bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal mortality as an indicator of obstetric care in Europe
Authors: Wildman Katherine , Bouvier‐Colle Marie‐Hélène ,   the MOMS group
Published: November 2010

Objective  This analysis considers the usefulness of maternal mortality ratio (MMR) as an indicator of obstetric care in the context of low overall maternal mortality. We explore whether variation in the level of MMR among European countries reflects differences in obstetric care.Design  The data presented in this article were collected as part of the European Concerted Action on Mothers' Mortality and Severe morbidity (MOMS). In this study, a panel of experts followed a protocol to determine cause of death and whether it was pregnancy‐related. This analysis uses the expert panel's confirmation of cause of death and obstetric attribution.Setting  All maternal deaths within 11 European countries.Population  Two hundred and ninety obstetric deaths occuring between 1992 and 1995.Methods  We present the results of a multivariable analysis that controls for cause of death, moment of death, place of death, pregnancy outcome, women's age and nationality.Main outcome measures  We test the hypothesis that countries with higher MMR would have proportionally more cases of direct obstetric death due to thromboembolism, hypertension, haemorrhage or infection compared with other countries in the study. We examine timing of death and maternal age to measure whether there are differences between country groups for older mothers.Results  We find distinct patterns in cause and timing of death and age‐specific mortality ratios between countries with different levels of MMR.Conclusions  Despite low rates of maternal mortality in Europe, between‐country differences follow patterns with respect to cause and timing of death and maternal age. In addition to representing an important indicator of health status in a country, differences in MMR among European countries provide insight to where obstetric care plays a role maternal deaths.
GSearcher: Agile Attribute Querying for Biological Networks
Authors: Su Gang , Athey Brian D. , Meng Fan 
Published: November 2010

Abstract
Summary: GSearcher provides a highly interactive user experience in navigating attribute data associated with large and complex biological networks. The user may either perform a quick search using keywords, phrases or regular expressions, or build a complex query with a group of filters for efficient and flexible exploration of large datasets.
Availability: http://brainarray.mbni.med.umich.edu/gsearcher/
Contact: sugang@umich.edu
SAMStat: monitoring biases in next generation sequencing data
Authors: Lassmann Timo , Hayashizaki Yoshihide , Daub Carsten O. 
Published: November 2010

Abstract
Motivation: The sequence alignment/map format (SAM) is a commonly used format to store the alignments between millions of short reads and a reference genome. Often certain positions within the reads are inherently more likely to contain errors due to the protocols used to prepare the samples. Such biases can have adverse effects on both mapping rate and accuracy. To understand the relationship between potential protocol biases and poor mapping we wrote SAMstat, a simple C program plotting nucleotide overrepresentation and other statistics in mapped and unmapped reads in a concise html page. Collecting such statistics also makes it easy to highlight problems in the data processing and enables non-experts to track data quality over time.
Results: We demonstrate that studying sequence features in mapped data can be used to identify biases particular to one sequencing protocol. Once identified, such biases can be considered in the downstream analysis or even be removed by read trimming or filtering techniques.
Availability: SAMStat is open source and freely available as a C program running on all Unix-compatible platforms. The source code is available from http://samstat.sourceforge.net.
Contact: timolassmann@gmail.com
Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons
Authors: Narzisi Giuseppe , Mishra Bud 
Published: November 2010

