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At least 757 records · Page 42Linked to original sources
PubMed2003

ESTprep: preprocessing cDNA sequence reads.

MOTIVATION: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases. RESULTS: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank. AVAILABILITY: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html

Algorithms↗
PubMed2005

Tag SNP selection in genotype data for maximizing SNP prediction accuracy.

MOTIVATION: The search for genetic regions associated with complex diseases, such as cancer or Alzheimer's disease, is an important challenge that may lead to better diagnosis and treatment. The existence of millions of DNA variations, primarily single nucleotide polymorphisms (SNPs), may allow the fine dissection of such associations. However, studies seeking disease association are limited by the cost of genotyping SNPs. Therefore, it is essential to find a small subset of informative SNPs (tag SNPs) that may be used as good representatives of the rest of the SNPs. RESULTS: We define a new natural measure for evaluating the prediction accuracy of a set of tag SNPs, and use it to develop a new method for tag SNPs selection. Our method is based on a novel algorithm that predicts the values of the rest of the SNPs given the tag SNPs. In contrast to most previous methods, our prediction algorithm uses the genotype information and not the haplotype information of the tag SNPs. Our method is very efficient, and it does not rely on having a block partition of the genomic region. We compared our method with two state-of-the-art tag SNP selection algorithms on 58 different genotype datasets from four different sources. Our method consistently found tag SNPs with considerably better prediction ability than the other methods. AVAILABILITY: The software is available from the authors on request.

Algorithms↗
PubMed1991

Analysis of coyote mitochondrial DNA genotype frequencies: estimation of the effective number of alleles.

A restriction-site survey of 327 coyotes (Canis latrans) from most parts of their North American range reveals 32 mitochondrial DNA (mtDNA) genotypes. The genotypes are not strongly partitioned in space, suggesting that there is high gene flow among coyote subpopulations. Consequently, each new geographic location added to the study has a decreasing probability of containing a mtDNA genotype that had not been previously discovered. This being the case, by using Monte Carlo sampling experiments, we can estimate the total number of genotypes that would be found if all possible localities were surveyed. This estimate of total genotypic variability agrees qualitatively with estimates based on theoretical considerations of the expected number of alleles in a stable population. We also predict effective population sizes from genotype data. The accuracy of these estimates is thought to be dependent on the fact that coyotes are not highly genetically structured, a situation which may apply to highly mobile species.

Alleles↗
PubMed2002

An overview of the cancer control programme in Singapore.

Singapore is a multiracial, multireligious and multicultural society. Today, cancer is the leading cause of death in Singapore and about one in four deaths is from cancer. The Singapore Cancer Registry has been in existence for more than 25 years and its accuracy of data for incidence, distribution, changing patterns, etc., is close to 100%. These statistics revealed that the incidence of cancer is related to the racial distribution of the population. A national concerted cancer control programme is targeted at prevention, early detection and integrated management. Strong laws against smoking and a national vaccination programme against hepatitis are in place.

Female↗
PubMed2002

Characterization of diet-dependent metabolic serotypes: proof of principle in female and male rats.

Our research seeks to identify a serum profile, or serotype, that reflects substantial changes in food intake. Earlier studies demonstrated that a number of low-molecular-weight, redox-active compounds of metabolome were sufficiently stable analytically and biologically to identify biomarkers of dietary restriction (DR, restriction of total food intake) in rats. A second initial requirement is to demonstrate feasibility, i.e., that concentration changes in selected serum metabolites can contain sufficient information to classify rats by diet. The current study distinguished 101 (female) and 112 (male) chromatographically identifiable compounds that differ between ad libitum (AL) consumption and DR 6-mo-old rats. In a cohort of female rats, both hierarchical cluster analysis (HCA) and principal component analyses (PCA) could distinguish dietary groups with 100% efficiency (101 metabolites). Repeating the classification studies using the 63 biologically and analytically most robust metabolites decreased noise without affecting categorical separation. In a cohort of male rats, PCA, but not HCA, distinguished the original dietary groups with 100% accuracy (112 metabolites). A subset of 52 of the 112 metabolites enabled both HCA and PCA to group the male rats with 100% accuracy. These data demonstrate that quantitative analysis of selected serum metabolites can yield sufficient information by which to classify the dietary intake of a group of rats, identify such markers chromatographically and set the stage for validation of these metabolic serotypes in independent datasets.

Animals↗
PubMed2003

RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis.

Here we devise a new method for high-throughput comparative sequence analysis. The developed protocol comprises a homogeneous in vitro transcription/RNase cleavage system with the accuracy and data acquisition speed of matrix-assisted laser desorption/ionization coupled with time-of-flight mass spectrometry (MALDI-TOF MS). In summary, the target region is PCR amplified using primers tagged with promoter sequences of T7 or SP6 RNA polymerase. Using RNase T1, the in vitro transcripts are base-specifically cleaved at every G-position. This reaction results in a characteristic pattern of fragment masses that is indicative of the original target sequence. To enable high-throughput analysis, samples are processed with automated liquid handling devices and nanoliter amounts are dispensed onto SpectroCHIP arrays for reliable and homogeneous MALDI preparation. This system enables rapid automated comparative sequence analysis for PCR products up to 1 kb in length. We demonstrate the feasibility of the devised method for analysis of single nucleotide polymorphisms (SNPs) and pathogen identification.

Apolipoproteins B↗
PubMed2005

Relationship of gender, age, and body mass index to errors in predicted kidney function.

