bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete catalytic cycle of cofactor‐independent phosphoglycerate mutase involves a spring‐loaded mechanism
Authors: Roychowdhury Amlan , Kundu Anirban , Bose Madhuparna , Gujar Akanksha , Mukherjee Somnath , Das Amit Kumar 
Published: January 2015

Cofactor‐independent phosphoglycerate mutase (iPGM), an important enzyme in glycolysis and gluconeogenesis, catalyses the isomerization of 2‐ and 3‐phosphoglycerates by an Mn2+‐dependent phospho‐transfer mechanism via a phospho‐enzyme intermediate. Crystal structures of bi‐domain iPGM from Staphylococcus aureus, together with substrate‐bound forms, have revealed a new conformation of the enzyme, representing an intermediate state of domain movement. The substrate‐binding site and the catalytic site are present in two distinct domains in the intermediate form. X–ray crystallography complemented by simulated dynamics has enabled delineation of the complete catalytic cycle, which includes binding of the substrate, followed by its positioning into the catalytic site, phospho‐transfer and finally product release. The present work describes a novel mechanism of domain movement controlled by a hydrophobic patch that is exposed on domain closure and acts like a spring to keep the protein in open conformation. Domain closing occurs after substrate binding, and is essential for phospho‐transfer, whereas the open conformation is a prerequisite for efficient substrate binding and product dissociation. A new model of catalysis has been proposed by correlating the hinge‐bending motion with the phospho‐transfer mechanism.
Forecasted coral reef decline in marine biodiversity hotspots under climate change
Authors: Descombes Patrice , Wisz Mary S. , Leprieur Fabien , Parravicini Valerianio , Heine Christian , Olsen Steffen M. , Swingedouw Didier , Kulbicki Michel , Mouillot David , Pellissier Loïc 
Published: January 2015

AbstractCoral bleaching events threaten coral reef habitats globally and cause severe declines of local biodiversity and productivity. Related to high sea surface temperatures (SST), bleaching events are expected to increase as a consequence of future global warming. However, response to climate change is still uncertain as future low‐latitude climatic conditions have no present‐day analogue. Sea surface temperatures during the Eocene epoch were warmer than forecasted changes for the coming century, and distributions of corals during the Eocene may help to inform models forecasting the future of coral reefs. We coupled contemporary and Eocene coral occurrences with information on their respective climatic conditions to model the thermal niche of coral reefs and its potential response to projected climate change. We found that under the RCP8.5 climate change scenario, the global suitability for coral reefs may increase up to 16% by 2100, mostly due to improved suitability of higher latitudes. In contrast, in its current range, coral reef suitability may decrease up to 46% by 2100. Reduction in thermal suitability will be most severe in biodiversity hotspots, especially in the Indo‐Australian Archipelago. Our results suggest that many contemporary hotspots for coral reefs, including those that have been refugia in the past, spatially mismatch with future suitable areas for coral reefs posing challenges to conservation actions under climate change.
Leaf and stem economics spectra drive diversity of functional plant traits in a dynamic global vegetation model
Authors: Sakschewski Boris , von Bloh Werner , Boit Alice , Rammig Anja , Kattge Jens , Poorter Lourens , Peñuelas Josep , Thonicke Kirsten 
Published: January 2015

