bluuebunny/crossref_metadata_2025_split huggingface dataset:
Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays
Authors: Gardner Shea N , Wagner Mark C 
Published: May 2005

Abstract
Background
Microbial forensics is important in tracking the source of a pathogen, whether the disease is a naturally occurring outbreak or part of a criminal investigation.

Results
A method and SPR Opt (S NP and P CR-R FLP Opt imization) software to perform a comprehensive, whole-genome analysis to forensically discriminate multiple sequences is presented. Tools for the optimization of forensic typing using Single Nucleotide Polymorphism (SNP) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) analyses across multiple isolate sequences of a species are described. The PCR-RFLP analysis includes prediction and selection of optimal primers and restriction enzymes to enable maximum isolate discrimination based on sequence information. SPR Opt calculates all SNP or PCR-RFLP variations present in the sequences, groups them into haplotypes according to their co-segregation across those sequences, and performs combinatoric analyses to determine which sets of haplotypes provide maximal discrimination among all the input sequences. Those set combinations requiring that membership in the fewest haplotypes be queried (i.e. the fewest assays be performed) are found. These analyses highlight variable regions based on existing sequence data. These markers may be heterogeneous among unsequenced isolates as well, and thus may be useful for characterizing the relationships among unsequenced as well as sequenced isolates. The predictions are multi-locus. Analyses of mumps and SARS viruses are summarized. Phylogenetic trees created based on SNPs, PCR-RFLPs, and full genomes are compared for SARS virus, illustrating that purported phylogenies based only on SNP or PCR-RFLP variations do not match those based on multiple sequence alignment of the full genomes.

Conclusion
This is the first software to optimize the selection of forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input. As more sequence data becomes available for multiple strains and isolates of a species, automated, computational approaches such as those described here will be essential to make sense of large amounts of information, and to guide and optimize efforts in the laboratory. The software and source code for SPR Opt is publicly available and free for non-profit use at http://www.llnl.gov/IPandC/technology/software/softwaretitles/spropt.php.
Synergistic effect of intrathecal fentanyl and bupivacaine in spinal anesthesia for cesarean section
Authors: Bogra Jaishri , Arora Namita , Srivastava Pratima 
Published: May 2005

Abstract
Background
Potentiating the effect of intrathecal local anesthetics by addition of intrathecal opiods for intra-abdominal surgeries is known. In this study by addition of fentanyl we tried to minimize the dose of bupivacaine, thereby reducing the side effects caused by higher doses of intrathecal bupivacaine in cesarean section.

Methods
Study was performed on 120 cesarean section parturients divided into six groups, identified as B8, B10 and B 12.5 8.10 and 12.5 mg of bupivacaine mg and FB8, FB10 and FB 12.5 received a combination of 12.5 μg intrathecal fentanyl respectively. The parameters taken into consideration were visceral pain, hemodynamic stability, intraoperative sedation, intraoperative and postoperative shivering, and postoperative pain.

Results
Onset of sensory block to T6 occurred faster with increasing bupivacaine doses in bupivacaine only groups and bupivacaine -fentanyl combination groups. Alone lower concentrations of bupivacaine could not complete removed the visceral pain. Blood pressure declined with the increasing concentration of Bupivacaine and Fentanyl. Incidence of nausea and shivering reduces significantly whereas, the postoperative pain relief and hemodynamics increased by adding fentanyl. Pruritis, maternal respiratory depression and changes in Apgar score of babies do not occur with fentanyl.

Conclusion
Spinal anesthesia among the neuraxial blocks in obstetric patients needs strict dose calculations because minimal dose changes, complications and side effects arise, providing impetus for this study. Here the synergistic, potentiating effect of fentanyl (an opiod) on bupivacaine (a local anesthetic) in spinal anesthesia for cesarian section is presented, fentanyl is able to reduce the dose of bupivacaine and therefore its harmful effects.
Recruitment of ethnic minority patients to a cardiac rehabilitation trial: The Birmingham Rehabilitation Uptake Maximisation (BRUM) study [ISRCTN72884263]
Authors: Jolly Kate , Lip Gregory Y , Taylor Rod S , Mant Jonathan W , Lane Deirdre A , Lee Kaeng W , Stevens Andrew J ,   the BRUM Steering Committee
Published: May 2005

