bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving classification in protein structure databases using text mining
Authors: Koussounadis Antonis , Redfern Oliver C , Jones David T 
Published: May 2009

Abstract

Background
The classification of protein domains in the CATH resource is primarily based on structural comparisons, sequence similarity and manual analysis. One of the main bottlenecks in the processing of new entries is the evaluation of 'borderline' cases by human curators with reference to the literature, and better tools for helping both expert and non-expert users quickly identify relevant functional information from text are urgently needed. A text based method for protein classification is presented, which complements the existing sequence and structure-based approaches, especially in cases exhibiting low similarity to existing members and requiring manual intervention. The method is based on the assumption that textual similarity between sets of documents relating to proteins reflects biological function similarities and can be exploited to make classification decisions.

Results
An optimal strategy for the text comparisons was identified by using an established gold standard enzyme dataset. Filtering of the abstracts using a machine learning approach to discriminate sentences containing functional, structural and classification information that are relevant to the protein classification task improved performance. Testing this classification scheme on a dataset of 'borderline' protein domains that lack significant sequence or structure similarity to classified proteins showed that although, as expected, the structural similarity classifiers perform better on average, there is a significant benefit in incorporating text similarity in logistic regression models, indicating significant orthogonality in this additional information. Coverage was significantly increased especially at low error rates, which is important for routine classification tasks: 15.3% for the combined structure and text classifier compared to 10% for the structural classifier alone, at 10-3 error rate. Finally when only the highest scoring predictions were used to infer classification, an extra 4.2% of correct decisions were made by the combined classifier.

Conclusion
We have described a simple text based method to classify protein domains that demonstrates an improvement over existing methods. The method is unique in incorporating structural and text based classifiers directly and is particularly useful in cases where inconclusive evidence from sequence or structure similarity requires laborious manual classification.
Isolation and characterization of a spontaneously immortalized bovine retinal pigmented epithelial cell line
Authors: Liggett Thomas E , Griffiths T Daniel , Gaillard Elizabeth R 
Published: May 2009

Abstract

Background
The Retinal Pigmented Epithelium (RPE) is juxtaposed with the photoreceptor outer segments of the eye. The proximity of the photoreceptor cells is a prerequisite for their survival, as they depend on the RPE to remove the outer segments and are also influenced by RPE cell paracrine factors. RPE cell death can cause a progressive loss of photoreceptor function, which can diminish vision and, over time, blindness ensues. Degeneration of the retina has been shown to induce a variety of retinopathies, such as Stargardt's disease, Cone-Rod Dystrophy (CRD), Retinitis Pigmentosa (RP), Fundus Flavimaculatus (FFM), Best's disease and Age-related Macular Degeneration (AMD). We have cultured primary bovine RPE cells to gain a further understanding of the mechanisms of RPE cell death. One of the cultures, named tRPE, surpassed senescence and was further characterized to determine its viability as a model for retinal diseases.

Results
The tRPE cell line has been passaged up to 150 population doublings and was shown to be morphologically similar to primary cells. They have been characterized to be of RPE origin by reverse transcriptase PCR and immunocytochemistry using the RPE-specific genes RPE65 and CRALBP and RPE-specific proteins RPE65 and Bestrophin. The tRPE cells are also immunoreactive to vimentin, cytokeratin and zonula occludens-1 antibodies. Chromosome analysis indicates a normal diploid number. The tRPE cells do not grow in suspension or in soft agar. After 3H thymidine incorporation, the cells do not appear to divide appreciably after confluency.

Conclusion
The tRPE cells are immortal, but still exhibit contact inhibition, serum dependence, monolayer growth and secrete an extra-cellular matrix. They retain the in-vivo morphology, gene expression and cell polarity. Additionally, the cells endocytose exogenous melanin, A2E and purified lipofuscin granules. This cell line may be a useful in-vitro research model for retinal maculopathies.
Characteristics of HIV seroprevalence of visitors to public health centers under the national HIV surveillance system in Korea: cross sectional study
Authors: Kee Mee-Kyung , Lee Jin-Hee , Chu Chaeshin , Lee Eun-Ju , Kim Sung-Soon 
Published: May 2009

Abstract

Background
In Korea, the cumulative number of HIV-infected individuals was smaller than those of other countries. Mandatory HIV tests, dominating method until 1990's, have been gradually changed to voluntary HIV tests. We investigated HIV seroprevalence status and its characteristics of visitors to Public Health Centers (PHCs), which conducted both mandatory test and voluntary test under the national HIV/STI surveillance program.

