bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of history science methods in exposure assessment for occupational health studies
Authors: Johansen K , Tinnerberg H , Lynge E 
Published: June 2005

Aims:To show the power of history science methods for exposure assessment in occupational health studies, using the dry cleaning industry in Denmark around 1970 as the example.Methods:Exposure data and other information on exposure status were searched for in unconventional data sources such as the Danish National Archives, the Danish Royal Library, archives of Statistics Denmark, the National Institute of Occupational Health, Denmark, and the Danish Labor Inspection Agency. Individual census forms were retrieved from the Danish National Archives.Results:It was estimated that in total 3267 persons worked in the dry cleaning industry in Denmark in 1970. They typically worked in small shops with an average size of 3.5 persons. Of these, 2645 persons were considered exposed to solvents as they were dry cleaners or worked very close to the dry cleaning process, while 622 persons were office workers, drivers, etc in shops with 10 or more persons. It was estimated that tetrachloroethylene constituted 85% of the dry cleaning solvent used, and that a shop would normally have two machines using 4.6 tons of tetrachloroethylene annually.Conclusion:The history science methods, including retrieval of material from the Danish National Archives and a thorough search in the Royal Library for publications on dry cleaning, turned out to be a very fruitful approach for collection of exposure data on dry cleaning work in Denmark. The history science methods proved to be a useful supplement to the exposure assessment methods normally applied in epidemiological studies.
Age at exposure to ionising radiation and cancer mortality among Hanford workers: follow up through 1994
Authors: Wing S , Richardson D B 
Published: June 2005

Background:Studies of workers at the plutonium production factory in Hanford, WA have led to conflicting conclusions about the role of age at exposure as a modifier of associations between ionising radiation and cancer.Aims:To evaluate the influence of age at exposure on radiation risk estimates in an updated follow up of Hanford workers.Methods:A cohort of 26 389 workers hired between 1944 and 1978 was followed through 1994 to ascertain vital status and causes of death. External radiation dose estimates were derived from personal dosimeters. Poisson regression was used to estimate associations between mortality and cumulative external radiation dose at all ages, and in specific age ranges.Results:A total of 8153 deaths were identified, 2265 of which included cancer as an underlying or contributory cause. Estimates of the excess relative risk per Sievert (ERR/Sv) for cumulative radiation doses at all ages combined were negative for all cause and leukaemia and positive for all cancer and lung cancer. Cumulative doses accrued at ages below 35, 35–44, and 45–54 showed little association with mortality. For cumulative dose accrued at ages 55 and above (10 year lag), the estimated ERR/Sv for all cancers was 3.24 (90% CI: 0.80 to 6.17), primarily due to an association with lung cancer (ERR/Sv: 9.05, 90% CI: 2.96 to 17.92).Conclusions:Associations between radiation and cancer mortality in this cohort are primarily a function of doses at older ages and deaths from lung cancer. The association of older age radiation exposures and cancer mortality is similar to observations from several other occupational studies.
A NOTE ON TWO-DIMENSIONAL DILATON GRAVITY WITH NON-SMOOTH POTENTIALS
Authors: BÖHMER CHRISTIAN G. , BRONOWSKI PIOTR 
Published: June 2005

Recent interest in brane world models motivates the investigation of generic first-order dilaton gravity actions, with potentials having some non-smoothness. We consider two different types of δ-like contributions in the action and analyse their effects on the solutions. Furthermore a second source of non-smoothness arises due to the remaining ambiguities in the solutions in the separated smooth patches, after fixing all other constants by matching and asymptotic conditions. If moreover staticity is assumed, we explicitly construct exact solutions. With the methods described, for example models with point like sources or brane world models (where the second source of non-smoothness becomes crucial), can now be treated as non-smooth dilaton gravity theories.
Thesaurus-based disambiguation of gene symbols
Authors: Schijvenaars Bob JA , Mons Barend , Weeber Marc , Schuemie Martijn J , van Mulligen Erik M , Wain Hester M , Kors Jan A 
Published: June 2005

Abstract
Background
Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.

