bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of polymorphisms in ERCC1, ASE-1 and RAIon the risk of colorectal carcinomas and adenomas: a case control study
Authors: Skjelbred Camilla F , Sæbø Mona , Nexø Bjørn A , Wallin Håkan , Hansteen Inger-Lise , Vogel Ulla , Kure Elin H 
Published: August 2006

Abstract

Background
The risk of sporadic colorectal cancer is mainly associated with lifestyle factors and may be modulated by several genetic factors of low penetrance. Genetic variants represented by single nucleotide polymorphisms in genes encoding key players in the adenoma carcinoma sequence may contribute to variation in susceptibility to colorectal cancer. In this study, we aimed to evaluate whether the recently identified haplotype encompassing genes of DNA repair and apoptosis, is associated with increased risk of colorectal adenomas and carcinomas.

Methods
We used a case-control study design (156 carcinomas, 981 adenomas and 399 controls) to test the association between polymorphisms in the chromosomal region 19q13.2-3, encompassing the genes ERCC1, ASE-1 and RAI, and risk of colorectal adenomas and carcinomas in a Norwegian cohort. Odds ratio (OR) and 95% confidence interval (CI) were estimated by binary logistic regression model adjusting for age and gender.

Results
The ASE-1 polymorphism was associated with an increased risk of adenomas, OR of 1.39 (95% CI 1.06–1.81), which upon stratification was apparent among women only, OR of 1.66 (95% CI 1.15–2.39). The RAI polymorphism showed a trend towards risk reduction for both adenomas (OR of 0.70, 95% CI 0.49–1.01) and carcinomas (OR of 0.49, 95% CI 0.21–1.13) among women, although not significant. Women who were homozygous carriers of the high risk haplotype had an increased risk of colorectal cancer, OR of 2.19 (95% CI 0.95–5.04) compared to all non-carriers although the estimate was not statistically significant.

Conclusion
We found no evidence that the studied polymorphisms were associated with risk of adenomas or colorectal cancer among men, but we found weak indications that the chromosomal region may influence risk of colorectal cancer and adenoma development in women.
Comorbidity in patients with diabetes mellitus: impact on medical health care utilization
Authors: Struijs Jeroen N , Baan Caroline A , Schellevis Francois G , Westert Gert P , van den Bos Geertrudis AM 
Published: August 2006

Abstract
Background
Comorbidity has been shown to intensify health care utilization and to increase medical care costs for patients with diabetes. However, most studies have been focused on one health care service, mainly hospital care, or limited their analyses to one additional comorbid disease, or the data were based on self-reported questionnaires instead of health care registration data. The purpose of this study is to estimate the effects a broad spectrum of of comorbidities on the type and volume of medical health care utilization of patients with diabetes.

Methods
By linking general practice and hospital based registrations in the Netherlands, data on comorbidity and health care utilization of patients with diabetes (n = 7,499) were obtained. Comorbidity was defined as diabetes-related comorbiiabetes-related comorbidity. Multilevel regression analyses were applied to estimate the effects of comorbidity on health care utilization.

Results
Our results show that both diabetes-related and non diabetes-related comorbidity increase the use of medical care substantially in patients with diabetes. Having both diabeterelated and non diabetes-related comorbidity incrases the demand for health care even more. Differences in health care utilization patterns were observed between the comorbidities.

Conclusion
Non diabetes-related comorbidity increases the health care demand as much as diabetes-related comorbidity. Current single-disease approach of integrated diabetes care should be extended with additional care modules, which must be generic and include multiple diseases in order to meet the complex health care demands of patients with diabetes in the future.
Mapping oral health related quality of life to generic health state values
Authors: Brennan David S , Spencer A John 
Published: August 2006

Abstract
Background
A summary utility index is useful for deriving quality-adjusted life years (QALY) for cost analyses or disability weights for burden of disease studies. However, many quality of life instruments provide descriptive profiles rather than a single utility index. Transforming quality of life instruments to a utility index could extend the use of quality of life instruments to costs analyses and burden of disease studies. The aims of the study were to map a specific oral health measure, the Oral Health Impact Profile to a generic health state measure, the EuroQol, in order to enable the estimation of health state values based on OHIP data.

