bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program
Authors: Laramie Jason M , Wilk Jemma B , Hunt Steven C , Ellison R Curtis , Chakravarti Aravinda , Boerwinkle Eric , Myers Richard H 
Published: March 2006

Abstract

Background
Elevated resting heart rate has been shown in multiple studies to be a strong predictor of cardiovascular disease. Previous family studies have shown a significant heritable component to heart rate with several groups conducting genomic linkage scans to identify quantitative trait loci.

Methods
We performed a genome-wide linkage scan to identify quantitative trait loci influencing resting heart rate among 3,282 Caucasians and 3,989 African-Americans in three independent networks comprising the Family Blood Pressure Program (FBPP) using 368 microsatellite markers. Mean heart rate measurements were used in a regression model including covariates for age, body mass index, pack-years, currently drinking alcohol (yes/no), hypertension status and medication usage to create a standardized residual for each gender/ethnic group within each study network. This residual was used in a nonparametric variance component model to generate a LOD score and a corresponding P value for each ethnic group within each study network. P values from each ethnic group and study network were merged using an adjusted Fisher's combining P values method and the resulting P values were converted to LOD scores. The entire analysis was redone after individuals currently taking beta-blocker medication were removed.

Results
We identified significant evidence of linkage (LOD = 4.62) to chromosome 10 near 142.78 cM in the Caucasian group of HyperGEN. Between race and network groups we identified a LOD score of 1.86 on chromosome 5 (between 39.99 and 45.34 cM) in African-Americans in the GENOA network and the same region produced a LOD score of 1.12 among Caucasians within a different network (HyperGEN). Combining all network and race groups we identified a LOD score of 1.92 (P = 0.0013) on chromosome 5p13-14. We assessed heterogeneity for this locus between networks and ethnic groups and found significant evidence for low heterogeneity (P ≤ 0.05).

Conclusion
We found replication (LOD > 1) between ethnic groups and between study networks with low heterogeneity on chromosome 5p13-14 suggesting that a gene in this region influences resting heart rate.
Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish
Authors: McCauley Jacob L , Hahs Daniel W , Jiang Lan , Scott William K , Welsh-Bohmer Kathleen A , Jackson Charles E , Vance Jeffery M , Pericak-Vance Margaret A , Haines Jonathan L 
Published: March 2006

AbstractBackgroundPopulation heterogeneity may be a significant confounding factor hampering detection and verification of late onset Alzheimer's disease (LOAD) susceptibility genes. The Amish communities located in Indiana and Ohio are relatively isolated populations that may have increased power to detect disease susceptibility genes.MethodsWe recently performed a genome scan of dementia in this population that detected several potential loci. However, analyses of these data are complicated by the highly consanguineous nature of these Amish pedigrees. Therefore we applied the Combinatorial Mismatch Scanning (CMS) method that compares identity by state (IBS) (under the presumption of identity by descent (IBD)) sharing in distantly related individuals from such populations where standard linkage and association analyses are difficult to implement. CMS compares allele sharing between individuals in affected and unaffected groups from founder populations. Comparisons between cases and controls were done using two Fisher's exact tests, one testing for excess in IBS allele frequency and the other testing for excess in IBS genotype frequency for 407 microsatellite markers.ResultsIn all, 13 dementia cases and 14 normal controls were identified who were not related at least through the grandparental generation. The examination of allele frequencies identified 24 markers (6%) nominally (p ≤ 0.05) associated with dementia; the most interesting (empiric p ≤ 0.005) markers were D3S1262, D5S211, and D19S1165. The examination of genotype frequencies identified 21 markers (5%) nominally (p ≤ 0.05) associated with dementia; the most significant markers were both located on chromosome 5 (D5S1480 and D5S211). Notably, one of these markers (D5S211) demonstrated differences (empiric p ≤ 0.005) under both tests.ConclusionOur results provide the initial groundwork for identifying genes involved in late-onset Alzheimer's disease within the Amish community. Genes identified within this isolated population will likely play a role in a subset of late-onset AD cases across more general populations. Regions highlighted by markers demonstrating suggestive allelic and/or genotypic differences will be the focus of more detailed examination to characterize their involvement in dementia.
Ascites due to right atrial myxoma in a haemodialysis patient
Authors: Banerjee Anindya , Davenport Andrew 
Published: March 2006

Abstract

Background
Persistent fluid overload in patients on renal replacement therapy despite good dialysis adequacy or obvious cardiac dysfunction should prompt a search for rarer causes.

Case presentation
We report here a rare cause of persistent peripheral oedema and ascites in a well-dialysed patient. CT scanning revealed a right atrial myxoma that was later confirmed on an echocardiogram.