Abstract
Motivation: Mired by its connection to a well-known 𝒩𝒫-complete combinatorial optimization problem—namely, the Shortest Common Superstring Problem (SCSP)—historically, the whole-genome sequence assembly (WGSA) problem has been assumed to be amenable only to greedy and heuristic methods. By placing efficiency as their first priority, these methods opted to rely only on local searches, and are thus inherently approximate, ambiguous or error prone, especially, for genomes with complex structures. Furthermore, since choice of the best heuristics depended critically on the properties of (e.g. errors in) the input data and the available long range information, these approaches hindered designing an error free WGSA pipeline.
Results: We dispense with the idea of limiting the solutions to just the approximated ones, and instead favor an approach that could potentially lead to an exhaustive (exponential-time) search of all possible layouts. Its computational complexity thus must be tamed through a constrained search (Branch-and-Bound) and quick identification and pruning of implausible overlays. For his purpose, such a method necessarily relies on a set of score functions (oracles) that can combine different structural properties (e.g. transitivity, coverage, physical maps, etc.). We give a detailed description of this novel assembly framework, referred to as Scoring-and-Unfolding Trimmed Tree Assembler (SUTTA), and present experimental results on several bacterial genomes using next-generation sequencing technology data. We also report experimental evidence that the assembly quality strongly depends on the choice of the minimum overlap parameter k.
Availability and Implementation: SUTTA's binaries are freely available to non-profit institutions for research and educational purposes at http://www.bioinformatics.nyu.edu.
Contact: narzisi@nyu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Fishery discards in the Irish Sea exhibit temporal oscillations and trends reflecting underlying processes at an annual scale
Authors: Viana Mafalda , Graham Norman , Wilson James G. , Jackson Andrew L. 
Published: November 2010

Abstract
Viana, M., Graham, N., Wilson, J. G., and Jackson, A. L. 2011. Fishery discards in the Irish Sea exhibit temporal oscillations and trends reflecting underlying processes at an annual scale. – ICES Journal of Marine Science, 68: 221–227. Non-inclusion of discard data in stock assessment can lead to underestimation of biomass and fishing mortality; this is of particular concern if there have been changes in discard practices over time. Although variability in space and time is a well-documented feature of discards, the temporal dynamics of the practice has received little detailed attention. The aim here is to characterize the temporal patterns of discarding practices in the Irish Sea (ICES Division VIIa) from 1994 to 2008. Trend and seasonality were explored in discards per unit effort (dpue) of haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus), and cod (Gadus morhua) through Bayesian harmonic regression (HREG) models. The HREG models reveal discarding of all three species in annual cycles, with a peak in the second quarter, perhaps reflecting species biology or fisher behaviour, or both. The dpue of cod cycled around a constant level throughout the observation period, but whiting and haddock dpue increased.
Environmental influences on stock abundance and fishing power in the silver-lipped pearl oyster fishery
Authors: Hart Anthony M. , Thomson Adrian W. , Murphy David 
Published: November 2010

Abstract
Hart, A. M., Thomson, A. W., and Murphy, D. 2011. Environmental influences on stock abundance and fishing power in the silver-lipped pearl oyster fishery. – ICES Journal of Marine Science, 68: . Stock variability, fishing power, and the contributing environmental factors were examined for the Australian silver-lipped pearl oyster, Pinctada maxima. The approach was to compare the longer-term time-series of stock abundance derived from catch per unit effort against the shorter-term 0+ spat-settlement index to seek agreement on causal factors. Indices of stock abundance were established with generalized linear models that simultaneously examined the influence of technological and environmental factors, resulting in a predictive model with a 3-year forecast. The advent of global positioning systems caused a 30% increase in fishing power. A negative relationship between abundance and rainfall, and a positive relationship between abundance and temperature, was detected for both spat settlement and fishery abundance. Northerly winds (negative northings) from December to February significantly enhanced settlement, but easterly winds (negative eastings) in the main fishing month of May influenced fishing power positively. After standardizing for the effects of fishing power, a 150% increase in stock abundance of the exploited component of P. maxima stocks was detected between 2004 and 2009. A major contributor to this increase was an exceptionally high settlement of spat in 2005, associated with a rare combination of environmental conditions. Once this year class grows beyond the target size classes, abundance is predicted to decrease to the normal levels.
Manganese Limitation Induces Changes in the Activity and in the Organization of Photosynthetic Complexes in the CyanobacteriumSynechocystissp. Strain PCC 6803
Authors: Salomon Eitan , Keren Nir 
Published: November 2010