Abstract

Background
Concerns have been raised about low participation rates of people from minority ethnic groups in clinical trials. However, the evidence is unclear as many studies do not report the ethnicity of participants and there is insufficient information about the reasons for ineligibility by ethnic group. Where there are data, there remains the key question as to whether ethnic minorities more likely to be ineligible (e.g. due to language) or decline to participate. We have addressed these questions in relation to the Birmingham Rehabilitation Uptake Maximisation (BRUM) study, a randomized controlled trial (RCT) comparing a home-based with a hospital-based cardiac rehabilitation programme in a multi-ethnic population in the UK.

Methods
Analysis of the ethnicity, age and sex of presenting and recruited subjects for a trial of cardiac rehabilitation in the West-Midlands, UK.
Participants: 1997 patients presenting post-myocardial infarction, percutaneous transluminal coronary angioplasty or coronary artery bypass graft surgery.
Data collected: exclusion rates, reasons for exclusion and reasons for declining to participate in the trial by ethnic group.

Results
Significantly more patients of South Asian ethnicity were excluded (52% of 'South Asian' v 36% 'White European' and 36% 'Other', p < 0.001). This difference in eligibility was primarily due to exclusion on the basis of language (i.e. the inability to speak English or Punjabi). Of those eligible, similar proportions were recruited from the different ethnic groups (white, South Asian and other). There was a marked difference in eligibility between people of Indian, Pakistani or Bangladeshi origin.

Conclusion
Once eligible for this trial, people from different ethnic groups were recruited in similar proportions. The reason for ineligibility in the BRUM study was the inability to support the range of minority languages.
Clinicians' management strategies for patients with dyspepsia: a qualitative approach
Authors: Knutsson Kerstin , Ohlsson Bodil , Troein Margareta 
Published: May 2005

Abstract
Background
Symptoms from the upper gastrointestinal tract are frequently encountered in clinical practice and may be of either organic or functional origin. For some of these conditions, according to the literature, certain management strategies can be recommended. For other conditions, the evidence is more ambiguous. The hypothesis that guided our study design was twofold: Management strategies and treatments suggested by different clinicians vary considerably, even when optimal treatment is clear-cut, as documented by evidence in the literature. Clinicians believe that the management strategies of their colleagues are similar to their own.

Methods
Simulated case histories of four patients with symptoms from the upper gastrointestinal tract were presented to 27 Swedish clinicians who were specialists in medical gastroenterology, surgery, and general practice and worked at three hospitals in the southern part of Sweden. The patients' histories contained information on the patient's sex and age and the localisation of the symptoms, but descriptions of subjective symptoms and findings from examinations differed from history to history. Interviews containing open-ended questions were conducted.

Results
For the same patient, the management strategies and treatments suggested by the clinicians varied widely, as did the strategies suggested by clinicians in the same speciality. Variation was more pronounced if the case history noted symptoms but no organic findings than if the case history noted unambiguous findings and symptoms. However, even in cases with a consensus in the scientific literature on treatment, the variations in clinicians' opinion on management were pronounced.

Conclusion
Despite these variations, the clinicians believed that the decisions made by their colleagues would be similar to their own. The overall results of this study indicate that we as researchers must make scientific evidence comprehensible and communicate evidence so that clinicians are able to interpret and implement it in practice. Of particular significance is that scientific evidence leads to an evidence-based care which is effective clinical practice and to the promotion of health from the perspective of the patient, together with cost-effectiveness as a priority.
Prevalence and risk factors of syphilis infection among drug addicts
Authors: Scherbaum Norbert , Baune Bernhard T , Mikolajczyk Rafael , Kuhlmann Thomas , Reymann Gerhard , Reker Martin 
Published: May 2005

Abstract

Background
Recent epidemiological data show an increased trend of official estimates for syphilis infection in the general population. Many of the infected cases remain undetected leaving an underestimation of the true prevalence of syphilis in the general population, but also among subpopulations such as illicit drug users. There is limited epidemiological data published on the proportion and risk factors of syphilis infections associated with illicit drug abuse.

