bluuebunny/crossref_metadata_2025_split huggingface dataset:
First measurements of nitrous oxide in Arctic sea ice
Authors: Randall Kevin , Scarratt Michael , Levasseur Maurice , Michaud Sonia , Xie Huixiang , Gosselin Michel 
Published: April 2012

Nitrous oxide (N2O) contributes ∼6% of the total radiative forcing from long‐lived greenhouse gases. While tropospheric concentrations have increased by 20% since the beginning of the industrial revolution, sources and sinks of N2O are still poorly quantified. In the Arctic, N2O atmospheric concentrations vary seasonally, due mainly to vertical mixing. The contributions of local natural sources to this cycle are still unknown. Here we report on N2O measurements conducted in the bottom 10 cm of the sea ice and in the underlying surface water (USW) from late March to early May 2008 in the southeastern Beaufort Sea and Amundsen Gulf. Bulk N2O concentrations in ice were low (∼6 nM) and were consistently undersaturated with respect to the USW (∼40% saturation) and the atmosphere (∼30% saturation). Loss of N2O via brine rejection during sea ice formation in fall and winter can explain these low N2O ice concentrations. An unknown fraction of this rejected N2O is likely ventilated to the atmosphere either directly from the ice or through leads during ice formation, while in spring and early summer, melting of the N2O‐depleted sea ice is expected to lower the partial pressure of N2O of newly open waters which could act as a sink for atmospheric N2O. These first measurements indicate that sea ice formation and melt has the potential to generate sea‐air or air‐sea fluxes of N2O, respectively.
Ozone and alkyl nitrate formation from the Deepwater Horizon oil spill atmospheric emissions
Authors: Neuman J. A. , Aikin K. C. , Atlas E. L. , Blake D. R. , Holloway J. S. , Meinardi S. , Nowak J. B. , Parrish D. D. , Peischl J. , Perring A. E. , Pollack I. B. , Roberts J. M. , Ryerson T. B. , Trainer M. 
Published: April 2012

Ozone (O3), alkyl nitrates (RONO2), and other photochemical products were formed in the atmosphere downwind from the Deepwater Horizon (DWH) oil spill by photochemical reactions of evaporating hydrocarbons with NOx (=NO + NO2) emissions from spill response activities. Reactive nitrogen species and volatile organic compounds (VOCs) were measured from an instrumented aircraft during daytime flights in the marine boundary layer downwind from the area of surfacing oil. A unique VOC mixture, where alkanes dominated the hydroxyl radical (OH) loss rate, was emitted into a clean marine environment, enabling a focused examination of O3 and RONO2 formation processes. In the atmospheric plume from DWH, the OH loss rate, an indicator of potential O3 formation, was large and dominated by alkanes with between 5 and 10 carbons per molecule (C5–C10). Observations showed that NOx was oxidized very rapidly with a 0.8 h lifetime, producing primarily C6–C10 RONO2 that accounted for 78% of the reactive nitrogen enhancements in the atmospheric plume 2.5 h downwind from DWH. Both observations and calculations of RONO2 and O3 production rates show that alkane oxidation dominated O3 formation chemistry in the plume. Rapid and nearly complete oxidation of NOx to RONO2 effectively terminated O3 production, with O3 formation yields of 6.0 ± 0.5 ppbv O3 per ppbv of NOx oxidized. VOC mixing ratios were in large excess of NOx, and additional NOx would have formed additional O3 in this plume. Analysis of measurements of VOCs, O3, and reactive nitrogen species and calculations of O3 and RONO2 production rates demonstrate that NOx‐VOC chemistry in the DWH plume is explained by known mechanisms.
Short‐term transport variability of the Antarctic Circumpolar Current from satellite gravity observations
Authors: Bergmann I. , Dobslaw H. 
Published: April 2012

