bluuebunny/crossref_metadata_2025_split huggingface dataset:
Professional Performance Review Process: Your Best PR Tool
Authors: Schraeder Patricia (Trici) 
Published: October 2009

Abstract
The Professional Performance Review Process (PPRP) was designed specifically for the school-based speech-language pathologist and enhances the four major purposes of professional performance review that have been identified in educational literature. The PPRP combines a formative self-reflection tool (including workload analysis) with a summative evaluation process.
Text Comprehension: Graphic Organizers to the Rescue
Authors: Proly Janet L. , Rivers Jessica , Schwartz Jamie 
Published: October 2009

Abstract
Graphic organizers are a research based strategy used for facilitating the reading comprehension of expository text. This strategy will be defined and the evolution and supporting evidence for the use of graphic organizers will be discussed. Various types of graphic organizers and resources for SLPs and other educators will also be discussed.
ABWGAT: anchor-based whole genome analysis tool
Authors: Das Sarbashis , Vishnoi Anchal , Bhattacharya Alok 
Published: October 2009

Abstract
Summary: Large numbers of genomes are being sequenced regularly and the rate will go up in future due to availability of new genome sequencing techniques. In order to understand genotype to phenotype relationships, it is necessary to identify sequence variations at the genomic level. Alignment of a pair of genomes and parsing the alignment data is an accepted approach for identification of variations. Though there are a number of tools available for whole-genome alignment, none of these allows automatic parsing of the alignment and identification of different kinds of genomic variants with high degree of sensitivity. Here we present a simple web-based interface for whole genome comparison named ABWGAT (Anchor-Based Whole Genome Analysis Tool) that is simple to use. The output is a list of variations such as SNVs, indels, repeat expansion and inversion.
Availability: The web server is freely available to non-commercial users at the following address http://abwgc.jnu.ac.in/_sarba. Supplementary data are available at http://abwgc.jnu.ac.in/_sarba/cgi-bin/abwgc_retrival.cgi using job id 524, 526 and 528.
Contact: dsarbashis@gmail.com; alok.bhattacharya@gmail.com
Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities
Authors: Schäfer Martin , Schwender Holger , Merk Sylvia , Haferlach Claudia , Ickstadt Katja , Dugas Martin 
Published: October 2009

Abstract
Motivation: The analysis of a number of different genetic features like copy number (CN) variation, gene expression (GE) or loss of heterocygosity has considerably increased in recent years, as well as the number of available datasets. This is particularly due to the success of microarray technology. Thus, to understand mechanisms of disease pathogenesis on a molecular basis, e.g. in cancer research, the challenge of analyzing such different data types in an integrated way has become increasingly important. In order to tackle this problem, we propose a new procedure for an integrated analysis of two different data types that searches for genes and genetic regions which for both inputs display strong equally directed deviations from the reference median. We employ this approach, based on a modified correlation coefficient and an explorative Wilcoxon test, to find DNA regions of such abnormalities in GE and CN (e.g. underexpressed genes accompanied by a loss of DNA material).
Results: In an application to acute myeloid leukemia, our procedure is able to identify various regions on different chromosomes with characteristic abnormalities in GE and CN data and shows a higher sensitivity to differences in abnormalities than standard approaches. While the results support various findings of previous studies, some new interesting DNA regions can be identified. In a simulation study, our procedure also shows more reliable results than standard approaches.
Availability: Code and data available as R packages edira and ediraAMLdata from http://www.statistik.tu-dortmund.de/~schaefer/
Contact: martin.schaefer@udo.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Airborne transmission of disease in hospitals
Authors: Eames I. , Tang J. W. , Li Y. , Wilson P. 
Published: October 2009

Hospital-acquired infection (HAI) is an important public health issue with unacceptable levels of morbidity and mortality, over the last 5 years. Disease can be transmitted by air (over large distances), by direct/indirect contact or a combination of both routes. While contact transmission of disease forms the majority of HAI cases, transmission through the air is harder to control, but one where the engineering sciences can play an important role in limiting the spread. This forms the focus of this themed volume.
In this paper, we describe the current hospital environment and review the contributions from microbiologists, mechanical and civil engineers, and mathematicians to this themed volume on the airborne transmission of infection in hospitals. The review also points out some of the outstanding scientific questions and possible approaches to mitigating transmission.
Cannabis and crime: findings from a longitudinal study
Authors: Pedersen Willy , Skardhamar Torbjørn 
Published: October 2009

