bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mixture models for analysis of the taxonomic composition of metagenomes
Authors: Meinicke Peter , Aßhauer Kathrin Petra , Lingner Thomas 
Published: May 2011

Abstract
Motivation: Inferring the taxonomic profile of a microbial community from a large collection of anonymous DNA sequencing reads is a challenging task in metagenomics. Because existing methods for taxonomic profiling of metagenomes are all based on the assignment of fragmentary sequences to phylogenetic categories, the accuracy of results largely depends on fragment length. This dependence complicates comparative analysis of data originating from different sequencing platforms or resulting from different preprocessing pipelines.
Results: We here introduce a new method for taxonomic profiling based on mixture modeling of the overall oligonucleotide distribution of a sample. Our results indicate that the mixture-based profiles compare well with taxonomic profiles obtained with other methods. However, in contrast to the existing methods, our approach shows a nearly constant profiling accuracy across all kinds of read lengths and it operates at an unrivaled speed.
Availability: A platform-independent implementation of the mixture modeling approach is available in terms of a MATLAB/Octave toolbox at http://gobics.de/peter/taxy. In addition, a prototypical implementation within an easy-to-use interactive tool for Windows can be downloaded.
Contact: pmeinic@gwdg.de; thomas@gobics.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Pathway analysis of high-throughput biological data within a Bayesian network framework
Authors: Isci Senol , Ozturk Cengizhan , Jones Jon , Otu Hasan H. 
Published: May 2011

AbstractMotivation: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network.Results: Proposed method takes into account the connectivity and relatedness between nodes of the pathway through factoring pathway topology in its model. Our simulations using synthetic data demonstrated robustness of our approach. We tested proposed method, Bayesian Pathway Analysis (BPA), on human microarray data regarding renal cell carcinoma (RCC) and compared our results with gene set enrichment analysis. BPA was able to find broader and more specific pathways related to RCC.Availability: Accompanying BPA software (BPAS) package is freely available for academic use at http://bumil.boun.edu.tr/bpa.Contact: hotu@bidmc.harvard.eduSupplementary information: Supplementary data are available at Bioinformatics online.
BINOCh: binding inference from nucleosome occupancy changes
Authors: Meyer Clifford A. , He Housheng H. , Brown Myles , Liu X. Shirley 
Published: May 2011

Abstract
Summary: Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation.
Availability: The BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license.
Contact: cliff@jimmy.harvard.edu; xsliu@jimmy.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Independent Predictors and Outcomes of Unanticipated Early Postoperative Tracheal Intubation after Nonemergent, Noncardiac Surgery
Authors: Ramachandran Satya Krishna , Nafiu Olubukola O. , Ghaferi Amir , Tremper Kevin K. , Shanks Amy , Kheterpal Sachin 
Published: May 2011

Background
Although the risk of hypoxemia is greatest during the first 72 h after surgery, little is known of the incidence of respiratory failure during this period. The authors studied the incidence and predictors of unanticipated early postoperative intubation (within 3 days) and its role in mortality.

Methods
A total of 222,094 adult patients undergoing nonemergent, noncardiac surgery in the American College of Surgeons-National Surgical Quality Improvement Program database were studied to determine the incidence and independent predictors of unanticipated early postoperative intubation. A risk-class model was developed and subsequently validated in 109,636 patients.

Results
Overall, 2,828 of 5,725 (49.4%) unanticipated tracheal intubations in a period of 30 days occurred within the first 3 days after surgery. The incidence of unanticipated early postoperative intubation was 0.83-0.9% in the derivation and validation cohorts. Independent predictors of unanticipated early postoperative intubation included current ethanol use, current smoker, dyspnea, chronic obstructive pulmonary disease, diabetes mellitus needing insulin therapy, active congestive heart failure, hypertension requiring medication, abnormal liver function, cancer, prolonged hospitalization, recent weight loss, body mass index less than 18.5 or ≥ 40 kg/m, medium-risk surgery, high-risk surgery, very-high-risk surgery, and sepsis. Unanticipated early postoperative intubation was an independent predictor of 30-day mortality, with an adjusted odds ratio of 9.2. Higher risk classes were associated with increasing incidence of unanticipated early postoperative intubation and death.

