bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic epidemiology and global diversity of the emerging bacterial pathogenElizabethkingia anophelis
Authors: Breurec Sebastien , Criscuolo Alexis , Diancourt Laure , Rendueles Olaya , Vandenbogaert Mathias , Passet Virginie , Caro Valérie , Rocha Eduardo P. C. , Touchon Marie , Brisse Sylvain 
Published: March 2016

ABSTRACTElizabethkingia anophelisis an emerging pathogen. Genomic analysis of strains from clinical, environmental or mosquito sources is needed to understand the epidemiological emergence ofE. anophelisand to uncover genetic elements implicated in antimicrobial resistance, pathogenesis, or niche adaptation. Here, the genomic sequences of two nosocomial isolates that caused neonatal meningitis in Bangui, Central African Republic, were determined and compared withElizabethkingiaisolates from other world regions and sources. Average nucleotide identity firmly confirmed thatE. anophelis, E. meningosepticaandE. miricolarepresent distinct genomic species and led to re-identification of several strains. Phylogenetic analysis ofE. anophelisstrains revealed several sublineages and demonstrated a single evolutionary origin of African clinical isolates, which carry unique antimicrobial resistance genes acquired by horizontal transfer. TheElizabethkingiagenus and the speciesE. anophelishad pan-genomes comprising respectively 7,801 and 6,880 gene families, underlining their genomic heterogeneity. African isolates were capsulated and carried a distinctive capsular polysaccharide synthesis cluster. A core-genome multilocus sequence typing scheme applicable to allElizabethkingiaisolates was developed, made publicly available (http://bigsdb.web.pasteur.fr/elizabethkingia), and shown to provide useful insights intoE. anophelisepidemiology. Furthermore, a clustered regularly interspaced short palindromic repeats (CRISPR) locus was uncovered inE. meningoseptica, E. miricolaand in a fewE. anophelisstrains. CRISPR spacer variation was observed between the African isolates, illustrating the value of CRISPR for strain subtyping. This work demonstrates the dynamic evolution ofE. anophelisgenomes and provides innovative tools forElizabethkingiaidentification, population biology and epidemiology.IMPORTANCEElizabethkingia anophelisis a recently recognized bacterial species involved in human infections and outbreaks in distinct world regions. Using whole-genome sequencing, we showed that the species comprises several sublineages, which differ markedly in their genomic features associated with antibiotic resistance and host-pathogen interactions. Further, we have devised high-resolution strain subtyping strategies and provide an open genomic sequence analysis tool, facilitating the investigation of outbreaks and tracking of strains across time and space. We illustrate the power of these tools by showing that two African healthcare-associated meningitis cases observed 5 years apart were caused by the same strain, providing evidence thatE. anopheliscan persist in the hospital environment.
Seven SNPs in the Coding Sequence of Leptin Receptor Gene in Long-term Selected Japanese Quail Lines
Authors: Karabağ Kemal , Alkan Sezai , Karlı Taki , İkten Cengiz , Şahin İnci , Balcıoğlu Murat Soner 
Published: March 2016

ABSTRACTThe objective of this study was to identify SNPs in the coding sequence of the leptin receptor gene and to test for their possible association with 20 economically advantageous traits in 15 generations of 2 selected (HBW and LBW) and a control of japanase quail. A 350-bp part of the leptin receptor coding region was amplified and sequenced and understood that the fragment contained 7 SNPs (GenBank:KP674322.1-KP674328.1) that were detected in 5 loci (T3216C, T3265C, T3265G, C3265G, T3303C, A3311G, and T3347C) in a total of 30 individuals. The T3216C and T3303C SNPs located at the end of the codon were synonymous and did not affect the presence of proline. However, phenylalanine, leucine and valine were produced when the T3265C, T3265G and C3265G SNPs, respectively, were present. Glutamine or arginine was produced when the A3311G SNP was A or G, respectively, and serine was produced when the T3347C SNP was C. Although codons and amino acid sequences changed due to the second SNP, the secondary protein structure was not changed. However, the fourth and fifth SNPs changed both the amino acid sequences and secondary protein structure.Pairing the SNP loci with phenotypic traits created haplogroups. When all individuals were evaluated together, some of the differences between the haplogroups were statistically significant (p<0.05; p<0.01). These results showed that both the sequence and structure of the leptin receptor gene could be altered by long-term selection. However, to achieve a more precise understanding of the role of leptin, entire coding sequences of leptin and the leptin receptor should be studied.
Sex beyond species: the first genetically analyzed case of intergeneric fertile hybridization in pinnipeds
Authors: Franco‐Trecu Valentina , Abud Carolina , Feijoo Matías , Kloetzer Guillermo , Casacuberta Marcelo , Costa‐Urrutia Paula 
Published: March 2016

