indicators, type of shop layout and performance metrics to evaluate the improvements implemented in the production system. The results provided evidence that the TOC and Lean are complementary approaches, and the individual gaps of each approach seem to be, in the most part, offset by the virtues of the other.Practical implicationsThis study enables decision makers and industrial managers to evaluate the practices adopted in the production environment, as well as the use of the different set of continuous improvement practices. This article also minimizes the literature gap regarding whether and how integrated Lean and TOC approach can be used in the firms.Originality/valueThis study contributes to the body of literature on Lean by comparing three different models integrating Lean and the TOC. Furthermore, a research agenda is suggested for future research aimed at developing new models integrating both approaches, aiming to increase the competitiveness of the production systems.