Methods
We used HIV-testing data from 246 PHCs in 2005 through the Health Care Information System. The number of test taker was calculated using the code distinguished by the residential identification number. The subjects were classified into four groups by reason for testing; General group, HIV infection suspected group (HIV ISG), HIV test recommended group (HIV TRG), and sexually transmitted infection (STI) risk group.

Results
People living with HIV/AIDS were 149 (124 male and 25 female) among 280,456 individuals tested at PHCs. HIV seroprevalence was 5.3 per 10,000 individuals. Overall, the male revealed significantly higher seroprevalence than the female (adjusted Odds Ratio (adj. OR): 6.2; CI 3.8–10.2). Individuals aged 30–39 years (adj. OR: 2.6; CI 1.7–4.0), and 40–49 years (adj. OR: 3.8; CI 2.4–6.0) had higher seroprevalence than 20–29 years. Seroprevalence of HIV ISG (voluntary test takers and cases referred by doctors) was significantly higher than those of others. Foreigners showed higher seroprevalence than native Koreans (adj. OR: 3.8; CI 2.2–6.4). HIV ISG (adj. OR: 4.9; CI 3.2–7.5), and HIV TRG (adj. OR: 2.6; CI 1.3–5.4) had higher seroprevalence than General group.

Conclusion
A question on the efficiency of current mandatory test is raised because the seroprevalence of mandatory test takers was low. However, HIV ISG included voluntary test takers was high in our result. Therefore, we suggest that Korea needs to develop a method encouraging more people to take voluntary tests at PHCs, also to expand the anonymous testing centers and Voluntary Counselling and Testing Program (VCT) for general population to easily access to HIV testing.
Physical activity, energy requirements, and adequacy of dietary intakes of older persons in a rural Filipino community
Authors: Risonar Maria Grace D , Rayco-Solon Pura , Ribaya-Mercado Judy D , Solon Juan Antonio A , Cabalda Aegina B , Tengco Lorena W , Solon Florentino S 
Published: May 2009

Abstract

Background
Aging is a process associated with physiological changes such as in body composition, energy expenditure and physical activity. Data on energy and nutrient intake adequacy among elderly is important for disease prevention, health maintenance and program development.

Methods
This descriptive cross-sectional study was designed to determine the energy requirements and adequacy of energy and nutrient intakes of older persons living in private households in a rural Filipino community. Study participants were generally-healthy, ambulatory, and community living elderly aged 60–100 y (n = 98), 88 of whom provided dietary information in three nonconsecutive 24-hour food-recall interviews.

Results
There was a decrease in both physical activity and food intake with increasing years. Based on total energy expenditure and controlling for age, gender and socio-economic status, the average energy requirement for near-old (≥ 60 to < 65 y) males was 2074 kcal/d, with lower requirements, 1919 and 1699 kcal/d for the young-old (≥ 65 to < 75 y) and the old-old (≥ 75 y), respectively. Among females, the average energy requirements for the 3 age categories were 1712, 1662, and 1398 kcal/d, respectively. Actual energy intakes, however, were only ~65% adequate for all subjects as compared to energy expenditure. Protein, fat, and micronutrients (vitamins A and C, thiamin, riboflavin, iron and calcium) intakes were only ~24–51% of the recommended daily intake. Among this population, there was a weight decrease of 100 g (p = 0.012) and a BMI decrease of 0.04 kg/m2 (p = 0.003) for every 1% decrease in total caloric intake as percentage of the total energy expenditure requirements.