Methods
Illicit drug addicts (n = 1223) in inpatients units in Germany were screened (2000–01) for syphilis and interviewed regarding patterns of drug use and sexual behaviour. TPHA-test for initial screening and FTA-ABS-IgM test in TPHA-positive patients were used.

Results
In total, TPHA-tests were positive in 39 (3.3%) and 7 patients (0.6%) were IgM positive. The prevalence rate for syphilis in males was 1.9% and for women it was 8.5%. Female patients were 4.56 (CI 95% 2.37–8.78) times more likely to have a positive TPHA test than males. Sexual behaviours such as high number of sexual partners, sex for drugs/money, sex on the first day were associated with syphilis infection only in women. Females with frequent sex for drugs or money had 4.31 (CI 95% 2.32–8.52) times more likely a reactive TPHA test than remaining patients. Neither the sociodemographic factors nor sexual behaviour were statistically significant associated with syphilis infection among men at all.

Conclusion
Our data suggest the need for screening for syphilis among these illicit drug users in inpatient settings, in particular among sexual active women. This conclusion is corroborated by the finding of increasing numbers of syphilis infections in the general population. The identification of syphilis cases among drug addicts would give treatment options to these individuals and would help to reduce the spread of infection in this population, but also a spread into heterosexual populations related to prostitution.
Echinococcal disease in Alberta, Canada: more than a calcified opacity
Authors: Somily Ali , Robinson Joan L , Miedzinski Lilly J , Bhargava Ravi , Marrie Thomas J 
Published: May 2005

Abstract

Background
Most cases of echinococcal disease (ED) acquired in Canada are thought to be due to the sylvatic form of Echinococcus granulosus, which may be more benign than ED due to either Echinococcus multilocularis or the pastoral form of E. granulosus. There are limited descriptions of the clinical course and outcome of Canadian patients with ED in the modern era.

Methods
A retrospective chart review was performed of patients hospitalized with echinococcal disease (ED) from 1991 to 2001 in Edmonton, Alberta.

Results
Forty-two cases of ED were identified of which 19 were definite, 3 probable, and 20 possible. Further analysis was limited to the 22 definite and probable cases, of which 77% were female and 41% aboriginal, with an age range of 5 to 87 years. Nine patients (40%) had pulmonary involvement and 11 (50%) hepatic involvement. One patient had an intracardiac mass presenting as a cerebrovascular event and one had a splenic cyst. Seven of the 22 patients had combined surgical resection and medical treatment, six had surgical resection of the cyst alone, four had cyst aspiration, one had medical treatment alone and four had no specific treatment. There was no mortality attributable to ED but three patients died of unrelated illnesses.

Conclusion
Echinococcal disease in northern Alberta has a marked diversity of clinical presentations, and generally has a good prognosis despite a wide variety of therapeutic interventions.
Hepatitis E virus infection in hemodialysis patients: A seroepidemiological survey in Iran
Authors: Taremi Mahnaz , Khoshbaten Manouchehr , Gachkar Latif , EhsaniArdakani MohammadJavad , Zali MohammadReza 
Published: May 2005

Abstract
Background
The hepatitis E virus (HEV) has a global distribution and is known to have caused large waterborne epidemics of icteric hepatitis. Transmission is generally via the fecal-oral route. Some reports have suggested parenteral transmission of HEV. Anti-HEV prevalence data among chronic hemodialysis (HD) patients are few and give conflicting results.

Methods
This cross-sectional study was conducted in August of 2004. We tested 324 chronic HD patients attending three different units in the city of Tabriz, northwestern part of Iran, for anti-HEV antibody. A specific solid- phase enzyme-linked immunoassay (Diapro, Italy) was used.

Results
The overall seroprevalence of hepatitis E was 7.4 %(95% CI: 4.6%–10.6%). The prevalence rate of HBV and HCV infection were 4.6% (95% CI: 2.3%–6.9%) and 20.4% (95% CI: 16%–24.8%), respectively. No significant association was found between anti-HEV positivity and age, sex, duration of hemodialysis, positivity for hepatitis B or C virus infection markers and history of transfusion.

