bluuebunny/crossref_metadata_2025_split huggingface dataset:
Palaeoenvironmental implications derived from a piston core from east lobe Bonney, Taylor Valley, Antarctica
Authors: Wagner Bernd , Ortlepp Sabrina , Kenig Fabien , Doran Peter T. , Melles Martin 
Published: August 2010

AbstractA 270 cm long sediment sequence was recovered with a piston corer from east lobe Bonney, Taylor Valley, Antarctica, and characterized according to its sedimentological, mineralogical, and geochemical properties. It is the first record of such length recovered from east lobe Bonney. The sediment core is mainly composed of halite crystals of different sizes, water, and a relatively low and stable proportion of clastic particles. Although the sediment surface was probably disturbed by the coring process and absence or low contents of organic material or carbonates hampers the establishment of a robust chronology by radiocarbon dating, the core probably contains at least several hundred years of information about the history of the lake and the Bonney basin. Variations in halite crystal sizes and amount as well as variations in the composition of clastic material can be related to past lake level changes and evaporation cycles.
Cognitive tests used in chronic adult human randomised controlled trial micronutrient and phytochemical intervention studies
Authors: Macready Anna L. , Butler Laurie T. , Kennedy Orla B. , Ellis Judi A. , Williams Claire M. , Spencer Jeremy P. E. 
Published: August 2010

In recent years there has been a rapid growth of interest in exploring the relationship between nutritional therapies and the maintenance of cognitive function in adulthood. Emerging evidence reveals an increasingly complex picture with respect to the benefits of various food constituents on learning, memory and psychomotor function in adults. However, to date, there has been little consensus in human studies on the range of cognitive domains to be tested or the particular tests to be employed. To illustrate the potential difficulties that this poses, we conducted a systematic review of existing human adult randomised controlled trial (RCT) studies that have investigated the effects of 24 d to 36 months of supplementation with flavonoids and micronutrients on cognitive performance. There were thirty-nine studies employing a total of 121 different cognitive tasks that met the criteria for inclusion. Results showed that less than half of these studies reported positive effects of treatment, with some important cognitive domains either under-represented or not explored at all. Although there was some evidence of sensitivity to nutritional supplementation in a number of domains (for example, executive function, spatial working memory), interpretation is currently difficult given the prevailing ‘scattergun approach’ for selecting cognitive tests. Specifically, the practice means that it is often difficult to distinguish between a boundary condition for a particular nutrient and a lack of task sensitivity. We argue that for significant future progress to be made, researchers need to pay much closer attention to existing human RCT and animal data, as well as to more basic issues surrounding task sensitivity, statistical power and type I error.
The impact of the food-based and nutrient-based standards on lunchtime food and drink provision and consumption in primary schools in England
Authors: Haroun Dalia , Harper Clare , Wood Lesley , Nelson Michael 
Published: August 2010

AbstractObjectiveTo assess lunchtime provision of food and drink in English primary schools and to assess both choices and consumption of food and drink by pupils having school lunches. These findings were compared with similar data collected in 2005.DesignCross-sectional data collected between February and April 2009. In each school, food and drink provision, including portion weights and number of portions of each item served at lunchtime, were recorded over five consecutive days. Caterers provided school lunchtime menus and recipes.SettingEngland.SubjectsA random selection of 6696 pupils having school lunches in a nationally representative sample of 136 primary schools in England.ResultsCompared with 2005, schools in 2009 provided significantly more fruit, fruit-based desserts, vegetables and salad, water and fruit juice, and less ketchup, sauces and gravy, starchy foods cooked in fat, snacks and confectionery (P < 0·01). Pupils were also making healthier choices, choosing an average of 2·2 portions of fruit and vegetables from their ‘five a day’, but about one-third to two-fifths of these were wasted.ConclusionsLunchtime food provision and consumption in primary schools have improved substantially since 2005, following the introduction of new standards for school food in 2008. However, improvements still need to be made to increase the Fe and Zn content and to decrease the Na content of recipes, and in encouraging pupils to eat more of the fruits and vegetables taken at lunchtime.
Choice and privatisation in Swedish primary care
Authors: Anell Anders 
Published: August 2010