Conclusion
These community living elderly suffer from lack of both macronutrient intake as compared with energy requirements, and micronutrient intake as compared with the standard dietary recommendations. Their energy intakes are ~65% of the amounts required based on their total energy expenditure. Though their intakes decrease with increasing age, so do their energy expenditure, making their relative insufficiency of food intake stable with age.
Cost-effectiveness of pioglitazone in type 2 diabetes patients with a history of macrovascular disease: a German perspective
Authors: Scherbaum Werner A , Goodall Gordon , Erny-Albrecht Katrina M , Massi-Benedetti Massimo , Erdmann Erland , Valentine William J 
Published: May 2009

Abstract

Background
The aim of this study was to project health-economic outcomes relevant to the German setting for the addition of pioglitazone to existing treatment regimens in patients with type 2 diabetes, evidence of macrovascular disease and at high risk of cardiovascular events.

Methods
Event rates corresponding to macrovascular outcomes from the Prospective Pioglitazone Clinical Trial in Macrovascular Events (PROactive) study of pioglitazone were used with a modified version of the CORE Diabetes Model to simulate outcomes over a 35-year time horizon. Direct medical costs were accounted from a healthcare payer perspective in year 2005 values. Germany specific costs were applied for patient treatment, hospitalization and management. Both costs and clinical benefits were discounted at 5.0% per annum.

Results
Over patient lifetimes pioglitazone treatment improved undiscounted life expectancy by 0.406 years and improved quality-adjusted life expectancy by 0.120 quality-adjusted life years (QALYs) compared to placebo. Direct medical costs (treatment plus complication costs) were marginally higher for pioglitazone treatment and calculation of the incremental cost-effectiveness ratio (ICER) produced a value of €13,294 per QALY gained with the pioglitazone regimen versus placebo. Acceptability curve analysis showed that there was a 78.2% likelihood that pioglitazone would be considered cost-effective in Germany, using a "good value for money" threshold of €50,000 per QALY gained. Sensitivity analyses showed that the results were most sensitive to changes in the simulation time horizon. After adjustment for the potential stabilization of pancreatic β-cell function with pioglitazone treatment, the ICER was €6,667 per QALY gained for pioglitazone versus placebo.

Conclusion
The findings of this modelling analysis indicated that, for patients with a history of macrovascular disease, addition of pioglitazone to existing therapy reduces the long-term cumulative incidence of diabetes-complications at a cost that would be considered to represent good value for money in the German setting.
F-actin-based extensions of the head cyst cell adhere to the maturing spermatids to maintain them in a tight bundle and prevent their premature release in Drosophila testis
Authors: Desai Bela S , Shirolikar Seema , Ray Krishanu 
Published: May 2009

Abstract

Background

In Drosophila, all the 64 clonally derived spermatocytes differentiate in syncytium inside two somatic-origin cyst cells. They elongate to form slender spermatids, which are individualized and then released into the seminal vesicle. During individualization, differentiating spermatids are organized in a tight bundle inside the cyst, which is expected to play an important role in sperm selection. However, actual significance of this process and its underlying mechanism are unclear.

Results

We show that dynamic F-actin-based processes extend from the head cyst cell at the start of individualization, filling the interstitial space at the rostral ends of the maturing spermatid bundle. In addition to actin, these structures contained lamin, beta-catenin, dynamin, myosin VI and several other filopodial components. Further, pharmacological and genetic analyses showed that cytoskeletal stability and dynamin function are essential for their maintenance. Disruption of these F-actin based processes was associated with spermatid bundle disassembly and premature sperm release inside the testis.

Conclusion

Altogether, our data suggests that the head cyst cell adheres to the maturing spermatid heads through F-actin-based extensions, thus maintaining them in a tight bundle. This is likely to regulate mature sperm release into the seminal vesicle. Overall, this process bears resemblance to mammalian spermiation.
Detection and phylogenetic analysis of Orf virus from sheep in Brazil: a case report
Authors: Abrahão Jônatas S , Campos Rafael K , Trindade Giliane S , Guedes Maria IM , Lobato Zélia IP , Mazur Carlos , Ferreira Paulo CP , Bonjardim Cláudio A , Kroon Erna G 
Published: May 2009

Abstract

Background

Orf virus (ORFV), the prototype of the genus Parapoxvirus (PPV), is the etiological agent of contagious ecthyma, a severe exanthematic dermatitis that afflicts domestic and wild small ruminants. Although South American ORFV outbreaks have occurred and diagnosed there are no South American PPV major membrane glycoprotein B2L gene nucleotide sequences available.

