bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-energy Spectra of Gamma-Ray Bursts from Cooling Electrons
Authors: Geng Jin-Jun , Huang Yong-Feng , Wu Xue-Feng , Zhang Bing , Zong Hong-Shi 
Published: January 2018

Abstract
The low-energy spectra of gamma-ray bursts’ (GRBs) prompt emission are closely related to the energy distribution of electrons, which is further regulated by their cooling processes. We develop a numerical code to calculate the evolution of the electron distribution with given initial parameters, in which three cooling processes (i.e., adiabatic, synchrotron, and inverse Compton cooling) and the effect of a decaying magnetic field are coherently considered. A sequence of results is presented by exploring the plausible parameter space for both the fireball and the Poynting flux–dominated regime. Different cooling patterns for the electrons can be identified, and they are featured by a specific dominant cooling mechanism. Our results show that the hardening of the low-energy spectra can be attributed to the dominance of synchrotron self-Compton cooling within the internal shock model or to decaying synchrotron cooling within the Poynting flux–dominated jet scenario. These two mechanisms can be distinguished by observing the hard low-energy spectra of isolated short pulses in some GRBs. The dominance of adiabatic cooling can also lead to hard low-energy spectra when the ejecta is moving at an extreme relativistic speed. The information from the time-resolved low-energy spectra can help to probe the physical characteristics of the GRB ejecta via our numerical results.
Reflection Spectra of the Black Hole Binary Candidate MAXI J1535-571 in the Hard State Observed by NuSTAR
Authors: Xu Yanjun , Harrison Fiona A. , García Javier A. , Fabian Andrew C. , Fürst Felix , Gandhi Poshak , Grefenstette Brian W. , Madsen Kristin K. , Miller Jon M. , Parker Michael L. , Tomsick John A. , Walton Dominic J. 
Published: January 2018

Abstract
We report on a Nuclear Spectroscopic Telescope Array (NuSTAR) observation of the recently discovered bright black hole candidate MAXI J1535-571. NuSTAR observed the source on MJD 58003 (five days after the outburst was reported). The spectrum is characteristic of a black hole binary in the hard state. We observe clear disk reflection features, including a broad Fe Kα line and a Compton hump peaking around 30 keV. Detailed spectral modeling reveals a narrow Fe Kα line complex centered around 6.5 keV on top of the strong relativistically broadened Fe Kα line. The narrow component is consistent with distant reflection from moderately ionized material. The spectral continuum is well described by a combination of cool thermal disk photons and a Comptonized plasma with the electron temperature

keV. An adequate fit can be achieved for the disk reflection features with a self-consistent relativistic reflection model that assumes a lamp-post geometry for the coronal illuminating source. The spectral fitting measures a black hole spin

, inner disk radius

, and a lamp-post height

(statistical errors, 90% confidence), indicating no significant disk truncation and a compact corona. Although the distance and mass of this source are not currently known, this suggests the source was likely in the brighter phases of the hard state during this NuSTAR observation.
Intégration, réseaux sociaux et représentations langagières de migrants en France
Authors: Biichlé Luc 
Published: January 2018

Fondé sur un corpus d’environ 300 entretiens dont 150 enregistrés, cet article propose l’étude du réseau social et des représentations de migrants originaires de onze pays différents ainsi que de leurs proches. En effet, la structure du réseau social, par la nature de ses liens, par les contacts qu’elle génère, détermine fortement les représentations et les pratiques, notamment langagières. Pour les migrants, la restructuration du réseau constitue donc une phase importante de l’insertion dans le nouveau pays. L’étude de ces réseaux ainsi que celle des représentations/pratiques des personnes montrent que l’on peut établir des corrélations entre la présence de liens faibles (réseaux ouverts) et les pratiques plurilingues (langue étrangère + français). À l’inverse, un réseau plus dense, moins ouvert, correspondra plutôt à des pratiques monolingues en langue(s) étrangère(s). Les processus intégrationnels, dont l’apprentissage de la langue, semblent donc largement subordonnés à la restructuration du réseau des migrants quelle que soit leur provenance.
L’évolution du niveau de vie des pauvres. La petite paysannerie de la région de Gérone (1750-1800)
Authors: Congost Rosa , Esteve Eulàlia , Serramontmany Albert , Detry Florence 
Published: January 2018