Results
We developed a simple thesaurus-based disambiguation algorithm that can operate with very little training data. The thesaurus comprises the information from five human genetic databases and MeSH. The extent of the homonym problem for human gene symbols is shown to be substantial (33% of the genes in our combined thesaurus had one or more ambiguous symbols), not only because one symbol can refer to multiple genes, but also because a gene symbol can have many non-gene meanings. A test set of 52,529 Medline abstracts, containing 690 ambiguous human gene symbols taken from OMIM, was automatically generated. Overall accuracy of the disambiguation algorithm was up to 92.7% on the test set.

Conclusion
The ambiguity of human gene symbols is substantial, not only because one symbol may denote multiple genes but particularly because many symbols have other, non-gene meanings. The proposed disambiguation approach resolves most ambiguities in our test set with high accuracy, including the important gene/not a gene decisions. The algorithm is fast and scalable, enabling gene-symbol disambiguation in massive text mining applications.
AnovArray: a set of SAS macros for the analysis of variance of gene expression data
Authors: Hennequet-Antier Christelle , Chiapello Hélène , Piot Karine , Degrelle Séverine , Hue Isabelle , Renard Jean-Paul , Rodolphe François , Robin Stéphane 
Published: June 2005

Abstract
Background
Analysis of variance is a powerful approach to identify differentially expressed genes in a complex experimental design for microarray and macroarray data. The advantage of the anova model is the possibility to evaluate multiple sources of variation in an experiment.

Results
AnovArray is a package implementing ANOVA for gene expression data using SAS® statistical software. The originality of the package is 1) to quantify the different sources of variation on all genes together, 2) to provide a quality control of the model, 3) to propose two models for a gene's variance estimation and to perform a correction for multiple comparisons.

Conclusion
AnovArray is freely available at http://www-mig.jouy.inra.fr/stat/AnovArray and requires only SAS® statistical software.
AutoFACT: An Auto matic F unctional A nnotation and C lassification T ool
Authors: Koski Liisa B , Gray Michael W , Lang B Franz , Burger Gertraud 
Published: June 2005

Abstract
Background
Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets.

Results
We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%.

Conclusion
AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at http://megasun.bch.umontreal.ca/Software/AutoFACT.htm.
The DiGEM trial protocol – a randomised controlled trial to determine the effect on glycaemic control of different strategies of blood glucose self-monitoring in people with type 2 diabetes [ISRCTN47464659]
Authors: Farmer Andrew , Wade Alisha , French David P , Goyder Elizabeth , Kinmonth Ann Louise , Neil Andrew 
Published: June 2005

Abstract

Background
We do not yet know how to use blood glucose self-monitoring (BGSM) most effectively in the self-management of type 2 diabetes treated with oral medication. Training in monitoring may be most effective in improving glycaemic control and well being when results are linked to behavioural change.

Methods/design

DiGEM is a three arm randomised parallel group trial set in UK general practices. A total of 450 patients with type 2 diabetes managed with lifestyle or oral glucose lowering medication are included. The trial compares effectiveness of three strategies for monitoring glycaemic control over 12 months (1) a control group with three monthly HbA1c measurements; interpreted with nurse-practitioner; (2) A self-testing of blood glucose group; interpreted with nurse- practitioner to inform adjustment of medication in addition to 1; (3) A self-monitoring of blood glucose group with personal use of results to interpret results in relation to lifestyle changes in addition to 1 and 2.
The trial has an 80% power at a 5% level of significance to detect a difference in change in the primary outcome, HbA1c of 0.5% between groups, allowing for an attrition rate of 10%. Secondary outcome measures include health service costs, well-being, and the intervention effect in sub-groups defined by duration of diabetes, current management, health status at baseline and co-morbidity. A mediation analysis will explore the extent to which changes in beliefs about self-management of diabetes between experimental groups leads to changes in outcomes in accordance with the Common Sense Model of illness. The study is open and has recruited more than half the target sample. The trial is expected to report in 2007.