AbstractManganese (Mn) ions are essential for oxygen evolution activity in photoautotrophs. In this paper, we demonstrate the dynamic response of the photosynthetic apparatus to changes in Mn bioavailability in cyanobacteria. Cultures of the cyanobacterium Synechocystis PCC 6803 could grow on Mn concentrations as low as 100 nm without any observable effect on their physiology. Below this threshold, a decline in the photochemical activity of photosystem II (PSII) occurred, as evident by lower oxygen evolution rates, lower maximal photosynthetic yield of PSII values, and faster QA reoxidation rates. In 77 K chlorophyll fluorescence spectroscopy, a peak at 682 nm was observed. After ruling out the contribution of phycobilisome and iron stress-induced IsiA proteins, this band was attributed to the accumulation of partially assembled PSII. Surprisingly, the increase in the 682-nm peak was paralleled by a decrease in the 720-nm peak, dominated by PSI fluorescence. The effect on PSI was confirmed by measurements of the P700 photochemical activity. The loss of activity was the result of two processes: loss of PSI core proteins and changes in the organization of PSI complexes. Blue native-polyacrylamide gel electrophoresis analysis revealed a Mn limitation-dependent dissociation of PSI trimers into monomers. The sensitive range for changes in the organization of the photosynthetic apparatus overlaps with the range of Mn concentrations measured in natural environments. We suggest that the ability to manipulate PSI content and organization allows cyanobacteria to balance electron transport rates between the photosystems. At naturally occurring Mn concentrations, such a mechanism will provide important protection against light-induced damage.
Oral administration of Parabacteroides distasonis antigens attenuates experimental murine colitis through modulation of immunity and microbiota composition
Authors: Kverka M , Zakostelska Z , Klimesova K , Sokol D , Hudcovic T , Hrncir T , Rossmann P , Mrazek J , Kopecny J , Verdu E F , Tlaskalova-Hogenova H 
Published: November 2010

Summary
Commensal bacteria have been shown to modulate the host mucosal immune system. Here, we report that oral treatment of BALB/c mice with components from the commensal, Parabacteroides distasonis, significantly reduces the severity of intestinal inflammation in murine models of acute and chronic colitis induced by dextran sulphate sodium (DSS). The membranous fraction of P. distasonis (mPd) prevented DSS-induced increases in several proinflammatory cytokines, increased mPd-specific serum antibodies and stabilized the intestinal microbial ecology. The anti-colitic effect of oral mPd was not observed in severe combined immunodeficient mice and probably involved induction of specific antibody responses and stabilization of the intestinal microbiota. Our results suggest that specific bacterial components derived from the commensal bacterium, P. distasonis, may be useful in the development of new therapeutic strategies for chronic inflammatory disorders such as inflammatory bowel disease.
ICT use in education: different uptake and practice in Hebrew‐speaking and Arabic‐speaking schools in Israel
Authors: Nachmias R. , Mioduser D. , Forkosh‐Baruch A. 
Published: November 2010

AbstractClosing educational gaps between sub‐populations in Israel, particularly between students in Hebrew‐speaking and Arabic‐speaking schools, persists to be one of the priorities of Israel's education system. In the field of information and communication technology (ICT), this goal refers to infrastructure as well as practice, i.e. teaching and learning. A secondary analysis of Second Information Technology in Education Study 2006 study findings portrays a multifaceted state of affairs on some issues, e.g. vision and goals, attitudes on ICT importance in general and as a lever for paradigmatic change in particular. This is contrary to expectations due to the inequality in allocation (mainly of infrastructure) between the two sectors. Arabic‐speaking mathematics teachers indicate greater ICT usage in their target class, while among science teachers, Hebrew‐speaking teachers report greater usage and influence on their pedagogy, indicating innovative usage. Conclusions suggest that further effort is needed to close the gaps between Hebrew‐ and Arabic‐speaking schools as well as collaboration and exchange of ideas, information and educational experience between staff members from both sectors.
Clinical audit and quality improvement – time for a rethink?
Authors: Bowie Paul , Bradley Nicholas A. , Rushmer Rosemary 
Published: November 2010