Certains débats historiographiques actuels, tels ceux qui concernent les inégalités sociales ou encore plus spécifiquement celui qui entoure la « révolution industrieuse », ont mis en lumière le défi que représente encore, pour l’histoire sociale et l’histoire économique, l’étude de l’évolution du niveau de vie des plus humbles. Cet article entend s’emparer de cette question par une approche régionale, en s’appuyant sur les sources considérées comme les plus significatives. Il apporte un faisceau de preuves pour témoigner d’une amélioration du niveau de vie des individus issus du groupe social des « travailleurs » ( treballadors ) dans la région de Gérone (située au nord-est de la péninsule Ibérique), grâce au croisement des données apportées par deux sources notariales : les contrats de mariage et les inventaires après décès, et par le témoignage direct d’un paysan ampurdanais, Sebastià Casanovas, durant la seconde moitié du XVIII e siècle.
Cutting Edge: Plasmodium falciparum Induces Trained Innate Immunity
Authors: Schrum Jacob E. , Crabtree Juliet N. , Dobbs Katherine R. , Kiritsy Michael C. , Reed George W. , Gazzinelli Ricardo T. , Netea Mihai G. , Kazura James W. , Dent Arlene E. , Fitzgerald Katherine A. , Golenbock Douglas T. 
Published: January 2018

Abstract
Malarial infection in naive individuals induces a robust innate immune response. In the recently described model of innate immune memory, an initial stimulus primes the innate immune system to either hyperrespond (termed training) or hyporespond (tolerance) to subsequent immune challenge. Previous work in both mice and humans demonstrated that infection with malaria can both serve as a priming stimulus and promote tolerance to subsequent infection. In this study, we demonstrate that initial stimulation with Plasmodium falciparum–infected RBCs or the malaria crystal hemozoin induced human adherent PBMCs to hyperrespond to subsequent ligation of TLR2. This hyperresponsiveness correlated with increased H3K4me3 at important immunometabolic promoters, and these epigenetic modifications were also seen in Kenyan children naturally infected with malaria. However, the use of epigenetic and metabolic inhibitors indicated that the induction of trained immunity by malaria and its ligands may occur via a previously unrecognized mechanism(s).
IL-10 Deficiency Reveals a Role for TLR2-Dependent Bystander Activation of T Cells in Lyme Arthritis
Authors: Whiteside Sarah K. , Snook Jeremy P. , Ma Ying , Sonderegger F. Lynn , Fisher Colleen , Petersen Charisse , Zachary James F. , Round June L. , Williams Matthew A. , Weis Janis J. 
Published: January 2018

AbstractT cells predominate the immune responses in the synovial fluid of patients with persistent Lyme arthritis; however, their role in Lyme disease remains poorly defined. Using a murine model of persistent Lyme arthritis, we observed that bystander activation of CD4+ and CD8+ T cells leads to arthritis-promoting IFN-γ, similar to the inflammatory environment seen in the synovial tissue of patients with posttreatment Lyme disease. TCR transgenic mice containing monoclonal specificity toward non–Borrelia epitopes confirmed that bystander T cell activation was responsible for disease development. The microbial pattern recognition receptor TLR2 was upregulated on T cells following infection, implicating it as marker of bystander T cell activation. In fact, T cell–intrinsic expression of TLR2 contributed to IFN-γ production and arthritis, providing a mechanism for microbial-induced bystander T cell activation during infection. The IL-10–deficient mouse reveals a novel TLR2-intrinsic role for T cells in Lyme arthritis, with potentially broad application to immune pathogenesis.
Continuity of Care in Resident Outpatient Clinics: A Scoping Review of the Literature
Authors: Walker Jeremey , Payne Brittany , Clemans-Taylor B. Lee , Snyder Erin Dunn 
Published: January 2018

ABSTRACT

Background
Continuity between patients and physicians is a core principle of primary care and an accreditation requirement. Resident continuity clinics face challenges in nurturing continuity for their patients and trainees.

Objective
We undertook a scoping review of the literature to better understand published benchmarks for resident continuity; the effectiveness of interventions to improve continuity; and the impact of continuity on resident and patient satisfaction, patient outcomes, and resident career choice.

Methods
We developed a MEDLINE search strategy to identify articles that defined continuity in residency programs in internal medicine, family medicine, and pediatrics published prior to December 31, 2015, and used a quality evaluation tool to assess included studies.

Results
The review includes 34 articles describing 12 different measures of continuity. The usual provider of care and continuity for physician formulas were most commonly utilized, and mean baseline continuity was 56 and 55, respectively (out of a total possible score of 100). Clinic and residency program redesign innovations (eg, advanced access scheduling, team-based care, and block scheduling) were studied and had mixed impact on continuity. Continuity in resident clinics is lower than published continuity rates for independently practicing physicians.