Case presentation
an outbreak of ovine contagious ecthyma in Midwest Brazil was investigated. The diagnosis was based on clinical examinations and molecular biology techniques. The molecular characterization of the virus was done using PCR amplification, cloning and DNA sequencing of the B2L gene. The phylogenetic analysis demonstrated a high degree of identity with ORFV strains, and the isolate was closest to the ORFV-India 82/04 isolate. Another Brazilian ORFV isolate, NE1, was sequenced for comparative analysis and also showed a high degree of identity with an Asian ORFV strain.

Conclusion
Distinct ORFV strains are circulating in Brazil. This is the first report on the phylogenetic analysis of an ORFV in South America.
Genetic and environmental pathways to complex diseases
Authors: Gohlke Julia M , Thomas Reuben , Zhang Yonqing , Rosenstein Michael C , Davis Allan P , Murphy Cynthia , Becker Kevin G , Mattingly Carolyn J , Portier Christopher J 
Published: May 2009

AbstractBackgroundPathogenesis of complex diseases involves the integration of genetic and environmental factors over time, making it particularly difficult to tease apart relationships between phenotype, genotype, and environmental factors using traditional experimental approaches.ResultsUsing gene-centered databases, we have developed a network of complex diseases and environmental factors through the identification of key molecular pathways associated with both genetic and environmental contributions. Comparison with known chemical disease relationships and analysis of transcriptional regulation from gene expression datasets for several environmental factors and phenotypes clustered in a metabolic syndrome and neuropsychiatric subnetwork supports our network hypotheses. This analysis identifies natural and synthetic retinoids, antipsychotic medications, Omega 3 fatty acids, and pyrethroid pesticides as potential environmental modulators of metabolic syndrome phenotypes through PPAR and adipocytokine signaling and organophosphate pesticides as potential environmental modulators of neuropsychiatric phenotypes.ConclusionIdentification of key regulatory pathways that integrate genetic and environmental modulators define disease associated targets that will allow for efficient screening of large numbers of environmental factors, screening that could set priorities for further research and guide public health decisions.
Enhanced reactivity to pain in patients with rheumatoid arthritis
Authors: Edwards Robert R , Wasan Ajay D , Bingham Clifton O , Bathon Joan , Haythornthwaite Jennifer A , Smith Michael T , Page Gayle G 
Published: May 2009

Abstract
Introduction
Maladaptive physiological responses to stress appear to play a role in chronic inflammatory diseases such as rheumatoid arthritis (RA). However, relatively little stress research in RA patients has involved the study of pain, the most commonly reported and most impairing stressor in RA. In the present study, we compared psychophysical and physiological responses to standardized noxious stimulation in 19 RA patients and 21 healthy controls.

Methods
Participants underwent a single psychophysical testing session in which responses to a variety of painful stimuli were recorded, and blood samples were taken at multiple time points to evaluate the reactivity of cortisol, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) to the experience of acute pain.

Results
The findings suggest that RA patients display a fairly general hyperalgesia to mechanical and thermal stimuli across several body sites. In addition, while serum cortisol levels did not differ at baseline or following pain testing in patients relative to controls, the RA patients tended to show elevations in serum IL-6 and demonstrated enhanced pain-reactivity of serum levels of TNF-α compared with the healthy controls (P < 0.05).

Conclusions
These findings highlight the importance of pain as a stressor in RA patients and add to a small body of literature documenting amplified responses to pain in RA. Future studies of the pathophysiology of RA would benefit from the consideration of acute pain levels when comparing RA patients with other groups, and future trials of analgesic interventions in RA patients may benefit from evaluating the effects of such interventions on inflammatory activity.
Long-term survival of chronic dialysis patients following survival from an episode of multiple-organ failure
Authors: Chapman Richard J , Templeton Maie , Ashworth Simon , Broomhead Robert , McLean Adam , Brett Stephen J 
Published: May 2009

Abstract
Introduction
This study aimed to examine the long-term outcome for patients with end-stage renal failure (ESRF) who survived multiple-organ failure.