AbstractFunctional diversity is critical for ecosystem dynamics, stability and productivity. However, dynamic global vegetation models (DGVMs) which are increasingly used to simulate ecosystem functions under global change, condense functional diversity to plant functional types (PFTs) with constant parameters. Here, we develop an individual‐ and trait‐based version of theDGVM LPJmL (Lund‐Potsdam‐Jena managed Land) calledLPJmL‐ flexible individual traits (LPJmL‐FIT) with flexible individual traits) which we apply to generate plant trait maps for the Amazon basin.LPJmL‐FITincorporates empirical ranges of five traits of tropical trees extracted from theTRYglobal plant trait database, namely specific leaf area (SLA), leaf longevity (LL), leaf nitrogen content (Narea), the maximum carboxylation rate of Rubisco per leaf area (), and wood density (WD). To scale the individual growth performance of trees, the leaf traits are linked by trade‐offs based on the leaf economics spectrum, whereas wood density is linked to tree mortality. No preselection of growth strategies is taking place, because individuals with unique trait combinations are uniformly distributed at tree establishment. We validate the modeled trait distributions by empirical trait data and the modeled biomass by a remote sensing product along a climatic gradient. Including trait variability and trade‐offs successfully predicts natural trait distributions and achieves a more realistic representation of functional diversity at the local to regional scale. As sites of high climatic variability, the fringes of the Amazon promote trait divergence and the coexistence of multiple tree growth strategies, while lower plant trait diversity is found in the species‐rich center of the region with relatively low climatic variability.LPJmL‐FITenables to test hypotheses on the effects of functional biodiversity on ecosystem functioning and to apply theDGVMto current challenges in ecosystem management from local to global scales, that is, deforestation and climate change effects.
Inclusion of ecologically based trait variation in plant functional types reduces the projected land carbon sink in an earth system model
Authors: Verheijen Lieneke M. , Aerts Rien , Brovkin Victor , Cavender‐Bares Jeannine , Cornelissen Johannes H. C. , Kattge Jens , van Bodegom Peter M. 
Published: January 2015

AbstractEarth system models demonstrate large uncertainty in projected changes in terrestrial carbon budgets. The lack of inclusion of adaptive responses of vegetation communities to the environment has been suggested to hamper the ability of modeled vegetation to adequately respond to environmental change. In this study, variation in functional responses of vegetation has been added to an earth system model (ESM) based on ecological principles. The restriction of viable mean trait values of vegetation communities by the environment, called ‘habitat filtering’, is an important ecological assembly rule and allows for determination of global scale trait–environment relationships. These relationships were applied to model trait variation for different plant functional types (PFTs). For three leaf traits (specific leaf area, maximum carboxylation rate at 25 °C, and maximum electron transport rate at 25 °C), relationships with multiple environmental drivers, such as precipitation, temperature, radiation, and CO2, were determined for the PFTs within the Max Planck Institute ESM. With these relationships, spatiotemporal variation in these formerly fixed traits in PFTs was modeled in global change projections (IPCC RCP8.5 scenario). Inclusion of this environment‐driven trait variation resulted in a strong reduction of the global carbon sink by at least 33% (2.1 Pg C yr−1) from the 2nd quarter of the 21st century onward compared to the default model with fixed traits. In addition, the mid‐ and high latitudes became a stronger carbon sink and the tropics a stronger carbon source, caused by trait‐induced differences in productivity and relative respirational costs. These results point toward a reduction of the global carbon sink when including a more realistic representation of functional vegetation responses, implying more carbon will stay airborne, which could fuel further climate change.
Self‐Activated Vanadate Compounds Toward Realization of Rare‐Earth‐Free Full‐Color Phosphors
Authors: Matsushima Yuta , Koide Takuhiro , Hiro‐Oka Masahiro , Shida Minori , Sato Akane , Sugiyama Sho , Ito Michimasa 
Published: January 2015

Rare‐earth‐free phosphors based on vanadate compounds were investigated, where the vanadates included chloride vanadates (MII2VO4Cl), pyrovanadates (MII2V2O7), orthovanadates (MII3(VO4)2) with divalent cations MII of Mg, Sr, Ba, and Zn, and oxofluorovanadates (AIVOF4) with an alkali metal AI. A chloride pyrolysis method and a liquid phase precipitation method were proposed for preparing the chloride vanadates and pyro‐ and orthovanadates, respectively. These vanadate compounds showed self‐activated photoluminescence (PL) based on the VO4 clusters against the ultraviolet (UV) light irradiation. The colors of PL covered almost the whole visible‐light region from blue to yellow as Sr2VO4Cl (deep blue), Ca2VO4Cl (sky blue), Ba2V2O7 (green), Sr2V2O7 (yellowish green), Zn3(VO4)2 (yellow), and Mg3(VO4)2 (yellow). A correlation was suggested from these compounds between the luminescent colors and the structural feature as the longer V–O distances in the VO4 tetrahedra in the crystal structures led to the longer wavelength in PL. This seemed to be also applicable for the oxofluorovanadates AIVOF4 (AI = K and Cs) which contain the VOF4 polyhedra with one O2− ion and four F‐ ions as the ligands, as they exhibited the reddish PL.
Improvements and Modifications to Room‐Temperature Fabrication Method for Dielectric Li2MoO4 Ceramics
Authors: Kähäri Hanna , Teirikangas Merja , Juuti Jari , Jantunen Heli 
Published: January 2015

