bluuebunny/crossref_metadata_2025_split huggingface dataset:
Han Receives 2009 Geodesy Section Award
Authors: Ray Richard D. , Jekeli Christopher 
Published: May 2010

It gives us great pleasure to see Shin‐Chan Han receive AGU's 2009 Geodesy Section Award, presented to a young scientist for major advances in the field of geodesy.Shin‐Chan burst upon the geodetic scene just before the launch of the Gravity Recovery and Climate Experiment (GRACE) satellites, and the timing could not have been more propitious—both for Shin‐Chan and for the GRACE project. His doctoral thesis at Ohio State University dealt with efficient methods for determining gravity from satellite‐to‐satellite tracking data, of the sort GRACE was soon providing. Soon thereafter a remarkable series of papers began to appear, as Shin‐Chan exploited the new time‐variable gravity measurements for applications ranging from surface water hydrology, to earthquake deformation, to ocean tides. All of these used new and highly original methods for extracting signals from the basic satellite tracking data. His analysis of the gravity changes associated with the great 2004 Sumatra earthquake was a revelation to many, for it emphasized the power of satellite gravity data to complement seismology, for example, by constraining the long‐wavelength viscoelastic relaxation and subsequent stress redistribution.
Rebuilding depleted fish stocks: biology, ecology, social science, and management strategies
Authors: Hammer Cornelius , Kjesbu Olav Sigurd , Kruse Gordon H. , Shelton Peter A. 
Published: May 2010

Abstract
Hammer, C., Kjesbu, O. S., Kruse, G. H., and Shelton, P. A. 2010. Rebuilding depleted fish stocks: biology, ecology, social science, and management strategies. – ICES Journal of Marine Science, 67: 1825–1829. This is an introduction to an ICES/PICES symposium entitled as in the title of this manuscript. During the symposium, five theme sessions embraced the subject material under the headings “Impact of fisheries and environmental impacts on stock structure, reproductive potential, and recruitment dynamics”, “Trophic controls on stock recovery”, “Methods for analysing and modelling stock recovery”, “Social and economic aspects of fisheries management and governance”, and “Management and recovery strategies”. A panel discussion provided a valuable overview of current understanding and research focus.
Morphological and genetic evidence that Octopus vulgaris Cuvier, 1797 inhabits Amsterdam and Saint Paul Islands (southern Indian Ocean)
Authors: Guerra Ángel , Roura Álvaro , González Ángel F. , Pascual Santiago , Cherel Yves , Pérez-Losada Marcos 
Published: May 2010

AbstractGuerra, Á., Roura, Á., González, Á. F., Pascual, S., Cherel, Y., and Pérez-Losada, M. 2010. Morphological and genetic evidence that Octopus vulgaris Cuvier, 1797 inhabits Amsterdam and Saint Paul Islands (southern Indian Ocean). – ICES Journal of Marine Science, 67: 1401–1407. The coastal octopus at Saint Paul and Amsterdam Islands is Octopus vulgaris Cuvier 1797. Meristic and morphological characters, along with phylogenetic analysis of COI and COIII DNA sequences, were used to identify 11 animals collected in 2000 or 2001. The range of the species is therefore expanded to include the oceanic islands of the central southern Indian Ocean. The trees also depicted the genus Octopus as polyphyletic and O. vulgaris sense Cuvier or sensu stricto as monophyletic.
Parental Perceptions of Research After Completion of Placebo‐controlled Trials in Pediatric Gastroenterology
Authors: Perez Maria E , Langseder Annette , Lazar Eric , Youssef Nader N 
Published: May 2010