Conclusions
One half of unanticipated tracheal intubations in a period of 30 days occurred within the first 3 days after nonemergent, noncardiac surgery and were independently associated with a 9-fold increase in mortality. The authors present a validated perioperative risk class index for determining risk of unanticipated early postoperative intubation.
Evidence‐based Guidelines From ESPGHAN and NASPGHAN for Helicobacter pylori Infection in Children
Authors: Koletzko Sibylle , Jones Nicola L. , Goodman Karen J. , Gold Benjamin , Rowland Marion , Cadranel Samy , Chong Sonny , Colletti Richard B. , Casswall Thomas , Elitsur Yoram , Guarner Jeannette , Kalach Nicolas , Madrazo Armando , Megraud Francis , Oderda Giuseppina ,   H pylori Working Groups of ESPGHAN and NASPGHAN
Published: May 2011

ABSTRACTObjective:As the clinical implications of Helicobacter pylori infection in children and adolescents continue to evolve, ESPGHAN and NASPGHAN jointly renewed clinical guidelines using a standardized evidence‐based approach to develop updated recommendations for children and adolescents in North America and Europe.Methods:An international panel of 11 pediatric gastroenterologists, 2 epidemiologists, 1 microbiologist, and 1 pathologist was selected by societies that developed evidence‐based guidelines based on the Delphi process with anonymous voting in a final face‐to‐face meeting. A systematic literature search was performed on 8 databases of relevance including publications from January 2000 to December 2009. After excluding nonrelevant publications, tables of evidence were constructed for different focus areas according to the Oxford classification. Statements and recommendations were formulated in the following areas: whom to test, how to test, whom to treat, and how to treat. Grades of evidence were assigned to each recommendation based on the GRADE system.Results:A total of 2290 publications were identified, from which 738 were finally reviewed. A total of 21 recommendations were generated, and an algorithm was proposed by the joint committee providing evidence‐based guidelines on the diagnostic workup and treatment of children with H pylori infection.Conclusions:These clinical practice guidelines represent updated, best‐available evidence and are meant for children and adolescents living in Europe and North America, but they may not apply to those living on other continents, particularly in developing countries with a high H pylori infection rate and limited health care resources.
Extended telephone‐based continuing care for alcohol dependence: 24‐month outcomes and subgroup analyses
Authors: McKay James R. , Van Horn Deborah , Oslin David W. , Ivey Megan , Drapkin Michelle L. , Coviello Donna M. , Yu Qin , Lynch Kevin G. 
Published: May 2011

ABSTRACTAims  To determine whether 18 months of telephone continuing care improves 24‐month outcomes for patients with alcohol dependence. Subgroup analyses were performed to identify patients who would benefit most from continuing care.Design  Comparative effectiveness trial of continuing care that consisted of monitoring and feedback only (TM) or monitoring and feedback plus counseling (TMC). Patients were randomized to treatment as usual (TAU), TAU plus TM or TAU plus TMC, and followed quarterly for 24 months.Setting  Publicly funded intensive out‐patient programs (IOP).Participants  A total of 252 alcohol‐dependent patients (49% with current cocaine dependence) who completed 3 weeks of IOP.Measurements  Percentage of days drinking, any heavy drinking and a composite good clinical outcome.Findings  In the intent‐to‐treat sample, group differences in alcohol outcomes out to 18 months favoring TMC over TAU were no longer present in months 19–24. There was also a non‐significant trend for TMC to perform better than usual care on the good clinical outcome measure (60% vs. 46% good clinical outcome in months 19–24). Overall significant effects favoring TMC and TM over TAU were seen for women; and TMC was also superior to TAU for participants with social support for drinking, low readiness to change and prior alcohol treatments. Most of these effects were obtained on at least two of three outcomes. However, no effects remained significant at 24 months.Conclusions  The benefits of an extended telephone‐based continuing care programme to treat alcohol dependence did not persist after the end of the intervention. A post‐hoc analysis suggested that women and individuals with social support for drinking, low readiness to change or prior alcohol treatments may benefit from the intervention.
Adoptive parents' suspicion of preadoption abuse of their adopted children and the use of support services
Authors: Ward B. W. 
Published: May 2011