Conclusion
Fluid overload states are common in patients on dialysis. Common causes are inadequacy of dialysis and non-compliance. Where aetiology is not easily apparent further investigations into rarer causes should be sought.
Carcinosarcoma of monoclonal origin arising in a dermoid cyst of ovary: a case report
Authors: Cabibi Daniela , Martorana Anna , Cappello Francesco , Barresi Elisa , Di Gangi Claudio , Rodolico Vito 
Published: March 2006

Abstract

Background
Transformation of a cystic benign teratoma of the ovary into a "carcinosarcoma" has very rarely been reported and its histogenetic origin is still debated.

Case presentation
A case of carcinosarcoma arising from a dermoid cyst is reported. The tumor showed cystic areas delimited by normal squamous epithelium, with transitional areas through dysplastic epithelium to "in situ" and infiltrating squamous cell carcinoma (SCC).
The sarcomatous component showed compact tissue composed of round cells concentrically arranged around small vessels, spindle, and pleomorphic cells with a high nuclear-cytoplasmic ratio.
Positive staining for vimentin, alpha smooth muscle actin and CD10, as well as P53 and P63, was found in the sarcomatous component and in some atypical basal cells of the squamous epithelium, which also showed the usual epithelial markers.

Conclusion
To the best of our knowledge, this is the first case of carcinosarcoma arising from a dermoid cyst in which a histogenetic origin from totipotent stem cells, located in the basal squamous layer, is supported by immunohistochemical findings.
The benefits and risks of bacille Calmette-Guérin vaccination among infants at high risk for both tuberculosis and severe combined immunodeficiency: assessment by Markov model
Authors: Clark Michael , Cameron D William 
Published: March 2006

AbstractBackgroundBacille Calmette-Guérin (BCG) vaccine is given to Canadian Aboriginal neonates in selected communities. Severe reactions and deaths associated with BCG have been reported among infants born with immunodeficiency syndromes. The main objective of this study was to estimate threshold values for severe combined immunodeficiency (SCID) incidence, above which BCG is associated with greater risk than benefit.MethodsA Markov model was developed to simulate the natural histories of tuberculosis (TB) and SCID in children from birth to 14 years. The annual risk of tuberculous infection (ARI) and SCID incidence were varied in analyses. The model compared a scenario of no vaccination to intervention with BCG. Appropriate variability and uncertainty analyses were conducted. Outcomes included TB incidence and quality-adjusted life years (QALYs).ResultsIn sensitivity analyses, QALYs were lower among vaccinated infants if the ARI was 0.1% and the rate of SCID was higher than 4.2 per 100,000. Assuming an ARI of 1%, this threshold increased to 41 per 100,000. In uncertainty analyses (Monte Carlo simulations) which assumed an ARI of 0.1%, QALYs were not significantly increased by BCG unless SCID incidence is 0. With this ARI, QALYs were significantly decreased among vaccinated children if SCID incidence exceeds 23 per 100,000. BCG is associated with a significant increase in QALYs if the ARI is 1%, and SCID incidence is below 5 per 100,000.ConclusionThe possibility that Canadian Aboriginal children are at increased risk for SCID has serious implications for continued BCG use in this population. In this context, enhanced TB Control – including early detection and treatment of infection – may be a safer, more effective alternative.
A cross-sectional study of the prevalence of intensity of infection with Schistosoma japonicumin 50 irrigated and rain-fed villages in Samar Province, the Philippines
Authors: Tarafder Mushfiqur R , Balolong Ernesto , Carabin Hélène , Bélisle Patrick , Tallo Veronica , Joseph Lawrence , Alday Portia , Gonzales Ryan O'Neil , Riley Steven , Olveda Remigio , McGarvey Stephen T 
Published: March 2006

Abstract

Background
Few studies have described heterogeneity in Schistosoma japonicum infection intensity, and none were done in Philippines. The purpose of this report is to describe the village-to-village variation in the prevalence of two levels of infection intensity across 50 villages of Samar Province, the Philippines.

Methods
This cross-sectional study was conducted in 25 rain-fed and 25 irrigated villages endemic for S. japonicum between August 2003 and November 2004. Villages were selected based on irrigation and farming criteria. A maximum of 35 eligible households were selected per village. Each participant was asked to provide stool samples on three consecutive days. All those who provided at least one stool sample were included in the analysis. A Bayesian three category outcome hierarchical cumulative logit regression model with adjustment for age, sex, occupation and measurement error of the Kato-Katz technique was used for analysis.

