bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil and Water Assessment Tool Soil Loss Simulation at the Sub‐Basin Scale in the Alt Penedès–Anoia Vineyard Region (Ne Spain) in the 2000s
Authors: Martínez‐Casasnovas José A. , Ramos Maria C. , Benites Grace 
Published: August 2013

AbstractThis paper evaluates soil loss due to water erosion in an area of 32,362 ha with a predominant land use of vineyards (Alt Penedès–Anoia region, Catalonia, Spain). The Soil and Water Assessment Tool (SWAT) was used incorporating daily climatic data for the period 2000–2010 and also detailed soil and land use maps. Particular attention was given to the universal soil loss equation cover and management factor (C factor) of vineyards, with a minimum value of 0·15 being determined for this crop. The model was calibrated using daily flow data for the year 2010, which yielded satisfactory results. Even so, significant differences were obtained on days with high‐intensity rainfall events, when the model overestimated runoff and peak discharge. In these vineyards, the simulated average soil losses per sub‐basin ranged between 0·13 and 9·73 Mg ha−1 y−1, with maximum values of between 26·32 and 42·60 Mg ha−1 y−1 registered in fine‐loamy soils developed on unconsolidated Tertiary marls. Other findings were related to problems associated with SWAT calibration under Mediterranean conditions characterised by major climate variability and high‐intensity rainfall events. Copyright © 2013 John Wiley & Sons, Ltd.
Influence of Different Bryophyte Carpets on Vascular Plant Establishment Around Pools in Restored Peatlands
Authors: Laberge Virginie , Hugron Sandrine , Rochefort Line , Poulin Monique 
Published: August 2013

AbstractVascular plants associated to natural peatland pools do not spontaneously colonize edges of man‐made pools in restored peatlands and have proven to be recalcitrant to the usual restoration techniques. The goal of this study was to evaluate the effect of the species used as a seedbed (Cladopodiella fluitans, Sphagnum cuspidatum, or Sphagnum magellanicum) and its developmental stage (established carpet or newly reintroduced fragments) on establishment success in the field of the seeds of four vascular species: Carex limosa, Carex magellanica, Carex oligosperma, and Scheuchzeria palustris. The germination rate was measured after one season and growth after two seasons. Seedbed composition and developmental stage had no effect on Carex, whereas the germination of S. palustris was higher on S. cuspidatum. Growth of vascular plants was slightly improved on S. magellanicum carpets and was lower on seedbeds of C. fluitans. Our results lead us to recommend seeding at the same time as bryophyte fragments are spread and fostering introduction of Sphagnum mosses, preferably to C. fluitans, around artificial pool edges. Copyright © 2013 John Wiley & Sons, Ltd.
Serum concentrations of perfluorinated alkyl acids and their associations with diet and personal characteristics among Swedish adults
Authors: Bjermo Helena , Darnerud Per Ola , Pearson Monika , Barbieri Heléne Enghardt , Lindroos Anna Karin , Nälsén Cecilia , Lindh Christian H. , Jönsson Bo A. G. , Glynn Anders 
Published: August 2013

ScopeIn this study, food is suggested as a major source of human exposure to perfluorinated alkyl acids (PFAA). We investigated relations between serum levels of PFAA in adults and diet/lifestyle factors nationwide in Sweden.Methods and resultsIn 2010–2011, adults (18–80 years, N = 270) recorded their diet for 4 days and answered a food frequency questionnaire. PFAA were measured in blood serum as well as v‐3 fatty acids in plasma phospholipids as a biomarker for fish consumption. Higher levels of PFAA were associated with male sex, increased age, and higher education. Women reporting full breastfeeding for ≥12 months had 32–44% lower levels of perfluorooctane sulfonate, perfluorooctanoic acid, and perfluorohexane sulfonate than women who never nursed their infants full‐time. Serum perfluorooctane sulfonate, perfluorononanoic acid, perfluorodecanoic acid, and perfluoroundecanoic acid were positively related to n‐3 fatty acids in plasma (partial r = 0.19–0.34, p ≤ 0.05).ConclusionThe relatively strong correlations between biomarkers of fish consumption and certain PFAA suggest that PFAA exposure should be taken into account in health risk and benefit assessment of fish consumption. Breastfeeding appears to be a major source of elimination of certain PFAA among women, and consequently PFAA exposure of nursed infants could be significant.
Minimal clinically important difference in myasthenia gravis: Outcomes from a randomized trial
Authors: Katzberg Hans D. , Barnett Carolina , Merkies Ingemar S.J. , Bril Vera 
Published: August 2013