AbstractBackground  Adopted children have a higher risk of developmental, mental, behavioural and social problems compared with non‐adopted children, and their use of postadoption support services is of interest. Little attention has been given to the impact of preadoption abuse on the use of these services, and therefore this study examines whether or not adoptive parents' suspicion of preadoption abuse has a significant impact on the use of support services by adopted children.Methods  Data from the National Survey of Adoptive Parents, a US nationally representative survey of adopted children, were used to examine parents' suspicion of preadoption abuse and its effects on the use of postadoption support services by children aged 6–17 years (n= 1411). Statistical analyses were used to examine the relationship between suspected abuse and the use of support services while controlling for characteristics of the adopted child and adoptive parents/household.Results  Seven out of 10 adopted children have used some form of support service, and a larger percentage of 6‐ to 12‐year‐old children suspected of experiencing preadoption abuse used a support service compared with children not suspected of experiencing abuse. Significant relationships existed between various types of suspected preadoption abuse and the use of different types of postadoption support services. These relationships may go unaccounted for when only examining if any preadoption abuse occurred, or if any support service was used.Conclusions  The type of preadoption abuse suspected appears to play a modest role in predicting the type of postadoption support services used by an adopted child. Giving further attention to understanding the relationship between different types of preadoption abuse and types of postadoption support services may help better understand the problems and difficulties experienced by adopted children.
Exploring nursing staff’s attitudes and use of music for older people with dementia in long‐term care facilities
Authors: Sung Huei‐Chuan , Lee Wen‐Li , Chang Shu‐Min , Smith Graeme D 
Published: May 2011

Aims.  This study aimed to explore nursing staff’s attitudes and use of music for older people with dementia in long‐term care facilities.Background.  Music has shown positive outcomes in managing behavioural symptoms of older people with dementia. Older people living in long‐term care facilities often do not have access to trained music therapists. Nursing staff provide the majority of direct care for institutionalised older people with dementia, therefore, will be the most appropriate personnel to learn and implement music therapy for those with dementia. To date, no studies have explored nursing staff’s attitudes and use of music for those with dementia.Design.  A cross‐sectional research design was used.Methods.  A convenience sample of 285 nursing staff caring for those with dementia in long‐term care facilities in Taiwan were recruited. Participants received a self‐administered questionnaire consisted of items exploring nursing staff’s attitude and use of music for those with dementia. A total of 214 participants completed the questionnaires, giving a response rate of 75·1%.Results.  Most nursing staff held positive attitudes towards use of music for older people with dementia (mean = 84·89, range 23–115), but only 30·6% (n = 66) had used music for those with dementia in practice. The majority perceived that they had limited knowledge and skills about use of music (72·9%). Over half of the participants reported that they lacked resources and time to implement music therapy in practice.Conclusions.  Nursing staff need more formal training to use music for those with dementia. Nursing staff can be the suitable personnel to learn easily and implement music therapy as a part of routine activity programmes for those with dementia.Relevance to clinical practice.  Appropriately trained nursing staff in long‐term care facilities who use music therapy may help improve the mental health of older people with dementia.
Factors influencing iron nutrition among one‐year‐old healthy children in Sweden
Authors: Bramhagen Ann‐Cathrine , Svahn Johan , Hallström Inger , Axelsson Irene 
Published: May 2011