Conclusions
Interventions to enhance continuity in resident clinics have mixed effects. More research is needed to understand how changes in continuity affect resident and patient satisfaction, patient outcomes, and resident career choice. A major challenge to research in this area is the lack of empanelment of residents' patients, creating difficulties in scheduling and measuring continuity visits.
Library instruction in medical education: a survey of current practices in the United States and Canada
Authors: Nevius Amanda M. , Ettien A’Llyn , Link Alissa P. , Sobel Laura Y. 
Published: January 2018

Objective: The most recent survey on instruction practices in libraries affiliated with accredited medical institutions in the United States was conducted in 1996. The present study sought to update these data, while expanding to include Canadian libraries. Additional analysis was undertaken to test for statistically significant differences between library instruction in the United States and Canada and between libraries affiliated with highly ranked and unranked institutions.Methods: A twenty-eight-question survey was distributed to libraries affiliated with accredited US and Canadian medical schools to assess what and how often librarians teach, as well as how librarians are involved in the curriculum committee and if they are satisfied with their contact with students and faculty. Quantitative data were analyzed with SAS, R, and MedCalc.Results: Most of the seventy-three responding libraries provided instruction, both asynchronously and synchronously. Library instruction was most likely to be offered in two years of medical school, with year one seeing the most activity. Database use was the most frequently taught topic, and libraries reported a median of five librarians providing instruction, with larger staffs offering slightly more education sessions per year. Libraries associated with highly ranked schools were slightly more likely to offer sessions that were integrated into the medical school curriculum in year four and to offer sessions in more years overall.Conclusions: In US and Canadian libraries, regardless of the rank of the affiliated medical school, librarians’ provision of instruction in multiple formats on multiple topics is increasingly common. This article has been approved for the Medical Library Association’s Independent Reading Program.
Spatial patterns of the Zostera noltei meadows across the Atlantic coast of Morocco: is there a latitudinal gradient?
Authors: Bououarour Oussama , El Kamcha Reda , Boutahar Loubna , Tnoumi Ali , Zourarah Bendahhou , Benhoussa Abdelaziz , Bazairi Hocein 
Published: January 2018

Seagrass meadows exist in most shallow, sheltered, soft-bottomed marine coastlines and estuaries throughout the world and rank among the most productive systems in the ocean. Zostera noltei Hornemann is a small seagrass largely widespread in intertidal areas of Western Europe and North-West Africa, the Mediterranean Sea and in the Black Sea.
In Morocco, intertidal Zostera noltei meadows were identified at six coastal ecosystems across c.a. 2500 km of its Atlantic coast (Tahaddart estuary, Moulay Bousselham, Sidi Moussa, Oualidia, Khnifiss lagoons and Dakhla Bay). The present work aimed at assessing the spatial and latitudinal variation of Z. noltei meadows by measuring the density of shoots, leaf biomass, root-rhizome biomass, number of leaf /shoot and the average length and width of leafs. Samples were conducted between December 2014 and January 2015, using a hand PVC corer (12.5 of diameter). When possible, a downstream and upstream comparison is performed in each site.
Density of shoots fluctuated between 1972 and 9833 shoots m-2. Leaves biomass varied between 32 and 259 gDW/m2 and root-rhizome biomass oscillated between 21 and 314 gDW/m2. Number of leaves per shoot fluctuated between 2.47 and 3.4 leaf per shoot, the leaf length between 4.9 and 30.8 cm and the leaf width 0.6 and 2 mm. These results showed, on the one hand, a clear spatial variation across a downstream-upstream gradient in each site and, on the other hand, a latitudinal pattern in the biomass and morphometry of the Z. noltei meadows across the Atlantic coast of Morocco. Significant differences were evidenced for all variables (ANOVA, p<0.05). The root-rhizome biomass and density of shoots are higher southward while the number of leaves per shoot, leaf biomass and the average length and width of the leaves are greater northward.
These results are compared with literature data from the distribution range of Z. noltei. Further analysis regarding the genetics, the associated benthic invertebrates and the sediment contamination are being performed and will increase the knowledge on such ecosystems and help in understanding their interaction with environment conditions.
Developing appropriate conservation measures for the seasonal whale shark feeding aggregation in Seychelles using ecological modeling tools
Authors: French Georgia C.A. , Bluemel Joanna K , Rowat David 
Published: January 2018

