bluuebunny/crossref_metadata_2025_split huggingface dataset:
Event-based prospective memory performance in autism spectrum disorder
Authors: Altgassen Mareike , Schmitz-Hübsch Maren , Kliegel Matthias 
Published: August 2009

Abstract
The purpose of the present study was to investigate event-based prospective memory performance in individuals with autism spectrum disorder and to explore possible relations between laboratory-based prospective memory performance and everyday performance. Nineteen children and adolescents with autism spectrum disorder and 19 matched neurotypical controls participated. The laboratory-based prospective memory test was embedded in a visuo-spatial working memory test and required participants to remember to respond to a cue-event. Everyday planning performance was assessed with proxy ratings. Although parents of the autism group rated their children’s everyday performance as significantly poorer than controls’ parents, no group differences were found in event-based prospective memory. Nevertheless, individual differences in laboratory-based and everyday performances were related. Clinical implications of these findings are discussed.
A Quality Committee's Evaluation of Surgical Intervention for Clostridium difficile Infection
Authors: Vasaly Fran White , Reines H. David 
Published: August 2009

ABSTRACTClostridium difficile (C diff) is an anaerobic bacterium that causes antibiotic‐associated colitis, which can progress to a life‐threatening illness for some patients. Clostridium difficile is highly transmissible in health care settings and has high morbidity and mortality rates. The increased prevalence of this bacterium and the consequences of infection necessitate an understanding of its transmission and use of stringent infection control practices.A two‐year retrospective evaluation was performed to examine the effectiveness of a screening tool for patients requiring surgical intervention for C diff and to determine whether treatment was timely and effective. Early, aggressive surgical intervention appears to be the single most effective treatment for fulminant C diff colitis. AORN J 90 (August 2009) 192–200. © AORN, Inc, 2009.
Antheraea pernyi silk fibroin maintains the immunosupressive properties of human bone marrow mesenchymal stem cells
Authors: Luan Xi‐Ying , Huo Guan‐Hua , Li Ming‐Zhong , Lu Shen‐Zhou , Zhang Xue‐Guang 
Published: August 2009

AbstractWe reported previously that regenerated Antheraea pernyi silk fibroin (A. pernyi SF) could support the attachment and growth of human bone marrow mesenchymal stem cells (hBMSCs). In this work, the immunosupressive effects of hBMSCs cultured on the A. pernyi SF films on T‐cells were investigated in vitro. The production of IL‐6, CD80, CD86 and HLA‐DR by the hBMSCs was also observed. The study showed that hBMSCs cultured on the regenerated A. pernyi SF films still kept their immunosupression on T‐cell proliferation and IL‐2 secretion. Moreover, regenerated A. pernyi SF like regenerated Bombyx mori SF and collagen did not elicit T‐cell proliferation but it could support the expression of IL‐6 and surface antigen of hBMSCs. Regenerated A. pernyi SF can maintain the function of hBMSCs in immunomodulation and cytokines production, which has the potential utility of hBMSCs combined with A. pernyi SF in tissue replacement and repair.
Short-term docosapentaenoic acid (22 : 5n-3) supplementation increases tissue docosapentaenoic acid, DHA and EPA concentrations in rats
Authors: Kaur Gunveen , Begg Denovan P. , Barr Daniel , Garg Manohar , Cameron-Smith David , Sinclair Andrew J. 
Published: August 2009

The metabolic fate of dietaryn-3 docosapentaenoic acid (DPA) in mammals is currently unknown. The aim of the present study was to determine the extent of conversion of dietary DPA to DHA and EPA in rats. Four groups of male weanling Sprague–Dawley rats (aged 5 weeks) were given 50 mg of DPA, EPA, DHA or oleic acid, daily for 7 d by gavage. At the end of the treatment period, the tissues were analysed for concentrations of long-chain PUFA. DPA supplementation led to significant increases in DPA concentration in all tissues, with largest increase being in adipose (5-fold) and smallest increase being in brain (1·1-fold). DPA supplementation significantly increased the concentration of DHA in liver and the concentration of EPA in liver, heart and skeletal muscle, presumably by the process of retroconversion. EPA supplementation significantly increased the concentration of EPA and DPA in liver, heart and skeletal muscle and the DHA concentration in liver. DHA supplementation elevated the DHA levels in all tissues and EPA levels in the liver. Adipose was the main tissue site for accumulation of DPA, EPA and DHA. These data suggest that dietary DPA can be converted to DHA in the liver, in a short-term study, and that in addition it is partly retroconverted to EPA in liver, adipose, heart and skeletal muscle. Future studies should examine the physiological effect of DPA in tissues such as liver and heart.
THE MONARCHICAL REPUBLIC OF MARY I
Authors: HUNT ALICE 
Published: August 2009