AbstractRationale and aim  Evidence of the benefits of clinical audit to patient care is limited, despite its longevity. Additionally, numerous attitudinal, professional and organizational barriers impede its effectiveness. Yet, audit remains a favoured quality improvement (QI) policy lever. Growing interest in QI techniques suggest it is timely to re‐examine audit. Clinical audit advisors assist health care teams, so hold unique cross‐cutting perspectives on the strategic and practical application of audit in NHS organizations. We aimed to explore their views and experiences of their role in supporting health care teams in the audit process.Method  Qualitative study using semi‐structured and focus group interviews. Participants were purposively sampled (n = 21) across health sectors in two large Scottish NHS Boards. Interviews were audio‐taped, transcribed and a thematic analysis performed.Results  Work pressure and lack of protected time were cited as audit barriers, but these hide other reasons for non‐engagement. Different professions experience varying opportunities to participate. Doctors have more opportunities and may dominate or frustrate the process. Audit is perceived as a time‐consuming, additional chore and a managerially driven exercise with no associated professional rewards. Management failure to support and resource changes fuels low motivation and disillusionment. Audit is regarded as a ‘political’ tool stifled by inter‐professional differences and contextual constraints.Conclusions  The findings echo previous studies. We found limited evidence that audit as presently defined and used is meeting policy makers' aspirations. The quality and safety improvement focus is shifting towards ‘alternative’ systems‐based QI methods, but research to suggest that these will be any more impactful is also lacking. Additionally, identified professional, educational and organizational barriers still need to be overcome. A debate on how best to overcome the limitations of audit and its place alongside other approaches to QI is necessary.
The application of pharmacoeconomic modelling to estimate a value‐based price for new cancer drugs
Authors: Dranitsaris George , Truter Ilse , Lubbe Martie S. , Cottrell Wayne , Spirovski Biljana , Edwards Jonathan 
Published: November 2010

AbstractRationale, aims and objectives  Value‐based pricing has recently been discussed by international bodies as a means to estimate a drug price that is linked to the benefits it offers patients and society. The World Health Organization (WHO) has recommended using three times a country's per capita gross domestic product (GDP) as the threshold for economic value. Using the WHO criteria, pharmacoeconomic modelling was used to illustrate the application of value‐based price towards bevacizumab, a relatively new drug that provides a 1.4‐month survival benefit to patients with metastatic colorectal cancer (mCRC).Methods  A decision model was developed to simulate outcomes in mCRC patients receiving chemotherapy ± bevacizumab. Clinical data were obtained from randomized trials and costs from Canadian cancer centres. Utility estimates were determined by interviewing 24 oncology nurses and pharmacists. A price per dose of bevacizumab was then estimated using a target threshold of $CAD117 000 per quality adjusted life year gained, which is three times the Canadian per capita GDP.Results  For a 1.4‐month survival benefit, a price of $CAD830 per dose would be considered cost‐effective from the Canadian public health care perspective. If the drug were able to improve patient quality of life or survival from 1.4 to 3 months, the drug price could increase to $CAD1560 and $CAD2180 and still be considered cost‐effective.Discussion  The use of the WHO criteria for estimating a value‐based price is feasible, but a balance between what patients/governments can afford to pay and the commercial viability of the product in the reference country would be required.
Measuring how well the NHS looks after its own staff: methodology of the first national clinical audits of occupational health services in the NHS
Authors: Williams Siân , Rogers Caroline , Peel Penny , Harvey Samuel B. , Henderson Max , Madan Ira , Smedley Julia , Grant Robert 
Published: November 2010