Discussion
The DiGEM intervention and trial design address weaknesses of previous research by use of a sample size with power to detect a clinically significant change in HbA1c, recruitment from a well-characterised primary care population, definition of feasible monitoring and behaviour change strategies based on psychological theory and evidence, and measures along the hypothesised causal path from cognitions to behaviours and disease and well being related outcomes. The trial will provide evidence to support, focus or discourage use of specific BGSM strategies.
The incidence of varicella and herpes zoster in Massachusetts as measured by the Behavioral Risk Factor Surveillance System (BRFSS) during a period of increasing varicella vaccine coverage, 1998–2003
Authors: Yih W Katherine , Brooks Daniel R , Lett Susan M , Jumaan Aisha O , Zhang Zi , Clements Karen M , Seward Jane F 
Published: June 2005

AbstractBackgroundThe authors sought to monitor the impact of widespread varicella vaccination on the epidemiology of varicella and herpes zoster. While varicella incidence would be expected to decrease, mathematical models predict an initial increase in herpes zoster incidence if re-exposure to varicella protects against reactivation of the varicella zoster virus.MethodsIn 1998–2003, as varicella vaccine uptake increased, incidence of varicella and herpes zoster in Massachusetts was monitored using the random-digit-dial Behavioral Risk Factor Surveillance System.ResultsBetween 1998 and 2003, varicella incidence declined from 16.5/1,000 to 3.5/1,000 (79%) overall with ≥66% decreases for all age groups except adults (27% decrease). Age-standardized estimates of overall herpes zoster occurrence increased from 2.77/1,000 to 5.25/1,000 (90%) in the period 1999–2003, and the trend in both crude and adjusted rates was highly significant (p < 0.001). Annual age-specific rates were somewhat unstable, but all increased, and the trend was significant for the 25–44 year and 65+ year age groups.ConclusionAs varicella vaccine coverage in children increased, the incidence of varicella decreased and the occurrence of herpes zoster increased. If the observed increase in herpes zoster incidence is real, widespread vaccination of children is only one of several possible explanations. Further studies are needed to understand secular trends in herpes zoster before and after use of varicella vaccine in the United States and other countries.
PI3K and PKC contribute to membrane depolarization mediated by α2-adrenoceptors in the canine isolated mesenteric vein
Authors: Yamboliev Ilia A , Mutafova-Yambolieva Violeta N 
Published: June 2005

Abstract
Background
Norepinephrine (NE), a classic neurotransmitter in the sympathetic nervous system, induces vasoconstriction of canine isolated mesenteric vein that is accompanied by a sustained membrane depolarization. The mechanisms underlying the NE-elicited membrane depolarization remain undefined. In the present study we hypothesized that phosphatidylinositol 3-kinase (PI3K) and protein kinase C (PKC) are involved in the electrical field stimulation (EFS)-induced slow membrane depolarization (SMD) in canine isolated mesenteric vein. EFS (0.1–2 Hz, 0.1 ms, 15V, 10 s)-induced changes in the membrane potential were recorded with a conventional intracellular microelectrode technique and evaluated in the absence and presence of inhibitors of neuronal activity, α-adrenoceptors, membrane ion channels, PI3K, inositol 1,4,5-triphosphate (InsP3) receptors, and PKC. Activation of PI3Kγ and PKCζ in response to exogenous NE and clonidine in the absence and presence of receptor and kinase inhibitors were also determined.

