bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane-inlet mass spectrometry reveals a high driving force for oxygen production by photosystem II
Authors: Shevela Dmitriy , Beckmann Katrin , Clausen Jürgen , Junge Wolfgang , Messinger Johannes 
Published: February 2011

Oxygenic photosynthesis is the basis for aerobic life on earth. The catalytic Mn
4
O

x

CaY

Z

center of photosystem II (PSII), after fourfold oxidation, extracts four electrons from two water molecules to yield dioxygen. This reaction cascade has appeared as a single four-electron transfer that occurs in typically 1 ms. Inevitable redox intermediates have so far escaped detection, probably because of very short lifetime. Previous attempts to stabilize intermediates by high O
2
-back pressure have revealed controversial results. Here we monitored by membrane-inlet mass spectrometry (MIMS) the production of

from
18
O-labeled water against a high background of

in a suspension of PSII-core complexes. We found neither an inhibition nor an altered pattern of O
2
production by up to 50-fold increased concentration of dissolved O
2
. Lack of inhibition is in line with results from previous X-ray absorption and visible-fluorescence experiments, but contradictory to the interpretation of previous UV-absorption data. Because we used essentially identical experimental conditions in MIMS as had been used in the UV work, the contradiction was serious, and we found it was not to be resolved by assuming a significant slowdown of the O
2
release kinetics or a subsequent slow conformational relaxation. This calls for reevaluation of the less direct UV experiments. The direct detection of O
2
release by MIMS shows unequivocally that O
2
release in PSII is highly exothermic. Under the likely assumption that one H
+
is released in the S
4
→ S
0
transition, the driving force at pH 6.5 and atmospheric O
2
pressure is at least 220 meV, otherwise 160 meV.
Synthesis, characterization and capacitive performance of hydrous manganese dioxide nanostructures
Authors: Zhang Jintao , Chu Wei , Jiang Jianwen , Zhao X S 
Published: February 2011

Hydrous manganese dioxide nanostructures were synthesized via a catalytic oxidation reaction mechanism at mild temperatures. It was found that the morphology of the manganese dioxide nanostructures was significantly influenced by the pH of the reaction system. With increasing pH the morphology of manganese dioxide nanostructures changed from urchin-like structures to nanobelts. The capacitive performance was investigated by using cycle voltammetry and galvanostatic charge/discharge techniques. Hydrous manganese dioxide nanostructures obtained from a basic solution exhibited a capacitance of 262 F g− 1at a current density of 250 mA g− 1and a capacitive retention of 75% after 1200 cycles, suggesting that this is a promising electrode material for supercapacitors. The high specific capacitance is attributed to the hydrous nature coupled with a high surface area (181 m2 g− 1) of the manganese dioxide nanostructure.
Improving SNP discovery by base alignment quality
Authors: Li Heng 
Published: February 2011

Abstract
Summary: I propose a new application of profile Hidden Markov Models in the area of SNP discovery from resequencing data, to greatly reduce false SNP calls caused by misalignments around insertions and deletions (indels). The central concept is per-Base Alignment Quality, which accurately measures the probability of a read base being wrongly aligned. The effectiveness of BAQ has been positively confirmed on large datasets by the 1000 Genomes Project analysis subgroup.
Availability: http://samtools.sourceforge.net
Contact: hengli@broadinstitute.org
Population structure of a deep-water squaloid shark, the Portuguese dogfish (Centroscymnus coelolepis)
Authors: Veríssimo Ana , McDowell Jan R. , Graves John E. 
Published: February 2011