ABSTRACTIntroduction: The minimal clinically important difference (MCID) is the smallest outcome change that has clinical significance. Its use has not been established in the study of myasthenia gravis (MG). Methods: Patients from a published intravenous immunoglobulin (IVIg) vs. placebo study were studied. One anchor‐based and 3 distribution‐based techniques were used to identify quantitative myasthenia gravis score (QMGS), repetitive nerve stimulation (RNS), and single‐fiber electromyography (SFEMG) MCID cut‐offs. Patients with a change‐score exceeding MCID cut‐offs were compared. Results: MCID cut‐offs were below a QMGS change of 3.0. Anchor‐based and 1 × SEM cut‐offs showed 58.3% vs. 30.7% responders (P = 0.017), ½ SD 54.2% vs. 19.2% responders (P = 0.018), and effect size 0.519 vs. 0.164 (P = 0.011) in IVIg vs. placebo. Anchor‐based (P = 0.73) and effect‐size (P = 0.41) MCID cut‐offs did not show a difference between IVIg and placebo. MCID methods did not produce meaningful RNS cut‐offs. Conclusions: QMGS MCID values provide clinically relevant information and are recommended in MG trials. MCID analysis shows that improvement in MG patients treated with IVIg reflects clinically meaningful changes. Muscle Nerve 49: 661–665, 2014
Testing the impact of diagenesis on the δ18O and δ13C of benthic foraminiferal calcite from a sediment burial depth transect in the equatorial Pacific
Authors: Edgar Kirsty M. , Pälike Heiko , Wilson Paul A. 
Published: August 2013

AbstractStable oxygen and carbon isotope (δ18O and δ13C) values measured in foraminiferal calcite are one of the primary tools used in paleoceanography. Diagenetic recrystallization of foraminiferal calcite can act to reset primary isotopic values, but its effects are typically poorly quantified. Here we test the impact of early stage diagenesis on stable isotope records generated from a suite of drill sites in the equatorial Pacific Ocean recovered during Ocean Drilling Program Leg 199 and Integrated Ocean Drilling Program Expedition 320. Our selected sites form paleowater and burial depth transects, with excellent stratigraphic control allowing us to confidently correlate our records. We observe large intersite differences in the preservation state of benthic foraminiferal calcite, implying very different recrystallization histories, but negligible intersite offsets in benthic δ18O and δ13C values. We infer that diagenetic alteration of benthic foraminiferal calcite (in sedimentary oozes) must predominantly occur at shallow burial depths (<100 m) where offsets in both the temperature and isotopic composition of waters in which the foraminifera calcified and pore waters in which diagenesis occurs are small. Our results suggest that even extensive recrystallization of benthic foraminiferal calcite results in minimal shifts from primary δ18O and δ13C values. This finding supports the long‐held suspicion that diagenetic alteration of foraminiferal calcite is less problematic in benthic than in planktic foraminifera and that in deep‐sea sediments routinely employed for paleoceanographic studies benthic foraminifera are robust recorders of stable isotope values in the fossil record.
Clinical characteristics and treatment outcome of childhood acute lymphoblastic leukemia in Saudi Arabia: A multi‐institutional retrospective national collaborative study
Authors: Al‐Sudairy Reem , Al‐Nasser Abdullah , Alsultan Abdulrahman , Ahmari Ali Al , Abosoudah Ibraheem , Al‐Hayek Reema , Al‐Harbi Talal , Al‐Manjomi Fahad , Al‐Harbi Musa , Al‐Ghamdi Hasna , Al‐Shahrani Mohammed , Belgaumi Asim F. 
Published: August 2013

AbstractBackgroundTreatment of childhood acute lymphoblastic leukemia (ALL) has been available in Saudi Arabia (SA) for over 30 years; however, only limited data have been published from there. This study was conducted to establish processes for collaborative data collection and provide clinical characteristics and outcome of children with ALL in SA.ProcedureClinical data for patients diagnosed from 2004 to 2008 were retrospectively collected at eight institutions and entered remotely into a custom‐built database. Statistics regarding clinical and genetic characteristics and treatment outcome were calculated.ResultsThe 594 evaluable patients had a median age of 4.37 years and 56.4% were boys. Majority of patients had B‐precursor ALL while 10.7% had T‐ALL. CNS leukemia was present in 5.2% of patients. The distribution of common genetic abnormalities was similar to that reported from western populations, with 24.6% hyperdiploidy, 21% RUNX1‐ETV6 positivity, 4.2% BCR‐ABL1 positivity, and 2.5% with MLL gene rearrangement. Patients received risk‐adapted therapy according to various protocols, although treatment strategies for the majority were similar. Five‐year OS, RFS and EFS were 86.9%, 79.1%, and 73.3%, respectively. The OS for patients with pre‐B ALL was significantly higher than for T‐ALL (88.0% vs. 71.8%; P = 0.019, Log‐Rank test). Patients with pre‐B ALL categorized as low‐risk by NCI/Rome criteria and those with hyperdiploidy had OS of 93.4% and 95.8%, respectively.ConclusionsThe characteristics of childhood ALL in SA are similar to those observed in developed countries. Future prospective studies utilizing unified national protocols are needed to further improve the outcome of our patients. Pediatr Blood Cancer 2014;61:74–80. © 2013 Wiley Periodicals, Inc.
Intensive induction chemotherapy followed by myeloablative chemotherapy with autologous hematopoietic progenitor cell rescue for young children newly‐diagnosed with central nervous system atypical teratoid/rhabdoid tumors: The head start III experience
Authors: Zaky Wafik , Dhall Girish , Ji Lingyun , Haley Kelley , Allen Jeffrey , Atlas Mark , Bertolone Salvatore , Cornelius Albert , Gardner Sharon , Patel Ramesh , Pradhan Kamnesh , Shen Violet , Thompson Stephen , Torkildson Joseph , Sposto Richard , Finlay Jonathan L. 
Published: August 2013