AbstractRationale, aims and objectives  Little is known about the quality of occupational health care provided to National Health Service (NHS) staff. We designed the first national clinical audits of occupational health care in England. We chose to audit depression and back pain as health care workers have high levels of both conditions compared with other employment sectors. The aim of the audits was to drive up quality of care for staff with these conditions. The object of this paper is to describe how we developed an audit methodology and overcame challenges presented by the organization and delivery of occupational health care for NHS staff.Methods  We designed two retrospective case note audits which ran simultaneously. Sites submitted up to 40 cases for each audit. We used duplicate case entry to test inter‐rater reliability and performed selection bias checks. Participants received their site's audit results, benchmarked against the national average, within 4 months of the end of the data entry period. We used electronic voting at a results dissemination conference to inform implementation activities.Results  Occupational Health departments providing services to 278 (83%) trusts in England participated in one or both audits. Median kappa scores were above 0.7 for both pilot and full audits, indicating ‘good’ levels of inter‐rater reliability.In total, 79% of participants at a dissemination conference said that they had changed their clinical practice either during data collection (52%) or following receipt of their audit results (27%).Conclusions  Clinical audit can be conducted successfully in the occupational health setting. We obtained meaningful data that have stimulated local and national quality improvement activities. Our methodology would be transferable to occupational health settings outside the NHS and in other countries.
Termination troubles in Escherichia coli K12
Authors: Dreyfus Marc , Heurgué‐Hamard Valérie 
Published: November 2010

SummaryIn this issue of Molecular Microbiology, Schaub and Hayes report that, compared with other enterobacteria, Escherichia coli K12 carries two mutations – one in the prfB gene encoding the release factor RF2, and the other in the rpsG gene encoding r‐protein S7 – that together concur in compromising translation termination at the essential rpsG gene. As a consequence, the growth of E. coli K12 is very sensitive to a further mutation (rluD‐) that depresses RF2 activity, whereas the growth of its close relative, E. coli B, is not. We tentatively discuss how the K12‐specific mutations in RF2 and S7 might have occurred and why inefficient translation termination at rpsG inhibits growth. The work of Schaub and Hayes illustrates the fact that, due probably to its long history in the laboratory, E. coli K12 has accumulated mutations that sometimes limit its value as a model for studying basic steps in prokaryotic gene expression.
The Arabidopsis tandem zinc finger protein AtTZF1 affects ABA‐ and GA‐mediated growth, stress and gene expression responses
Authors: Lin Pei‐Chi , Pomeranz Marcelo C. , Jikumaru Yusuke , Kang Shin Gene , Hah Cyrus , Fujioka Shozo , Kamiya Yuji , Jang Jyan‐Chyun 
Published: November 2010

SummaryTandem zinc finger (TZF) proteins are characterized by two zinc‐binding CCCH motifs arranged in tandem. Human TZFs such as tristetraproline (TTP) bind to and trigger the degradation of mRNAs encoding cytokines and various regulators. Although the molecular functions of plant TZFs are unknown, recent genetic studies have revealed roles in hormone‐mediated growth and environmental responses, as well as in the regulation of gene expression. Here we show that expression of AtTZF1 (AtCTH/AtC3H23) mRNA is repressed by a hexokinase‐dependent sugar signaling pathway. However, AtTZF1 acts as a positive regulator of ABA/sugar responses and a negative regulator of GA responses, at least in part by modulating gene expression. RNAi of AtTZF1–3 caused early germination and slightly stress‐sensitive phenotypes, whereas plants over‐expressing AtTZF1 were compact, late flowering and stress‐tolerant. The developmental phenotypes of plants over‐expressing AtTZF1 were only partially rescued by exogenous application of GA, implying a reduction in the GA response or defects in other mechanisms. Likewise, the enhanced cold and drought tolerance of plants over‐expressing AtTZF1 were not associated with increased ABA accumulation, suggesting that it is mainly ABA responses that are affected. Consistent with this notion, microarray analysis showed that over‐expression of AtTZF1 mimics the effects of ABA or GA deficiency on gene expression. Notably, a gene network centered on a GA‐inducible and ABA/sugar‐repressible putative peptide hormone encoded by GASA6 was severely repressed by AtTZF1 over‐expression. Hence AtTZF1 may serve as a regulator connecting sugar, ABA, GA and peptide hormone responses.