ABSTRACTAim  To examine the association between cannabis use during adolescence and young adulthood, and subsequent criminal charges.Methods  Data were obtained from the Young in Norway Longitudinal Study. A population‐based sample (n = 1353) was followed from 13 to 27 years of age. Data were gathered on cannabis use, alcohol consumption and alcohol problems, and use of other illegal substances such as amphetamines, cocaine and opiates. In addition, extensive information on socio‐demographic, family and personal factors was collected. This data set was linked to individual‐level information from official Norwegian crime statistics.Findings  We found robust associations between cannabis use and later registered criminal charges, both in adolescence and in young adulthood. These associations were adjusted for a range of confounding factors, such as family socio‐economic background, parental support and monitoring, educational achievement and career, previous criminal charges, conduct problems and history of cohabitation and marriage. In separate models, we controlled for alcohol measures and for use of other illegal substances. After adjustment, we still found strong associations between cannabis use and later criminal charges. However, when eliminating all types of drug‐specific charges from our models, we no longer observed any significant association with cannabis use.Conclusions  The study suggests that cannabis use in adolescence and early adulthood may be associated with subsequent involvement in criminal activity. However, the bulk of this involvement seems to be related to various types of drug‐specific crime. Thus, the association seems to rest on the fact that use, possession and distribution of drugs such as cannabis is illegal. The study strengthens concerns about the laws relating to the use, possession and distribution of cannabis.
Relationship of abdominal obesity with cardiovascular disease, diabetes and hyperlipidaemia in Spain
Authors: Casanueva Felipe F. , Moreno Basilio , Rodríguez‐Azeredo Rosario , Massien Christine , Conthe Pedro , Formiguera Xavier , Barrios Vivencio , Balkau Beberly 
Published: October 2009

SummaryObjectives  To evaluate the relevance of obesity and abdominal obesity in the prevalence of cardiovascular disease (CVD), diabetes mellitus, hyperlipidaemia and hypertension in primary care patients and to ascertain whether waist circumference (WC) measurement should be included in routine clinical practice in addition to body mass index (BMI).Methods  As part of the IDEA study, primary care physicians from Spain recruited patients aged 18–80 years. WC and BMI and the presence of CVD, diabetes mellitus, hyperlipidaemia and hypertension were recorded. Finally, 17 980 were analysed.An age‐related increase in adiposity was observed. Overall 33% were obese by BMI, and 51% of subjects presented abdominal obesity by the National Cholesterol Education Program Adult Treatment Panel III (NCEP‐ATPIII) (WC > 102 cm for men and > 88 cm for women). Although there was a correlation between BMI and WC, they presented different distribution patterns. Women, but not men, with a high level of education, professional activity and smoking were associated with a lower WC. Abdominal obesity was significantly associated with CVD. Some subjects with abdominal obesity but lean by BMI, showed an increased prevalence of CVD and diabetes. Furthermore, abdominal obesity was strongly associated with dyslipidaemia and hypertension.Conclusions  Half of the primary care patients studied showed abdominal obesity as measured by WC, whereas one‐third was obese by BMI. Abdominal obesity was strongly associated with CVD and diabetes, even in patients lean by BMI. WC should be included in the routine clinical practice in addition to BMI.
Maternal thyroid function during gestation is related to breech presentation at term
Authors: Kuppens S. M. I. , Kooistra L. , Wijnen H. A. , Crawford S. , Vader H. L. , Hasaart T. H. M. , Oei S. G. , Pop V. J. 
Published: October 2009