Conclusion
We observed high anti-HEV antibody prevalence; there was no association between HEV and blood borne infections (HBV, HCV, and HIV) in our HD patients. This is the first report concerning seroepidemiology of HEV infection in a large group of chronic HD individuals in Iran.
Rural residence is not a risk factor for frequent mental distress: a behavioral risk factor surveillance survey
Authors: Rohrer James E , Borders Tyrone F , Blanton Jimmy 
Published: May 2005

AbstractBackgroundResidents of rural areas may be at increased risk of mental health problems. If so, public health programs aimed at preventing poor mental health may have to be customized for delivery to rural areas. The purpose of this study was to examine the relationship between residing in a rural area and frequent mental distress, which is one indicator of poor mental health.MethodsThe Behavioral Risk Factor Surveillance System (BRFSS) survey for the state of Texas was the source of information about obesity, demographic characteristics, and frequent mental distress (FMD). FMD was defined as poor self-rated mental health during at least half of the days in the last month. Adjusted odds for FMD were computed for rural and suburban respondents relative to urban respondents.ResultsFMD was found to be independently associated with lower education, being younger, being non-Hispanic, being unmarried, and being female. FMD also was associated with being obese or underweight and suburban residence (relative to metro-central city). FMD was not more common among rural respondents than in the metro-central city.ConclusionRural respondents were not at greater risk of frequent mental distress than urban respondents in this sample. Programs seeking to improve community mental health should target persons with less education and extremes in body weight, along with women and single persons, regardless of whether they live in rural or urban areas.
Prevalence of nonvitamin, nonmineral supplement usage among students in a Turkish university
Authors: Ayranci Unal , Son Nazan , Son Osman 
Published: May 2005

Abstract
Background
There have been multiple studies carried out in many countries with regard to the use of nonvitamin, nonmineral (NVNM) supplements. These studies have shown that the use of NVNM supplements is on the increase throughout the world, particularly in western countries. The aim of this study was to assess the extent of NVNM supplement use among Turkish university students.

Methods
The survey was conducted between September and December 2004 at Osmangazi University, a public university located in the west of Turkey. Responses were analysed, using the chi-square (x2) test, t test and percent (%) ratios, according to gender and consumers. Differences were considered significant for p ≤ 0.05.

Results
Of 2253 students attending the university, 1871 participated in the survey (909 men and 962 women). Overall, the prevalence of NVNM supplement use was 16.5% (16.6% in men and 16.3% in women, p < 0.05).
The three most commonly given reasons for use were 'improvement of energy and vitality (78.6%)', 'promotion of weight loss (71.1%)', followed by 'enhancement of athletic performance (64.3%)'. Twenty-six of the 308 reported NVNM users (26/308, 8.4%) reported having experienced an adverse reaction. Television (76.3%), magazines/newspapers (41.5%) and internet websites (37.3%) were the most frequently used sources for obtaining information about NVNM supplements. The three most frequently used NVNM supplements were echinacea, ginseng, and gingko biloba (38.6%, 36.4%, and 32.8%, respectively). Nutritional scores were higher in NVNM supplement users than in non-users (66.510.8 vs. 62.712.7) (p < 0.001). Users and nonusers of NVNM supplements differed significantly according to sex, age, Body Mass Index (BMI) values, types of school, mother and fathers' education levels, family income, most permanent place of residence up to the time of survey, smoking status, and participating in sports.

Conclusion
The results indicate that the prevalence of NVNM supplement use is relatively modest among Turkish university students and more information is needed on why people use particular NVNM supplements.
Screening for asthma in Cantonese-speaking immigrant children
Authors: Greenfield Robyn O , Lee Angela C , Tang Roland , Brugge Doug 
Published: May 2005

Abstract
Background
Asthma prevalence among Chinese immigrant children is poorly understood and attempts to screen these children have produced varied outcomes. We sought to learn how to improve screening for asthma in Chinese immigrant children.