Results
Contractile responses to NE and clonidine (0.05 – 10 μM) were significantly diminished in the presence of yohimbine (0.1 μM). Exogenous NE (0.1 μM) and clonidine (1 μM) elicited SMD. The resting membrane potential of canine mesenteric vein smooth muscle cells was -68.8 ± 0.8 mV. EFS elicited a biphasic depolarization comprised of excitatory junction potentials and SMD that are purinergic and adrenergic in nature, respectively. The magnitude of the SMD in response to EFS at 0.5 Hz was 9.4 ± 0.7 mV. This response was reduced by 65–98% by the fast Na+ channel inhibitor tetrodotoxin (1 μM), by the inhibitor of N-type Ca2+ channels ω-conotoxin GVIA (5 nM), the non-selective α-adrenoceptor blocker phentolamine (1 μM), the selective α2-adrenoceptor blocker yohimbine (0.1 μM), the ion channel inhibitors niflumic acid (NFA, 100 μM), 5-nitro-2-(3-phenylpropylamino) benzoic acid (NPPB, 30 μM), 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS, 200 μM), and Gd3+ (30 μM), and the PI3K inhibitors wortmannin (100 nM) and LY-294002 (10 μM). The SMD remained unchanged in the presence of the L-type Ca2+ channel blocker nicardipine (1 μM) and the InsP3 receptor blockers 2-aminoethoxydiphenylborate (2APB, 50 μM) and xestospongin C (3 μM). The inhibitor of PKC chelerythrine (1 μM), but not calphostin C (10 μM), diminished the SMD. Exogenous NE and clonidine (1 μM each) activated both PI3Kγ and PKCζ, and the activation of these kinases was abolished by preincubation of tissue with the α2-adrenoceptor blocker yohimbine.

Conclusion
Neuronally-released NE stimulates smooth muscle α2-adrenoceptors and activates PI3K and atypical PKC in the canine mesenteric vein. Events downstream of PKC lead to SMD and vasoconstriction. This represents a novel pathway for NE-induced membrane depolarization in a vascular smooth muscle preparation.
Quantification of resting myocardial blood flow velocity in normal humans using real-time contrast echocardiography. A feasibility study
Authors: Malm Siri , Frigstad Sigmund , Helland Frode , Oye Kjetil , Slordahl Stig , Skjarpe Terje 
Published: June 2005

Abstract

Background
Real-time myocardial contrast echocardiography (MCE) is a novel method for assessing myocardial perfusion. The aim of this study was to evaluate the feasibility of a very low-power real-time MCE for quantification of regional resting myocardial blood flow (MBF) velocity in normal human myocardium.

Methods
Twenty study subjects with normal left ventricular (LV) wall motion and normal coronary arteries, underwent low-power real-time MCE based on color-coded pulse inversion Doppler. Standard apical LV views were acquired during constant IV. infusion of SonoVue®. Following transient microbubble destruction, the contrast replenishment rate (β), reflecting MBF velocity, was derived by plotting signal intensity vs. time and fitting data to the exponential function; y (t) =A (1-e-β(t-t0)) + C.

Results
Quantification was feasible in 82%, 49% and 63% of four-chamber, two-chamber and apical long-axis view segments, respectively. The LAD (left anterior descending artery) and RCA (right coronary artery) territories could potentially be evaluated in most, but contrast detection in the LCx (left circumflex artery) bed was poor. Depending on localisation and which frames to be analysed, mean values of "Equation missing" were 0.21–0.69 s-1, with higher values in medial than lateral, and in basal compared to apical regions of scan plane (p = 0.03 and p < 0.01). Higher β-values were obtained from end-diastole than end-systole (p < 0.001), values from all-frames analysis lying between.

Conclusion
Low-power real-time MCE did have the potential to give contrast enhancement for quantification of resting regional MBF velocity. However, the technique is difficult and subjected to several limitations. Significant variability in β suggests that this parameter is best suited for with-in patient changes, comparing values of stress studies to baseline.
Cancer history and other personal factors affect quality of life in patients with hepatitis C
Authors: Olson Sara H , Iyer Sandy , Scott Jennifer , Erez Orry , Samuel Shelby , Markovits Temima , Schwartz Myron , Toro Charlene , Gambarin-Gelwan Maya , Kurtz Robert C 
Published: June 2005

Abstract

Background
Although patients with chronic hepatitis C (CHC) have been found to have reduced quality of life, little is known about how other characteristics affect their quality of life. The purpose of this study was to investigate the effect of other characteristics, including history of cancer, on quality of life in patients with CHC.

Methods
One hundred forty patients from clinics at three hospitals in New York City completed a detailed epidemiologic interview about demographic and lifestyle characteristics and the SF-36 measuring health-related quality of life. We compared results from our patients to normative data using t-tests of differences between means. We used multivariate analyses to determine other personal and health-related factors associated with quality of life outcomes.