AbstractVeríssimo, A., McDowell, J. R., and Graves, J. E. 2011. Population structure of a deep-water squaloid shark, the Portuguese dogfish (Centroscymnus coelolepis). – ICES Journal of Marine Science, 68: . The genetic population structure of the deep-water squaloid Centroscymnus coelolepis (the Portuguese dogfish) in the eastern Atlantic was investigated using eight polymorphic nuclear microsatellite markers and a 496-bp fragment of the mitochondrial DNA control region (mtDNA CR). Samples (20–50 individuals per location) were collected off Ireland, Portugal, Madeira, Mauritania, South Africa, and the Azores (Mid-Atlantic Ridge). High levels of genetic diversity were found at the nuclear microsatellite loci (mean A = 17.3; overall Ho = 0.77), although there was low diversity at the mtDNA CR (h = 0.65, π = 0.0018). Genetic diversity for the Portuguese dogfish was homogeneously distributed among sampling locations, resulting in low and non-significant indices of genetic differentiation (e.g. FST = −0.0013 to 0.0096, ΦST = −0.017 to 0.033; p > 0.5), consistent with the absence of population structure within the area sampled. The results indicate that C. coelolepis has a high dispersal potential within the eastern Atlantic, and its apparent spatial segregation by size and maturity stage suggest large-scale migration associated with the reproductive cycle.
Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean
Authors: Bolon Yung-Tsi , Haun William J. , Xu Wayne W. , Grant David , Stacey Minviluz G. , Nelson Rex T. , Gerhardt Daniel J. , Jeddeloh Jeffrey A. , Stacey Gary , Muehlbauer Gary J. , Orf James H. , Naeve Seth L. , Stupar Robert M. , Vance Carroll P. 
Published: February 2011

Abstract
Mutagenized populations have become indispensable resources for introducing variation and studying gene function in plant genomics research. In this study, fast neutron (FN) radiation was used to induce deletion mutations in the soybean (Glycine max) genome. Approximately 120,000 soybean seeds were exposed to FN radiation doses of up to 32 Gray units to develop over 23,000 independent M2 lines. Here, we demonstrate the utility of this population for phenotypic screening and associated genomic characterization of striking and agronomically important traits. Plant variation was cataloged for seed composition, maturity, morphology, pigmentation, and nodulation traits. Mutants that showed significant increases or decreases in seed protein and oil content across multiple generations and environments were identified. The application of comparative genomic hybridization (CGH) to lesion-induced mutants for deletion mapping was validated on a midoleate x-ray mutant, M23, with a known FAD2-1A (for fatty acid desaturase) gene deletion. Using CGH, a subset of mutants was characterized, revealing deletion regions and candidate genes associated with phenotypes of interest. Exome resequencing and sequencing of PCR products confirmed FN-induced deletions detected by CGH. Beyond characterization of soybean FN mutants, this study demonstrates the utility of CGH, exome sequence capture, and next-generation sequencing approaches for analyses of mutant plant genomes. We present this FN mutant soybean population as a valuable public resource for future genetic screens and functional genomics research.
Variability in the population pharmacokinetics of isoniazid in South African tuberculosis patients
Authors: Wilkins Justin J. , Langdon Grant , McIlleron Helen , Pillai Goonaseelan , Smith Peter J. , Simonsson Ulrika S. H. 
Published: February 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • The pharmacokinetic properties of isoniazid are well characterized, having been studied in seminal work beginning in the early 1950s. Pharmacokinetic models have been published in other populations. WHAT THIS PAPER ADDS • This work provides a population model for isoniazid pharmacokinetics in a South African population from a tuberculosis‐endemic region, of potential use in investigating the complex exposure‐response relationships found in the first line treatment of pulmonary tuberculosis. Previous work has been performed in smaller groups of healthy volunteers or predominantly Caucasian or Asian patients, but the pharmacokinetics of isoniazid in the population in this study are significantly different from those previously reported in other populations. The developed model will provide a basis for estimation of optimal doses in children.AIM This study was designed to characterize the population pharmacokinetics of isoniazid in South African pulmonary tuberculosis patients.METHODS Concentration–time measurements obtained from 235 patients receiving oral doses of isoniazid as part of routine tuberculosis chemotherapy in two clinical studies were pooled and subjected to nonlinear mixed‐effects analysis.RESULTS A two‐compartmental model, including first‐order absorption and elimination with allometric scaling, was found to describe the observed dose‐exposure relationship for oral isoniazid adequately. A mixture model was used to characterize dual rates of isoniazid elimination. Estimates of apparent clearance in slow and fast eliminators were 9.70 and 21.6 l h−1, respectively. The proportion of fast eliminators in the population was estimated to be 13.2%. Central volume of distribution was estimated to be 10% smaller in female patients and clearance was found to be 17% lower in patients with HIV. Variability in absorption rate (90%) was completely interoccasional in nature, whereas in relative bioavailability, interoccasional variability (8.4%) was lower than interindividual variability (26%). Oral doses, given once daily according to dosing policies at the time, were sufficient to reach therapeutic concentrations in the majority of the studied population, regardless of eliminator phenotype. Simulations suggested that current treatment guidelines (5 mg kg−1) may be suboptimal in fast eliminators with low body weight.CONCLUSIONS A population pharmacokinetic model was developed to characterize the highly variable pharmacokinetics of isoniazid in a South African pulmonary tuberculosis patient population. Current treatment guidelines may lead to underexposure in rapid isoniazid eliminators.
Influence of genetic, biological and pharmacological factors on warfarin dose in a Southern Brazilian population of European ancestry
Authors: Botton Mariana Rodrigues , Bandinelli Eliane , Rohde Luis Eduardo Paim , Amon Luis Carlos , Hutz Mara Helena 
Published: February 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Warfarin is an oral anticoagulant widely used for thromboembolic disease prophylaxis. The pharmacokinetics and pharmacodynamics of this drug vary with environmental and genetic factors. Several algorithms including genetic and non‐genetic factors have been developed for different populations. These investigations have shown that polymorphisms in CYP2C9 and VKORC1 genes are related to warfarin dose variation. WHAT THIS STUDY ADDS • This study confirms that CYP2C9 and VKORC1 genes are the main predictors of warfarin dose, but there are other genes with smaller effects that can improve the algorithm for better dose prediction.• This study observed for the first time an effect of the F2 gene on warfarin dose prediction.• The inclusion for the first time of co‐medication with amlodipine, carbamazepine, β‐adrenoceptor blockers and diuretics refined the construction of an algorithm for dose prediction.AIMS To investigate the influence of polymorphisms in CYP2C9, VKORC1, CYP4F2 and F2 genes on warfarin dose–response and develop a model including genetic and non‐genetic factors for warfarin dose prediction needed for each patient.METHODS A total of 279 patients of European ancestry on warfarin medication were investigated. Genotypes for −1639G>A, 1173C>T, and 3730G>A SNPs in the VKORC1 gene, CYP2C9*2 and CYP2C9*3, 1347C>T in the CYP4F2 gene and 494C>T in the F2 gene were determined by allelic discrimination with Taqman 5'‐nuclease assays.RESULTS The CYP2C9*2 and CYP2C9*3 polymorphisms in the CYP2C9 gene, −1639G>A and 1173C>T in the VKORC1 gene and 494C>T in the F2 gene are responsible for lower anticoagulant doses. In contrast, 1347C>T in the CYP4F2 gene and 3730G>A in the VKORC1 gene are responsible for higher doses of warfarin. An algorithm including genetic, biological and pharmacological factors that explains 63.3% of warfarin dose variation was developed.CONCLUSION The model suggested has one of the highest coefficients of determination among those described in the literature.
A cautious iodization programme bringing iodine intake to a low recommended level is associated with an increase in the prevalence of thyroid autoantibodies in the population
Authors: Pedersen Inge B. , Knudsen Nils , Carlé Allan , Vejbjerg Pernille , Jørgensen Torben , Perrild Hans , Ovesen Lars , Rasmussen Lone B. , Laurberg Peter 
Published: February 2011