AbstractIn 2007, a new wave of local reforms involving choice for the population and privatisation of providers was initiated in Swedish primary care. Important objectives behind reforms were to strengthen the role of primary care and to improve performance in terms of access and responsiveness. The purpose of this article was to compare the characteristics of the new models and to discuss changes in financial incentives for providers and challenges regarding governance from the part of county councils. A majority of the models being introduced across the 21 county councils can best be described as innovative combinations between a comprehensive responsibility for providers and significant degrees of freedom regarding choice for the population. Key financial characteristics of fixed payment and comprehensive financial responsibility for providers may create financial incentives to under-provide care. Informed choices by the population, in combination with reasonably low barriers for providers to enter the primary care market, should theoretically counterbalance such incentives. To facilitate such competition is indeed a challenge, not only because of difficulties in implementing informed choices but also because the new models favour large and/or horizontally integrated providers. To prevent monopolistic behaviour, county councils may have to accept more competition as well as more governance over clinical practice than initially intended.
Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913
Authors: Qin Qi-Long , Li Yang , Zhang Yan-Jiao , Zhou Zhe-Min , Zhang Wei-Xin , Chen Xiu-Lan , Zhang Xi-Ying , Zhou Bai-Cheng , Wang Lei , Zhang Yu-Zhong 
Published: August 2010

Abstract
Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. In this study, the complete genome of deep-sea sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913 was less tolerant of H2O2 than TAC125. SM9913 has gene clusters related to both polar and lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea bacteria and absent in the related surface bacteria, are important for the survival of SM9913 in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal resistance. Many signal transduction genes and a glycogen production operon were also present in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy in a deep-sea environment.
Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time
Authors: Hall Edward K , Singer Gabriel A , Pölzl Marvin , Hämmerle Ieda , Schwarz Christian , Daims Holger , Maixner Frank , Battin Tom J 
Published: August 2010

Abstract
Stoichiometry of microbial biomass is a key determinant of nutrient recycling in a wide variety of ecosystems. However, little is known about the underlying causes of variance in microbial biomass stoichiometry. This is primarily because of technological constraints limiting the analysis of macromolecular composition to large quantities of microbial biomass. Here, we use Raman microspectroscopy (MS), to analyze the macromolecular composition of single cells of two species of bacteria grown on minimal media over a wide range of resource stoichiometry. We show that macromolecular composition, determined from a subset of identified peaks within the Raman spectra, was consistent with macromolecular composition determined using traditional analytical methods. In addition, macromolecular composition determined by Raman MS correlated with total biomass stoichiometry, indicating that analysis with Raman MS included a large proportion of a cell's total macromolecular composition. Growth phase (logarithmic or stationary), resource stoichiometry and species identity each influenced each organism's macromolecular composition and thus biomass stoichiometry. Interestingly, the least variable peaks in the Raman spectra were those responsible for differentiation between species, suggesting a phylogenetically specific cellular architecture. As Raman MS has been previously shown to be applicable to cells sampled directly from complex environments, our results suggest Raman MS is an extremely useful application for evaluating the biomass stoichiometry of environmental microorganisms. This includes the ability to partition microbial biomass into its constituent macromolecules and increase our understanding of how microorganisms in the environment respond to resource heterogeneity.
Effect of degree of fluid saturation on transport coefficients in disturbed soils
Authors: Tuli A. , Hopmans J. W. 
Published: August 2010

SummaryTo improve the predictive capability of transport models in soils we need experimental data that improve their understanding of properties at the scale of pores, including the effect of degree of fluid saturation. All transport occurs in the same soil pore space, so that one may intuitively expect a link between the different transport coefficients and key geometrical characteristics of the pores such as tortuosity and connectivity, and pore‐size distribution. To understand the combined effects of pore geometry and pore‐size distribution better, we measured the effect of degree of water saturation on hydraulic conductivity and bulk soil electrical conductivity, and of degree of air saturation on air conductivity and gaseous diffusion for a fine sand and a sandy loam soil. To all measured data were fitted a general transport model that includes both pore geometry and pore‐size distribution parameters. The results show that both pore geometry and pore‐size distribution determine the functional relations between degree of saturation, hydraulic conductivity and air conductivity. The control of pore size on convective transport is more for soils with a wider pore‐size distribution. However, the relative contribution of pore‐size distribution is much larger for the unsaturated hydraulic conductivity than for gaseous phase transport. For the other transport coefficients, their saturation dependency could be described solely by the pore‐geometry term. The contribution of the latter to transport was much larger for transport in the air phase than in the water phase, supporting the view that connectivity dominates gaseous transport. Although the relation between effective fluid saturation and all four relative transport coefficients for the sand could be described by a single functional relation, the presence of a universal relationship between fluid saturation and transport for all soils is doubtful.
Sequence dependence of DNA bending rigidity
Authors: Geggier Stephanie , Vologodskii Alexander 
Published: August 2010

