bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
Authors: Hu Pingzhao , Greenwood Celia MT , Beyene Joseph 
Published: May 2005

AbstractBackgroundWith the explosion of microarray studies, an enormous amount of data is being produced. Systematic integration of gene expression data from different sources increases statistical power of detecting differentially expressed genes and allows assessment of heterogeneity. The challenge, however, is in designing and implementing efficient analytic methodologies for combination of data generated by different research groups.ResultsWe extended traditional effect size models to combine information from different microarray datasets by incorporating a quality measure for each gene in each study into the effect size estimation. We illustrated our method by integrating two datasets generated using different Affymetrix oligonucleotide types. Our results indicate that the proposed quality-adjusted weighting strategy for modelling inter-study variation of gene expression profiles not only increases consistency and decreases heterogeneous results between these two datasets, but also identifies many more differentially expressed genes than methods proposed previously.ConclusionData integration and synthesis is becoming increasingly important. We live in a high-throughput era where technologies constantly change leaving behind a trail of data with different forms, shapes and sizes. Statistical and computational methodologies are therefore critical for extracting the most out of these related but not identical sources of data.
A new approach for the analysis of bacterial microarray-based Comparative Genomic Hybridization: insights from an empirical study
Authors: Taboada Eduardo N , Acedillo Rey R , Luebbert Christian C , Findlay Wendy A , Nash John HE 
Published: May 2005

Abstract

Background
Microarray-based Comparative Genomic Hybridization (M-CGH) has been used to characterize the extensive intraspecies genetic diversity found in bacteria at the whole-genome level. Although conventional microarray analytical procedures have proved adequate in handling M-CGH data, data interpretation using these methods is based on a continuous character model in which gene divergence and gene absence form a spectrum of decreasing gene conservation levels. However, whereas gene divergence may yet be accompanied by retention in gene function, gene absence invariably leads to loss of function. This distinction, if ignored, leads to a loss in the information to be gained from M-CGH data.
We present here results from experiments in which two genome-sequenced strains of C. jejuni were compared against each other using M-CGH. Because the gene content of both strains was known a priori, we were able to closely examine the effects of sequence divergence and gene absence on M-CGH data in order to define analytical parameters for M-CGH data interpretation. This would facilitate the examination of the relative effects of sequence divergence or gene absence in comparative genomics analyses of multiple strains of any species for which genome sequence data and a DNA microarray are available.

Results
As a first step towards improving the analysis of M-CGH data, we estimated the degree of experimental error in a series of experiments in which identical samples were compared against each other by M-CGH. This variance estimate was used to validate a Log Ratio-based methodology for identification of outliers in M-CGH data. We compared two genome strains by M-CGH to examine the effect of probe/target identity on the Log Ratios of signal intensities using prior knowledge of gene divergence and gene absence to establish Log Ratio thresholds for the identification of absent and conserved genes.

Conclusion
The results from this empirical study validate the Log Ratio thresholds that have been used in other studies to establish gene divergence/absence. Moreover, the analytical framework presented here enhances the information content derived from M-CGH data by shifting the focus from divergent/absent gene detection to accurate detection of conserved and absent genes. This approach closely aligns the technical limitations of M-CGH analysis with practical limitations on the biological interpretation of comparative genomics data.
Variability and conservation in hepatitis B virus core protein
Authors: Chain Benjamin M , Myers Richard 
Published: May 2005

Abstract
Background
Hepatitis B core protein (HBVc) has been extensively studied from both a structural and immunological point of view, but the evolutionary forces driving sequence variation within core are incompletely understood.

Results
In this study, the observed variation in HBVc protein sequence has been examined in a collection of a large number of HBVc protein sequences from public sequence repositories. An alignment of several hundred sequences was carried out, and used to analyse the distribution of polymorphisms along the HBVc. Polymorphisms were found at 44 out of 185 amino acid positions analysed and were clustered predominantly in those parts of HBVc forming the outer surface and spike on intact capsid. The relationship between HBVc diversity and HBV genotype was examined. The position of variable amino acids along the sequence was examined in terms of the structural constraints of capsid and envelope assembly, and also in terms of immunological recognition by T and B cells.

Conclusion
Over three quarters of amino acids within the HBVc sequence are non-polymorphic, and variation is focused to a few amino acids. Phylogenetic analysis suggests that core protein specific forces constrain its diversity within the context of overall HBV genome evolution. As a consequence, core protein is not a reliable predictor of virus genotype. The structural requirements of capsid assembly are likely to play a major role in limiting diversity. The phylogenetic analysis further suggests that immunological selection does not play a major role in driving HBVc diversity.
Reporting of unintended events in an intensive care unit: comparison between staff and observer
Authors: Capuzzo Maurizia , Nawfal Imad , Campi Matilde , Valpondi Vanna , Verri Marco , Alvisi Raffaele 
Published: May 2005

Abstract
Background
In order to identify relevant targets for change, it is essential to know the reliability of incident staff reporting. The aim of this study is to compare the incidence and type of unintended events (UE) reported by facilitated Intensive Care Unit (ICU) staff with those recorded concurrently by an observer.