Methods
Data were collected from patients treated by a random sample of South Australian dentists in 2001–02 using mailed self-complete questionnaires. Dentists recorded the diagnosis of dental conditions and provided patients with self-complete questionnaires to record the nature, severity and duration of symptoms using the EuroQol (EQ-5D) and 14-item version of the Oral Health Impact Profile (OHIP-14) instruments. Data were available from 375 patients (response rate = 72%). A random two-thirds sample of patients was used in tobit regressions of EQ-5D health state values estimated using OHIP-14 in a model with categories of OHIP responses as indicator variables and in a model with OHIP responses as continuous variables. Age and sex were included as covariates in both models. The remaining one-third sample of patients was used to test the models.

Results
The OHIP item 'painful aching in mouth' was significantly related to health state values in both models while 'life less satisfying' was also significant in the continuous model. Mean forecast errors relative to the mean observed health state value were higher when fitted to the categorical model (17.4%) compared to the continuous model (15.2%) (P < 0.05).

Conclusion
The findings enable health state values to be derived from OHIP-14 scores for populations where utility has not or cannot be measured directly.
The chaperone DnaK controls the fractioning of functional protein between soluble and insoluble cell fractions in inclusion body-forming cells
Authors: González-Montalbán Nuria , García-Fruitós Elena , Ventura Salvador , Arís Anna , Villaverde Antonio 
Published: August 2006

AbstractBackgroundThe molecular mechanics of inclusion body formation is still far from being completely understood, specially regarding the occurrence of properly folded, protein species that exhibit natural biological activities. We have here comparatively explored thermally promoted,in vivoprotein aggregation and the formation of bacterial inclusion bodies, from both structural and functional sides. Also, the status of the soluble and insoluble protein versions in both aggregation systems have been examined as well as the role of the main molecular chaperones GroEL and DnaK in the conformational quality of the target polypeptide.ResultsWhile thermal denaturation results in the formation of heterogeneous aggregates that are rather stable in composition, protein deposition as inclusion bodies renders homogenous but strongly evolving structures, which are progressively enriched in the main protein species while gaining native-like structure. Although both type of aggregates display common features, inclusion body formation but not thermal-induced aggregation involves deposition of functional polypeptides that confer biological activity to such particles, at expenses of the average conformational quality of the protein population remaining in the soluble cell fraction. In absence of DnaK, however, the activity and conformational nativeness of inclusion body proteins are dramatically impaired while the soluble protein version gains specific activity.ConclusionThe chaperone DnaK controls the fractioning of active protein between soluble and insoluble cell fractions in inclusion body-forming cells but not during thermally-driven protein aggregation. This cell protein, probably through diverse activities, is responsible for the occurrence and enrichment in inclusion bodies of native-like, functional polypeptides, that are much less represented in other kind of protein aggregates.
Clear cell sarcoma of the scapula. A case report and review of the literature
Authors: Kazakos Constantinos J , Galanis Vasilios G , Giatromanolaki Alexandra , Verettas Dennis-Alexander J , Sivridis Efthimios 
Published: August 2006

AbstractBackgroundClear cell sarcoma of tendons and aponeuroses (CCSTA) appears usually in the extremities and rarely in the trunk.Case presentationWe present an unusual case of CCSTA overlying the scapular region and with secondary osseous extension in the lower scapula. The patient underwent a wide local excision with removal of the tumor and the lower two thirds of the scapula. He had no local recurrences but he developed lung metastases after 5 months in spite of postoperative chemotherapy. He finally died ten months later.ConclusionThe patients with CCSTA have a variable unpredictable course. Despite treatment the overall prognosis is poor.
Effects of dopexamine on the intestinal microvascular blood flow and leucocyte activation in a sepsis model in rats
Authors: Birnbaum Jürgen , Klotz Edda , Spies Claudia D , Lorenz Björn , Stuebs Patrick , Hein Ortrud Vargas , Gründling Matthias , Pavlovic Dragan , Usichenko Taras , Wendt Michael , Kox Wolfgang J , Lehmann Christian 
Published: August 2006

Abstract
Introduction
Dopexamine may be a therapeutic option to improve hepatosplanchnic perfusion in sepsis. To investigate this possibility, we administered dopexamine in an experimental sepsis model in rats.

