bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Risk, Perceived Risk, and Cancer Worry in Daughters of Breast Cancer Patients
Authors: Quillin John M. , Bodurtha Joann N. , McClish Donna , Wilson Diane Baer 
Published: December 2010

AbstractThis study explored relationships between worry, perceived risk for breast cancer, consulting a genetic counselor, having genetic testing, and genetic risk for women whose mothers had breast cancer. Analyses involved data from a community‐based phone survey of women whose mothers had breast cancer. Participants were categorized as having low, intermediate, or high genetic risk based on their reported family history, in accordance with an accepted classification scheme. The Lerman Breast Cancer Worry Scale measured worry, and participants reported their perceived lifetime likelihood of breast cancer, risk compared to others, and chance from 1 to 100. ANOVA, chi‐square, and multiple regression analyses were conducted as appropriate. One hundred‐fifty women participated. Mean age was 38 years, and 81% were Caucasian. Fifty‐two women had low, 74 had intermediate, and 24 had high genetic risk for breast cancer. There were no significant differences in worry or perceived risk by hereditary risk category. Most high‐risk women (91%) had not spoken with a genetic counselor, and no one had previous genetic testing. These findings suggest perceived risk, worry about breast cancer, and use of expert consultation do not match the genetic contribution to risk. There is a need for effectively stratifying and communicating risk in the community and providing tailored reassurance or referral for high‐risk assessment.
Ozonolysis of Canola Oil: A Study of Product Yields and Ozonolysis Kinetics in Different Solvent Systems
Authors: Omonov Tolibjon S. , Kharraz Ereddad , Curtis Jonathan M. 
Published: December 2010

AbstractThe use of ozonolysis has been proposed as a step in the production of vegetable‐oil‐based polyols as replacements for the equivalent petrochemicals. As part of an evaluation of the commercial viability of ozonolysis, the intermediates and products formed from the ozonolysis of canola oil using different protic and aprotic solvents and solvent mixtures were systematically studied by GC‐FID and size‐exclusion chromatography with refractive index detection (SEC‐RI). It was found that the use of an aprotic solvent (ethyl acetate) leads to the formation of oligomeric ozonolysis products whereas alcohols and/or mixtures of ethyl acetate with alcohols for the ozonolysis of canola oil do not form high molecular weight compounds. In addition, when ethyl acetate is used as the solvent, the formation of carboxylic acids is observed in the early stages of ozonolysis whereas the use of alcohols significantly reduces acid formation. As expected, extending the ozonolysis time led to extensive carboxylic acid formation, especially using ethyl acetate as a solvent. It was found that the optimum time for the complete ozonolysis of canola oil was largely independent of the solvent used for ozonolysis. However, the yield of ozonolysis products differs considerably depending on the solvents employed. Overall, a clear correlation between the ozonolysis time, product yields and the reaction exothermicity was observed.
Enhancing Communication in Surgery Through Team Training Interventions: A Systematic Literature Review
Authors: Gillespie Brigid M. , Chaboyer Wendy , Murray Patrick 
Published: December 2010

AbstractIn surgery, up to 70% of adverse events are attributable to failures in communication. The purpose of this systematic literature review was to critically assess the results of team training interventions used in the OR. In the 12 studies that met the inclusion criteria, there were statistically significant before‐and‐after improvements in teamwork practices and in some secondary outcomes such as complication rates. Our findings suggest that team training interventions have utility in enhancing team communication and cohesion. Team training interventions that are developed in response to the nuances of the context are more likely to become embedded in clinical practice. The introduction of more complex interventions has implications for resources and staffing. Further research is needed to identify and evaluate strategies that address the sustainability of complex team training interventions across multiple OR contexts.
Clinical Issues—December 2010
Authors: Burlingame Byron 
Published: December 2010

This MonthPerioperative fire prevention recommendation changesKey words: fire safety, ECRI, Anesthesia Patient Safety Foundation, National Fire Protection Association, AORN Fire Safety Tool Kit.New relative humidity standards for health care facilitiesKey words: American Society of Healthcare Engineers humidity standards; National Fire Protection Agency humidity standards; safe environment of care; heating, ventilating, and air conditioning; HVAC system.Prevention of venous stasis in outpatient settingsKey words: deep vein thrombosis prophylaxis, DVT prevention protocol.Mechanical deep vein thrombosis (DVT) prophylaxisKey words: deep vein thrombosis, DVT prophylaxis, mechanical DVT prophylaxis.
DNA methylation patterns in luminal breast cancers differ from non‐luminal subtypes and can identify relapse risk independent of other clinical variables
Authors: Kamalakaran Sitharthan , Varadan Vinay , Giercksky Russnes Hege E. , Levy Dan , Kendall Jude , Janevski Angel , Riggs Michael , Banerjee Nilanjana , Synnestvedt Marit , Schlichting Ellen , Kåresen Rolf , Shama Prasada K. , Rotti Harish , Rao Ramachandra , Rao Laxmi , Eric Tang Man-Hung , Satyamoorthy K. , Lucito Robert , Wigler Michael , Dimitrova Nevenka , Naume Bjorn , Borresen-Dale Anne-Lise , Hicks James B. 
Published: December 2010