Methods
The study is a prospective data collection performed in two 4-bed multidisciplinary ICUs of a teaching hospital. The format of the UE reporting system was voluntary, facilitated and not necessarily anonymous, and used a structured form with a predetermined list of items. UEs were reported by ICU staff over a period of 4 weeks. The reporting incidence during the first fourteen days was compared with that during the second fourteen. During morning shifts in the second fourteen days, one observer in each ICU recorded any UE seen. The staff was not aware of the observers' study. The incidence of UEs reported by staff was compared with that recorded by the observers.

Results
The staff reported 36 UEs in the first fourteen days and 31 in the second.. The incidence of UE detection during morning shifts was significantly higher than during afternoon or night shifts (p < 0.001). Considering only working day morning shifts, the rate of UE reporting by the staff per 100 patient days was 26.9 (CI 95% 16.9–37.0) in the first fourteen day period and 20.3 (CI 95% 10.3–30.4) in the second. The rate of UE detection by the observers was 53.1 per 100 patient days (CI 95% 40.6–65.6), significantly higher (p < 0.001) than that reported concurrently by the staff. There was excellent agreement between staff and observers about the severity of the UEs recorded (Intraclass Correlation Coefficient 0.869). The observers recorded mainly UEs involving Airway/mechanical ventilation and Patient management, and the staff Catheter/Drain/Probe and Medication errors (p = 0.025).

Conclusion
UE incidence is strongly underreported by staff in comparison with observers. Also the types of UEs reported are different. Invaluable information about incidents in ICU can be obtained in a few days by observer monitoring.
Embolic stroke complicating Staphylococcus aureusendocarditis circumstantially linked to rectal trauma from foreign body: a first case report
Authors: Pandey Braj B , Dang Tuan C , Healy John F 
Published: May 2005

Abstract

Background
Diagnostic and therapeutic instrumentation of the lower gastrointestinal tract has been reported to result in bacteremia and endocarditis. No such case has been reported in persons with a history of rectal foreign body insertion despite its potential for greater trauma.

Case presentation
A 58-year-old male was admitted with confusion and inability to speak. His past history was notable for hospitalization to extract a retained plastic soda bottle from the rectosigmoid two years prior. On examination, he was febrile, tachycardic and hypotensive. There was an apical pansystolic murmur on cardiac examination. He had a mixed receptive and expressive aphasia, and a right hemiparesis. On rectal examination he had perianal erythema and diminished sphincter tone. Magnetic resonance imaging of the brain showed infarction of the occipital and frontal lobes. Transesophageal Echocardiography of the heart revealed vegetations on the mitral valve. All of his blood culture bottles grew methicillin sensitive Staphylococcus aureus. He was successfully treated for bacterial endocarditis with intravenous nafcillin and gentamicin. The rectum is frequently colonized by Staphylococcus aureus and trauma to its mucosa can lead to bacteremia and endocarditis with this organism.
In the absence of corroborative evidence such as presented here, it is difficult to make a correlation between staphylococcal endocarditis and anorectal foreign body insertion due to patients being less than forthcoming

Conclusion
There is a potential risk of staphylococcal bacteremia and endocarditis with rectal foreign body insertion. Further studies are needed to explore this finding. Detailed sexual history and patient counseling should be made a part of routine primary care.
Effects of diabetes and hypertension on macrophage infiltration and matrix expansion in the rat kidney
Authors: Hartner Andrea , Veelken Roland , Wittmann Michael , Cordasic Nada , Hilgers Karl F 
Published: May 2005

Abstract
Background
In experimental models of diabetes mellitus, aggravation of renal injury by concomitant hypertension has been described. Inflammatory mechanisms contribute to renal damage in both diseases. We investigated whether hypertension and diabetes mellitus act synergistically to induce macrophage infiltration and matrix expansion in the kidney.

Methods
Insulin-dependent diabetes mellitus was induced by streptozotocin injections to hypertensive mRen2-transgenic rats (TGR) and normotensive Sprague-Dawley control rats. Quantitative immunohistochemical examination of kidney tissue sections was used to measure macrophage infiltration and matrix expansion. The expression of MCP-1, Osteopontin, RANTES, ICAM-1 and VCAM-1 was evaluated by real-time RT-PCR. The localization of MCP-1 was studied by immunohistochemistry.