Methods
This prospective, randomized, controlled laboratory study was conducted in 42 Wistar rats. The animals were divided into three groups. Group 1 served as the control group (CON group). The animals in both groups 2 (LPS group) and 3 (DPX group) received an endotoxin (lipopolysaccharide from Escherichia coli – LPS) infusion (20 mg/kg for 15 minutes). DPX group additionally received dopexamine (0.5 μg/kg per minute over four hours). One half of the animals in each group underwent studies of intestinal microvascular blood flow (IMBF) using laser Doppler fluxmetry. In the other half an intravital microscopic evaluation of leucocyte-endothelial cell interaction in intestinal microcirculation was conducted. Functional capillary density (FCD) in the intestinal mucosa and in the circular as well as longitudinal muscle layer was estimated.

Results
One hour after endotoxin challenge, IMBF decreased significantly in LPS group to 51% compared with baseline (P < 0.05). In DPX group (endotoxin plus dopexamine) we found IMBF values significantly higher than those in LPS group (approximately at the level of controls). The impaired FCD following endotoxin challenge was improved by dopexamine in the longitudinal muscle layer (+33% in DPX group versus LPS group; P < 0.05) and in the circular muscle layer (+48% in DPX group versus LPS group; P < 0.05). In DPX group, dopexamine administration reduced the number of firmly adherent leucocytes (-31% versus LPS group; P < 0.05). Plasma levels of tumour necrosis factor-α were reduced by dopexamine infusion (LPS group: 3637 ± 553 pg/ml; DPX group: 1933 ± 201 pg/ml) one hour after endotoxin challenge.

Conclusion
Dopexamine administration improved IMBF and FCD (markers of intestinal microcirculation) and reduced leucocyte activation (a marker of inflammation) in experimental sepsis.
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
Authors: Stanke Mario , Tzvetkova Ana , Morgenstern Burkhard 
Published: August 2006

Abstract
Background
A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were systematically evaluated and compared on test data from the human genome. AUGUSTUS was among the tools that were tested in this project.

Results
AUGUSTUS can be used as an ab initio program, that is, as a program that uses only one single genomic sequence as input information. In addition, it is able to combine information from the genomic sequence under study with external hints from various sources of information. For EGASP, we used genomic sequence alignments as well as alignments to expressed sequence tags (ESTs) and protein sequences as additional sources of information. Within the category of ab initio programs AUGUSTUS predicted significantly more genes correctly than any other ab initio program. At the same time it predicted the smallest number of false positive genes and the smallest number of false positive exons among all ab initio programs. The accuracy of AUGUSTUS could be further improved when additional extrinsic data, such as alignments to EST, protein and/or genomic sequences, was taken into account.

Conclusion
AUGUSTUS turned out to be the most accurate ab initio gene finder among the tested tools. Moreover it is very flexible because it can take information from several sources simultaneously into consideration.
A computational approach for identifying pseudogenes in the ENCODE regions
Authors: Zheng Deyou , Gerstein Mark B 
Published: August 2006

Abstract
Background
Pseudogenes are inheritable genetic elements showing sequence similarity to functional genes but with deleterious mutations. We describe a computational pipeline for identifying them, which in contrast to previous work explicitly uses intron-exon structure in parent genes to classify pseudogenes. We require alignments between duplicated pseudogenes and their parents to span intron-exon junctions, and this can be used to distinguish between true duplicated and processed pseudogenes (with insertions).

Results
Applying our approach to the ENCODE regions, we identify about 160 pseudogenes, 10% of which have clear 'intron-exon' structure and are thus likely generated from recent duplications.

