bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate, female traits and population features as drivers of breeding timing in Mediterranean red deer populations
Authors: PELÁEZ Marta , SAN MIGUEL Alfonso , RODRÍGUEZ‐VIGAL Carlos , PEREA Ramón 
Published: January 2017

AbstractUnderstanding the factors that lead to variation in the timing of breeding in widespread species such as red deer (Cervus elaphus) is crucial to predict possible responses of wild populations to different climate scenarios. Here, we sought to further understand the causes of inter‐annual variation in the reproduction timing of female deer in Mediterranean environments. An integrative approach was used to identify the relative importance of individual, population and climate traits in the date of conception of free‐ranging deer, based on a dataset of 829 hinds culled during 12 years. We found that a population trait, density, was the most important factor explaining the variation in conception dates, with greater densities causing later conception dates. Body mass was the second in importance, with heavier females conceiving earlier than lighter ones. Almost equally important was the spring real bioclimatic index, a measure of plant productivity, causing later conception dates in the least productive springs (drier and hotter). Another climatic component, the end of summer drought, showed that the sooner the autumn arrives (greater rainfalls and cooler temperatures) the earlier the conception dates. Interestingly, age class was found to be a minor factor in determining conception date. Only older females (≥10 years old) conceived significantly later, suggesting reproductive senescence. This study highlights not only the importance of population and individual traits but also the influence of climatic parameters on the deer reproductive cycle in Mediterranean environments, giving valuable insight into how reproductive phenology may respond to seasonality and global climate changes.
Taxonomic research on deep‐sea macrofauna in the South China Sea using the Chinese deep‐sea submersible Jiaolong
Authors: LI Xinzheng 
Published: January 2017

AbstractThis paper reviews the taxonomic and biodiversity studies of deep‐sea invertebrates in the South China Sea based on the samples collected by the Chinese manned deep‐sea submersible Jiaolong. To date, 6 new species have been described, including the sponges Lophophysema eversa, Saccocalyx microhexactin and Semperella jiaolongae as well as the crustaceans Uroptychus jiaolongae, Uroptychus spinulosus and Globospongicola jiaolongi; some newly recorded species from the South China Sea have also been reported. The Bathymodiolus platifrons–Shinkaia crosnieri deep‐sea cold seep community has been reported by Li (2015), as has the mitochondrial genome of the glass sponge L. eversa by Zhang et al. (2016). The population structures of two dominant species, the shrimp Shinkaia crosnieri and the mussel Bathymodiolus platifrons, from the cold seep Bathymodiolus platifrons–Shinkaia crosnieri community in the South China Sea and the hydrothermal vents in the Okinawa Trough, were compared using molecular analysis. The systematic position of the shrimp genus Globospongicola was discussed based on 16S rRNA gene sequences.
New species of the giant deep‐sea isopod genus Bathynomus (Crustacea, Isopoda, Cirolanidae) from Hainan Island, South China Sea
Authors: KOU Qi , CHEN Jun , LI Xinzheng , HE Lisheng , WANG Yong 
Published: January 2017

AbstractSeveral specimens of the giant deep‐sea isopod genus Bathynomus were collected by a deep‐sea lander at a depth of 898 m near Hainan Island in the northern South China Sea. After careful examination, this material and the specimens collected from the Gulf of Aden, north‐western Indian Ocean, previously reported as Bathynomus sp., were identified to be the same as a new species to the genus. Bathynomus jamesi sp. nov. can be distinguished from the congeners by: the distal margin of pleotelson with 11 or 13 short straight spines and central spine not bifid; uropodal endopod and exopod with distolateral corner slightly pronounced; clypeus with lateral margins concave; and antennal flagellum extending when extended posteriorly reaches the pereonite 3. In addition, Bathynomus jamesi sp. nov. is also supported by molecular analyses based on mitochondrial COI and 16S rRNA gene sequences. The distribution range of the new species includes the western Pacific and north‐western Indian Ocean.
Vitamin D insufficiency in the first 6 months of infancy and challenge‐proven IgE‐mediated food allergy at 1 year of age: a case‐cohort study
Authors: Molloy J. , Koplin J. J. , Allen K. J. , Tang M. L. K. , Collier F. , Carlin J. B. , Saffery R. , Burgner D. , Ranganathan S. , Dwyer T. , Ward A. C. , Moreno‐Betancur M. , Clarke M. , Ponsonby A. L. , Vuillermin P. ,   the BIS Investigator Group
Published: January 2017