Ocean bottom pressure gradients deduced from the satellite gravity mission Gravity Recovery and Climate Experiment (GRACE) were previously shown to provide barotropic transport variations of the Antarctic Circumpolar Current (ACC) with up to monthly resolution. Here, bottom pressure distributions from GRACE with monthly (GFZ RL04) and higher temporal resolution (CNES/GRGS with 10 days, ITG‐GRACE2010 with daily resolution) are evaluated over the ACC area. Even on time scales shorter than 10 days, correlations with in situ bottom pressure records frequently exceed 0.6 with positive explained variances, giving evidence that high‐frequency nontidal ocean mass variability is captured by the daily ITG‐GRACE2010 solutions not already included in the applied background models. Bottom pressure is subsequently taken to calculate the barotropic component of the ACC transport variability across Drake Passage. For periods longer than 30 days, transport shows high correlations between 0.4 and 0.5 with several tide gauge records along the coast of Antarctica. Still significant correlations around 0.25 are obtained even for variability with periods shorter than 10 days. Since transport variations are predominantly affected by time‐variable surface winds, GRACE‐based transports are contrasted against an atmospheric index of the Southern Annular Mode (SAM), which represents the Southern Hemispheric wind variability. Correlations between the SAM and GRACE‐based transports are consistently higher than correlations between any of the available sea level records in all frequency bands considered, indicating that GRACE is indeed able to accurately observe a hemispherically consistent pattern of bottom pressure (and hence ACC transport) variability that is otherwise at least partially masked in tide gauge records due to local weather effects, sea ice presence and steric signals.
Stress and Coping in Parents of Children and Adolescents with Spinal Muscular Atrophy
Authors: von Gontard A. , Rudnik-Schöneborn S. , Zerres K. 
Published: April 2012

AbstractChronic illness and disability is not only associated with higher rates of behavioural problems in children, but also parental stress which requires active coping. The aim of the study was to analyse stress and coping, as well as their mediating variables, in parents of children and adolescents with Spinal Muscular Atrophy (SMA).96 children and adolescents with SMA aged 6;0 to 18;11 years were compared to 59 age, sex and SES matched controls. Parental stress was measured with the QRS, coping with the F-COPES and social support with the F-SOZU questionnaires.Parental stress was significantly higher in the SMA families for the total score and all subscales of the QRS. Stress was higher in families with severely affected SMA types I and II. The greatest percentage of variance contributing to stress could be explained by lack of social support, degree of disability and behavioural problems in the child. Although social support was reduced, the actual coping abilities of the families did not differ.Families with children and adolescents with SMA show high degrees of stress and strain which are associated with the severity of the disease, reduced social support and child behaviour. Despite these stresses they manage and cope no differently from families with healthy children.
The role of plant viroids in diseases - new developments.
Authors: Serio F. di , Torchetti E. M. , Flores R. , Navarro B. 
Published: April 2012

Abstract
Viroids are tiny infectious agents of plants, consisting exclusively of a small (246-401 nucleotides) circular RNA lacking protein-coding ability. Likely mimicking structural features of cellular RNAs, they can redirect the pre-existing host transcription and RNA trafficking machineries for their own replication and spread, and by doing so they eventually elicit severe diseases. Therefore, in addition to causing phytopathological problems, viroids also offer opportunities for basic research on cellular RNA-based networks. After briefly summarizing the biological, molecular and epidemiological properties of viroids, this review focuses on relevant novelties of these infectious agents, with major emphasis on the molecular pathways presumably mediating viroid pathogenesis and on current phytosanitary emergences in Europe associated with the dissemination of viroids potentially causing severe diseases in vegetable crops.
Bpipe: a tool for running and managing bioinformatics pipelines
Authors: Sadedin Simon P. , Pope Bernard , Oshlack Alicia 
Published: April 2012

Abstract
Summary: Bpipe is a simple, dedicated programming language for defining and executing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, Bpipe is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.
Availability and implementation: Bpipe is freely available from http://bpipe.org under a BSD License.
Contact: simon.sadedin@mcri.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
ChemSpot: a hybrid system for chemical named entity recognition
Authors: Rocktäschel Tim , Weidlich Michael , Leser Ulf 
Published: April 2012