Conclusion
Detailed examination of our results and comparison of our annotation with the GENCODE reference annotation demonstrate that our computation pipeline provides a good balance between identifying all pseudogenes and delineating the precise structure of duplicated genes.
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA
Authors: Djebali Sarah , Delaplace Franck , Crollius Hugues Roest 
Published: August 2006

Abstract
Background
Accurate and automatic gene identification in eukaryotic genomic DNA is more than ever of crucial importance to efficiently exploit the large volume of assembled genome sequences available to the community. Automatic methods have always been considered less reliable than human expertise. This is illustrated in the EGASP project, where reference annotations against which all automatic methods are measured are generated by human annotators and experimentally verified. We hypothesized that replicating the accuracy of human annotators in an automatic method could be achieved by formalizing the rules and decisions that they use, in a mathematical formalism.

Results
We have developed Exogean, a flexible framework based on directed acyclic colored multigraphs (DACMs) that can represent biological objects (for example, mRNA, ESTs, protein alignments, exons) and relationships between them. Graphs are analyzed to process the information according to rules that replicate those used by human annotators. Simple individual starting objects given as input to Exogean are thus combined and synthesized into complex objects such as protein coding transcripts.

Conclusion
We show here, in the context of the EGASP project, that Exogean is currently the method that best reproduces protein coding gene annotations from human experts, in terms of identifying at least one exact coding sequence per gene. We discuss current limitations of the method and several avenues for improvement.
Comparison of the Medical Priority Dispatch System to an Out‐of‐hospital Patient Acuity Score
Authors: Feldman Michael J. , Verbeek P. Richard , Lyons David G. , Chad Sandra J. , Craig Alan M. , Schwartz Brian 
Published: August 2006

Abstract
Background:
Although the Medical Priority Dispatch System (MPDS) is widely used by emergency medical services (EMS) dispatchers to determine dispatch priority, there is little evidence that it reflects patient acuity. The Canadian Triage and Acuity Scale (CTAS) is a standard patient acuity scale widely used by Canadian emergency departments and EMS systems to prioritize patient care requirements.
Objectives:
To determine the relationship between MPDS dispatch priority and out‐of‐hospital CTAS.
Methods:
All emergency calls on a large urban EMS communications database for a one‐year period were obtained. Duplicate calls, nonemergency transfers, and canceled calls were excluded. Sensitivity and specificity to detect high‐acuity illness, as well as positive predictive value (PPV) and negative predictive value (NPV), were calculated for all protocols.
Results:
Of 197,882 calls, 102,582 met inclusion criteria. The overall sensitivity of MPDS was 68.2% (95% confidence interval [CI] = 67.8% to 68.5%), with a specificity of 66.2% (95% CI = 65.7% to 66.7%). The most sensitive protocol for detecting high acuity of illness was the breathing‐problem protocol, with a sensitivity of 100.0% (95% CI = 99.9% to 100.0%), whereas the most specific protocol was the one for psychiatric problems, with a specificity of 98.1% (95% CI = 97.5% to 98.7%). The cardiac‐arrest protocol had the highest PPV (92.6%, 95% CI = 90.3% to 94.3%), whereas the convulsions protocol had the highest NPV (85.9%, 95% CI = 84.5% to 87.2%). The best‐performing protocol overall was the cardiac‐arrest protocol, and the protocol with the overall poorest performance was the one for unknown problems. Sixteen of the 32 protocols performed no better than chance alone at identifying high‐acuity patients.
Conclusions:
The Medical Priority Dispatch System exhibits at least moderate sensitivity and specificity for detecting high acuity of illness or injury. This performance analysis may be used to identify target protocols for future improvements.
Kinetics and Dynamics of Multi-Channel Unimolecular Reactions of Alkoxyl Radicals Over an Extended Range of Temperature and Pressure. A Combined Quantum Chemical/RRKM Dynamical Study
Authors: Somnitz Holger , Zellner Reinhard 
Published: August 2006