Aims and objectives. To describe possible social, nutritional and biological factors influencing iron intake and iron status among healthy one‐year‐old children in southern Sweden.Background. Iron deficiency is one of the most important nutritional disorders and increases the risk of delayed mental and motor development. Children are at risk because of rapid growth, which entails relatively high requirements of iron.Design. A prospective study using survey methods.Method. Randomly selected one‐year‐old children (n = 90) and their parents participated. Parents answered a questionnaire enquiring about demographic data and the child’s feeding and health during the first year. The child’s total food intake and blood samples (haemoglobin, mean corpuscular volume, S‐ferritin and transferring receptor) were obtained.Results. Twenty‐seven per cent of the children had an iron intake below the Nordic Nutrition Recommendations of 8 mg/day (NNR 2004). Follow‐on formula and iron‐fortified porridge contributed to 64% of the child’s total iron intake. Partial breastfeeding and low maternal education correlated negatively with iron intake from complementary food. In total, 10·3% (n = 9) of the children were found to be iron‐depleted (S‐ferritin ≤12 μg/l), and 2·3% (n = 2) had iron deficiency with or without anaemia (Hb ≤100 g/l).Conclusions. One‐year‐old children in Sweden may be at risk of developing iron deficiency, but information about iron‐rich food can improve iron status.Relevance to clinical practice. Knowledge about factors influencing children’s iron intake and iron status may improve the nutritional advice and education from the Child Health Services to prevent or detect iron deficiency.
PIPKs are essential for rhizoid elongation and caulonemal cell development in the moss Physcomitrella patens
Authors: Saavedra Laura , Balbi Virginia , Lerche Jennifer , Mikami Koji , Heilmann Ingo , Sommarin Marianne 
Published: May 2011

SummaryPtdIns‐4,5‐bisphosphate is a lipid messenger of eukaryotic cells that plays a critical role in processes such as cytoskeleton organization, intracellular vesicular trafficking, secretion, cell motility, regulation of ion channels and nuclear signalling pathways. The enzymes responsible for the synthesis of PtdIns(4,5)P2 are phosphatidylinositol phosphate kinases (PIPKs). The moss Physcomitrella patens contains two PIPKs, PpPIPK1 and PpPIPK2. To study their physiological role, both genes were disrupted by targeted homologous recombination and as a result mutant plants with lower PtdIns(4,5)P2 levels were obtained. A strong phenotype for pipk1, but not for pipk2 single knockout lines, was obtained. The pipk1 knockout lines were impaired in rhizoid and caulonemal cell elongation, whereas pipk1‐2 double knockout lines showed dramatic defects in protonemal and gametophore morphology manifested by the absence of rapidly elongating caulonemal cells in the protonemal tissue, leafy gametophores with very short rhizoids, and loss of sporophyte production. pipk1 complemented by overexpression of PpPIPK1 fully restored the wild‐type phenotype whereas overexpression of the inactive PpPIPK1E885A did not. Overexpression of PpPIPK2 in the pipk1‐2 double knockout did not restore the wild‐type phenotype demonstrating that PpPIPK1 and PpPIPK2 are not functionally redundant. In vivo imaging of the cytoskeleton network revealed that the shortened caulonemal cells in the pipk1 mutants was the result of the absence of the apicobasal gradient of cortical F‐actin cables normally observed in wild‐type caulonemal cells. Our data indicate that both PpPIPKs play a crucial role in the development of the moss P. patens, and particularly in the regulation of tip growth.
Phylogenetic variation in glycosidases and glycanases acting on plant cell wall polysaccharides, and the detection of transglycosidase and trans‐β‐xylanase activities
Authors: Franková Lenka , Fry Stephen C. 
Published: May 2011