ABSTRACTIn his celebrated 1987 essay, ‘The monarchical republic of Queen Elizabeth I’, Patrick Collinson wrote that ‘Elizabethan England was a republic which also happened to be a monarchy: or vice versa.’ Since then, the idea of an Elizabethan ‘monarchical republic’ has been tested, challenged, and developed, with precedents found in Henry VIII's and Edward VI's reigns. Mary I's reign has not, however, been considered for its contribution to the debates. Yet, in 1553, the unique circumstances of Mary's accession as England's first queen regnant, who was also still legally a bastard, exacerbated sixteenth-century anxieties about monarchical authority, and about the correct relationship between a monarch and parliament. Prior to Mary's coronation, her council put forward an unprecedented proposal: they wanted parliament to sit before Mary was anointed and crowned queen. This article explores this proposal, in conjunction with two texts, Richard Taverner'sAn oration gratulatory made upon the joyfull proclayming of the moste noble Princes Quene Mary Quene of Englandeand the playRespublica, to argue that, at the beginning of her reign, significant pressure was put on Mary to rule her country as a ‘monarchical republic’.
PRESBYTERIAN RELIGION, HISTORIOGRAPHY, AND ULSTER SCOTS IDENTITY, c. 1800 TO 1914
Authors: HOLMES ANDREW R. 
Published: August 2009

ABSTRACTThe links between Presbyterians in Scotland and the north of Ireland are obvious but have been largely ignored by historians of the nineteenth century. This article addresses this gap by showing how Ulster Presbyterians considered their relationship with their Scottish co-religionists and how they used the interplay of religious and ethnic considerations this entailed to articulate an Ulster Scots identity. For Presbyterians in Ireland, their Scottish origins and identity represented a collection of ideas that could be deployed at certain times for specific reasons – theological orthodoxy, civil and religious liberty, and certain character traits such as hard work, courage, and soberness. Ideas about the Scottish identity of Presbyterianism were reawakened for a more general audience in the first half of the nineteenth century, during the campaign for religious reform and revival within the Irish church, and were expressed through a distinctive denominational historiography inaugurated by James Seaton Reid. The formulation of a coherent narrative of Presbyterian religion and the improvement of Ulster laid the religious foundations of a distinct Ulster Scots identity and its utilization by unionist opponents of Home Rule between 1885 and 1914.
A taxonomic revision ofCaloplaca herbidellaandC. furfuracea
Authors: ARUP Ulf , ÅKELIUS Elin 
Published: August 2009

AbstractCaloplaca herbidella(Hue) H. Magn. andC. furfuraceaH. Magn. are two isidiate, epiphytic species in the large genusCaloplaca.Caloplaca herbidellain a strict sense is normally grey and fertile with thick, somewhat coralloid isidia, but orange, sterile forms with thin isidia also occur.Caloplaca furfuraceais superficially similar morphologically toC. herbidellas. str. but has thinner, more granular isidia and generally a darker grey colour. Doubts have been raised as to whetherC. furfuraceashould be acknowledged as a proper species or incorporated inC. herbidella. Using morphometric methods and molecular analysis of the nrITS DNA gene we show thatC. herbidellaandC. furfuraceaare two clearly separated species. Furthermore, the mainly sterile, orange form ofC. herbidellacan be regarded as a separate species that is here described asC. corallizaArup & Åkelius. All three species are described in detail, including photographs and notes on their ecology. Finally, new distribution maps for Europe show thatC. herbidellaandC. corallizaare widespread in Europe, but the latter is probably less common than the former.Caloplaca furfuraceais clearly very rare in Europe with only few collections from Switzerland and Sweden, but seems to be more common in North America.
The pattern and course of cognitive impairment in late-life depression
Authors: Köhler S. , Thomas A. J. , Barnett N. A. , O'Brien J. T. 
Published: August 2009