Background: The whale shark feeding aggregation in the Seychelles has been studied in detail since 2002, including aerial survey and collection of environmental data. In these coastal waters previous tagging studies have shown whale sharks spend considerable time in the top 10m of water (44-60% of daylight hours). Although protected locally there is currently no management structure to conserve them outside of protected areas. This is the first attempt to develop Temporary Protected Areas using statistical modeling of their ecological distribution to conserve the aggregation.
Methods: Data on whale shark occurrence and distribution were collected via standardized aerial surveys from microlight aircraft that also recorded locations of surface-feeding schools of fish and environmental variables. These data were input into Geographical Information System (GIS) software to create density distribution maps; further layers generated included distance from the coastline, and chlorophyll-a (Chl-a) concentration (from MODIS satellite imagery). MAXENT ecological modeling software and Kernel Density Estimate analysis were used to produce a habitat suitability map and probability distribution estimate. The MAXENT model was tested using pseudo-absence data in a binomial generalized linear model.
Results: Chl-a concentration, distance from coast and fish schools were all found to influence whale shark presence and Maxent results closely matched those from the Kernel Density Estimate analysis. Predictions of suitable habitat for whale sharks avoided higher Chl-a concentrations, but showed positive correlations with schools of fish, possibly acting as a direct indication of zooplankton abundance. Whale sharks preferentially selected feeding areas close to the coast.
Conclusion: Maxent and Kernel Density Estimates can provide useful tools to guide the development of appropriate conservation and management of this species that take into consideration temporal behavior and ecology.
Data reuse and scholarly reward: understanding practice and building infrastructure
Authors: Vision Todd J , Piwowar Heather A 
Published: January 2018

Recently introduced funding agency policies seek to increase the availability of data from individual published studies for reuse by the research community at large. The success of such policies can be measured both by data input (“is useful data being made available?”) and research output (“are these data being reused by others?”). A key determinant of data input is the extent to which data producers receive adequate professional credit for making data available. One of us (HP) previously reported a large citation difference for published microarray studies with and without data available in a public repository. Analysis of a much larger sample, with more covariates, provides a more reliable estimate of this citation boost, as well as additional insights into patterns of reuse and how the availability of data affects publication impact. A more recent study tracking the reuse of 100 datasets from each of ten different primary data repositories reveals large variation in patterns of reuse and citation. Our findings (a) illuminate ways in which the reuses of archived data tend to differ in purpose from that of the original producers; (b) inform data archiving policy, such as how long data embargoes need to be in order to protect the proprietary interests of producers; (c) and allow us to answer the vexing question of what the return on investment is for data archiving. In conducting these studies, we have become aware of gaps in data citation practice and infrastructure that limit the extent to which researchers receive credit for their contributions. We describe early efforts to bake good data citation and usage tracking into cyberinfrastructure as part of DataONE, the Data Observation Network for Earth. Finally, we introduce total-impact, a tool that allows researchers to track the diverse impacts of all their research outputs, including data, and empowers them to be recognized for their scholarly work on their own terms.
Software and Data Availability:
Research software and data: https://github.com/hpiwowar (CCZero for data where possible, MIT for code);
Dryad: new BSD license: http://code.google.com/p/dryad;
DataONE: Apache license: http://www.dataone.org/developer-resources;
total-impact: MIT license: https://github.com/total-impact.
This is an abstract that was submitted to the iEvoBio 2012 conference, held on July 10-11, 2012, in Ottawa, Canada.
Accessing biological data in R with semantic web technologies
Authors: Willighagen Egon 
Published: January 2018

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.
Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.
Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. The third example shows how the package can be used to handle RDF returned by OpenTox web services.
Discussion. The two provided library bring basic semantic web technologies to R. This paper only shows examples from the biology domain, but we believe the approaches are generally applicable. It currently only exposes a subset of key Apache Jena, but the rrdf package makes it easy to make more of the library's functionality, such as the shortest path finding. The rrdf libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.
Shades of yellow: interactive effects of visual and odour cues in a pest beetle
Authors: Arnold Sarah EJ , Stevenson Philip C , Belmain Steven R 
Published: January 2018

Background. The visual ecology of pest insects is poorly studied compared to the role of odour cues in determining their behaviour. Furthermore, the combined effects of both odour and vision on insect orientation are frequently ignored, but could impact behavioural responses.
Methods. A locomotion compensator was used to evaluate use of different visual stimuli by a major coleopteran pest of stored grains ( Sitophilus zeamais ), with and without the presence of host odours (known to be attractive to this species), in an open-loop setup.
Results. Some visual stimuli – in particular, one shade of yellow, solid black and high contrast black-against-white stimuli – elicited positive orientation behaviour from the beetles in the absence of odour stimuli. When host odours were also present, at 90° to the source of the visual stimulus, the beetles presented with yellow and vertical black-on-white grating patterns changed their walking course and typically adopted a path intermediate between the two stimuli. The beetles presented with a solid black-on-white target continued to orient more strongly towards the visual than the odour stimulus.
Discussion. Visual stimuli can strongly influence orientation behaviour, even in species where use of visual cues is sometimes assumed to be unimportant, while the outcomes from exposure to multimodal stimuli are unpredictable and need to be determined under differing conditions. The importance of the two modalities of stimulus (visual and olfactory) in food location is likely to depend upon relative stimulus intensity and motivational state of the insect.