SummaryObjective  To study the relationship between suboptimal maternal thyroid function during gestation and breech presentation at term.Design  Prospective follow‐up study during three trimesters of gestation.Patients  A total of 1058 Dutch Caucasian healthy pregnant women were prospectively followed from 12 weeks gestation until term (≥37 weeks) delivery.Measurements  Maternal thyroid parameters [TSH, free T4 (FT4) and auto‐antibodies to thyroid peroxidase] were assessed at 12, 24 and 36 weeks gestation as well as foetal presentation at term.Results  At term, 58 women (5·5%) presented in breech. Compared with women with foetuses in the cephalic position, those women who presented in breech at term had significantly higher TSH concentrations, but only at 36 weeks gestation (P = 0·007). No between group differences were obtained for FT4 level at any assessment. The prevalence of breech presentation in the subgroup of women with TSH ≥ 2·5 mIU/l (90th percentile) at 36 weeks gestation was 11%, compared with 4·8% in the women with TSH < 2·50 mIU/l (P = 0·006). Women with TSH below the 5th percentile had no breech presentations. Breech position was significantly and independently related to high maternal TSH concentration (≥2·5 mIU/l) at 36 weeks gestation (O.R.: 2·23, 95% CI: 1·14–4·39), but not at 12 and 24 weeks gestation.Conclusions  Women with TSH levels above 2·5 mIU/l during end gestation are at risk for breech presentation, and as such for obstetric complications.
An audit of liquid‐based cervical cytology screening samples (ThinPrep and SurePath) reported as glandular neoplasia
Authors: Thiryayi S. A. , Marshall J. , Rana D. N. 
Published: October 2009

S. A. Thiryayi, J. Marshall and D. N. Rana An audit of liquid‐based cervical cytology screening samples (ThinPrep and SurePath) reported as glandular neoplasiaObjectives:  The aims of this study were to assess the number of cases diagnosed as glandular neoplasia (national report code 6) of cervical (6A) and non‐cervical (6B) types on ThinPrep (TP) and SurePath (SP) liquid‐based cytology (LBC) samples and to calculate the positive predictive value (PPV) of these diagnoses for significant glandular and/or squamous pathology for local audit and as a contribution to national data on glandular neoplasia.Methods:  A computerized search identified all screening LBC samples reported as glandular neoplasia during the 24‐month period from January 2006 to December 2007. Corresponding histology samples were identified, with a minimum follow‐up period of 6 months for each case.Results:  A total of 70 samples, representing 70 patients, were reported as glandular neoplasia, 39 TP (55.7%) and 31 SP (44.3%), with 46 samples (31 TP, 15 SP) reported as 6A and 24 samples (eight TP, 16 SP) as 6B. PPV of glandular neoplasia was calculated for a biopsy diagnosis of cervical glandular intraepithelial neoplasia/adenocarcinoma and/or cervical intraepithelial neoplasia (CIN) 2 or worse. The PPV of 6A was 100% for both TP and SP. The PPV of 6B for adenocarcinoma was 62.5% for TP and 66.7% for SP. The combined PPV for 6A + 6B was 92.3% for TP, 83.3% for SP and 88.4% combined. The overall pick‐up rates for the two methods were significantly different (TP 0.031%, SP 0.052%; P = 0.014). Histology showed only CIN3 with endocervical crypt involvement in nine TP cases and one SP case.
Modified Papanicolaou staining protocol with minimum alcohol use: a cost‐cutting measure for resource‐limited settings
Authors: Gupta S. , Chachra K. L. , Bhadola P. , Sodhani P. 
Published: October 2009