Results
Macrophage infiltration was present in the kidney of normotensive diabetic rats. Hypertensive rats exhibited a more marked infiltration of macrophages, regardless of whether diabetes was present or not. Gene expression of ICAM-1, VCAM-1 and RANTES was unaltered whereas Osteopontin and MCP-1 were induced by hypertension. Immunoreactive MCP-1 was slightly increased in diabetic rat kidney podocytes, and more markedly increased in hypertensive animals. Glomerular matrix accumulation was induced by diabetes and hypertension to a similar degree, and was highest in hypertensive, diabetic animals.

Conclusion
Diabetes mellitus caused a mild, and angiotensin-dependent hypertension a more marked infiltration of macrophages in the kidney. Combination of both diseases led to additive effects on matrix expansion but not on inflammation. Hypertension appears to be a much stronger stimulus for inflammation of the kidney than STZ diabetes, at least in mRen2-transgenic rats.
Accumulation of health risk behaviours is associated with lower socioeconomic status and women's urban residence: a multilevel analysis in Japan
Authors: Fukuda Yoshiharu , Nakamura Keiko , Takano Takehito 
Published: May 2005

Abstract
Background
Little is known about the socioeconomic differences in health-related behaviours in Japan. The present study was performed to elucidate the effects of individual and regional socioeconomic factors on selected health risk behaviours among Japanese adults, with a particular focus on regional variations.

Methods
In a nationally representative sample aged 25 to 59 years old (20,030 men and 21,076 women), the relationships between six risk behaviours (i.e., current smoking, excessive alcohol consumption, poor dietary habits, physical inactivity, stress and non-attendance of health check-ups), individual characteristics (i.e., age, marital status, occupation and household income) and regional (N = 60) indicators (per capita income and unemployment rate) were examined by multilevel analysis.

Results
Divorce, employment in women, lower occupational class and lower household income were generally associated with a higher likelihood of risk behaviour. The degrees of regional variation in risk behaviour and the influence of regional indicators were greater in women than in men: higher per capita income was significantly associated with current smoking, excessive alcohol consumption, stress and non-attendance of health check-ups in women.

Conclusion
Individual lower socioeconomic status was a substantial predictor of risk behaviour in both sexes, while a marked regional influence was observed only in women. The accumulation of risk behaviours in individuals with lower socioeconomic status and in women in areas with higher income, reflecting an urban context, may contribute to their higher mortality rates.
Topical immunotherapy of severe alopecia areata with diphenylcyclopropenone (DPCP): experience in an Iranian population
Authors: Aghaei Shahin 
Published: May 2005

AbstractBackgroundHighly variable results of topical diphenylcyclopropenone (DPCP) in the treatment of alopecia areata have been reported so far. The purposes of the present study were to evaluate the efficacy and tolerability of DPCP treatment in severe alopecia areata.MethodsTwenty-eight patients (16 female and 12 male, 10–35 years old, mean age 25 years) with extensive alopecia areata were enrolled in an open-label clinical trial. After sensitization with 2% DPCP, progressively higher concentrations beginning at 0.001% were applied weekly for 6 months to one side of the scalp, after which, if terminal hair growth was noted, the entire scalp was then treated under the same weekly protocol. The maximum concentration of DPCP in acetone was 2%.ResultsTwenty-seven of 28 patients completed therapy. The overall response rate was 81.5% (22/27), complete remission (90%-100% terminal hair re-growth) was obtained 22.2% (6/27) and partial remission (10%-90% terminal hair re-growth) in 59.3% (16/27). In all patients an eczematous reaction consisting of erythema, itching, and scaling at the site of application were observed. During therapy, other side effects including, occipital lymphadenopathy 40.7% (11/27), severe eczema/blister formation 40.7% (11/27), hyperpigmentation 18.5% (5/27) were observed, but no hypopigmentation, vitiligo, contact urticaria, and erythema multiforme-like reaction were seen in the patients. Nineteen of 27 (70.4%) patients had at least one side effect, other than eczematous reaction. Notably, partial recurrence was observed in 50.9% (13/22) of these patients after 6 to 12 months of follow-up. During the follow-up time the maintenance DPCP immunotherapy was continued.ConclusionTopical DPCP treatment for alopecia areata is an effective therapy with a slightly high relapse rate during bilateral maintenance treatment. According to the author's knowledge this is the first experience with DPCP in Iran.
General practitioners with a special interest in respiratory medicine: national survey of UK primary care organisations
Authors: Pinnock Hilary , Netuveli Gopalakrishnan , Price David , Sheikh Aziz 
Published: May 2005

Abstract

Background
To meet the universally recognised challenge of caring for people with long-term diseases many healthcare cultures are encouraging family physicians to develop specialist skills. We aimed to determine the major factors influencing the appointment of respiratory General Practitioners with a Special Interest (GPwSI) in the UK, and to determine the priority attached to the potential roles, perceived barriers to implementation, and monitoring planned.