SummaryWall polysaccharide chemistry varies phylogenetically, suggesting a need for variation in wall enzymes. Although plants possess the genes for numerous putative enzymes acting on wall carbohydrates, the activities of the encoded proteins often remain conjectural. To explore phylogenetic differences in demonstrable enzyme activities, we extracted proteins from 57 rapidly growing plant organs with three extractants, and assayed their ability to act on six oligosaccharides ‘modelling’ selected cell‐wall polysaccharides. Based on reaction products, we successfully distinguished exo‐ and endo‐hydrolases and found high taxonomic variation in all hydrolases screened: β‐d‐xylosidase, endo‐(1→4)‐β‐d‐xylanase, β‐d‐mannosidase, endo‐(1→4)‐β‐d‐mannanase, α‐d‐xylosidase, β‐d‐galactosidase, α‐l‐arabinosidase and α‐l‐fucosidase. The results, as GHATAbase, a searchable compendium in Excel format, also provide a compilation for selecting rich sources of enzymes acting on wall carbohydrates. Four of the hydrolases were accompanied, sometimes exceeded, by transglycosylase activities, generating products larger than the substrate. For example, during β‐xylosidase assays on (1→4)‐β‐d‐xylohexaose (Xyl6), Marchantia, Selaginella and Equisetum extracts gave negligible free xylose but approximately equimolar Xyl5 and Xyl7, indicating trans‐β‐xylosidase activity, also found in onion, cereals, legumes and rape. The yield of Xyl9 often exceeded that of Xyl7–8, indicating that β‐xylanase was accompanied by an endotransglycosylase activity, here called trans‐β‐xylanase, catalysing the reaction 2Xyl6→ Xyl3 + Xyl9. Similar evidence also revealed trans‐α‐xylosidase, trans‐α‐arabinosidase and trans‐α‐arabinanase activities acting on xyloglucan oligosaccharides and (1→5)‐α‐l‐arabino‐oligosaccharides. In conclusion, diverse plants differ dramatically in extractable enzymes acting on wall carbohydrate, reflecting differences in wall polysaccharide composition. Besides glycosidase and glycanase activities, five new transglycosylase activities were detected. We propose that such activities function in the assembly and re‐structuring of the wall matrix.
Large‐scale detection of rare variants via pooled multiplexed next‐generation sequencing: towards next‐generation Ecotilling
Authors: Marroni Fabio , Pinosio Sara , Di Centa Eleonora , Jurman Irena , Boerjan Wout , Felice Nicoletta , Cattonaro Federica , Morgante Michele 
Published: May 2011

SummaryCommon variants, such as those identified by genome‐wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome‐wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next‐generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non‐synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub‐sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost‐effective compared to individual sequencing.
Additive inheritance of histone modifications in Arabidopsis thaliana intra‐specific hybrids
Authors: Moghaddam Ali M. Banaei , Roudier Francois , Seifert Michael , Bérard Caroline , Magniette Marie‐Laure M. , Ashtiyani Raheleh Karimi , Houben Andreas , Colot Vincent , Mette Michael F. 
Published: May 2011

SummaryPlant genomes are earmarked with defined patterns of chromatin marks. Little is known about the stability of these epigenomes when related, but distinct genomes are brought together by intra‐species hybridization. Arabidopsis thaliana accessions and their reciprocal hybrids were used as a model system to investigate the dynamics of histone modification patterns. The genome‐wide distribution of histone modifications H3K4me2 and H3K27me3 in the inbred parental accessions Col‐0, C24 and Cvi and their hybrid offspring was compared by chromatin immunoprecipitation in combination with genome tiling array hybridization. The analysis revealed that, in addition to DNA sequence polymorphisms, chromatin modification variations exist among accessions of A. thaliana. The range of these variations was higher for H3K27me3 (typically a repressive mark) than for H3K4me2 (typically an active mark). H3K4me2 and H3K27me3 were rather stable in response to intra‐species hybridization, with mainly additive inheritance in hybrid offspring. In conclusion, intra‐species hybridization does not result in gross changes to chromatin modifications.