SummaryAutoantibodies against the thyroid gland with thyroid peroxidase antibody (TPO‐Ab) and thyroglobulin antibody (Tg‐Ab) as the most common can often be demonstrated in serum. The effect of public iodization programmes on antibody prevalence is uncertain.Aim  To measure the concentrations of thyroid autoantibodies in the Danish population before and after mandatory iodization of salt.Methods  Two identical cross‐sectional population studies were performed before (Cohort 1 (C1), year 1997–1998, n = 4649, median urinary iodine 61 μg/l) and 4–5 years after (Cohort 2 (C2), year 2004–2005, n = 3570, median urinary iodine 101 μg/l) mandatory iodine fortification of salt was implemented in Denmark. Blood tests were analysed for TPO‐Ab and Tg‐Ab using sensitive assays.Results  Antibodies were more frequent in C2 than in C1: TPO‐Ab > 30 U/ml, C1 vs C2: 14·3 vs 23·8% (P < 0·001) and Tg‐Ab > 20 U/ml, C1 vs C2: 13·7 vs 19·9% (P < 0·001). The C2 vs C1 effect was confirmed in multivariate regression models (C1 reference): TPO‐Ab: OR (95% CI): 1·80 (1·59–2·04) and Tg‐Ab: 1·49 (1·31–1·69). The increase in the frequency of thyroid antibodies was most pronounced in young women and especially observed at low concentrations of antibodies.Conclusion  The prevalence of both TPO‐Ab and Tg‐Ab was higher 4–5 years after a cautious iodine fortification of salt was introduced in Denmark. The increase was most pronounced in young women and in the low concentrations of antibody. Further studies are needed to evaluate the long‐term effects of increased iodine intake on thyroid autoimmunity in the population.
Investigation of the significance of Oil Red O‐positive macrophage excess in bronchoalveolar lavage fluid during HIV infection
Authors: Lacoste‐Collin L. , Martin‐Blondel G. , Basset‐Léobon C. , Lauwers‐Cancès V. , d’Aure D. , Aziza J. , Berry A. , Marchou B , Delisle M. B. , Courtade‐Saïdi M. 
Published: February 2011