Results
A total of 1427 households and 6917 individuals agreed to participate in the study. A total of 5624 (81.3%) participants provided at least one stool sample. The prevalences of those lightly and at least moderately infected varied from 0% (95% Bayesian credible interval (BCI): 0%–3.1%) to 45.2% (95% BCI: 36.5%–53.9%) and 0% to 23.0% (95% BCI: 16.4%–31.2%) from village-to-village, respectively. Using the 0–7 year old group as a reference category, the highest odds ratio (OR) among males and females were that of being aged 17–40-year old (OR = 8.76; 95% BCI: 6.03–12.47) and 11–16-year old (OR = 8.59; 95% BCI: 4.74–14.28), respectively. People who did not work on a rice farm had a lower prevalence of infection than those working full time on a rice farm. The OR for irrigated villages compared to rain-fed villages was 1.41 (95% BCI: 0.50–3.21).

Discussion
We found very important village-to-village variation in prevalence of infection intensity. This variation is probably due to village-level variables other than that explained by a crude classification of villages into the irrigated and non-irrigated categories. We are planning to capture this spatial heterogeneity by updating our initial transmission dynamics model with the data reported here combined with 1-year post-treatment follow-up of study participants.
A family of E. coliexpression vectors for laboratory scale and high throughput soluble protein production
Authors: Cabrita Lisa D , Dai Weiwen , Bottomley Stephen P 
Published: March 2006

Abstract

Background
In the past few years, both automated and manual high-throughput protein expression and purification has become an accessible means to rapidly screen and produce soluble proteins for structural and functional studies. However, many of the commercial vectors encoding different solubility tags require different cloning and purification steps for each vector, considerably slowing down expression screening. We have developed a set of E. coli expression vectors with different solubility tags that allow for parallel cloning from a single PCR product and can be purified using the same protocol.

Results
The set of E. coli expression vectors, encode for either a hexa-histidine tag or the three most commonly used solubility tags (GST, MBP, NusA) and all with an N-terminal hexa-histidine sequence. The result is two-fold: the His-tag facilitates purification by immobilised metal affinity chromatography, whilst the fusion domains act primarily as solubility aids during expression, in addition to providing an optional purification step. We have also incorporated a TEV recognition sequence following the solubility tag domain, which allows for highly specific cleavage (using TEV protease) of the fusion protein to yield native protein. These vectors are also designed for ligation-independent cloning and they possess a high-level expressing T7 promoter, which is suitable for auto-induction. To validate our vector system, we have cloned four different genes and also one gene into all four vectors and used small-scale expression and purification techniques. We demonstrate that the vectors are capable of high levels of expression and that efficient screening of new proteins can be readily achieved at the laboratory level.

Conclusion
The result is a set of four rationally designed vectors, which can be used for streamlined cloning, expression and purification of target proteins in the laboratory and have the potential for being adaptable to a high-throughput screening.
Fold classification based on secondary structure – how much is gained by including loop topology?
Authors: Jeong Jieun , Berman Piotr , Przytycka Teresa 
Published: March 2006

AbstractBackgroundIt has been proposed that secondary structure information can be used to classify (to some extend) protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms.We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample.We investigate alternative ways of computing and presenting this information.ResultsWe used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance.Parameters of local alignment function were optimized using a genetic algorithm.Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction.ConclusionWe found that, on average, properly presented information about the loop topology improves noticeably the accuracy of the method but the benefits vary between fold families as measured by log-odds cluster score.
A thyroid tumor extending to the parapharyngeal space
Authors: Cetik Fikret , Yazici Demet , Uguz Aysun 
Published: March 2006

Abstract

Background
The metastasis of papillary thyroid carcinoma to the parapharyngeal space is rare and discussed in the English literature before. Encountering a parapharyngeal mass with cystic appearance on imaging, one should rule out thyroid malignancy as differential diagnosis.

Case presentation
The case presented here is a 22-year-old woman who was referred to our clinic with complaints of painless neck mass, dysphagia and hoarseness for two years. After radiologic and pathological examination, the mass thought to be relevant with the thyroid gland. Peroperatively, the tumor was found to originate from the superior pole of the right thyroid gland, with a narrow stalk, and extended following the neurovascular bundle to the lower part of the parapharyngeal space. The bulk was removed via transservical approach with total thyroidectomy.

Conclusion
The occurrence of the follicular variant of papillary thyroid carcinoma in the parapharyngeal space is extremely rare. The management of this rare case was discussed with the review of literature.
Is general inpatient obstetrics and gynaecology evidence-based? A survey of practice with critical review of methodological issues
Authors: Khan Aamir T , Mehr M Nauman , Gaynor Anne-Marie , Bowcock Malcolm , Khan Khalid S 
Published: March 2006

Abstract

Background
To examine the rates of evidence-supported care provided in an obstetrics-gynaecology unit.