Dielectric properties of lithium molybdate disks fabricated by moistening water‐soluble Li2MoO4 powder, compressing it, and postprocessing the samples at 120°C, were improved by the optimization of powder particle size, sample pressing pressure, and postprocessing time. It appeared that the postprocessing temperature of the Li2MoO4 ceramics could be chosen so as to be applicable to the associated integrated materials as long as the postprocessing time was adequately adjusted to ensure the removal of the residual water. In addition, the dielectric properties of Li2MoO4 ceramic were modified with an inclusion of suitable additives. For example, at 1 GHz the relative permittivity of Li2MoO4 disks fabricated at room temperature and postprocessed at 120°C was increased from 6.4 to 8.8 with an addition of 10 vol% of rutile TiO2 and to 9.7 with an addition of 10 vol% of BaTiO3. At the same time the loss tangent value increased from 0.0006 to 0.0014 and to 0.011, respectively.
Transcontinental migratory connectivity predicts parasite prevalence in breeding populations of the European barn swallow
Authors: von Rönn J. A. C. , Harrod C. , Bensch S. , Wolf J. B. W. 
Published: January 2015

AbstractParasites exert a major impact on the eco‐evolutionary dynamics of their hosts and the associated biotic environment. Migration constitutes an effective means for long‐distance invasions of vector‐borne parasites and promotes their rapid spread. Yet, ecological and spatial information on population‐specific host–parasite connectivity is essentially lacking. Here, we address this question in a system consisting of a transcontinental migrant species, the European barn swallow (Hirundo rustica) which serves as a vector for avian endoparasites in the genera Plasmodium, Haemoproteus and Leucocytozoon. Using feather stable isotope ratios as geographically informative markers, we first assessed migratory connectivity in the host: Northern European breeding populations predominantly overwintered in dry, savannah‐like habitats in Southern Africa, whereas Southern European populations were associated with wetland habitats in Western Central Africa. Wintering areas of swallows breeding in Central Europe indicated a migratory divide with both migratory programmes occurring within the same breeding population. Subsequent genetic screens of parasites in the breeding populations revealed a link between the host's migratory programme and its parasitic repertoire: controlling for effects of local breeding location, prevalence of Africa‐transmitted Plasmodium lineages was significantly higher in individuals overwintering in the moist habitats of Western Central Africa, even among sympatrically breeding individuals with different overwintering locations. For the rarer Haemoproteus parasites, prevalence was best explained by breeding location alone, whereas no clear pattern emerged for the least abundant parasite Leucocytozoon. These results have implications for our understanding of spatio‐temporal host–parasite dynamics in migratory species and the spread of avian borne diseases.
An emergency response‐type rainfall‐runoff‐inundation simulation for 2011 Thailand floods
Authors: Sayama T. , Tatebe Y. , Tanaka S. 
Published: January 2015

AbstractA devastating flood disaster occurred in Thailand in 2011. In case of such large‐scale flooding, it is important to predict the dynamics of inundation on a near real‐time basis for safe evacuation. To predict widespread inundation, where both rainfall‐runoff from surrounding mountains and rainfall on floodplains contribute to the event, this paper applied a rainfall‐runoff‐inundation (RRI) model to the entire Chao Phraya River basin (160 000 km2). Near real‐time simulation was conducted for emergency responses with globally available dataset including satellite‐based topography (HydroSHEDS derived from SRTM) and rainfall (TRMM 3B42RT) during the disaster. Post‐flood simulation was also carried out with more local information. The RRI model was found capable of representing the peak inundation extent with an acceptable accuracy and correctly predicting a 1‐month lasting inundation in the lower part of the basin. On the other hand, the prediction overestimated the river discharge by 40% and the inundation water level by 2 m mainly due to the neglect of the evapotranspiration effect. The post‐flood simulation improved its accuracy by up to 10% for river discharges and 1 m for peak inundation water levels, but it did not lead to better agreement of flood extents with those based on the remote sensing. Further study is recommended to improve accuracy for modelling of spatial extent of flooding. Furthermore, sensitivity analysis with different input suggested what information should be prioritised for emergency response‐type flood simulations.
Prevalence of gastroesophageal reflux disease in children, adults, and elderly in the same community
Authors: Okimoto Eiko , Ishimura Norihisa , Morito Yoshiya , Mikami Hironobu , Shimura Shino , Uno Goichi , Tamagawa Yuji , Aimi Masahito , Oshima Naoki , Kawashima Kousaku , Kazumori Hideaki , Sato Shuichi , Ishihara Shunji , Kinoshita Yoshikazu 
Published: January 2015