SUMMARYA species, according to the biological concept, is a natural group of potentially interbreeding individuals isolated by diverse mechanisms. Hybridization is considered the production of offspring resulting from the interbreeding of two genetically distinct taxa. It has been documented in over 10% of wild animals, and at least in 34 cases for Artic marine mammals. In Otariids, intergeneric hybridization has been reported though neither confirming it through genetic analyses nor presenting evidence of fertile offspring. In this study, we report the finding of a hybrid adult female between a South American fur seal (Arctocephalus australis) and a South American sea lion (Otaria byronia), and its offspring, a male pup, in Uruguay. Further based on morphological constraints and breeding seasons, sex‐biased hybridization between the two species is hypothesized. Morphological and genetic (nuclear and mitochondrial) results confirm de hybrid nature of the female‐pup pair. Here we discuss a genetic dilution effect, considering other hybridization events must be occurring, and how isolation mechanisms could be circumvented. Moreover, the results obtained from stable isotope analysis suggest feeding habits may be a trait transmitted maternally, leading to consider broader issues regarding hybridization as an evolutionary innovation phenomenon.
Estimation of saturated hydraulic conductivity from double‐ring infiltrometer measurements
Authors: Fatehnia M. , Tawfiq K. , Ye M. 
Published: March 2016

SummaryThis research aims to determine soil vertical saturated hydraulic conductivity (Ks) in situ from the measured steady infiltration rate (I), initial soil properties and double‐ring infiltrometer (DRI) test data. Characterizing the effects of these variables on the measured steady infiltration rate will enable more accurate prediction of Ks. We measured the effects of the ring diameter, head of ponding, ring depth, initial effective saturation and soil macroscopic capillary length on measured steady infiltration rates. We did this by simulating 864 DRI tests with the finite element program HYDRUS‐2D and by conducting 39 full‐scale in situ DRI tests, 30 Mini‐Disk infiltrometer experiments and four Guelph Permeameter tests. The M5′ model trees and genetic programming (GP) methods were applied to the data to establish formulae to predict the Ks of sandy to sandy‐clay soils. The nine field DRI tests were used to verify the computer models. We determined the accuracy of the methods with 30% of the simulated DRI data to compare I/KS values of the finite element models with estimates from the suggested formulae. We also used the suggested formulae to predict the Ks values of 30 field DRI experiments and compared them with values measured by Guelph Permeameter tests. Compared with the GP method, the M5′ model was better at predicting KS, with a correlation coefficient of 0.862 and root mean square error (RMSE) of 0.282 cm s−1. In addition, the latter method estimated Ksvalues of the field experiments more accurately, with an RMSE of 0.00346 cm s−1.
The effect of pre‐industrial charcoal kilns on chemical properties of forest soil of Wallonia, Belgium
Authors: Hardy B. , Cornelis J.‐T. , Houben D. , Lambert R. , Dufey J. E. 
Published: March 2016