The diversity of breast cancers reflects variations in underlying biology and affects the clinical implications for patients. Gene expression studies have identified five major subtypes– Luminal A, Luminal B, basal‐like, ErbB2+ and Normal‐Like. We set out to determine the role of DNA methylation in subtypes by performing genome‐wide scans of CpG methylation in breast cancer samples with known expression‐based subtypes. Unsupervised hierarchical clustering using a set of most varying loci clustered the tumors into a Luminal A majority (82%) cluster, Basal‐like/ErbB2+ majority (86%) cluster and a non‐specific cluster with samples that were also inconclusive in their expression‐based subtype correlations. Contributing methylation loci were both gene associated loci (30%) and non‐gene associated (70%), suggesting subtype dependant genome‐wide alterations in the methylation landscape. The methylation patterns of significant differentially methylated genes in luminal A tumors are similar to those identified in CD24 + luminal epithelial cells and the patterns in basal‐like tumors similar to CD44 + breast progenitor cells. CpG islands in the HOXA cluster and other homeobox (IRX2, DLX2, NKX2‐2) genes were significantly more methylated in Luminal A tumors. A significant number of genes (2853, p < 0.05) exhibited expression–methylation correlation, implying possible functional effects of methylation on gene expression. Furthermore, analysis of these tumors by using follow‐up survival data identified differential methylation of islands proximal to genes involved in Cell Cycle and Proliferation (Ki‐67, UBE2C, KIF2C, HDAC4), angiogenesis (VEGF, BTG1, KLF5), cell fate commitment (SPRY1, OLIG2, LHX2 and LHX5) as having prognostic value independent of subtypes and other clinical factors.
Sentence interpretation in bilingual speakers of English and Dutch
Authors: Mcdonald Janet L. 
Published: December 2010

ABSTRACTSpeakers of English and Dutch vary in how strongly they use various syntactic (e.g., word order, prepositions, case inflection) and semantic (e.g., noun animacy) cues to interpret native language sentences. For example, in simple NVN sentences, English speakers rely heavily on word order, while Dutch speakers rely on case inflection. This paper compares the cue usage of English/Dutch and Dutch/English bilinguals with varying amounts of second language exposure to that of native speaker control groups. For all constructions tested, dative constructions, simple NVN sentences, and relative clauses, it was found that with increasing exposure, cue usage in the second language gradually shifts from that appropriate to the first language to that appropriate to the second. A model of cue learning originally proposed to account for monolingual data is found to be compatible with the learning pattern exhibited by bilinguals.
Sentence interpretation strategies in adult Dutch–English bilinguals
Authors: Kilborn Kerry , Cooreman Ann 
Published: December 2010

ABSTRACTThis study is concerned with the probabilistic nature of processing strategies in bilingual speakers of Dutch and English. We used a sentence interpretation task designed to set up various “coalitions” and “competitions” among a restricted set of grammatical entities (i.e., word order, animacy, agreement). Performance in English paralleled that in Dutch in large measure, but where it diverged it approached performance on similar tasks by English monolinguals (Bates et al., 1982). These findings are interpreted on the basis of the “competition model,” a probabilistic theory of grammatical processing which provides a formalism for explaining what it means for a second language user to be “between” languages.
The recruitment of early retirees: a vignette study of the factors that affect managers' decisions
Authors: KARPINSKA KASIA , HENKENS KÈNE , SCHIPPERS JOOP 
Published: December 2010

ABSTRACTRetirement is characterised as a dynamic process that has several different outcomes, from early retirement to re-entry to the labour force. Recent studies of the Dutch population show that a substantial number of early retirees re-enter the workforce after early retirement, but others do not succeed even though they want to return to paid work. An often-named reason for their failures is bias in the selection process. This raises the questions as to what restrictions do early retirees face in the labour market and what are the characteristics that enhance or limit their hiring chances? The aim of this study was to identify the individual and organisational characteristics that influence managers' hiring decisions, and for the purpose a vignette study among Dutch managers and business students was conducted. Profiles of hypothetical early retirees were presented to the respondents who were then asked to make decisions whether of not to employ the individual. The results show that hiring early retirees is of low priority to both managers and students, and depends to a large extent on organisational factors (such as personnel shortages) and the age of the retiree. The findings suggest that despite equal opportunities policies, age discrimination is still present on the Dutch labour market and that managers generally hinder the re-employment of workers approaching the retirement age.
A review of recent research (2000–2008) on applied linguistics and language teaching with specific reference to L2 Spanish
Authors: Antón Marta 
Published: December 2010