ABSTRACTBackground and Objectives:Investigators may have concerns that parents will not allow their children to participate in placebo‐controlled trials (PCTs). The aim of the present study was to identify potential differences between parental perceptions in families who successfully completed (CO) a clinical trial compared with those who were noncompleters (NC).Patients and Methods:Parents of both CO and NC children enrolled in pediatric gastrointestinal studies performed in the previous year were eligible. NC were defined as those who were screen failures or treatment nonresponders or had adverse events. One hundred seven parents were identified and mailed a 26‐item questionnaire eliciting perceptions regarding participation in research. Questionnaires were sent 6 months after participation in research ended.Results:Seventy‐eight (69%) parents returned the survey. Characteristics included maternal responders (98%), English as primary language (97%), and education beyond high school (85%). Five parents (4.7%) had children involved in previous research trials. There were no significant differences in responses found between CO (n = 49; 63%) and NC (n = 29; 37%) in regard to importance of research, perceptions of risk to child, benefits to child, and more attention in the study. Statistical significance was approached in regard to the comfort with the research team, with a greater portion of CO stating that the researcher put the parent at ease and the NC feeling less positive about the interaction (P = 0.05).Conclusions:A positive perception about participation in research is not stratified by successful completion of a PCT. These results should encourage investigators and institutional review boards that if properly designed and conducted, pediatric PCTs can result in a positive experience for parents.
A Comparison of Presentation and Management Trends in Acute Pancreatitis Between Infants/Toddlers and Older Children
Authors: Park Alexander J , Latif Sahibzada U , Ahmad Mahwish U , Bultron Gilberto , Orabi Abrahim I , Bhandari Vineet , Husain Sohail Z 
Published: May 2010

ABSTRACTObjectives:Acute pancreatitis is a necroinflammatory disease that leads to 210,000 hospitalizations in the United States annually. Recent reports suggest that there may be important differences in clinical features between infants/toddlers and older children. Thus, in this study we make a direct comparison between the pediatric age groups in presentation and management trends of acute pancreatitis.Patients and Methods:We examined all children (ages 0 to 20 years) admitted to Yale‐New Haven Children's Hospital with pancreatitis between 1994 and 2007.Results:Two hundred seventy‐one cases met inclusion criteria for acute pancreatitis. Infants and toddlers manifested fewer signs and symptoms of abdominal pain, epigastric tenderness, and nausea compared with older children (43% vs 93%; 57% vs 90%; and 29% vs 76%, respectively; P < 0.05 for all comparisons). They were more likely to be diagnosed by serum lipase than by amylase and to undergo radiographic evaluation (P < 0.05). They had a longer hospital stay (19.5 vs 4 days; P < 0.05) and were less likely to be directly transitioned to oral nutrition (14% vs 71%; P < 0.05).Conclusions:Infants and toddlers with acute pancreatitis present with fewer classical symptoms and are managed differently from older children. We believe these data will be helpful in evaluating and understanding treatment practices in this age group.
Development and Assessment of a Modified Pediatric Crohn Disease Activity Index
Authors: Leach Steven T , Nahidi Lily , Tilakaratne Samantha , Day Andrew S , Lemberg Daniel A 
Published: May 2010

ABSTRACTThe Pediatric Crohn Disease Activity Index (PCDAI) is an established and validated measure of disease activity in children with Crohn disease. However, its use in the research setting can be limited because of ambiguity of the subjective and anthropometric components of the index. Here we propose and evaluate a modified PCDAI (Mod PCDAI) consisting of the laboratory measures of the PCDAI plus C‐reactive protein. This Mod PCDAI can provide an indication of disease activity because it correlates with the PCDAI, physicians' global assessment, and fecal calprotectin, and therefore may provide a suitable alternative to the PCDAI when required.
Gastric Electrical Activity Becomes Abnormal in the Upright Position in Patients With Postural Tachycardia Syndrome
Authors: Safder Shaista , Chelimsky Thomas C , O'Riordan Mary Ann , Chelimsky Gisela 
Published: May 2010

ABSTRACTObjectives:Some patients with functional abdominal pain report worsening of symptoms in the upright position. Many of these have a postural tachycardia syndrome (POTS). We investigated whether the electrical activity of the stomach changes during the upright portion of a tilt table test in patients with and without POTS.Patients and Methods:All of the children undergoing autonomic testing were offered enrollment in this institutional review board–approved prospective study between October 2007 and January 2009. Electrogastrography was recorded 10 minutes in the supine position and during the entire upright portion of tilt. Children were divided into 2 groups: POTS and No‐POTS. Findings were correlated with this grouping using Fisher exact test and either Student t test or Wilcoxon rank sum test as appropriate.Results:Forty‐nine patients participated (35 girls), with a mean age of 14.7 + 3.5 years, 25 with POTS and 24 without. The POTS and No‐POTS groups did not differ in baseline normal gastric activity. The change from supine to standing showed a significant difference in the electrogastrographic tracing between the POTS and No‐POTS groups (P < 0.04–0.09), best seen in channels 1 and 4. In particular, gastric activity became more abnormal in the upright position in the POTS group, whereas the opposite occurred in the No‐POTS group.Conclusions:The electrical activity of the stomach changes during the upright position in children with POTS, but not in children without this diagnosis. These changes could relate to their report of worsening pain in the upright position.
β‐Carotene Deficiency in Cholestatic Liver Disease of Childhood Is Caused by β‐Carotene Malabsorption
Authors: Socha Piotr , Skorupa Ewa , Pawlowska Joanna , Wierzbicka Aldona , Dhawan Anil , Jankowska Irena , Karczmarewicz Ela , Kubalska Jolanta , Łukaszkiewicz Jacek , Lorenc Roman 
Published: May 2010