Abstract
Motivation: The accurate identification of chemicals in text is important for many applications, including computer-assisted reconstruction of metabolic networks or retrieval of information about substances in drug development. But due to the diversity of naming conventions and traditions for such molecules, this task is highly complex and should be supported by computational tools.
Results: We present ChemSpot, a named entity recognition (NER) tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and International Union of Pure and Applied Chemistry entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It achieves an F1 measure of 68.1% on the SCAI corpus, outperforming the only other freely available chemical NER tool, OSCAR4, by 10.8 percentage points.
Availability: ChemSpot is freely available at: http://www.informatik.hu-berlin.de/wbi/resources
Contact: leser@informatik.hu-berlin.de
Multiple potential regulatory sites of TLR4 activation induced by LPS as revealed by novel inhibitory human TLR4 mAbs
Authors: Tsukamoto Hiroki , Fukudome Kenji , Takao Shoko , Tsuneyoshi Naoko , Ihara Hideyuki , Ikeda Yoshitaka , Kimoto Masao 
Published: April 2012

Abstract
Recognition of LPS by the toll-like receptor 4 (TLR4)/MD-2 complex is a trigger of innate immune defense against bacterial invasion. However, excessive immune activation by this receptor complex causes septic shock and autoimmunity. Manipulation of TLR4 signaling represents a potential therapy that would avoid the detrimental consequences of unnecessary immune responses. In this study, we established two novel mAbs that inhibit LPS-induced human TLR4 activation. HT52 and HT4 mAbs inhibited LPS-induced nuclear factor-κB activation in TLR4/MD-2-expressing Ba/F3-transfected cells and cytokine production and up-regulation of CD86 in the human cell line U373 and PBMCs. These inhibitory activities were stronger than that of HTA125 mAb, which we previously reported. Immunofluorescent and biochemical studies using TLR4 deletion mutants revealed that HT52 and HT4 recognized spatially distinct regions on TLR4 irrespective of MD-2 association. The HT52 and HTA125 epitopes were localized within aa 50–190, while the HT4 epitope was formed only by the full length of TLR4. In addition, we demonstrated that HT52 and HT4 failed to compete with LPS for binding to TLR4/MD-2 but inhibited LPS-induced TLR4 internalization. Inhibitory activities were not due to the interaction with the Fcγ receptor CD32. Our finding that binding of mAbs to at least two distinct regions on TLR4 inhibits LPS-dependent activation provides a novel method for manipulating TLR4 activation and also a rationale for designing drugs targeted to TLR4.
Human microdose evaluation of the novel EP1 receptor antagonist GSK269984A
Authors: Ostenfeld Thor , Beaumont Claire , Bullman Jonathan , Beaumont Maria , Jeffrey Phillip 
Published: April 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• The microdose administration of novel drug candidates to humans in early development is currently undergoing evaluation as a cost‐efficient approach to the early assessment of pharmacokinetics (PK) before the commitment of resources required to support formal phase 1 studies.• The microdose approach assumes that PK can be extrapolated linearly over the full range of exposures achieved with sub‐pharmacological doses up to the therapeutic dose range.• Few microdose studies have been undertaken in the context of pharmaceutical drug development and their precise role in the selection of candidates for further clinical evaluation at therapeutic doses has yet to be fully substantiated.WHAT THIS STUDY ADDS• The present study describes the elective application of a human microdose study with a novel EP1 receptor antagonist, GSK269984A, to address a critical development liability posed by uncertainty with respect to the predicted human PK profile.• Microdose data revealed a favourable PK profile, consistent with a clinically acceptable dosing regimen. These data support the value of undertaking a microdose study early in the drug discovery process to facilitate risk evaluation and to enable decision‐making.AIM The primary objective was to evaluate the pharmacokinetics (PK) of the novel EP1 antagonist GSK269984A in human volunteers after a single oral and intravenous (i.v.) microdose (100 µg).METHOD GSK269984A was administered to two groups of healthy human volunteers as a single oral (n= 5) or i.v. (n= 5) microdose (100 µg). Blood samples were collected for up to 24 h and the parent drug concentrations were measured in separated plasma using a validated high pressure liquid chromatography‐tandem mass spectrometry method following solid phase extraction.RESULTS Following the i.v. microdose, the geometric mean values for clearance (CL), steady‐state volume of distribution (Vss) and terminal elimination half‐life (t1/2) of GSK269984A were 9.8 l h−1, 62.8 l and 8.2 h. Cmax and AUC(0,∞) were 3.2 ng ml−1 and 10.2 ng ml−1 h, respectively; the corresponding oral parameters were 1.8 ng ml−1 and 9.8 ng ml−1 h, respectively. Absolute oral bioavailability was estimated to be 95%. These data were inconsistent with predictions of human PK based on allometric scaling of in vivo PK data from three pre‐clinical species (rat, dog and monkey).CONCLUSION For drug development programmes characterized by inconsistencies between pre‐clinical in vitro metabolic and in vivo PK data, and where uncertainty exists with respect to allometric predictions of the human PK profile, these data support the early application of a human microdose study to facilitate the selection of compounds for further clinical development.
A randomized study of sodium hypochlorite versus formocresol pulpotomy in primary molar teeth
Authors: RUBY JOHN D. , COX CHARLES F. , MITCHELL STEPHEN C. , MAKHIJA SONIA , CHOMPU‐INWAI PAPIMON , JACKSON JANICE 
Published: April 2012