AbstractBackgroundEcological evidence suggests vitamin D insufficiency (VDI) due to lower ambient ultraviolet radiation (UVR) exposure may be a risk factor for IgE‐mediated food allergy. However, there are no studies relating directly measured VDI during early infancy to subsequent challenge‐proven food allergy.ObjectiveTo prospectively investigate the association between VDI during infancy and challenge‐proven food allergy at 1 year.MethodsIn a birth cohort (n = 1074), we used a case‐cohort design to compare 25‐hydroxyvitamin D3 (25(OH)D3) levels among infants with food allergy vs a random subcohort (n = 274). The primary exposures were VDI (25(OH)D3 <50 nM) at birth and 6 months of age. Ambient UVR and time in the sun were combined to estimate UVR exposure dose. IgE‐mediated food allergy status at 1 year was determined by formal challenge. Binomial regression was used to examine associations between VDI, UVR exposure dose and food allergy and investigate potential confounding.ResultsWithin the random subcohort, VDI was present in 45% (105/233) of newborns and 24% (55/227) of infants at 6 months. Food allergy prevalence at 1 year was 7.7% (61/786), and 6.5% (53/808) were egg‐allergic. There was no evidence of an association between VDI at either birth (aRR 1.25, 95% CI 0.70–2.22) or 6 months (aRR 0.93, 95% CI 0.41–2.14) and food allergy at 1 year.ConclusionsThere was no evidence that VDI during the first 6 months of infancy is a risk factor for food allergy at 1 year of age. These findings primarily relate to egg allergy, and larger studies are required.
The difficulties of systematic reviews
Authors: Westgate Martin J. , Lindenmayer David B. 
Published: January 2017

AbstractThe need for robust evidence to support conservation actions has driven the adoption of systematic approaches to research synthesis in ecology. However, applying systematic review to complex or open questions remains challenging, and this task is becoming more difficult as the quantity of scientific literature increases. We drew on the science of linguistics for guidance as to why the process of identifying and sorting information during systematic review remains so labor intensive, and to provide potential solutions. Several linguistic properties of peer‐reviewed corpora—including nonrandom selection of review topics, small‐world properties of semantic networks, and spatiotemporal variation in word meaning—greatly increase the effort needed to complete the systematic review process. Conversely, the resolution of these semantic complexities is a common motivation for narrative reviews, but this process is rarely enacted with the rigor applied during linguistic analysis. Therefore, linguistics provides a unifying framework for understanding some key challenges of systematic review and highlights 2 useful directions for future research. First, in cases where semantic complexity generates barriers to synthesis, ecologists should consider drawing on existing methods—such as natural language processing or the construction of research thesauri and ontologies—that provide tools for mapping and resolving that complexity. These tools could help individual researchers classify research material in a more robust manner and provide valuable guidance for future researchers on that topic. Second, a linguistic perspective highlights that scientific writing is a rich resource worthy of detailed study, an observation that can sometimes be lost during the search for data during systematic review or meta‐analysis. For example, mapping semantic networks can reveal redundancy and complementarity among scientific concepts, leading to new insights and research questions. Consequently, wider adoption of linguistic approaches may facilitate improved rigor and richness in research synthesis.
Monte Carlo decision curve analysis using aggregate data
Authors: Hozo Iztok , Tsalatsanis Athanasios , Djulbegovic Benjamin 
Published: January 2017

AbstractBackgroundDecision curve analysis (DCA) is an increasingly used method for evaluating diagnostic tests and predictive models, but its application requires individual patient data. The Monte Carlo (MC) method can be used to simulate probabilities and outcomes of individual patients and offers an attractive option for application of DCA.Materials and methodsWe constructed a MC decision model to simulate individual probabilities of outcomes of interest. These probabilities were contrasted against the threshold probability at which a decision‐maker is indifferent between key management strategies: treat all, treat none or use predictive model to guide treatment. We compared the results of DCA with MC simulated data against the results of DCA based on actual individual patient data for three decision models published in the literature: (i) statins for primary prevention of cardiovascular disease, (ii) hospice referral for terminally ill patients and (iii) prostate cancer surgery.ResultsThe results of MC DCA and patient data DCA were identical. To the extent that patient data DCA were used to inform decisions about statin use, referral to hospice or prostate surgery, the results indicate that MC DCA could have also been used. As long as the aggregate parameters on distribution of the probability of outcomes and treatment effects are accurately described in the published reports, the MC DCA will generate indistinguishable results from individual patient data DCA.ConclusionsWe provide a simple, easy‐to‐use model, which can facilitate wider use of DCA and better evaluation of diagnostic tests and predictive models that rely only on aggregate data reported in the literature.
Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180T grown photoautotrophically and photoheterotrophically
Authors: Tang T. , Mohr W. , Sattin S. R. , Rogers D. R. , Girguis P. R. , Pearson A. 
Published: January 2017

AbstractAnoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism—permitting either autotrophic or heterotrophic growth—is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur‐oxidizing bacterium, Allochromatium vinosum DSM180T. In one treatment, A. vinosum was grown with CO2 as the sole carbon source, while in a second treatment, it was grown on acetate. Different intracellular isotope patterns were observed for fatty acids, phytol, individual amino acids, intact proteins, and total RNA between the two experiments. Photoautotrophic CO2 fixation yielded typical isotopic ordering for the lipid biomarkers: δ13C values of phytol > n‐alkyl lipids. In contrast, growth on acetate greatly suppressed intracellular isotopic heterogeneity across all molecular classes, except for a marked 13C‐depletion in phytol. This caused isotopic “inversion” in the lipids (δ13C values of phytol < n‐alkyl lipids). The finding suggests that inverse δ13C patterns of n‐alkanes and pristane/phytane in the geologic record may be at least in part a signal for photoheterotrophy. In both experimental scenarios, the relative isotope distributions could be predicted from an isotope flux‐balance model, demonstrating that microbial carbon metabolisms can be interrogated by combining compound‐specific stable isotope analysis with metabolic modeling. Isotopic differences among molecular classes may be a means of fingerprinting microbial carbon metabolism, both in the modern environment and the geologic record.
Effects of amphibian phylogeny, climate and human impact on the occurrence of the amphibian‐killing chytrid fungus
Authors: Bacigalupe Leonardo D. , Soto‐Azat Claudio , García‐Vera Cristobal , Barría‐Oyarzo Ismael , Rezende Enrico L. 
Published: January 2017

AbstractChytridiomycosis, due to the fungusBatrachochytrium dendrobatidis(Bd), has been associated with the alarming decline and extinction crisis of amphibians worldwide. Because conservation programs are implemented locally, it is essential to understand how the complex interactions among host species, climate and human activities contribute toBdoccurrence at regional scales. Using weighted phylogenetic regressions and model selection, we investigated geographic patterns ofBdoccurrence along a latitudinal gradient of 1500 km within a biodiversity hot spot in Chile (1845 individuals sampled from 253 sites and representing 24 species), and its association with climatic, socio‐demographic and economic variables. Analyses show thatBdprevalence decreases with latitude although it has increased by almost 10% between 2008 and 2013, possibly reflecting an ongoing spread ofBdfollowing the introduction ofXenopus laevis. Occurrence ofBdwas higher in regions with high gross domestic product (particularly near developed centers) and with a high variability in rainfall regimes, whereas models including other bioclimatic or geographic variables, including temperature, exhibited substantially lower fit and virtually no support based on Akaike weights. In addition,Bdprevalence exhibited a strong phylogenetic signal, with five species having high numbers of infected individuals and higher prevalence than the average of 13.3% across all species. Taken together, our results highlight thatBdin Chile might still be spreading south, facilitated by a subset of species that seem to play an important epidemiological role maintaining this pathogen in the communities, in combination with climatic and human factors affecting the availability and quality of amphibian breeding sites. This information may be employed to design conservation strategies and mitigate the impacts ofBdin the biodiversity hot spot of southern Chile, and similar studies may prove useful to disentangle the role of different factors contributing to the emergence and spread of this catastrophic disease.
Moving forward socio‐economically focused models of deforestation
Authors: Dezécache Camille , Salles Jean‐Michel , Vieilledent Ghislain , Hérault Bruno 
Published: January 2017