SummaryIn Wallonia, Belgium, intensive in situ charcoal production that was linked closely to pre‐industrial smelting and steel‐making affected a large part of the forested area in the late eighteenth century. Charcoal kiln relics can be detected under forest as domes of about 10 m in diameter, with the topsoil greatly enriched with charcoal residues. We sampled 19 charcoal kiln sites and the adjacent reference soil by soil horizon on four different soil types (Arenosols, Luvisols, Cambisols and Podzols). Data were analysed with linear mixed models to assess the effect of the charcoal kiln site on soil properties in relation to depth and soil conditions. We also addressed the evolution of soil properties over time by a comparison of the soil characteristics at a currently active kiln site. The charcoal‐rich topsoil has a larger C:N ratio and cation exchange capacity (CEC) per unit of organic carbon than the reference soil. The largest CECs per unit of carbon were observed on soil with coarser textures. On acidic soil, the increase in base saturation in the subsoil reflects the past liming effect of ash produced by wood charring, whereas the topsoil is re‐acidified. The acidity of carbonate‐rich Cambisols, however, is not reduced. Regardless of soil type, the kiln topsoil is greatly depleted in exchangeable K+ and available P, which may be attributed to the small affinity of the exchange complex of charcoal for K+ and a decrease in P availability with time. Therefore, we recommend further research on the long‐term effects of biochar on the dynamics of plant nutrients.
Effects of compost, biochar and manure on carbon mineralization of biogas residues applied to soil
Authors: Coban H. , Miltner A. , Centler F. , Kästner M. 
Published: March 2016

SummaryBiogas residues contain microbial biomass, which contributes to the formation of soil organic matter. Whether the potential of biogas residues to increase soil organic matter can be enhanced by co‐application with compost, biochar or manure is unknown, however. The aim of this paper is to evaluate the effects of co‐amendment on the mineralization of biogas residues, carbon dioxide emissions and the carbon flow within the microbial food web. We determined the fate of 13C‐labelled microbial biomass present in biogas residues applied together with compost, biochar and manure to soil, by analysing CO2 and biomarker phospholipid fatty acids. Although the rate of mineralization constant of the slowly degrading carbon pool was not affected by co‐amendments, co‐amendment with manure resulted in a larger rate of mineralization constant of the readily degrading carbon pool of biogas residues. The incorporation of carbon was mainly to Gram‐negative biomass and was the smallest with manure co‐amendment, which indicated differences in bioavailability of the carbon source.
Skin cancer risk in outdoor workers: a European multicenter case–control study
Authors: Trakatelli M. , Barkitzi K. , Apap C. , Majewski S. , De Vries E. ,   the EPIDERM group
Published: March 2016

AbstractBackgroundExposure to ultraviolet radiation (UVR) is the most important external risk factor for skin cancer. Outdoor workers, who are exposed to high ambient UVR levels are at increased risk.ObjectiveTo compare outdoor with indoor workers in terms of: (i) skin cancer risk factors, and (ii) risk of developing skin cancer.MethodsUsing descriptive methods and a large multicenter European case–control study, we compared risk factor patterns between outdoor (N = 1416) and indoor workers (N = 1863). Risk of developing basal cell carcinoma (BCC), squamous cell carcinoma (SCC), melanoma and actinic keratosis (AK) were analysed by type of work using multivariate logistic regression models, for three categories of work: indoor; farming/construction; other outdoor work.ResultsAlthough skin phototype was equally distributed by type of work, significantly less outdoor than indoor workers used sunscreen in their own country (44.3% vs. 60.2%), but had more outdoor hobbies (66.2% vs. 58.2%). Outdoor workers had lower educational levels, and felt less confident in understanding medical information and filling medical forms (all P < 0.001). Outdoor workers had more signs of photodamage (78.1% vs. 65.5%) and among the skin cancer patients, 37.7% of outdoor workers vs. 28.6% of indoor workers had ≥2 skin cancers diagnosed during their lifetime. Multivariate logistic regression models showed significantly increased risk of outdoor vs. indoor work for AK (ORother outdoor = 1.55, ORfarming/construction = 2.58), SCC (ORother outdoor = 1.32, ORfarming/construction = 2.77) and BCC (ORother outdoor = 1.53, ORfarming/construction = 1.83). No significant associations were found for melanoma. The risk of all types of skin cancer and AK was significantly increased for workers with ≥5 years of outdoor work.ConclusionsOutdoor workers had more risk behaviour with similar constitutional skin cancer risk factors: more UV exposure (both occupational and leisure) and less sunscreen use and lower health literacy. This results in higher exposure, more photodamage and an increased risk of developing AK, BCC and SCC.
The European Status Quo in legal recognition and patient‐care services of occupational skin cancer
Authors: Ulrich C. , Salavastru C. , Agner T. , Bauer A. , Brans R. , Crepy M.N. , Ettler K. , Gobba F. , Goncalo M. , Imko‐Walczuk B. , Lear J. , Macan J. , Modenese A. , Paoli J. , Sartorelli P. , Stageland K. , Weinert P. , Wroblewski N. , Wulf H.C. , John S.M. 
Published: March 2016