S. Gupta, K. L. Chachra, P. Bhadola and P. Sodhani Modified Papanicolaou staining protocol with minimum alcohol use: a cost‐cutting measure for resource‐limited settingsObjective:  To devise a simple, cost‐effective protocol for Papanicolaou (Pap) staining of cervicovaginal smears.Methods:  Five hundred coded paired cervical smears were collected from women as part of routine cervical cancer screening. One set of smears was stained by conventional Pap staining protocol (CP) and the other by a modified protocol (MP) in which alcohol was replaced by 1% acetic acid in all the steps except during fixation and prior to mounting; in addition, one alcohol‐based counterstain, OG, was omitted. The smears were examined blindly by the pathologists and then decoded. Each pair of smears was compared and the two protocols were analysed for staining quality and diagnoses by McNemar and chi‐square tests.Results:  The staining quality in the MP was satisfactory. The nuclear and cytoplasmic features were comparable to the CP. Cytoplasmic transparency was maintained in the MP and the differential staining of blue/green and pink was acceptable to the pathologists and technicians. The diagnoses agreed in all cases and there was no compromise in interpreting the smears. With MP it took only 3–4 minutes to stain a batch of 50 slides. in contrast to the 20 minutes taken by CP. The MP used almost one‐seventh of the amount of alcohol compared with CP, which translated into a significant cost reduction per smear.Conclusions:  The improvised Pap staining protocol with minimum alcohol use is a simple, cost‐effective and technician‐friendly procedure that can be easily adopted in high‐volume, resource‐limited laboratories for mass cervical cancer screening.
Activated complement is more extensively present in diseased aortic valves than naturally occurring complement inhibitors: a sign of ongoing inflammation
Authors: Ter Weeme M. , Vonk A. B. A. , Kupreishvili K. , Van Ham M. , Zeerleder S. , Wouters D. , Stooker W. , Eijsman L. , Van Hinsbergh V. W. M. , Krijnen P. A. J. , Niessen H. W. M. 
Published: October 2009

Eur J Clin Invest 2010; 40 (1): 4–10AbstractBackground  Recent studies indicate a role for complement in the pathogenesis of aortic valve disease. However, the role of naturally occurring anti‐complement mediators in this context is unknown. In this study, we have analysed this in three different pathological conditions of the aortic valve: degeneration, atherosclerosis and bacterial endocarditis.Materials and methods  Human aortic valves were obtained at autopsy (n = 30): 5 control valves, 10 aortic valves with atherosclerotic changes, 10 aortic valves with degenerative changes and 5 degenerative changed aortic valves with bacterial infection. These valves were analysed immunohistochemically for the presence of activated complement (C3d and C5b9) and the complement inhibitors C1‐inh and clusterin. Areas of positivity were then quantified.Results  C3d, C5b9 and the complement inhibitors C1‐inh and clusterin depositions were mainly found in the endothelium and extracellular matrix in aortic valves. All these mediators were already present in control valves, but the area of positivity increased significantly in response to the different diseases, with the highest increase in response to bacterial endocarditis. Interestingly, in all three aortic diseases, the depositions of complement were significantly more widespread than that of their inhibitors.Conclusions  Our study indicates that anti‐complement mediators (C1‐inh and clusterin) are deposited in diseased aortic valves together with activated complement, indicating an existing counter response against complement locally in the valve. However, deposition of activated complement is significantly more widespread than that of its inhibitors, which could explain ongoing inflammation in those diseased aortic valves.
Sperm chromatin structure assay as an independent predictor of fertility in vivo: a case–control study
Authors: Giwercman Aleksander , Lindstedt Lars , Larsson Mattias , Bungum Mona , Spano Marcello , Levine Richard J. , Rylander Lars 
Published: October 2009

SummaryStandard sperm parameters have a limited power for prediction of the chance of natural conception. Recent studies have indicated that the sperm chromatin structure assay (SCSA) DNA fragmentation index (DFI), a measure for the fraction of sperms with DNA damage, is associated with fertility in vivo. The aim of this study was to evaluate the value of this parameter for prediction of infertility. One hundred and twenty‐seven men from infertile couples with no known female factor and 137 men with proven fertility were included. Semen analysis was performed as recommended by the WHO. DFI was assessed using SCSA. Logistic binary regression was used to compute the odds ratios (OR) for infertility. As compared with men with a DFI <10%, men with a DFI between 10% and 20% had an increased risk for infertility (OR 2.5, 95% CI: 1.0–6.1). This was also true for men with a DFI >20% (OR 8.4; 95% CI: 3.0–23). In men with normal standard semen parameters (sperm concentration, motility and morphology) the OR for infertility was increased with DFI >20% (OR 5.1, 95% CI: 1.2–23), whereas if one of the standard semen parameters was abnormal, the OR for infertility was increased already at DFI above 10% (OR 16, 95% CI: 4.2–60). We conclude that SCSA DFI adds to the value of semen analysis in prediction of the chance of natural conception.
Dietary Approaches to Stop Hypertension (DASH) diet: applicability and acceptability to a UK population
Authors: Harnden K. E. , Frayn K. N. , Hodson L. 
Published: October 2009