Esta reseña presenta una visión general de los estudios sobre español como segunda lengua en contextos educativos. La temática y el ámbito geográfico es amplio a fin de captar la diversidad de alumnos y contextos de aprendizaje de español L2 a sólo dos décadas de que la enseñanza de este idioma adquiriera ímpetu a nivel global. Los alumnos tradicionales de segunda lengua o lengua extranjera, hablantes de herencia, inmigrantes y niños indígenas presentan una variedad de contextos de investigación que contribuye y expande las disciplinas de enseñanza y aprendizaje de segunda lengua/lengua extranjera, lingüística aplicada y sociolingüística. Siguiendo tendencias iniciadas en años anteriores en adquisición de segunda lengua, y en relación con investigaciones sobre otros idiomas, los temas principales en este periodo reciente han sido la adquisición y enseñanza del sistema lingüístico, procesos de aprendizaje y su contexto social. La reseña se organiza temáticamente según estas categorías principales.This review presents a broad picture of recent work on L2 Spanish1in educational contexts. The thematic and geographic scope of the review is wide, in order to capture the diversity of learners and learning contexts of L2 Spanish, just two decades after teaching and learning the language gained impetus worldwide. Traditional second or foreign language learners, heritage learners, immigrants and indigenous children provide a variety of contexts for research that builds on and expands the fields of second and foreign language learning and teaching, applied linguistics and sociolinguistics. Continuing the trend from previous years in SLA, and in connection with research on learners of other languages, main themes in this time period have been the acquisition and teaching of the language system, learning processes, and social contexts of learning. The review is organized thematically according to these main categories.
Second Language Research Forum Colloquia 2009
Authors: Hansen Lynne 
Published: December 2010

Presented at the Second Language Research Forum, Michigan State University, USA; 30 October 2009Recent years have brought increasing attention to studies of language acquisition in a country where the language is spoken, as opposed to formal language study in classrooms. Research on language learners in immersion contexts is important, as the question of whether study abroad is valuable is still somewhat controversial among researchers (DeKeyser 2007; Sunderman & Kroll 2009). In the introduction to a pioneering volume on language study abroad, Freed (1995, pp. 17–18) noted that a vital question concerns the relative linguistic benefits of a summer, a semester or a year in the foreign environment. Our purpose in this colloquium, which was organized by Lynne Hansen, was to introduce a new line of research which allows comparisons of L2 attainment over these exposure times as well as longer periods. Tens of thousands of young missionaries for the Church of Jesus Christ of Latter-day Saints (also known as the LDS or Mormon Church), advanced speakers of some fifty languages, return home annually after two years of language learning abroad. This natural sample of learners, in its relative uniformity of learner characteristics and learning contexts, allows for the control of variables in SLA research which can be problematic in studies of more heterogeneous groups.
Contributions of phonetic token variability and word-type frequency to phonological representations
Authors: RICHTSMEIER PETER , GERKEN LOUANN , OHALA DIANE 
Published: December 2010

ABSTRACTThe experiments here build on the widely reported finding that children are most accurate when producing phonotactic sequences with high ambient-language frequency. What remains controversial is a description of the input that children must be tracking for this effect to arise. We present a series of experiments that compare two ambient-language properties, token and type frequency, as they contribute to phonotactic learning. Token frequency is the raw number of exposures children have to a particular pattern; type frequency refers to a count of abstract entities, such as unique words. Our results suggest that children's production accuracy is most sensitive to a combination of type and token frequency: children were able to generalize a target phonotactic sequence to a new word when familiarized with multiple word-types across tokens from multiple talkers, but not when presented with either word-types with no talker variability or multiple talker-tokens of a single word.
Morphological Confocal Microscopy in Arthropods and the Enhancement of Autofluorescence after Proteinase K Extraction
Authors: Valdecasas Antonio G. , Abad Angela 
Published: December 2010

AbstractProcedures to study the molecular and morphological characteristics of microscopic organisms are often incompatible with each other. Therein, the realization of alternatives that make the characterization of these features compatible and simultaneously permit the deposition of the original material as a voucher sample into a reference collection is one of the foremost goals of biodiversity studies. In this study, we show that genomic extraction does not necessarily compromise the detailed study of the external morphology of microscopic organisms, and to do so, we used a group of aquatic mites (Acari, Hydrachnidia) as a test group. Hydrachnidia morphology is difficult to study when specimens have been stored in pure ethanol; however, proteinase K extraction leaves them flexible and easy to dissect, while, at the same time, maintaining all of their diagnostic features intact. Furthermore, autofluorescence is significantly enhanced after proteinase extraction. Our study was conducted with aquatic mites that were stored in absolute ethanol in the field and processed for DNA extraction using a Qiagen QIAamp minikit. Before and after molecular extraction, a laser scanning confocal microscopy morphological examination was carried out.
MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks
Authors: Gori Fabio , Folino Gianluigi , Jetten Mike S. M. , Marchiori Elena 
Published: December 2010