AbstractBackgroundSkin cancer is the most common malignancy in Caucasian populations worldwide and ultraviolet radiation (UVR) is known for being the number one carcinogen. As, especially in outdoor workers, UVR is an inevitable carcinogen, the prevention and management of UVR‐related skin cancers in these at‐risk populations represent a collective challenge for dermatologists and healthcare policymakers likewise.ObjectiveTo provide an overview on the current regulations on the acknowledgement and management of work‐related skin cancer in 11 European countries.MethodsDermatologists from 11 countries networking within the EU Horizon 2020 COST Action TD1206 ‘StanDerm’ contributed to a standardized survey regarding current national regulations, implemented for the recognition, prevention and management as well as possible compensation regulations in their individual country of residence.ResultsTen of 11 participating countries in this survey reported the existence of an established programme available on certain occupational diseases; work‐related skin diseases were only specifically recognized in eight countries. Seven of 11 countries recognize cutaneous squamous cell carcinoma in outdoor workers as ‘occupational skin cancer’. Basal cell carcinoma (6 of 11), actinic keratosis (5 of 11), Bowen's disease (5 of 11) and malignant melanoma (5 of 11) are not as regularly approved as potentially ‘work‐induced’. Only a few of the countries included into this survey established a general documentation system (national registry) on occupational skin diseases. So far, representatives of only three countries of this survey referred to a specific established national programme for the prevention, management or compensation of occupational skin cancers acquired during work‐related UVR exposure.ConclusionThis survey highlights the need for mandatory regulations on the prevention, management and potential compensation of work‐related UV‐induced skin cancer across Europe. Against the background of a joint European domestic market, equal standards of occupational safety across Europe should include binding regulations for the protection and management of work‐related skin cancer. The design of a common regulation to meet the increasing incidence of skin cancers in outdoor workers should become part of the European agenda, ensuring equal working and living conditions in the member states.
Socio‐economic stratification of English in globalized landscapes: A market‐oriented perspective
Authors: Vandenbroucke Mieke 
Published: March 2016

Globalization has dramatically altered the urban societies of Amsterdam and Brussels over recent decades, with intensified socio‐economic inequality, unprecedented levels of multilingualism and the increasing importance of English. In this paper, I examine the use of English in the linguistic landscape of socio‐economically stratified commercial shopping streets in these two second‐tier global cities. I adopt a market‐oriented, contextualized approach to quantitative and qualitative variability in how English emerges in these particular commercial ‘linguistic markets’. McDonaldization in midscale shopping streets occurs alongside downscale and upscale uses of English which are more susceptible to local commercial dynamics, in particular in Brussels. As such, global English in these single city contexts emerges as a heterogeneous and scaled phenomenon shaped by specific local commercial and linguistic market conditions.
Grassland root functional parameters vary according to a community‐level resource acquisition–conservation trade‐off
Authors: Fort Florian , Cruz Pablo , Lecloux Eric , Bittencourt de Oliveira Leandro , Stroia Ciprian , Theau Jean‐Pierre , Jouany Claire 
Published: March 2016

AbstractQuestionsThe fundamental trade‐off between fine root trait attributes related to resource acquisition and conservation is well documented at species and community levels. However, relations remain unclear between this trade‐off and community adaptation to environmental factors. As a result we ask: (1) how do fertility changes influence community position along the root acquisition–conservation trade‐off; (2) how does root position along the soil profile influence its functional parameter; and (3) do fertility and soil depth have an interactive effect on community root parameters?LocationNative multi‐species temperate grassland in the French Massif Central.MethodsWe assessed botanical composition and measured community root functional parameters (at plot and soil layer levels) in 16 plots differentiated by the amounts of N and P fertilizers applied over 16 yr and a soil depth gradient. Structural equation models were used to analyse relations among environmental factors, botanical composition and root functional parameters.ResultsBotanical composition and plot‐level root functional parameters vary according to fertility and soil depth. Communities from low fertility plots display a resource conservation strategy, i.e. high root tissue density, low specific root length (SRL) and low root length density (RLD), while communities from high fertility plots display a resource acquisition strategy, i.e. opposite parameter values. This demonstrates the importance of root resource management strategies in community adaptation to resource acquisition. Roots display different parameter values with soil depth. Roots in the surface horizon have small diameters and high SRL and RLD, suggesting intensive soil exploration and a high nutrient acquisition capacity. Roots in deep horizons have large diameters and low SRL, suggesting high water transport capacity per root length unit. This pattern is affected by plot fertility, i.e. communities from high fertility plots show higher root strategy differentiation with depth than communities from low fertility plots. We hypothesize that this root specialization along the soil profile enables species to be competitive for nutrient uptake in shallow soil layers and water uptake and transport in deep soil layers.ConclusionOur study provides evidence that fertility and soil depth modified root functional parameters, in agreement with predictions from the economics spectrum theory.
Lower Gastrointestinal Bleeding and Ischemic Colitis
Authors: Newman Jamie R , Cooper Mary Anne 
Published: March 2016