AbstractBackground:  The Dietary Approaches to Stop Hypertension (DASH) diet is widely promoted in the USA for the prevention and treatment of high blood pressure. It is high in fruit and vegetables, low‐fat dairy and wholegrain foods and low in saturated fat and refined sugar. To our knowledge, the use of this dietary pattern has not been assessed in a free‐living UK population.Methods:  The DASH diet was adapted to fit UK food preferences and portion sizes. Fourteen healthy subjects followed the adapted DASH diet for 30 days in which they self‐selected all food and beverages. Dietary intake was assessed by 5‐day food diaries completed before and towards the end of the study. Blood pressure was measured at the beginning and end of the study to assess compliance to the DASH style diet.Results:  The DASH diet was easily adapted to fit with UK food preferences. Furthermore, it was well tolerated and accepted by subjects. When on the DASH style diet, subjects reported consuming significantly (P < 0.01) more carbohydrate and protein and less total fat (5%, 6% and 9% total energy, respectively). Sodium intakes decreased by 860 mg day−1 (P < 0.001). Systolic and diastolic blood pressure decreased significantly (P < 0.05) by 4.6 and 3.9 mmHg, respectively when on the DASH style diet.Conclusions:  The DASH style diet was well accepted and was associated with a decrease in blood pressure in normotensive individuals and should be considered when giving dietary advice to people with elevated blood pressure in the UK.
Functional stratification of the Spitzenkörper of Neurospora crassa
Authors: Verdín Jorge , Bartnicki‐Garcia Salomon , Riquelme Meritxell 
Published: October 2009

SummaryGS‐1 (ncu04189) is a protein required for the synthesis of β‐1,3‐glucan in Neurospora crassa. As chitin, β‐1,3‐glucan is a morphogenetically relevant component of the fungal cell wall. Previously, we showed that chitin synthases are delivered to the growing hyphal tip of N. crassa by secretory microvesicles that follow an unconventional route and accumulate in the core of the Spitzenkörper (Spk). Tagged with the green fluorescent protein (GFP), GS‐1 accumulated in the hyphal apex forming a dynamic and pleomorphic ring‐like structure (‘Spitzenring’) that corresponded to the Spk outer macrovesicular stratum and surrounded the inner core of chitin synthase‐containing microvesicles. TIRF microscopy revealed that GS‐1‐GFP reached the hyphal apex as a population of heterogeneous‐size particles that moved along defined paths. On sucrose density gradients, GS‐1‐associated particles mainly sedimented in a high density range 1.1272–1.2124 g ml−1. Clearly, GS‐1 and chitin synthases of N. crassa are contained in two different types of secretory vesicles that accumulate in different strata of the Spk, a differentiation presumably related to the spatial control of cell‐wall synthesis.
Distinct β‐clamp interactions govern the activities of the Y family PolIV DNA polymerase
Authors: Wagner Jérôme , Etienne Hélène , Fuchs Robert P. , Cordonnier Agnes , Burnouf Dominique 
Published: October 2009

SummaryThe prototypic Y family DNA polymerase IV (PolIV) of Escherichia coli is involved in multiple replication‐associated processes including spontaneous mutagenesis, translesion synthesis (TLS), cell fitness, survival under stressful conditions and checkpoint like functions. It interacts physically and functionally with the replisome's β processivity clamp through the canonical PolIV C‐terminal peptide (CTP). A second interaction that involves a portion of the little finger (LF) domain of PolIV has been structurally described. Here we show that the LF–β interaction stabilizes the clamp–polymerase complex in vitro and is necessary for the access of PolIV to ongoing replication forks in vivo. However, in contrast to the CTP–β, the LF–β interaction is dispensable for the role of the polymerase in TLS. This discloses two independent modes of action for PolIV and, in turn, uncovers a novel way by which the cell may regulate the potentially deleterious effect of such low fidelity polymerases during replication.