AbstractBackgroundAtypical teratoid/rhabdoid tumor (AT/RT) of the central nervous system (CNS) is a rare embryonal neoplasm of early childhood with dismal outcome and no current uniformly accepted treatment. Given its highly aggressive nature and predilection for dissemination at diagnosis, intensive multimodal therapy is required.Materials and MethodsNineteen children with newly diagnosed CNS AT/RT were treated on the head start (HS) III protocol. Treatment consisted of surgical resection, 5 cycles of induction chemotherapy, followed by consolidation with myeloablative chemotherapy and autologous hematopoietic progenitor cell rescue (AuHCR). Irradiation was given following recovery from consolidation based on patient age, disease extent at diagnosis, and treatment response to induction.ResultsNineteen children (median age of 14 months) were treated on HS III between 2003 and 2009. Only four finished induction and three proceeded to consolidation. There are presently four survivors at 40, 42, 46, and 79 months from study enrollment. Eleven patients experienced tumor progression at a median time to progression of 4.1 months of whom 10 died with a median time from progression to death of 2.6 months. Five toxic deaths occurred, three of them while on the study. The 3‐year event‐free survival (EFS) and overall survival (OS) for the whole group was 21 ± 9% and 26 ± 10%, respectively. Five patients received irradiation at progression with only one long‐term survivor.ConclusionA minority of children with CNS AT/RT treated on HS III may be long‐term survivors without irradiation. More effective therapies are desperately needed. Pediatr Blood Cancer 2014;61:95–101. © 2013 Wiley Periodicals, Inc.
Estimating the excess of inappropriate prescriptions of anti‐dopaminergic anti‐emetics during acute gastroenteritis epidemics in France
Authors: Roussel Victoire , Tritz Thomas , Souty Cécile , Turbelin Clément , Arena Christophe , Lambert Bruno , Lillo‐LeLouët Agnès , Kernéis Solen , Blanchon Thierry , Hanslik Thomas 
Published: August 2013

ABSTRACTPurposeAnti‐dopaminergic anti‐emetics (ADA) use for the treatment of nausea associated with gastroenteritis (GE) can be considered inappropriate, as their effects are not supported by evidence of clinical efficacy and can potentially induce serious adverse events.ObjectiveThis study quantifies the suboptimal consumption of ADA attributable to seasonal GE epidemics in France and its cost.MethodsGE epidemiological data were collected and transmitted by the general practitioners (GPs) of Sentinelles network. Epidemic periods were identified by periodic regression. Drug sales data were obtained from pharmacies, and costs data were obtained from the French National Social Security. The ADA use and costs incurred by seasonal GE epidemics were calculated.ResultsDuring the epidemic periods considered in this study, the median age of patients seen by GPs for GE was 24 years old. During each epidemic, a sale increase by 14% for domperidone, by 15% for metoclopramide and 30% for metopimazine was observed. The average cost attributable to seasonal GE epidemic was 5 030 000 Euros, of which 2 160 000 Euros were incurred by the French National Social Security.ConclusionLinking epidemiological databases helped to identify and quantify inappropriate ADA prescriptions. GE treatment guidelines should be disseminated more widely. Copyright © 2013 John Wiley & Sons, Ltd.
Automatic detection of adverse events to predict drug label changes using text and data mining techniques
Authors: Gurulingappa Harsha , Toldo Luca , Rajput Abdul Mateen , Kors Jan A. , Taweel Adel , Tayrouz Yorki 
Published: August 2013