L. Lacoste‐Collin, G. Martin‐Blondel, C. Basset‐Léobon, V. Lauwers‐Cancès, D. d’Aure, J. Aziza, A. Berry, B Marchou, M.B. Delisle and M. Courtade‐SaïdiInvestigation of the significance of Oil Red O‐positive macrophage excess in bronchoalveolar lavage fluid during HIV infectionObjective:  To assess the significance of increased levels of Oil Red O‐positive macrophages (ORO‐PM) in bronchoalveolar lavage fluids (BALFs) from HIV‐positive patients.Methods:  Cytological data for seventy BALF samples from 66 consecutive HIV‐infected patients were analysed according to antiretroviral therapy regimen, presence of Pneumocystis jiroveci infection, blood CD4+T cell count, HIV‐1 viral load and plasma lipid levels. Non‐parametric tests were used to compare the values between groups.Results:  The percentages of ORO‐PM were high in this group: 40% [6–80] (median [interquartile range]). They were positively correlated with the BALF total cell count, 21% [5–48.5] for <300 cells/mm3 and 60% [26.5–80] for >300 cells/mm3 (P < 0.01) but inversely correlated with the percentage of BALF lymphocytes, 50% [20–80] for <15% lymphocytes and 11.5% [2–47] for ≥15% lymphocytes (P < 0.01). Antiretroviral therapy with or without protease inhibitors, plasma lipid levels, HIV‐1 viral load, blood CD4+T cell count or presence of a Pneumocystis jiroveci infection were not correlated with the ORO‐PM status.Conclusion:  Significantly increased numbers of ORO‐PM were correlated with high total cell counts and low lymphocyte counts in BALF, irrespective of disease activity or treatment. Extended work on a larger series of patients needs to be conducted.
A Taiwanese version of the International Consultation on Incontinence Questionnaire – Urinary Incontinence Short Form for pregnant women: instrument validation
Authors: Chang Shiow‐Ru , Chen Kuang‐Ho , Chang Ting‐Chen , Lin Ho‐Hsiung 
Published: February 2011

Aim.  To translate the International Consultation on Incontinence Questionnaire – Urinary Incontinence Short Form (ICIQ‐UI SF) from English to Taiwanese and to evaluate its reliability and validity for pregnant Taiwanese women.Background.  Urinary incontinence in pregnant women has been little investigated in Taiwan. A validated assessment instrument for urinary incontinence is needed for pregnant Taiwanese women.Design.  A non‐experimental design was used to test the psychometric properties of the Taiwanese version of the ICIQ‐UI SF.Method.  The internal consistency reliability and construct validity of the Taiwanese version of the ICIQ‐UI SF for pregnant women were evaluated in a random sample of 121 pregnant women at a medical center in Taiwan. Test–retest reliability was assessed for a sample of 55 pregnant women who completed this version at two time points in four weeks. Construct validity was verified with three questions and seven urinary‐leakage situations by factor analysis.Results.  The Taiwanese version of the ICIQ‐UI SF showed adequate test–retest reliability in pregnant Taiwanese women. The Pearson’s correlation coefficient of the total score was 0·75, kappa statistics showed excellent or good reproducibility for most items and McNemar’s test confirmed that there was no significant difference in the test–retest pair for each item of the scale. The internal consistency reliability of the scale was good, with Cronbach’s α = 0·80. Three factors were extracted and identified with an eigenvalue ≥1·04, explaining 65·64% the total variance. The first, second and third factors were ‘symptom and quality of life’, ‘stress incontinence or other types’ and ‘urge or overflow incontinence’.Conclusions.  The results provide evidence of the validity and reliability of the psychometric properties of the Taiwanese version of the ICIQ‐UI SF for pregnant women.Relevance to clinical practice.  This questionnaire is a suitable instrument for evaluating urinary incontinence in pregnant Taiwanese women.
Use of polyurethane foam inside plaster casts to prevent the onset of heel sores in the population at risk. A controlled clinical study
Authors: Forni Cristiana , Loro Loretta , Tremosini Morena , Mini Sandra , Pignotti Elettra , Bigoni Ombretta , Guzzo Giuseppe , Bellini Laura , Trofa Carmela , Di Cataldo Anna M , Guzzi Marilena 
Published: February 2011