Results
Compared to normative data, these patients had reduced quality of life, particularly on physical functioning. The summary Physical Component Score (PCS) was 45.4 ± 10.6 and the Mental Component Score (MCS) was 48.2 ± 11.1, vs norms of 50 ± 10.0; p-values were <0.0001 and <0.05, respectively. In multivariate analyses, the PCS was significantly lower among those with cancer history, ≥ 2 other chronic conditions, less education, low physical activity, and higher alanine aminotransferase (ALT) levels. Cancer was more important for men, while other chronic conditions were more important for women. On the MCS, history of depression, low physical activity, alcohol use, and female gender were independently associated with poorer scores.

Conclusion
Several health and lifestyle factors independently influence quality of life in CHC patients. Different factors are important for men and women.
The role of vocal individuality in conservation
Authors: Terry Andrew MR , Peake Tom M , McGregor Peter K 
Published: June 2005

AbstractIdentifying the individuals within a population can generate information on life history parameters, generate input data for conservation models, and highlight behavioural traits that may affect management decisions and error or bias within census methods. Individual animals can be discriminated by features of their vocalisations. This vocal individuality can be utilised as an alternative marking technique in situations where the marks are difficult to detect or animals are sensitive to disturbance. Vocal individuality can also be used in cases were the capture and handling of an animal is either logistically or ethically problematic. Many studies have suggested that vocal individuality can be used to count and monitor populations over time; however, few have explicitly tested the method in this role. In this review we discuss methods for extracting individuality information from vocalisations and techniques for using this to count and monitor populations over time. We present case studies in birds where vocal individuality has been applied to conservation and we discuss its role in mammals.
Epigenetic silencing of DSC3 is a common event in human breast cancer
Authors: Oshiro Marc M , Kim Christina J , Wozniak Ryan J , Junk Damian J , Muñoz-Rodríguez José L , Burr Jeanne A , Fitzgerald Matthew , Pawar Sangita C , Cress Anne E , Domann Frederick E , Futscher Bernard W 
Published: June 2005

Abstract
Introduction
Desmocollin 3 (DSC3) is a member of the cadherin superfamily of calcium-dependent cell adhesion molecules and a principle component of desmosomes. Desmosomal proteins such as DSC3 are integral to the maintenance of tissue architecture and the loss of these components leads to a lack of adhesion and a gain of cellular mobility. DSC3 expression is down-regulated in breast cancer cell lines and primary breast tumors; however, the loss of DSC3 is not due to gene deletion or gross rearrangement of the gene. In this study, we examined the prevalence of epigenetic silencing of DSC3 gene expression in primary breast tumor specimens.

Methods
We used bisulfite genomic sequencing to analyze the methylation state of the DSC3 promoter region from 32 primary breast tumor specimens. We also used a quantitative real-time RT-PCR approach, and analyzed all breast tumor specimens for DSC3 expression. Finally, in addition to bisulfite sequencing and RT-PCR, we used an in vivo nuclease accessibility assay to determine the chromatin architecture of the CpG island region from DSC3-negative breast cancer cells lines.

Results
DSC3 expression was downregulated in 23 of 32 (72%) breast cancer specimens comprising: 22 invasive ductal carcinomas, 7 invasive lobular breast carcinomas, 2 invasive ductal carcinomas that metastasized to the lymph node, and a mucoid ductal carcinoma. Of the 23 specimens showing a loss of DSC3 expression, 13 (56%) were associated with cytosine hypermethylation of the promoter region. Furthermore, DSC3 expression is limited to cells of epithelial origin and its expression of mRNA and protein is lost in a high proportion of breast tumor cell lines (79%). Lastly, DNA hypermethylation of the DSC3 promoter is highly correlated with a closed chromatin structure.

Conclusion
These results indicate that the loss of DSC3 expression is a common event in primary breast tumor specimens, and that DSC3 gene silencing in breast tumors is frequently linked to aberrant cytosine methylation and concomitant changes in chromatin structure.