Methods
Children (n = 152) were administered the Brief Pediatric Asthma Screen in either Cantonese or English, they then viewed and reacted to a video showing people wheezing and subsequently took a pulmonary function test.

Results
The diagnosed asthma prevalence for our study population was 27.0%, with another 5.3% having possible undiagnosed asthma. Very few children had spirometry findings below normal. In multivariate analysis, being native born (p = 0.002) and having a family history of asthma (p = 0.003) were statistically associated with diagnosis of asthma. After viewing the video, 35.6% of respondents indicated that the images differed from their conception of wheezing. Of four translations of the word "wheeze" no single word was chosen by a majority.

Conclusion
Our findings suggest that asthma diagnoses are higher for Chinese children who were born in the US suggesting that desegregation of data might reveal at risk subpopulations. Care needs to be taken when diagnosing asthma for Cantonese speakers because of the centrality of the word wheeze and the challenges of translation.
Metabolic effect of telmisartan and losartan in hypertensive patients with metabolic syndrome
Authors: Vitale Cristiana , Mercuro Giuseppe , Castiglioni Carlotta , Cornoldi Alessandra , Tulli Arianna , Fini Massimo , Volterrani Maurizio , Rosano Giuseppe MC 
Published: May 2005

Abstract

Background
Metabolic syndrome is a cluster of common cardiovascular risk factors that includes hypertension and insulin resistance. Hypertension and diabetes mellitus are frequent comorbidities and, like metabolic syndrome, increase the risk of cardiovascular events. Telmisartan, an antihypertensive agent with evidence of partial peroxisome proliferator-activated receptor activity-gamma (PPARγ) activity, may improve insulin sensitivity and lipid profile in patients with metabolic syndrome.

Methods
In a double-blind, parallel-group, randomized study, patients with World Health Organization criteria for metabolic syndrome received once-daily doses of telmisartan (80 mg, n = 20) or losartan (50 mg, n = 20) for 3 months. At baseline and end of treatment, fasting and postprandial plasma glucose, insulin sensitivity, glycosylated haemoglobin (HBA1c) and 24-hour mean systolic and diastolic blood pressures were determined.

Results
Telmisartan, but not losartan, significantly (p < 0.05) reduced free plasma glucose, free plasma insulin, homeostasis model assessment of insulin resistance and HbAic. Following treatment, plasma glucose and insulin were reduced during the oral glucose tolerance test by telmisartan, but not by losartan. Telmisartan also significantly reduced 24-hour mean systolic blood pressure (p < 0.05) and diastolic blood pressure (p < 0.05) compared with losartan.

Conclusion
As well as providing superior 24-hour blood pressure control, telmisartan, unlike losartan, displayed insulin-sensitizing activity, which may be explained by its partial PPARγ activity.
Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system
Authors: Gosset Guillermo 
Published: May 2005

Abstract
The application of metabolic engineering in Escherichia coli has resulted in the generation of strains with the capacity to produce metabolites of commercial interest. Biotechnological processes with these engineered strains frequently employ culture media containing glucose as the carbon and energy source. In E. coli, the phosphoenolpyruvate:sugar phosphotransferase system (PTS) transports glucose when this sugar is present at concentrations like those used in production fermentations. This protein system is involved in phosphoenolpyruvate-dependent sugar transport, therefore, its activity has an important impact on carbon flux distribution in the phosphoenolpyruvate and pyruvate nodes. Furthermore, PTS has a very important role in carbon catabolite repression. The properties of PTS impose metabolic and regulatory constraints that can hinder strain productivity. For this reason, PTS has been a target for modification with the purpose of strain improvement. In this review, PTS characteristics most relevant to strain performance and the different strategies of PTS modification for strain improvement are discussed. Functional replacement of PTS by alternative phosphoenolpyruvate-independent uptake and phosphorylation activities has resulted in significant improvements in product yield from glucose and productivity for several classes of metabolites. In addition, inactivation of PTS components has been applied successfully as a strategy to abolish carbon catabolite repression, resulting in E. coli strains that use more efficiently sugar mixtures, such as those obtained from lignocellulosic hydrolysates.