AbstractBackground and AimThe prevalence of gastroesophageal reflux disease (GERD) in adults is increasing in Japan as well as worldwide likely due to increasing obesity and the decreasing rate of Helicobacter pylori infection. However, data regarding the prevalence of GERD in children and adolescents in Japan are lacking. We investigated the prevalence of GERD in children, adults, and elderly living in the same community.MethodsWe surveyed employees of Shimane University Hospital and a related facility and their families using the Gastroesophageal Reflux Disease Questionnaire (GerdQ) and Izumo Scale instruments with demographic information (age, sex, body height, and body weight) and information regarding concurrent medication being taken for GERD. The presence of GERD was defined as a GerdQ score of ≥ 8.ResultsA total of 1859 subjects (771 males, 1088 females; 6–96 years old) were eligible for assessment. The prevalence of GERD in those under 20 years old was 4.4%, which was approximately one third of the rate in adults (11.6%). GERD prevalence was closely associated with obesity in adults, but not in subjects under 20 years old. GERD and other gastrointestinal symptoms frequently overlapped in both adults and younger subjects.ConclusionWe found that the prevalence of GERD in subjects under 20 years of age was lower than that in adults and not associated with obesity. Nevertheless, it is important to be aware of symptoms such as heartburn and/or regurgitation when children and adolescents seek routine clinical care.
Interleukin‐8: A critical chemokine in biliary atresia
Authors: Dong Rui , Zheng Shan 
Published: January 2015

AbstractBiliary atresia (BA) is characterized by periductular inflammation and fibrosis and is associated with the progressive obliteration of the bile ducts. The induction and maintenance of systemic and local inflammatory responses plays a pivotal role in this process. Interleukin‐8 (IL‐8) is an important mediator of inflammation and the immune response in human disease. IL‐8 is overexpressed in BA, and its expression positively correlates with inflammation and liver fibrosis. In this review, we focus on the available evidence, recent insights, and future clinical and preclinical possibilities regarding the role of IL‐8 in BA.
Ideal colonoscopic surveillance intervals to reduce incidence of advanced adenoma and colorectal cancer
Authors: Good Norm M , Macrae Finlay A , Young Graeme P , O'Dywer John , Slattery Masha , Venables William , Lockett Trevor J , O'Dwyer Marilla 
Published: January 2015

AbstractBackground and AimsThere is limited information about the interplay between multiple risk factors contributing to the risk of advanced neoplasia. We determined the actual risk for advanced neoplasia in relation to lapsed time between colonoscopies in people enrolled in a structured surveillance program. This risk information can be used to guide the selection of optimal surveillance intervals.MethodsPatients were recruited into programs at two major tertiary hospitals, with a personal or family history of advanced neoplasia. Five thousand one hundred forty‐one patients had an index and one or more surveillance colonoscopies. Fifty‐one percent had a family history of colorectal neoplasia while the remainder had a personal history.ResultsPatients with an immediately prior colonoscopy result (prior result) of advanced adenoma had a risk for advanced neoplasia 7.1 times greater than those with a normal prior result. Cancer as a prior result did not confer a greater risk than either a hyperplastic polyp or a nonadvanced adenoma. Being female reduced risk, age increased risk. Only a family history of a first‐degree relative diagnosed under 55, or definite or suspected hereditary nonpolyposis colorectal cancer (HNPCC) conferred an increased risk over a personal history of advanced neoplasia.ConclusionsMost family history categories did not confer excess risk above personal history of advanced neoplasia. A prior cancer poses less of a risk than a prior advanced adenoma. Based on our models, a person with an advanced adenoma should be scheduled for colonoscopy at 3 years, corresponding to a 15% risk of advanced neoplasia for a male aged under 56. Guidelines should be updated that uses a 15% risk as a benchmark for calculating surveillance intervals.
The biosynthesis and wall‐binding of hemicelluloses in cellulose‐deficient maize cells: An example of metabolic plasticity
Authors: de Castro María , Miller Janice G. , Acebes José Luis , Encina Antonio , García‐Angulo Penélope , Fry Stephen C. 
Published: January 2015