Methods
We performed a review of databases from the renal medicine service and intensive care units (ICU) of the participating hospitals within Imperial College Healthcare NHS Trust, London, UK. Patients with ESRF admitted to ICU who required support of two or more organ systems or were ventilated for more than 36 hours were included. To provide a comparison we examined the survival of a comparator group of ESRF patients in the general population with similar demographic and disease characteristics to our study group. We also examined the outcome for ESRF patients admitted to ICU who died prior to discharge.

Results
Survival data for two years following discharge from ICU were examined for the impact of age, prior dialysis history, Acute Physiology and Chronic Health Evaluation (APACHE) II scores and medical or surgical status. Of the 199 patients who met the inclusion criteria, 111 (56%) survived their ICU stay. Sixty-two (56%) of the survivors remained alive two years following discharge. There was no group difference in survival with regards to age, dialysis history or APACHE II scores. Those admitted with a medical rather than surgical diagnosis were less likely to survive two years (P < 0.01). Patients who died in ICU had higher APACHE II scores (P < 0.0001) and were more likely to have a medical diagnosis. By log rank analysis two-year mortality was significantly higher (P = 0.003) in the ICU survivors than the comparator group with ESRF. This difference was lost when patients who died within a month of discharge were excluded.

Conclusions
ESRF patients with multiple-organ failure have a high mortality, with the increased risk of death continuing into the early post-ICU period. Those with non-surgical diagnoses have the highest risk. Survival within the group who live beyond the early post-ICU period appears similar to the background population of ESRF patients.
Evaluation of the Optimal Number of Lesions Needed for Tumor Evaluation Using the Response Evaluation Criteria in Solid Tumors: A North Central Cancer Treatment Group Investigation
Authors: Hillman Shauna L. , An Ming-Wen , O'Connell Michael J. , Goldberg Richard M. , Schaefer Paul , Buckner Jan C. , Sargent Daniel J. 
Published: May 2009

Purpose In February 2000, the criteria for measuring tumor shrinkage as an indicator of antitumor activity were redefined by the Response Evaluation Criteria in Solid Tumors (RECIST). This resulted in simplifying bidimensional to unidimensional measurement of lesions. Under RECIST, all lesions, up to 10, must be measured. Scanning and measuring multiple lesions is costly, time-consuming, and a disincentive to participation in clinical trials. We investigated whether fewer than 10 lesions can be measured without compromising the accuracy of assessing a regimen's activity. Patients and Methods Thirty-two North Central Cancer Treatment Group trials including 2,374 patients were analyzed. Twelve studies were conducted before RECIST; 20 were conducted post-RECIST. Agreement between objective status by cycle, confirmed response, overall response rate, and time to progression (TTP) was evaluated based on all 10 versus the largest one through five lesions. Results The median number of lesions reported on RECIST trials did not differ from pre-RECIST trials (median = 2.0). One lesion at baseline was reported in 49% of patients, two lesions in 28% of patients, three lesions in 12% of patients, four lesions in 6% of patients, and five lesions in 5% of patients in post-RECIST trials. Utilizing the largest two lesions produced excellent concordance with that using all lesions for all end points. In no trial did the overall response rate differ by more than 3% when two versus all lesions were considered. Evaluating more than two lesions did not significantly improve agreement. Conclusion Based on these trials, the assessment of more than two lesions did not alter the conclusions regarding a treatment's efficacy as judged by response rate or TTP.
Research governance delays for a multicentre non-interventional study
Authors: Mallick Andrew A , O'Callaghan Finbar JK 
Published: May 2009

Summary Objectives To evaluate the delay in research governance approval for a non-interventional, multicentre study in the United Kingdom. Design The times taken from application to the granting of research governance approval for an observational study of childhood stroke with ethical approval were prospectively recorded. Setting Ninety-two acute NHS Trusts in the United Kingdom. Main outcome measures Median delay (in working days) between application and research governance approval. Results The median delay between application and research governance approval was 43 working days (interquartile range 27–62, range 0–147). The reason for delay beyond 43 working days was inexplicable in 30 (70%) of 44 trusts. Conclusions There is considerable variation in the processes undertaken by research and development departments that can lead to significant delays in commencing an ethically approved study. Any improvements to the systems for gaining approval are welcome.