BackgroundCognitive deficits persist despite clinical recovery in subjects with late-life depression, but more needs to be known about their longer-term outcome and factors affecting their course. To investigate this, we followed the pattern of cognitive impairments over time and examined the effects of current mood, remission status, age of depression onset and antidepressant (AD) treatment on these deficits.MethodSixty-seven subjects aged ⩾60 years with DSM-IV major depressive disorder and 36 healthy comparison subjects underwent tests of global cognition, memory, executive functioning and processing speed at baseline, 6 and 18 months, with some subjects tested again after 4 years. z scores were compared between groups, with analyses of clinical factors that may have influenced cognitive performance in depressed subjects.ResultsHalf of the patients exhibited a generalized cognitive impairment (GCI) that persisted after 18 months. Patients performed worse across all cognitive domains at all time points, without substantial variability due to current mood, remission status or AD treatment. Late age of onset was associated significantly with decline in memory and executive functioning. Impaired processing speed may be a partial mediator of some deficits, but was insufficient to explain differences between patients and controls. Four-year follow-up data suggest impairments persist, but do not further decline.ConclusionsCognitive deficits in late-life depression persist up to 4 years, affect multiple domains and are related to trait rather than state effects. Differences in severity and course between early and late onset depression suggest different pathogenic processes.
Thinking about stratigraphic sequence in social terms
Authors: McAnany Patricia A. , Hodder Ian 
Published: August 2009

AbstractFor archaeologists, stratification is an important character of archaeological deposits. Through it, layering is discerned and cultural and evolutionary interpretations are proposed. Archaeologists possess much implicit knowledge about the social practices that produce stratigraphic sequence and the specific, contextualized manner in which layers were built upon or cut into previous deposits. The aim of this paper is to gather together and formalize this knowledge so as to codify conceptual ‘tools to think by’ when recording and interpreting stratigraphy. Relevant literature is widely dispersed and here can only be sampled; authors consider stratigraphy in terms of (1) techniques of terraforming, (2) processes enacted and (3) meaning and interpretation. Techniques and processes are discussed within larger social interpretations such as memory, history-building, forgetting, renewing, cleansing and destroying. Examples are drawn from the Turkish Neolithic site of Çatalhöyük and the ancestral Maya site of K'axob in Belize, Central America, to illustrate the applicability of an approach that here is called ‘social stratigraphy’. A practice-based history of stratigraphy – the recording and interpretation of strata – within archaeology is problematized in reference to codependence with geology, the deployment of labour and centralized authority within the emergent 19th- to early 20th-century field of archaeology. The contributions of and conflicts between British and American stratigraphic schools are considered in light of a potential rapprochement. Contested issues of cultural heritage – such as preservation of selected strata – suggest that thinking about stratigraphic sequence in social terms is more than an academic exercise.
DUALITY FOR CONVEX POLYTOPES
Authors: ROMANOWSKA A. B. , ŚLUSARSKI P. , SMITH J. D. H. 
Published: August 2009

AbstractThis paper establishes a duality between the category of polytopes (finitely generated real convex sets considered as barycentric algebras) and a certain category of intersections of hypercubes, considered as barycentric algebras with additional constant operations.
What is microbial community ecology?
Authors: Konopka Allan 
Published: August 2009

Abstract
The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.
Upcoming challenges for multiple sequence alignment methods in the high-throughput era
Authors: Kemena Carsten , Notredame Cedric 
Published: August 2009

AbstractThis review focuses on recent trends in multiple sequence alignment tools. It describes the latest algorithmic improvements including the extension of consistency-based methods to the problem of template-based multiple sequence alignments. Some results are presented suggesting that template-based methods are significantly more accurate than simpler alternative methods. The validation of existing methods is also discussed at length with the detailed description of recent results and some suggestions for future validation strategies. The last part of the review addresses future challenges for multiple sequence alignment methods in the genomic era, most notably the need to cope with very large sequences, the need to integrate large amounts of experimental data, the need to accurately align non-coding and non-transcribed sequences and finally, the need to integrate many alternative methods and approaches.Contact: cedric.notredame@crg.es
CMap 1.01: a comparative mapping application for the Internet
Authors: Youens-Clark Ken , Faga Ben , Yap Immanuel V. , Stein Lincoln , Ware Doreen 
Published: August 2009

Abstract
Summary:CMap is a web-based tool for displaying and comparing maps of any type and from any species. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can run on a variety of database engines and uses only free and open software components.
Availability: http://www.gmod.org/cmap
Contact: kclark@cshl.edu
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
Authors: Cloonan Nicole , Xu Qinying , Faulkner Geoffrey J. , Taylor Darrin F. , Tang Dave T. P. , Kolle Gabriel , Grimmond Sean M. 
Published: August 2009