International Journal of Paediatric Dentistry 2013; 23: 145–152
Background.  Alternatives to vital pulpotomy treatment in primary teeth are being sought because of the high formaldehyde content of traditional formocresol (FC) pulpotomy medicaments.Aim.  The aim was to compare the clinical and radiographic success of vital pulpotomy treatment in primary molars using 3% sodium hypochlorite (NaOCl) versus a 1 : 5 dilution of Buckley’s FC.Design.  Pulpotomies were performed in primary molars of healthy children between 3 and 10 years old. Sixty‐five primary teeth were randomized into two groups that were evaluated for treatment outcomes. Following treatment, the pulp chamber was filled with zinc oxide eugenol (ZnOE) and restored with a stainless steel crown cemented with glass ionomer cement. Clinical and radiographic outcomes were recorded at 6 and 12 months.Results.  The control (FC) and experimental (NaOCl) groups demonstrated 100% clinical success at 6 and 12 months. The NaOCl group had 86% (19/22) radiographic success at 6 months and 80% (12/15) at 12 months. The FC group had 84% (21/25) radiographic success at 6 months and 90% (9/10) at 12 months. No significant differences were found in the radiographic outcomes between the two groups at 6 and 12 months (Fisher’s exact test; P = 0.574 and P = 0.468, respectively).Conclusion.  NaOCl demonstrated clinical and radiographic success comparable to FC.
GABRA2 markers moderate the subjective effects of alcohol
Authors: Uhart Magdalena , Weerts Elise M. , McCaul Mary E. , Guo Xiuqing , Yan Xiaofei , Kranzler Henry R. , Li Ning , Wand Gary S. 
Published: April 2012

ABSTRACTIndividual differences in subjective responses (SRs) to alcohol are moderated by genetic variants and may be risk factors for the development of alcohol use disorders. Variation in the GABAAα2 receptor subunit gene (GABRA2) has been associated with alcohol dependence (AD). Therefore, we examined whether individual differences in SRs, which reflect sensitivity to the effects of alcohol, are associated with variation in GABRA2. Sixty‐nine healthy subjects (21–30 years) underwent a laboratory‐based within‐session cumulative oral alcohol dosing procedure, achieving a mean peak blood alcohol level of 100.4 mg/dl (standard error = 2.5). Subjective assessments were obtained throughout the session, including ascending and descending limbs of the alcohol curve. We genotyped single nucleotide polymorphisms (SNPs) across the chromosome 4 region spanning GABRA2 and analyzed the effect of genotype and haplotypes on subjective responses to alcohol. Population substructure was characterized through the use of ancestry informative markers. Individual SNP analysis demonstrated that carriers of the minor alleles for SNPs rs279858, rs279844, rs279845, rs279826, rs279828 and rs279836 had lower ‘Negative’ alcohol effects scores than individuals homozygous for the common allele at each SNP (P = 0.0060, P = 0.0035, P = 0.0045, P = 0.0043, P = 0.0037 and P = 0.0061, respectively). Haplotype effects of block 1 showed concordant results with SNPs in this block (P = 0.0492 and P = 0.0150 for haplotypes 1 and 4, respectively). The minor alleles for several of these SNPs have previously been associated with AD. Our findings provide further evidence that variation within GABRA2 is associated with attenuated negative responses to alcohol, a known risk factor for vulnerability to alcohol use disorders.
Xenotransplantation‐associated infectious risk: a WHO consultation
Authors: Fishman Jay A. , Scobie Linda , Takeuchi Yasuhiro 
Published: April 2012