Rate coefficients and branching ratios for unimolecular reactions of alkoxyl radicals in the temperature range 200 to 1500 K and in the pressure range 10−2 to 104 bar are presented. Special emphasis is given to the change of the relative importance of different reaction channels. This is evident for longer chain alkoxyl radicals which at lower temperatures undergo isomerisation via an energetically favourable six-member ring transition state. At temperatures above >600 K, however, the rates of the alternative decomposition pathways become faster than that of isomerisation.
The theoretical approach to derive unimolecular rate coefficients makes use of extensive (G2/G3) ab initio calculations. These are used as input data for RRKM calculations to which a tunnelling probability of the generalised Eckart type has been included on the microcanonical level. A subsequent multi-channel master equation (ME) treatment yields thermal rate coefficients and complete fall-off curves for arbitrary pressure and temperature conditions.
The kinetics of two linear chain alkoxyl radicals, 1-butoxyl and 2-pentoxyl, have been analysed to show the expected complex temperature and pressure behaviour resulting from the competition of multiple accessible reaction channels, each with its specific p,T-dependence. Additional results are reported for the minimum temperatures where channel switching can occur, the trajectory of these characteristic points on the p,T-surface, and the temperature dependence of the fractional ratios of the unimolecular reaction channels and the bimolecular reaction with oxygen at ambient atmospheric pressure.
Cognitive Function and Behavior of Children With Adenotonsillar Hypertrophy Suspected of Having Obstructive Sleep-Disordered Breathing
Authors: Suratt Paul M. , Peruggia Mario , D'Andrea Lynn , Diamond Robert , Barth Jeffrey T. , Nikova Margarita , Perriello Vito A. , Johnson Michael L. 
Published: August 2006

OBJECTIVE. The purpose of this study was to determine whether risks of impaired cognitive function could be predicted for children or groups of children with adenotonsillar hypertrophy who were suspected of having obstructive sleep-disordered breathing, from historical and polysomnographic variables used separately or in combination.METHODS. We studied 114 consecutive 6- to 12-year-old children with adenotonsillar hypertrophy, who were referred because of suspected obstructive sleep-disordered breathing, with questionnaires, assessment of tonsil size, general and memory cognitive tests, and attended polysomnography with the use of nasal pressure recording to detect flow.RESULTS. There were important significant relationships between snore group (snored every night versus less often), sleep efficiency, and race and 2 of 3 general cognitive tests (vocabulary and similarities). Significant but weaker relationships were observed between sleep latency and 2 memory indices (verbal memory and general memory) and between sleep efficiency and 2 behavior indices (attention-deficit/hyperactivity disorder summary and hyperactive-impulsive summary). The number of episodes of apnea and hypopnea per 1 hour of sleep predicted the vocabulary score as well as did the snore group, but it did not predict other tests as well as other variables. Tonsil size did not predict any cognitive or behavior score. Confidence intervals for group means were small, whereas prediction intervals for individual children were large.CONCLUSIONS. Risk of impaired cognitive function and behavior can be predicted from snoring history, sleep efficiency, sleep latency, and race but not tonsil size. The combination of snoring history and polysomnographic variables predicted impaired cognitive scores better than did either alone. The snoring history predicted more test scores than the number of episodes of apnea and hypopnea per 1 hour of sleep.
Distributed attitude alignment in spacecraft formation flying
Authors: Ren Wei 
Published: August 2006

AbstractIn this paper, we consider a distributed attitude alignment problem for a team of deep space formation flying spacecraft through local information exchange. We propose control laws for three different cases. In the first case, multiple spacecraft converge to their (possibly time‐varying) desired attitudes while maintaining the same attitude or given relative attitudes during formation maneuvers under an undirected communication graph. In the second case, multiple spacecraft converge to the same rotation rate while aligning their attitudes during formation maneuvers under an undirected communication graph. In the third case, attitude alignment under a directed information exchange graph is addressed. Simulation results for attitude alignment among six spacecraft demonstrate the effectiveness of our approach. Copyright © 2006 John Wiley & Sons, Ltd.