ABSTRACTBackground:Depletion of β‐carotene (b‐c) has not been extensively studied in children with chronic cholestatic liver disease.Patients and Methods:We assessed b‐c serum concentration in 53 children with cholestatic liver disease: 19 patients operated on for biliary atresia, 12 with Alagille syndrome, and 22 with progressive familial intrahepatic cholestasis. To test b‐c absorption, 6 children with chronic cholestasis received a load of 10 mg b‐c/kg body weight.Results:We found decreased b‐c concentrations in 45 patients. The absorption of b‐c was not detectable in 5 of 6 children studied.Conclusions:b‐c depletion is a common problem of chronic cholestatic liver disease in childhood that can be attributed to disturbed intestinal absorption.
Intestinal Microbiota of 6‐week‐old Infants Across Europe: Geographic Influence Beyond Delivery Mode, Breast‐feeding, and Antibiotics
Authors: Fallani Matteo , Young David , Scott Jane , Norin Elisabeth , Amarri Sergio , Adam Rüdiger , Aguilera Marga , Khanna Sheila , Gil Angel , Edwards Christine A , Doré Joël ,   Other Members of the INFABIO Team
Published: May 2010

ABSTRACTObjectives:There are many differences in diet and lifestyle across Europe that may influence the development of the infant gut microbiota. This work aimed to assess the impact of geographic area, mode of delivery, feeding method, and antibiotic treatment on the fecal microbiota of infants from 5 European countries with different lifestyle characteristics: Sweden, Scotland, Germany, Italy, and Spain.Patients and Methods:Fecal samples from 606 infants (age 6 weeks) recruited within the European project INFABIO were analyzed by fluorescent in situ hybridization combined with flow cytometry using a panel of 10 rRNA targeted group‐ and species‐specific oligonucleotide probes. Information on factors potentially affecting gut microbiota composition was collected with questionnaires and associations were evaluated with multivariate analyses.Results:The Bifidobacterium genus was predominant (40% average proportion of total detectable bacteria), followed by Bacteroides (11.4%) and enterobacteria (7.5%). Northern European countries were associated with higher proportions of bifidobacteria in infant feces, whereas a more diverse microbiota with more bacteroides characterized southern countries. Bifidobacteria dominated the microbiota of breast‐fed infants, whereas formula‐fed babies had significantly higher proportions of Bacteroides and members of the Clostridium coccoides and Lactobacillus groups. Newborns delivered by cesarean section or from mothers treated with antibiotics perinatally had lower proportions of Bacteroides and members of the Atopobium cluster.Conclusions:Delivery mode and feeding method influenced the fecal microbiota of European infants at 6 weeks, as expected, but the effect of country of birth was more pronounced, with dominant bifidobacteria in northern countries and greater early diversification in southern European countries.
Medical Management of Alagille Syndrome
Authors: Kamath Binita M , Loomes Kathleen M , Piccoli David A 
Published: May 2010

ABSTRACTAlagille syndrome is a highly variable, autosomal dominant disorder that affects the liver, heart, eyes, face, skeleton, kidneys, and vascular system. Much has been learned about the genetics of this disorder, which is caused primarily by mutations in the Notch signaling pathway ligandJAGGED1; however, the medical management of this condition is complex and continues to generate controversy. The significant variability of organ involvement requires the managing physician to have an understanding of the breadth and interplay of the variable manifestations. Furthermore, the liver disease in particular requires an appreciation of the natural history and evolution of the profound cholestasis.
Overexpression of AtDOF4.7, an Arabidopsis DOF Family Transcription Factor, Induces Floral Organ Abscission Deficiency in Arabidopsis
Authors: Wei Peng-Cheng , Tan Feng , Gao Xin-Qi , Zhang Xiu-Qing , Wang Gao-Qi , Xu Heng , Li Li-Juan , Chen Jia , Wang Xue-Chen 
Published: May 2010