Fishman JA, Scobie L, Takeuchi Y. Xenotransplantation‐associated infectious risk: a WHO consultation. Xenotransplantation 2012; 19: 72–81. © 2012 John Wiley & Sons A/S.Abstract:  Xenotransplantation carries the potential risk of the transmission of infection with the cells or tissues of the graft. The degree of risk is unknown in the absence of clinical trials. The clinical application of xenotransplantation has important implications for infectious disease surveillance, both at the national and international levels. Preclinical data indicate that infectious disease events associated with clinical xenotransplantation from swine, should they occur, will be rare; data in human trials are limited but have demonstrated no transmission of porcine microorganisms including porcine endogenous retrovirus. Xenotransplantation will necessitate the development of surveillance programs to detect known infectious agents and, potentially, previously unknown or unexpected pathogens. The development of surveillance and safety programs for clinical trials in xenotransplantation is guided by a “Precautionary Principle,” with the deployment of appropriate screening procedures and assays for source animals and xenograft recipients even in the absence of data suggesting infectious risk. All assays require training, standardization and validation, and sharing of laboratory methods and expertise to optimize the quality of the surveillance and diagnostic testing. Investigation of suspected xenogeneic infection events (xenosis, xenozoonosis) should be performed in collaboration with an expert data safety review panel and the appropriate public health and competent authorities. It should be considered an obligation of performance of xenotransplantation trials to report outcomes, including any infectious disease transmissions, in the scientific literature. Repositories of samples from source animals and from recipients prior to, and following xenograft transplantation are essential to the investigation of possible infectious disease events. Concerns over any potential hazards associated with xenotransplantation may overshadow potential benefits. Careful microbiological screening of source animals used as xenotransplant donors may enhance the safety of transplantation beyond that of allotransplant procedures. Xenogeneic tissues may be relatively resistant to infection by some human pathogens. Moreover, xenotransplantation may be made available at the time when patients require organ replacement on a clinical basis. Insights gained in studies of the microbiology and immunology of xenotransplantation will benefit transplant recipients in the future. This document summarizes approaches to disease surveillance in individual recipients of nonhuman tissues.
Upper limit of normal serum alanine and aspartate aminotransferase levels in Korea
Authors: Sohn Won , Jun Dae Won , Kwak Min Jung , Park Quehn , Lee Kang Nyeong , Lee Hang Lak , Lee Oh Young , Yoon Byung Chul , Choi Ho Soon 
Published: April 2012

AbstractBackground and Aim:  The widely accepted range of upper limits of normal (ULN) alanine aminotransferase (ALT) levels (ULN < 40 U/L) was recently challenged by several reports. Both ALT and aspartate aminotransferase (AST) are commonly used as surrogate markers of liver disease, but almost all studies of aminotransferase activity were conducted on ALT. We investigated not only ULN of ALT but also AST activity and to identify factors modulating them in healthy Korean.Methods:  A cross‐sectional study of 411 240 registered blood donors in all nationwide blood banks belonging to the Korean Red Cross were conducted. ULN of ALT and AST was evaluated adjusting their age according to the national population census database. “Decision tree model” was used to identify the affecting factors of ALT and AST and optimal cut‐off points of affecting factors.Results:  “ULN of ALT” was 34 U/L in men and 24 U/L in women and “ULN of AST” was 32 U/L in men and 26 U/L in women in the blood donor database. Decision tree analysis showed that ALT levels were mostly influenced by body mass index level and its critical two cut‐off points were 23.5 kg/m2 and 25.8 kg/m2, respectively. The most affecting factor of AST was gender.Conclusion:  Upper limits of normal of ALT and AST in Koreans were lower than conventional accepted values (< 40 U/L) but higher than recently suggested values (male < 30 U/L and female < 19 U/L). Body mass index was the most determining factor for ALT and gender was the most influencing factor for AST activity.