For many aspects of DNA–protein interaction, it is vital to know how DNA bending rigidity (or persistence length,
a
) depends on its sequence. We addressed this problem using the method based on cyclization of short DNA fragments, which allows very accurate determination of
a
. Our approach was based on assigning specific values of
a
to each of 10 distinct dinucleotide steps. We prepared DNA fragments, each about 200 bp in length, with various quasi-periodic sequences, measured their cyclization efficiencies (
j
factors), and fitted the data by the theoretical equation to obtain the values of
a
for each fragment. From these data, we obtained a set of
a
for the dinucleotide steps. To test this set, we used it to design DNA sequences that should correspond to very low and very high values of
a
, prepared the corresponding fragments, and determined their values of
a
experimentally. The measured and calculated values of
a
were very close to one another, confirming that we have found the correct solution to this long-standing problem. The same experimental data also allowed us to determine the sequence dependence of DNA helical repeat.
MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation
Authors: Biswas Ambarish , Mynampati Kalyan C. , Umashankar Shivshankar , Reuben Sheela , Parab Gauri , Rao Raghuraj , Kannan Velayutham S. , Swarup Sanjay 
Published: August 2010

Abstract
Summary: Analysis of high throughput metabolomics experiments is a resource-intensive process that includes pre-processing, pre-treatment and post-processing at each level of experimental hierarchy. We developed an interactive user-friendly online software called Metabolite Data Analysis Tool (MetDAT) for mass spectrometry data. It offers a pipeline of tools for file handling, data pre-processing, univariate and multivariate statistical analyses, database searching and pathway mapping. Outputs are produced in the form of text and high-quality images in real-time. MetDAT allows users to combine data management and experiment-centric workflows for optimization of metabolomics methods and metabolite analysis.
Availability: MetDAT is available free for academic use from http://smbl.nus.edu.sg/METDAT2/.
Contact: sanjay@nus.edu.sg
Identifying informative subsets of the Gene Ontology with information bottleneck methods
Authors: Jin Bo , Lu Xinghua 
Published: August 2010

Abstract
Motivation: The Gene Ontology (GO) is a controlled vocabulary designed to represent the biological concepts pertaining to gene products. This study investigates the methods for identifying informative subsets of GO terms in an automatic and objective fashion. This task in turn requires addressing the following issues: how to represent the semantic context of GO terms, what metrics are suitable for measuring the semantic differences between terms, how to identify an informative subset that retains as much as possible of the original semantic information of GO.
Results: We represented the semantic context of a GO term using the word-usage-profile associated with the term, which enables one to measure the semantic differences between terms based on the differences in their semantic contexts. We further employed the information bottleneck methods to automatically identify subsets of GO terms that retain as much as possible of the semantic information in an annotation database. The automatically retrieved informative subsets align well with an expert-picked GO slim subset, cover important concepts and proteins, and enhance literature-based GO annotation.
Availability: http://carcweb.musc.edu/TextminingProjects/
Contact: xinghua@pitt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Cross-species queries of large gene expression databases
Authors: Le Hai-Son , Oltvai Zoltán N. , Bar-Joseph Ziv 
Published: August 2010