Abstract
After flower pollination, a programmed process called abscission occurs in which unwanted floral organs are actively shed from the main plant body. We found that a member of the DOF (for DNA binding with one finger) transcription factor family, Arabidopsis (Arabidopsis thaliana) DOF4.7, was expressed robustly in the abscission zone. The Arabidopsis 35S::AtDOF4.7 lines with constitutive expression of AtDOF4.7 exhibited an ethylene-independent floral organ abscission deficiency. In these lines, anatomical analyses showed that the formation of the abscission zone was normal. However, dissolution of the middle lamella failed to separate between the cell walls. AtDOF4.7 was identified as a nucleus-localized transcription factor. This protein had both in vitro and in vivo binding activity to typical DOF cis-elements in the promoter of an abscission-related polygalacturonase (PG) gene, PGAZAT. Overexpression of AtDOF4.7 resulted in down-regulation of PGAZAT. AtDOF4.7 interacted with another abscission-related transcription factor, Arabidopsis ZINC FINGER PROTEIN2. Taken together, our results suggest that AtDOF4.7 participates in the control of abscission as part of the transcription complex that directly regulates the expression of cell wall hydrolysis enzymes.
Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants
Authors: Nakagami Hirofumi , Sugiyama Naoyuki , Mochida Keiichi , Daudi Arsalan , Yoshida Yuko , Toyoda Tetsuro , Tomita Masaru , Ishihama Yasushi , Shirasu Ken 
Published: May 2010

Abstract
Knowledge of phosphorylation events and their regulation is crucial to understand the functional biology of plants. Here, we report a large-scale phosphoproteome analysis in the model monocot rice (Oryza sativa japonica ‘Nipponbare’), an economically important crop. Using unfractionated whole-cell lysates of rice cells, we identified 6,919 phosphopeptides from 3,393 proteins. To investigate the conservation of phosphoproteomes between plant species, we developed a novel phosphorylation-site evaluation method and performed a comparative analysis of rice and Arabidopsis (Arabidopsis thaliana). The ratio of tyrosine phosphorylation in the phosphoresidues of rice was equivalent to those in Arabidopsis and human. Furthermore, despite the phylogenetic distance and the use of different cell types, more than 50% of the phosphoproteins identified in rice and Arabidopsis, which possessed ortholog(s), had an orthologous phosphoprotein in the other species. Moreover, nearly half of the phosphorylated orthologous pairs were phosphorylated at equivalent sites. Further comparative analyses against the Medicago phosphoproteome also showed similar results. These data provide direct evidence for conserved regulatory mechanisms based on phosphorylation in plants. We also assessed the phosphorylation sites on nucleotide-binding leucine-rich repeat proteins and identified novel conserved phosphorylation sites that may regulate this class of proteins.
DIBER: protein, DNA or both?
Authors: Chojnowski Grzegorz , Bochtler Matthias 
Published: May 2010

The programDIBER(an acronym for DNA and FIBER) requires only native diffraction data to predict whether a crystal contains protein, B-form DNA or both. In standalone mode, the classification is based on the cube root of the reciprocal unit-cell volume and the largest local average of diffraction intensities at 3.4 Å resolution. In combined mode, thePhaserrotation-function score (for the 3.4 Å shell and a canonical B-DNA search model) is also taken into account. In standalone (combined) mode,DIBERclassifies 87.4 ± 0.2% (90.2 ± 0.3%) of protein, 69.1 ± 0.3% (78.8 ± 0.3%) of protein–DNA and 92.7 ± 0.2% (90.0 ± 0.2%) of DNA crystals correctly. Reliable predictions with a correct classification rate above 80% are possible for 36.8 ± 1.0% (60.2 ± 0.4%) of the protein, 43.6 ± 0.5% (59.8 ± 0.3%) of the protein–DNA and 83.3 ± 0.3% (82.6 ± 0.4%) of the DNA structures. Surprisingly, selective use of the diffraction data in the 3.4 Å shell improves the overall success rate of the combined-mode classification. An open-sourceCCP4/CCP4i-compatible version ofDIBERis available from the authors' website at http://www.iimcb.gov.pl/diber and is subject to the GNU Public License.
Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa
Authors: Ascone Isabella , Savino Carmelinda , Kahn Richard , Fourme Roger 
Published: May 2010