Abstract
Motivation: Metagenomics is a recent field of biology that studies microbial communities by analyzing their genomic content directly sequenced from the environment. A metagenomic dataset consists of many short DNA or RNA fragments called reads. One interesting problem in metagenomic data analysis is the discovery of the taxonomic composition of a given dataset. A simple method for this task, called the Lowest Common Ancestor (LCA), is employed in state-of-the-art computational tools for metagenomic data analysis of very short reads (about 100 bp). However LCA has two main drawbacks: it possibly assigns many reads to high taxonomic ranks and it discards a high number of reads.
Results: We present MTR, a new method for tackling these drawbacks using clustering at Multiple Taxonomic Ranks. Unlike LCA, which processes the reads one-by-one, MTR exploits information shared by reads. Specifically, MTR consists of two main phases. First, for each taxonomic rank, a collection of potential clusters of reads is generated, and each potential cluster is associated to a taxon at that rank. Next, a small number of clusters is selected at each rank using a combinatorial optimization algorithm. The effectiveness of the resulting method is tested on a large number of simulated and real-life metagenomes. Results of experiments show that MTR improves on LCA by discarding a significantly smaller number of reads and by assigning much more reads at lower taxonomic ranks. Moreover, MTR provides a more faithful taxonomic characterization of the metagenome population distribution.
Availability: Matlab and C++ source codes of the method available at http://cs.ru.nl/˜gori/software/MTR.tar.gz.
Contact: gori@cs.ru.nl; elenam@cs.ru.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence
Authors: Shao Xiaojian , Tan Chris S. H. , Voss Courtney , Li Shawn S. C. , Deng Naiyang , Bader Gary D. 
Published: December 2010

Abstract
Motivation: Predicting protein interactions involving peptide recognition domains is essential for understanding the many important biological processes they mediate. It is important to consider the binding strength of these interactions to help us construct more biologically relevant protein interaction networks that consider cellular context and competition between potential binders.
Results: We developed a novel regression framework that considers both positive (quantitative) and negative (qualitative) interaction data available for mouse PDZ domains to quantitatively predict interactions between PDZ domains, a large peptide recognition domain family, and their peptide ligands using primary sequence information. First, we show that it is possible to learn from existing quantitative and negative interaction data to infer the relative binding strength of interactions involving previously unseen PDZ domains and/or peptides given their primary sequence. Performance was measured using cross-validated hold out testing and testing with previously unseen PDZ domain–peptide interactions. Second, we find that incorporating negative data improves quantitative interaction prediction. Third, we show that sequence similarity is an important prediction performance determinant, which suggests that experimentally collecting additional quantitative interaction data for underrepresented PDZ domain subfamilies will improve prediction.
Availability and Implementation: The Matlab code for our SemiSVR predictor and all data used here are available at http://baderlab.org/Data/PDZAffinity.
Contact: gary.bader@utoronto.ca; dengnaiyang@cau.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
New approach for segmentation and quantification of two-dimensional gel electrophoresis images
Authors: dos Anjos António , Møller Anders L. B. , Ersbøll Bjarne K. , Finnie Christine , Shahbazkia Hamid R. 
Published: December 2010

Abstract
Motivation: Detection of protein spots in two-dimensional gel electrophoresis images (2-DE) is a very complex task and current approaches addressing this problem still suffer from significant shortcomings. When quantifying a spot, most of the current software applications include a lot of background due to poor segmentation. Other software applications use a fixed window for this task, resulting in omission of part of the protein spot, or including background in the quantification. The approach presented here for the segmentation and quantification of 2-DE aims to minimize these problems.
Results: Five sections from different gels are used to test the performance of the presented method concerning the detection of protein spots, and three gel sections are used to test the quantification of sixty protein spots. Comparisons with a state-of-the-art commercial software and an academic state-of-the-art approach are presented. It is shown that the proposed approach for segmentation and quantification of 2-DE images can compete with the available commercial and academic software packages.
Availability: A command-line prototype may be downloaded, for non-commercial use, from http://w3.ualg.pt/~aanjos/prototypes.html.
Contact: antoniodosanjos@gmail.com
Supplementary information: Supplementary data are available at Bioinformtaics online.