Abstract
Motivation: Expression databases, including the Gene Expression Omnibus and ArrayExpress, have experienced significant growth over the past decade and now hold hundreds of thousands of arrays from multiple species. Since most drugs are initially tested on model organisms, the ability to compare expression experiments across species may help identify pathways that are activated in a similar way in humans and other organisms. However, while several methods exist for finding co-expressed genes in the same species as a query gene, looking at co-expression of homologs or arbitrary genes in other species is challenging. Unlike sequence, which is static, expression is dynamic and changes between tissues, conditions and time. Thus, to carry out cross-species analysis using these databases, we need methods that can match experiments in one species with experiments in another species.
Results: To facilitate queries in large databases, we developed a new method for comparing expression experiments from different species. We define a distance metric between the ranking of orthologous genes in the two species. We show how to solve an optimization problem for learning the parameters of this function using a training dataset of known similar expression experiments pairs. The function we learn outperforms previous methods and simpler rank comparison methods that have been used in the past for single species analysis. We used our method to compare millions of array pairs from mouse and human expression experiments. The resulting matches can be used to find functionally related genes, to hypothesize about biological response mechanisms and to highlight conditions and diseases that are activating similar pathways in both species.
Availability: Supporting methods, results and a Matlab implementation are available from http://sb.cs.cmu.edu/ExpQ/
Contact: zivbj@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
NoiseMaker: simulated screens for statistical assessment
Authors: Kwan Phoenix , Birmingham Amanda 
Published: August 2010

Abstract
Summary: High-throughput screening (HTS) is a common technique for both drug discovery and basic research, but researchers often struggle with how best to derive hits from HTS data. While a wide range of hit identification techniques exist, little information is available about their sensitivity and specificity, especially in comparison to each other. To address this, we have developed the open-source NoiseMaker software tool for generation of realistically noisy virtual screens. By applying potential hit identification methods to NoiseMaker-simulated data and determining how many of the pre-defined true hits are recovered (as well as how many known non-hits are misidentified as hits), one can draw conclusions about the likely performance of these techniques on real data containing unknown true hits. Such simulations apply to a range of screens, such as those using small molecules, siRNAs, shRNAs, miRNA mimics or inhibitors, or gene over-expression; we demonstrate this utility by using it to explain apparently conflicting reports about the performance of the B score hit identification method.
Availability and implementation: NoiseMaker is written in C#, an ECMA and ISO standard language with compilers for multiple operating systems. Source code, a Windows installer and complete unit tests are available at http://sourceforge.net/projects/noisemaker. Full documentation and support are provided via an extensive help file and tool-tips, and the developers welcome user suggestions.
Contact: amanda.birmingham@thermofisher.com
Supplementary information: Supplementary data are available at Bioinformatics online.
RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression
Authors: Na Dokyun , Lee Doheon 
Published: August 2010

Abstract
Motivation: RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes. BMC Syst. Biol., 4, 71). The program additionally incorporates the effect on translation efficiency of the spacer length between a Shine–Dalgarno (SD) sequence and an AUG codon, which is crucial for the incorporation of fMet-tRNA into the ribosome. RBSDesigner provides a graphical user interface (GUI) for the convenient design of synthetic RBSs.
Availability: RBSDesigner is written in Python and Microsoft Visual Basic 6.0 and is publicly available as precompiled stand-alone software on the web (http://rbs.kaist.ac.kr).
Contact: dhlee@kaist.ac.kr
Families' Perspectives on the Effect of Constipation and Fecal Incontinence on Quality of Life
Authors: Kaugars Astrida Seja , Silverman Alan , Kinservik Margo , Heinze Susan , Reinemann Lisa , Sander Megan , Schneider Brian , Sood Manu 
Published: August 2010

ABSTRACTObjectives:Understanding families' quality of life can be important for interdisciplinary treatment planning. The present study examined child and parent perspectives about how constipation and fecal incontinence affect families' quality of life.Patients and Methods:Semistructured interviews were conducted with 8 children/adolescents and 8 caregivers. All of the children met Rome II criteria for functional constipation. Interviews were analyzed by an interdisciplinary team using a content analysis approach, which included developing a coding manual that described emergent themes from the interview transcripts.Results:Qualitative and quantitative responses revealed the varied experiences of participating families. Child and parent views may be misaligned, which can affect treatment planning and effectiveness. Families described variable satisfaction with the treatment recommendations they had been offered and experienced difficulty finding appropriate care. Children's social and family functioning were significantly affected by constipation and fecal incontinence difficulties. Both children and parents described the challenges of discussing the problems with others.Conclusions:Multiple domains of individual and family functioning are affected by children's constipation and fecal incontinence difficulties, thereby affecting the quality of life of both children and their parents. The findings underscore the need for providers to consider the influence of symptoms on adjustment to both the medical condition and treatment adherence and discuss concerns with children and parents. The results provide the foundation for developing a standardized tool for quantitative assessment of quality of life for children with constipation.