Methods
The main diagnosis-intervention set was established for a sample of 325 consecutive inpatient admissions in 1998–99 in a prospective study in a UK tertiary care centre. A comprehensive literature search was conducted to obtain the evidence supporting the intervention categorised according to the following hierarchy: Grade A, care supported by evidence from randomised controlled trials; Grade B, care supported by evidence from controlled observational studies and convincing non-randomised evidence; and Grade C, care without substantial research evidence.

Results
Of the 325 admissions, in 135 (42%) the quality of care was based on Grade A evidence, in 157 (48%) it was based on Grade B evidence, and in 33 (10%) it was based on Grade C evidence. The patterns of care were not different amongst patients sampled in 1998 and 1999.

Conclusion
A significant majority (90%) of obstetric and gynaecological care was found to be supported by substantial research evidence.
Knowledge, attitudes and practices on cervical cancer screening among the medical workers of Mulago Hospital, Uganda
Authors: Mutyaba Twaha , Mmiro Francis A , Weiderpass Elisabete 
Published: March 2006

Abstract

Background
Cervical cancer is the commonest cancer of women in Uganda. Over 80% of women diagnosed in Mulago national referral and teaching hospital, the biggest hospital in Uganda, have advanced disease. Pap smear screening, on opportunistic rather than systematic basis, is offered free in the gynaecological outpatients clinic and the postnatal/family planning clinics. Medical students in the third and final clerkships are expected to learn the techniques of screening. Objectives of this study were to describe knowledge on cervical cancer, attitudes and practices towards cervical cancer screening among the medical workers of Mulago hospital.

Methods
In a descriptive cross-sectional study, a weighted sample of 310 medical workers including nurses, doctors and final year medical students were interviewed using a self-administered questionnaire. We measured knowledge about cervical cancer: (risk factors, eligibility for screening and screening techniques), attitudes towards cervical cancer screening and practices regarding screening.

Results
Response rate was 92% (285). Of these, 93% considered cancer of the cervix a public health problem and knowledge about Pap smear was 83% among respondents. Less than 40% knew risk factors for cervical cancer, eligibility for and screening interval. Of the female respondents, 65% didn't feel susceptible to cervical cancer and 81% had never been screened. Of the male respondents, only 26% had partners who had ever been screened. Only 14% of the final year medical students felt skilled enough to use a vaginal speculum and 87% had never performed a pap smear.

Conclusion
Despite knowledge of the gravity of cervical cancer and prevention by screening using a Pap smear, attitudes and practices towards screening were negative. The medical workers who should be responsible for opportunistic screening of women they care for are not keen on getting screened themselves. There is need to explain/understand the cause of these attitudes and practices and identify possible interventions to change them. Medical students leave medical school without adequate skills to be able to effectively screen women for cervical cancer wherever they go to practice. Medical students and nurses training curricula needs review to incorporate practical skills on cervical cancer screening.
A critical evaluation of the electronic surgical logbook
Authors: Achuthan R , Grover K , MacFie J 
Published: March 2006

Abstract

Background
The Association of Surgeons of Great Britain and Ireland (ASGBI) devised the electronic surgical logbook (version 2.4) for higher trainees in General Surgery enabling trainees to compile a uniform data set of their operative and training experience. This is in use by higher surgical trainees (HST) in the United Kingdom. This logbook permits trainees to submit data centrally into a Regional Analysis Database (RAD). With the implementation of the European Working Time Directive (EWTD) there is need for reliable data to assess the effects of the directive on training. In order to draw meaningful conclusions from the database the quality of data needs to be validated. We critically analysed the RAD in the Yorkshire region for a one-year period.

Methods
The RAD from the ASGBI for the Yorkshire region was analysed. Data for the period 01/10/2002–30/09/2003 was identified and interrogated using Microsoft Excel (2000 version). The RAD was compared with information obtained from the Regional Surgical Advisor for Yorkshire with respect to hospitals, surgical consultants and HST's in the region during the study period.

Results
There were 13,755 operations entered for the study period. 579 corrections to the data had to be made (4.2%) and a further 1140 entries were deleted (8.2%). Following corrections and deletions 12,615 operative entries were available for analysis. Overall 12.5% of the data required either correction or exclusion from the database prior to analysis.

Conclusion
The RAD has a large dataset useful to monitor and assess training. However, the quality of the data needs to be verified prior to use. Recommendations have been made to develop the ASGBI logbook, which would eventually translate to improved data reliability of the RAD.