Methods
We sent a piloted semi-structured questionnaire to a random sample of 50% of English and Welsh primary care organisations (PCOs) (n = 161) during winter 2003. In addition to descriptive statistics, we used hierarchical cluster analysis to classify service priorities. Free-text responses to open-ended questions were analysed qualitatively by a multidisciplinary group to identify emerging themes.

Results
Of the 111 (69%) PCOs who responded, 7 (6%) already have, and a further 35 (32%) are planning, a respiratory GPwSI service. This proportion is considerably lower than in specialities linked to National Health Service clinical priorities. Local needs and pressure on hospital beds were the main described motives for developing a service. Stated service priorities were to relieve pressure on secondary care and to improve quality of care, including the strategic planning of respiratory services within PCOs.

Conclusion
The relatively few respiratory GPwSIs currently in post reflects the lack of government prioritisation of respiratory care. However, respiratory GPwSI services are increasingly being considered as a local strategy for reducing pressure on secondary care respiratory services and raising standards of chronic disease management in primary care.
Development of a semi-quantitative food frequency questionnaire for use in United Arab Emirates and Kuwait based on local foods
Authors: Dehghan Mahshid , Al Hamad Nawal , Yusufali AfzalHussein , Nusrath Fathimunissa , Yusuf Salim , Merchant Anwar T 
Published: May 2005

Abstract

Background
The Food Frequency Questionnaire (FFQ) is one of the most commonly used tools in epidemiologic studies to assess long-term nutritional exposure. The purpose of this study is to describe the development of a culture specific FFQ for Arab populations in the United Arab Emirates (UAE) and Kuwait.

Methods
We interviewed samples of Arab populations over 18 years old in UAE and Kuwait assessing their dietary intakes using 24-hour dietary recall. Based on the most commonly reported foods and portion sizes, we constructed a food list with the units of measurement. The food list was converted to a Semi-Quantitative Food Frequency Questionnaire (SFFQ) format following the basic pattern of SFFQ using usual reported portions. The long SFFQ was field-tested, shortened and developed into the final SFFQ.
To estimate nutrients from mixed dishes we collected recipes of those mixed dishes that were commonly eaten, and estimated their nutritional content by using nutrient values of the ingredients that took into account method of preparation from the US Department of Agriculture's Food Composition Database.

Results
The SFFQs consist of 153 and 152 items for UAE and Kuwait, respectively. The participants reported average intakes over the past year. On average the participants reported eating 3.4 servings/d of fruits and 3.1 servings/d of vegetables in UAE versus 2.8 servings/d of fruits and 3.2 servings/d of vegetables in Kuwait. Participants reported eating cereals 4.8 times/d in UAE and 5.3 times/d in Kuwait. The mean intake of dairy products was 2.2/d in UAE and 3.4 among Kuwaiti.

Conclusion
We have developed SFFQs to measure diet in UAE and Kuwait that will serve the needs of public health researchers and clinicians and are currently validating those instruments.
Octacalcium phosphate crystals directly stimulate expression of inducible nitric oxide synthase through p38 and JNK mitogen-activated protein kinases in articular chondrocytes
Authors: Ea Hang-Korng , Uzan Benjamin , Rey Christian , Lioté Frédéric 
Published: May 2005

AbstractBasic calcium phosphate (BCP) crystals, including hydroxyapatite, octacalcium phosphate (OCP) and carbonate-apatite, have been associated with severe osteoarthritis and several degenerative arthropathies. Most studies have considered the chondrocyte to be a bystander in the pathogenesis of calcium crystal deposition disease, assuming that synovial cell cytokines were the only triggers of chondrocyte activation. In the present study we identified direct activation of articular chondrocytes by OCP crystals, which are the BCP crystals with the greatest potential for inducing inflammation. OCP crystals induced nitric oxide (NO) production and inducible nitric oxide synthase (NOS) mRNA expression by isolated articular chondrocytes and cartilage fragments, in a dose-dependent manner and with variations over time. OCP crystals also induced IL-1β mRNA expression. Using pharmacological and cytokine inhibitors, we observed that OCP crystals induced NO production and inducible NOS mRNA activation were regulated at both the transcriptional and the translational levels; were independent from IL-1β gene activation; and involved p38 and c-Jun amino-terminal kinase (JNK) mitogen-activated protein kinase (MAPK) pathways, as further confirmed by OCP crystal-induced p38 and JNK MAPK phosphorylation. Taken together, our data suggest that the transcriptional inducible NOS response to OCP crystals involved both the p38 and the JNK MAPK pathways, probably under the control of activator protein-1. NO, a major mediator of cartilage degradation, can be directly produced by BCP crystals in chondrocytes. Together with synovial activation, this direct mechanism may be important in the pathogenesis of destructive arthropathies triggered by microcrystals.