Abstract
Summary: Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA. For example, tags that cross exon-junction boundaries will often not map to a reference genome, and the strand specificity of the data needs to be retained. Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome. Maximizing the mappable tags can provide significant savings in the cost of sequencing experiments. This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context.
Availability: Executables, source code, and exon-junction libraries are available from http://grimmond.imb.uq.edu.au/RNA-MATE/
Contact: n.cloonan@imb.uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics Online.
Gene ranking and biomarker discovery under correlation
Authors: Zuber Verena , Strimmer Korbinian 
Published: August 2009

Abstract
Motivation: Biomarker discovery and gene ranking is a standard task in genomic high-throughput analysis. Typically, the ordering of markers is based on a stabilized variant of the t-score, such as the moderated t or the SAM statistic. However, these procedures ignore gene–gene correlations, which may have a profound impact on the gene orderings and on the power of the subsequent tests.
Results: We propose a simple procedure that adjusts gene-wise t-statistics to take account of correlations among genes. The resulting correlation-adjusted t-scores (‘cat’ scores) are derived from a predictive perspective, i.e. as a score for variable selection to discriminate group membership in two-class linear discriminant analysis. In the absence of correlation the cat score reduces to the standard t-score. Moreover, using the cat score it is straightforward to evaluate groups of features (i.e. gene sets). For computation of the cat score from small sample data, we propose a shrinkage procedure. In a comparative study comprising six different synthetic and empirical correlation structures, we show that the cat score improves estimation of gene orderings and leads to higher power for fixed true discovery rate, and vice versa. Finally, we also illustrate the cat score by analyzing metabolomic data.
Availability: The shrinkage cat score is implemented in the R package ‘st’, which is freely available under the terms of the GNU General Public License (version 3 or later) from CRAN (http://cran.r-project.org/web/packages/st/).
Contact: strimmer@uni-leipzig.de
Methyl side-chain dynamics prediction based on protein structure
Authors: Carbonell Pablo , Sol Antonio del 
Published: August 2009

Abstract
Motivation: Protein dynamics is believed to influence protein function through a variety of mechanisms, some of which are not fully understood. Thus, prediction of protein flexibility from sequence or structural characteristics would assist in comprehension of the ways dynamics is linked to function, and would be important in protein modeling and design. In particular, quantitative description of side-chain dynamics would allow us to understand the role of side-chain flexibility in different functional processes, such as protein–ligand and protein–protein interactions.
Results: Using a dataset of 18 proteins, we trained a neural network for the prediction of methyl-bearing side-chain dynamics as described by the methyl side-chain generalized order parameters (S2) inferred from NMR data. The network uses 10 input parameters extracted from 3D structures. The average correlation coefficient between the experimental and predicted generalized order parameters is r = 0.71 ± 0.029. Further analysis revealed that the order parameter depends more strongly on the methyl carbon packing density, the methyl carbon distance to the Cα atom, and the knowledge-based pair-wise contact potential between the methyl carbon and neighboring amino acids. In general, we observed an improvement in the prediction of methyl order parameters by our network in comparison with molecular dynamics simulations. The sensitivity of the predictions to minor structural changes was illustrated in two examples (calmodulin and barnase) by comparing the S2 predictions for the unbound and ligand-bound structures. The method was able to correctly predict most of the significant changes in side-chain dynamics upon ligand binding, and identified some residues involved in long-range communications or protein–ligand binding.
Availability: http://epigenomique.genopole.fr/∼carbonell
Contact: antdelsol@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Network analyses in systems pharmacology
Authors: Berger Seth I. , Iyengar Ravi 
Published: August 2009

Abstract
Systems pharmacology is an emerging area of pharmacology which utilizes network analysis of drug action as one of its approaches. By considering drug actions and side effects in the context of the regulatory networks within which the drug targets and disease gene products function, network analysis promises to greatly increase our knowledge of the mechanisms underlying the multiple actions of drugs. Systems pharmacology can provide new approaches for drug discovery for complex diseases. The integrated approach used in systems pharmacology can allow for drug action to be considered in the context of the whole genome. Network-based studies are becoming an increasingly important tool in understanding the relationships between drug action and disease susceptibility genes. This review discusses how analysis of biological networks has contributed to the genesis of systems pharmacology and how these studies have improved global understanding of drug targets, suggested new targets and approaches for therapeutics, and provided a deeper understanding of the effects of drugs. Taken together, these types of analyses can lead to new therapeutic options while improving the safety and efficacy of existing medications.
Contact: ravi.iyengar@mssm.edu