ABSTRACTPurposeThe aim of this study was to assess the impact of automatically detected adverse event signals from text and open‐source data on the prediction of drug label changes.MethodsOpen‐source adverse effect data were collected from FAERS, Yellow Cards and SIDER databases. A shallow linguistic relation extraction system (JSRE) was applied for extraction of adverse effects from MEDLINE case reports. Statistical approach was applied on the extracted datasets for signal detection and subsequent prediction of label changes issued for 29 drugs by the UK Regulatory Authority in 2009.Results76% of drug label changes were automatically predicted. Out of these, 6% of drug label changes were detected only by text mining. JSRE enabled precise identification of four adverse drug events from MEDLINE that were undetectable otherwise.ConclusionsChanges in drug labels can be predicted automatically using data and text mining techniques. Text mining technology is mature and well‐placed to support the pharmacovigilance tasks. Copyright © 2013 John Wiley & Sons, Ltd.
Exhaustive comparison and classification of ligand‐binding surfaces in proteins
Authors: Murakami Yoichi , Kinoshita Kengo , Kinjo Akira R. , Nakamura Haruki 
Published: August 2013

AbstractMany proteins function by interacting with other small molecules (ligands). Identification of ligand‐binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand‐binding protein sequences and functions. Consequently, we classified the patches into ∼2000 well‐characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross‐fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes.
An automated approach to network features of protein structure ensembles
Authors: Bhattacharyya Moitrayee , Bhat Chanda R. , Vishveshwara Saraswathi 
Published: August 2013

AbstractNetwork theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone‐efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user‐friendly, standalone program package named PSN‐Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X‐ray structures. The novelty in network construction lies in the explicit consideration of side‐chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long‐range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross‐correlation/interaction energy in PSN‐Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN‐Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin‐conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN‐Ensemble for single‐static structures of active/inactive states of β2‐adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN‐Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN‐Ensemble/psn_index.html.
Sparsely populated residue conformations in protein structures: Revisiting “experimental” Ramachandran maps
Authors: Kalmankar Neha V. , Ramakrishnan C. , Balaram P. 
Published: August 2013

ABSTRACTThe Ramachandran map clearly delineates the regions of accessible conformational (φ–ψ) space for amino acid residues in proteins. Experimental distributions of φ, ψ values in high‐resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely “arid”, fully allowed region in the top left quadrant establishes that side‐chain and backbone interactions may provide the energetic compensation necessary for populating this region of φ–ψ space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II′ β turns (Bin 13). Of the 516 non‐Gly residues in Bin 13, 384 occupied the i + 1 position of Type II′ β turns. Further examination of these turn segments revealed a high propensity to occur at the N‐terminus of helices and as a tight turn in β hairpins. The β strand–helix motif with the Type II′ β turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101–1112. © 2013 Wiley Periodicals, Inc.
Leonidas Zervas award lecture: Abiotic ligands for new quaternary architectures of peptides and proteins
Authors: Jensen Knud J. 
Published: August 2013

AbstractThis review is the result of a kind invitation to provide a report on the basis of the Leonidas Zervas award lecture at the 32nd European Peptide Society in Athens, Greece, September 2012. The lecture covered several topics including contributions toward new methods for the assembly of peptides and chemical modification of proteins. The present review will focus on another topic from the Zervas lecture, namely, our recent efforts at creating new, artificial architectures for the organization of the quaternary structure of proteins. Crucially, this is achieved with abiotic ligands and not protein surface engineering. This concept was demonstrated for the important biopharmaceutical peptide insulin, by using both abiotic metal ion binding ligands and perfluoroalkyl chains. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Self‐trapping of the d‐d charge transfer exciton in rock‐salt structured Zn1–xNixO evidenced by soft X‐ray excited luminescence
Authors: Sokolov V. I. , Pustovarov V. A. , Churmanov V. N. , Ivanov V. Yu. , Gruzdev N. B. , Sokolov P. S. , Baranov A. N. , Moskvin A. S. 
Published: August 2013

AbstractLuminescence spectra of NiO and solid solutions Zn1–xNixO have been investigated under vacuum ultra‐violet (VUV) and soft X‐ray (XUV) excitation (DESY, Hamburg). Photoluminescence (PL) spectra show broad emission violet and green bands centered at about 3.2 and 2.6 eV, respectively. The PL excitation (PLE) spec‐tral evolution and lifetime measurements reveal that the two mechanisms with short and long decay times, at‐tributed to the d(eg)‐d(eg) and p(π)‐d charge transfer (CT) transitions in the range 4–6 eV, respectively, are responsible for the observed emissions. The XUV excitation makes it possible to avoid the predominant role of the surface effects in luminescence and reveal a bulk violet luminescence with puzzling well isolated doublet of very narrow lines. These lines with close energies near 3.3 eV are attributed to recombination transitions in the self‐trapped d‐d CT excitons formed by the coupled Jahn‐Teller Ni+ and Ni3+ centers. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)