OBJECTIVE: To compare the incidence and clinical characteristics of lower gastrointestinal (LGI) bleeding due to ischemic colitis with those with LGI bleeding of other causes.METHODS: A chart review was performed of patients admitted with LGI bleeding to Sunnybrook and Women’s College Health Sciences Centre, Toronto, Ontario, between July 1, 1997 and January 31, 2000.RESULTS: Of 124 patients with LGI bleeding, 24 cases were due to ischemic colitis, 62 to diverticulosis, 11 to inflammatory bowel disease (IBD) and 27 to all other causes (‘others’). The average ages of patients in each group were 66.5, 76.5, 40.5 and 77.5 years, respectively. Patients with ischemic colitis were statistically younger than those with diverticular bleeding and ‘others’. Patients with IBD were younger than those in the other three groups. The only statistical difference for vascular disease risks was hypertension, because of its absence from the IBD group. Three patients with ischemic colitis underwent blood transfusions, while 23 with diverticulosis, 15 ‘others’ and none with IBD received blood. Three patients with ischemic colitis and one patient from the ‘others’ group died. More women (75) than men (49) had LGI bleeding - in total and within each subgroup. Of women with LGI bleeding, many more with ischemic colitis (44.4%) than with diverticulosis (3.0%), IBD (0%) or ‘others’ (5.6%) were taking estrogen.CONCLUSIONS: Ischemic colitis was the second most common cause of LGI bleeding. LGI bleeding from all causes was more common in women than in men. Many more women in the ischemic colitis group than in the other groups were using estrogen therapy.
Motion – The Available Treatments for Hepatitis C Are Cost Effective: Arguments against the Motion
Authors: Kim W Ray 
Published: March 2016

Hepatitis C is a prevalent infection in North America. However, the natural history of hepatitis C virus (HCV) infection in the general population is not fully understood. Available cohortbased studies suggest that only a relative minority of patients develop significant liver disease, such as cirrhosis and/or hepatocellular carcinoma. Other studies, mostly conducted based on referral patients with established disease, portray much more serious consequences of HCV infection. Although a substantial improvement has been made in the treatment for HCV, the overall impact of antiviral therapy in altering the natural course of HCV infection remains uncertain. Therapeutic trials involve narrow selection criteria that would exclude the majority of hepatitis C patients in the community, and are conducted in ideal settings that may not be generalizable to the average practice setting. Demographic groups that are at high risk of developing severe liver disease include older male patients who consume alcohol. In contrast, antiviral therapy is more effective in young and female patients and those who do not drink alcohol. Thus, patients who appear to be successfully treated may not be those for whom clearance of the virus would be beneficial. Cost-effectiveness studies published to date have not been able to fully address the complex and heterogeneous matrix of the factors that influence the natural history of HCV infection and treatment response.In summary, there is a significant degree of uncertainty about many assumptions that are necessary in creating computer models to estimate the cost-effectiveness of HCV therapy. When interpreting the results of cost effectiveness analyses regarding the treatment of HCV infection, it is important to be aware of the underlying assumptions that are incorporated in the model and the data on which they are based. Given these limitations, vis-à-vis the expense, toxicity and yet limited effectiveness of the currently available antiviral agents, one should not blindly accept a conclusion that treatment for hepatitis C is cost effective.