AbstractWhilst high‐resolution spatial variables contribute to a good fit of spatially explicit deforestation models, socio‐economic processes are often beyond the scope of these models. Such a low level of interest in the socio‐economic dimension of deforestation limits the relevancy of these models for decision‐making and may be the cause of their failure to accurately predict observed deforestation trends in the medium term. This study aims to propose a flexible methodology for taking into account multiple drivers of deforestation in tropical forested areas, where the intensity of deforestation is explicitly predicted based on socio‐economic variables. By coupling a model of deforestation location based on spatial environmental variables with several sub‐models of deforestation intensity based on socio‐economic variables, we were able to create a map of predicted deforestation over the period 2001–2014 in French Guiana. This map was compared to a reference map for accuracy assessment, not only at the pixel scale but also over cells ranging from 1 to approximately 600 sq. km. Highly significant relationships were explicitly established between deforestation intensity and several socio‐economic variables: population growth, the amount of agricultural subsidies, gold and wood production. Such a precise characterization of socio‐economic processes allows to avoid overestimation biases in high deforestation areas, suggesting a better integration of socio‐economic processes in the models. Whilst considering deforestation as a purely geographical process contributes to the creation of conservative models unable to effectively assess changes in the socio‐economic and political contexts influencing deforestation trends, this explicit characterization of the socio‐economic dimension of deforestation is critical for the creation of deforestation scenarios in REDD+ projects.
Detection of the MYD88 mutation by the combination of the allele‐specific PCR and quenching probe methods
Authors: Nogami S. , Kawaguchi‐Ihara N. , Shiratori E. , Ohtaka M. , Itoh M. , Tohda S. 
Published: January 2017

SummaryIntroductionThe MYD88 missense mutation c.794T>C, p.Leu265Pro, is found in patients with Waldenstörm's macroglobulinemia and lymphoma. Direct sequencing, allele‐specific PCR (AS‐PCR), PCR‐restriction fragment length polymorphism (PCR‐RFLP), and high‐resolution melting analysis (HRM) are currently used to detect the mutation; however, they are either time‐consuming or have low detection sensitivity. Here, we developed a novel highly sensitive and rapid detection method based on the quenching probe (QP) technique and AS‐PCR.MethodA lymphoma cell line heterozygous for the MYD88 mutation, two wild‐type cell lines, and two samples from Waldenstörm's macroglobulinemia patients were analyzed by AS‐PCR, PCR‐RFLP, HRM, and QP, and their detection sensitivity was examined using the mixtures of the mutant and wild‐type DNA.ResultsFor mutation‐carrying heterozygous samples, the QP method produced W‐shaped melting profiles presenting curves derived from the wild‐type and mutant alleles. The QP analysis was performed in 2 h and demonstrated the detection limit of 5%, which was similar to that of the other methods. However, the combination of AS‐PCR and QP (AS‐QP) improved the sensitivity to 0.62% of the mutant allele.ConclusionThe AS‐QP analysis is rapid and minimally improves detection sensitivity compared to the AS‐PCR.
The influence of Sb on glass‐forming ability of Ga‐containing As2Se3 glasses
Authors: Shpotyuk Yaroslav , Boussard‐Pledel Catherine , Nazabal Virginie , Bureau Bruno 
Published: January 2017

AbstractEffect of As to Sb substitution on glass‐forming ability of As2Se3 glass under Ga additions was comprehensively studied using optical spectroscopy in visible and IR regions, differential scanning calorimetry, X‐ray diffraction as well as Raman scattering techniques. The crystallization processes enhanced by Ga additions to As2Se3 glass were significantly suppressed under such As to Sb substitution. Following conventional synthesis, it was possible to substitute up to 50% of As by Sb within Gay(As0.40−xSbxSe0.60)100−y cut‐section without essential impact on glassy state, thus improving optical properties in the IR region by lowering the phonon energy. In the case of Gay(As0.28Sb0.12Se0.60)100−y cut‐section, up to 8 at.% of Ga can be introduced without crystallization, whereas in case of Gay(As0.40Se0.60)100−y system, glass‐forming ability is limited just up to 3 at.% of Ga. The prepared Ga5(As0.28Sb0.12Se0.60)95 glass composition was shown to be the richest in Ga keeping its vitreous state, good optical and thermodynamic properties allowing further rare‐earth doping and fiber drawing.
Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula
Authors: Ziegler Maren , Arif Chatchanit , Burt John A. , Dobretsov Sergey , Roder Cornelia , LaJeunesse Todd C. , Voolstra Christian R. 
Published: January 2017

AbstractAimCoral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth.LocationShallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG).MethodsNext‐generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera.ResultsCorals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C‐ to D‐dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)‐based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera.Main conclusionsOur study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host–symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing ‘Future Ocean’ conditions.