The 2 Å resolution crystal structure of bovine erythrocyte Cu,Zn superoxide dismutase (CuZnSOD) has been determined by X-ray diffraction at high pressure (0.57 GPa) and room temperature. At 0.57 GPa the secondary, tertiary and quaternary structures are similar to other previously determined bovine erythrocyte CuZnSOD structures. Nevertheless, pressure has a localized impact on the atomic coordinates of Cαatoms and on side chains. The compression of the crystal and of the protein backbone is anisotropic. This anisotropy is discussed, taking into account intermolecular contacts and protein conformation. Pressure perturbation highlights the more flexible zones in the protein such as the electrostatic loop. At 0.57 GPa, a global shift of the dimetallic sites in both subunits and changes in the oxidation state of Cu were observed. The flexibility of the electrostatic loop may be useful for the interaction of different metal carriers in the copper-uptake process, whereas the flexibility of the metal sites involved in the activity of the protein could contribute to explaining the ubiquitous character of CuZnSODs, which are found in organisms living in very different conditions, including the deep-sea environment. This work illustrates the potential of combining X-ray crystallography with high pressure to promote and stabilize higher energy conformational substates.
Structure ofArabidopsischloroplastic monothiol glutaredoxin AtGRXcp
Authors: Li Lenong , Cheng Ninghui , Hirschi Kendal D. , Wang Xiaoqiang 
Published: May 2010

Monothiol glutaredoxins (Grxs) play important roles in maintaining redox homeostasis in living cells and are conserved across species.Arabidopsis thalianamonothiol glutaredoxin AtGRXcp is critical for protection from oxidative stress in chloroplasts. The crystal structure of AtGRXcp has been determined at 2.4 Å resolution. AtGRXcp has a glutaredoxin/thioredoxin-like fold with distinct structural features that differ from those of dithiol Grxs. The structure reveals that the putative active-site motif CGFS is well defined and is located on the molecular surface and that a long groove extends to both sides of the catalytic Cys97. Structural comparison and molecular modeling suggest that glutathione can bind in this groove and form extensive interactions with conserved charged residues including Lys89, Arg126 and Asp152. Further comparative studies reveal that a unique loop with five additional residues adjacent to the active-site motif may be a key structural feature of monothiol Grxs and may influence their function. This study provides the first structural information on plant CGFS-type monothiol Grxs, allowing a better understanding of the redox-regulation mechanism mediated by these plant Grxs.
Hepatitis C virus risk behaviors within the partnerships of young injecting drug users
Authors: Hahn Judith A. , Evans Jennifer L. , Davidson Peter J. , Lum Paula J. , Page Kimberly 
Published: May 2010

ABSTRACTAims  Young injection drug users (IDU) are at high risk for hepatitis C virus (HCV). We sought to determine whether perceiving one's injecting partner to be HCV positive was associated with decreased odds of engaging in receptive needle/syringe sharing (RNS) or ancillary equipment sharing (AES) with that partner.Design  Cross sectional study.Setting  2003 to 2007 in San Francisco.Participants  212 young (under age 30) IDU who were HCV antibody negative reported on 492 injecting partnerships.Measurements  Self‐reported RNS and AES within injecting partnerships.Findings  RNS and AES (in the absence of RNS) occurred in 23% and 64% of injecting partnerships in the prior month. The odds of engaging in RNS were significantly lower for relationships in which the participant reported that his/her partner was HCV positive (odds ratio [OR] 0.49; 95% confidence interval [CI] 0.25–0.95). This association was attenuated when adjusted for reusing one's own needle/syringe (adjusted OR 0.57; 95% CI 0.28–1.15). The odds of engaging in AES were lower for participants who did not know the HCV status of their partner, only among non‐sexual partnerships (OR 0.47; 95% CI 0.29–0.76).Conclusions  Because perceiving one's partner to be HCV positive was associated with decreased RNS, increased HCV testing and partner disclosure may be warranted. AES was common and was decreased only among non‐sexual partnerships in which the HCV status of the partner was not known. This suggests that interventions to reduce AES in young IDU must be widespread.