AbstractCell‐suspension cultures (Zea mays L., Black Mexican sweet corn) habituated to 2,6‐dichlorobenzonitrile (DCB) survive with reduced cellulose owing to hemicellulose network modification. We aimed to define the hemicellulose metabolism modifications in DCB‐habituated maize cells showing a mild reduction in cellulose at different stages in the culture cycle. Using pulse‐chase radiolabeling, we fed habituated and non‐habituated cultures with [3H]arabinose, and traced the distribution of 3H‐pentose residues between xylans, xyloglucans and other polymers in several cellular compartments for 5 h. Habituated cells were slower taking up exogenous [3H]arabinose. Tritium was incorporated into polysaccharide‐bound arabinose and xylose residues, but habituated cells diverted a higher proportion of their new [3H]xylose residues into (hetero) xylans at the expense of xyloglucan synthesis. During logarithmic growth, habituated cells showed slower vesicular trafficking of polymers, especially xylans. Moreover, habituated cells showed a decrease in the strong wall‐binding of all pentose‐containing polysaccharides studied; correspondingly, especially in log‐phase cultures, habituation increased the proportion of 3H‐hemicelluloses ([3H]xylans and [3H]xyloglucan) sloughed into the medium. These findings could be related to the cell walls' cellulose‐deficiency, and consequent reduction in binding sites for hemicelluloses; the data could also reflect the habituated cells' reduced capacity to integrate arabinoxylans by extra‐protoplasmic phenolic cross‐linking, as well as xyloglucans, during wall assembly.
Evaluation of the immunomodulatory effect of melatonin on the T‐cell response in peripheral blood from systemic lupus erythematosus patients
Authors: Medrano‐Campillo Pablo , Sarmiento‐Soto Helia , Álvarez‐Sánchez Nuria , Álvarez‐Ríos Ana I. , Guerrero Juan M. , Rodríguez‐Prieto Ismael , Castillo‐Palma María Jesús , Lardone Patricia J. , Carrillo‐Vico Antonio 
Published: January 2015

AbstractSystemic lupus erythematosus (SLE) is an autoimmune disorder characterized by the production of antinuclear autoantibodies. In addition, the involvement of CD4+ T‐helper (Th) cells in SLE has become increasingly evident. Although the role of melatonin has been tested in some experimental models of lupus with inconclusive results, there are no studies evaluating the melatonin effect on cells from patients with SLE. Therefore, the aim of this study was to analyse the role of in vitro administered melatonin in the immune response of peripheral leukocytes from treated patients with SLE (n = 20) and age‐ and sex‐matched healthy controls. Melatonin was tested for its effect on the production of key Th1, Th2, Th9, Th17 and innate cytokines. The frequency of T regulatory (Treg) cells and the expression of FOXP3 and BAFF were also explored. Our results are the first to show that melatonin decreased the production of IL‐5 and to describe the novel role of melatonin in IL‐9 production by human circulating cells. Additionally, we highlighted a two‐faceted melatonin effect. Although it acted as a prototypical anti‐inflammatory compound, reducing exacerbated Th1 and innate responses in PHA‐stimulated cells from healthy subjects, it caused the opposite actions in immune‐depressed cells from patients with SLE. Melatonin also increased the number of Treg cells expressing FOXP3 and offset BAFF overexpression in SLE patient cells. These findings open a new field of research in lupus that could lead to the use of melatonin as treatment or cotreatment for SLE.