Aim.  The aim of this study was to test the effectiveness of polyurethane foam in contact with the heel inside a plaster cast to decrease the rate of pressure sores in the population at most risk.Background.  The rate of pressure sores caused by the plaster cast is reported to be 14–15% in the paediatric population, 33·3% in patients having undergone chemotherapy for bone tumours and 43% in orthopaedic patients who already have sore skin when the cast is applied (grade 1 lesion) to the heel.Design.  Controlled clinical trial.Methods.  From November 2007–January 2009, all consecutive subjects requiring lower limb casts having undergone chemotherapy and/or presenting heel soreness received polyurethane foam in contact with the skin of the heel before applying the cast. The results were compared with those of patients with the same risk factors but were not administered the foam and were enrolled from May 2005–August 2006.Results.  In total, 156 patients were enrolled, 85 in the control group and 71 in the experimental group. In the experimental group, 2 of the 56 patients (3·6%) with sore skin developed a pressure sore compared with 21 of 49 (42·9%) in the control group without polyurethane foam (p < 0·0005). In the experimental group, one of the 24 patients (4·2%) patients undergoing chemotherapy developed a pressure sore compared with 18 of 54 (33·3%) in the control group (p = 0·005).Conclusions.  Placing polyurethane foam in contact with the skin of the heel inside a plaster cast prevents the formation of pressure sores.Relevance to clinical practice.  This study provides evidence that using polyurethane foam to prevent sores even inside plaster casts in populations at most risk is a simple and cost‐effective strategy and decreases the discomfort, pain and risks in these patients.
The adoption, local implementation and assimilation into routine nursing practice of a national quality improvement programme: the Productive Ward in England
Authors: Robert Glenn , Morrow Elizabeth , Maben Jill , Griffiths Peter , Callard Lynn 
Published: February 2011

Aim and objective.  To explore why innovations in service and delivery are adopted and how they are then successfully implemented and eventually assimilated into routine nursing practice.Background.  The ‘Productive Ward’ is a national quality improvement programme that aims to engage nursing staff in the implementation of change at ward level.Design.  Mixed methods (analysis of routine data, online survey, interviews) to apply an evidence‐based diffusion of innovations framework.Method.  (1) Broad and narrow indicators of the timing of ‘decisions to adopt’ the Productive Ward were applied. (2) An online survey explored the perceptions of 150 respondents involved with local implementation. (3) Fifty‐eight interviews in five organisational case studies to explore the process of assimilation in each context.Results.  Since the launch of the programme in May 2008 staff in approximately 85% of NHS acute hospitals had either downloaded Productive Ward materials or formally purchased a support package (as of March 2009). On a narrower measure, 40% (140) of all NHS hospitals had adopted the programme (i.e. purchased a support package) with large variation between geographical regions. Four key interactions in the diffusion of innovations framework appeared central to the rapid adoption of the programme. Despite widespread perception of significant benefits, frontline nursing staff report that more needs to be carried out to ensure that impact can be demonstrated in quantifiable terms and include patient perspectives.Conclusions.  The programme has been rapidly adopted by NHS hospitals in England. A variety of implementation approaches are being employed, which are likely to have implications for the successful assimilation of the programme into routine nursing practice.Relevance to clinical practice.  This paper summarises the perceived benefits of the Productive Ward programme and highlights important lessons for nurse leaders who are designing (or adapting) and then implementing quality improvement programmes locally, particularly in terms of how to frame such initiatives – and provide support to – ward‐level staff.