BACKGROUND: Previous studies have shown conflicting data on accuracy of equations for kidney function prediction. The present work analysed the relationship of gender, age and body mass index (BMI) to error of predictions by the Cockcroft-Gault equation (CG(eq)), the simplified equation of the Modification of Renal Diseases Study (MDRD(eq)) and the Mayo Clinic equation (Mayo(eq)). METHODS: Inulin clearance (glomerular filtration rate; GFR) and other variables were measured in 380 subjects of both sexes, aged 18-88 years, with and without kidney disease. GFR was defined as low when <60 ml/min x 1.73 m2. BMI was used for definition of underweight/overweight. Relative error of predictions was used as an index of bias. It was calculated as prediction minus GFR (positive values =overestimates, negative values = underestimates) and expressed as a percentage of the GFR. Absolute error was used as an index of imprecision and was calculated as the absolute value of relative error. RESULTS: CG(eq) relative error was inversely associated with age and directly associated with BMI (P<0.001), but not with gender or GFR. MDRD(eq) relative error was inversely associated with female gender and GFR (P<0.001), but not with age or BMI. Mayo(eq) relative error was directly associated with male gender, BMI and GFR (P<0.01), but not with age. Absolute error was higher for CG(eq) than for MDRD(eq) but only at low GFR (P<0.001). Mayo(eq) had a higher absolute error than CG(eq) and MDRD(eq) (P<0.01). CONCLUSIONS: Errors of predictions varied not only with GFR but also with gender, age and BMI. Without using creatinine assay calibration, Mayo(eq) was less accurate than both MDRD(eq) and CG(eq), whereas MDRD(eq) was slightly more precise than CG(eq) but only at low GFR.

Adult↗
PubMed1997

Three-dimensional endosonography for staging of rectal cancer.

OBJECTIVE: This prospective study was conducted to investigate the value of three-dimensional (3D) endosonography for staging of rectal cancer. SUMMARY BACKGROUND DATA: Transrectal ultrasound is the most sensitive technique for peroperative staging and follow-up of rectal cancer. Major limitations of this technique include the complexity of image interpretation and the inability to examine stenotic tumors or to identify recurrent rectal cancer. METHODS: Three-dimensional endosonography was performed in 100 patients with rectal tumors. Transrectal volume scans were obtained using a 3D multiplane transducer (7.5/10.0 MHz). Stenotic tumors were examined with a 3D frontfire transducer (5.0/7.5 MHz). The volume scans were processed and analyzed on a Combison 530 workstation (Kretztechnik, Zipf, Austria). RESULTS: The 3D endosonography and conventional endosonography were performed in 49 patients with nonstenotic rectal cancer. Display of volume data in three perpendicular planes or as 3D view facilitated the interpretation of ultrasound images and enhanced the diagnostic information of the data. The accuracy of 3D endosonography in the assessment of infiltration depth was 88% compared to 82% with the conventional technique. In the determination of lymph node involvement, 3D and two-dimensional endosonography provided accuracy rates of 79% and 74%, respectively. The 3D scanning allowed the visualization of obstructing tumors using reconstructed planes in front of the transducer. Correct assessment of the infiltration depth was possible in 15 of 21 patients with obstructing tumors (accuracy, 76%). Three-dimensional endosonography displayed suspicious pararectal lesions in 30 patients. Transrectal ultrasound-guided biopsy was extremely precise (accuracy, 98%) and showed malignancy in 10 of 30 patients. Histologic analysis changed the endosonographic diagnosis in 8 (27%) of the patients. CONCLUSIONS: The 3D endosonography permits examination of rectal cancer using previously unattainable planes and 3D views. The 3D imaging and ultrasound-guided biopsy seem capable to improve staging of rectal cancer and should be evaluated in further studies.

Endosonography↗
PubMed2004

First trimester prenatal diagnosis.

PURPOSE OF REVIEW: The recent developments in first trimester sonography promise to greatly enhance our diagnostic capabilities for detection of aneuploidies. Collateral benefits of nuchal translucency measurements include the prediction of non-chromosomal adverse outcomes. These advances will fundamentally change clinical practices. All obstetricians must therefore have a working knowledge of the expanding literature in this field. RECENT FINDINGS: The review covers developments in nuchal translucency based first trimester detection of chromosomal anomalies and discusses the recent literature on the use of fetal nasal bone measurements to further improve diagnostic accuracy. Emerging data on the relationship between nuchal fluid measurement and the risk of cardiac anomaly will also be presented. SUMMARY: It is likely that the emphasis in obstetric clinical care will shift substantially towards the first trimester. With the enhanced diagnostic capabilities, greater research emphasis will inevitably need to be placed on the first trimester treatment of fetal disorders.

Aneuploidy↗
PubMed1999

Repetitive transcranial magnetic stimulation has a beneficial effect on bradykinesia in Parkinson's disease.

The effect of focal 5 Hz repetitive transcranial magnetic stimulation (rTMS) of the motor hand area (M1) on bradykinesia was studied in 12 unmedicated patients with Parkinson's disease (PD). On 2 separate days, a real-rTMS was applied to M1 contralaterally to the more severely affected limb or a frontal sham-rTMS was applied 3 cm anteriorly to Fz in a random order. Stimulus intensity was 10% below resting motor threshold. Before and 20 min after rTMS, patients performed 15 consecutive pointing movements with the index finger contralaterally to the stimulated M1. Compared with sham-rTMS, real-rTMS over the contralateral M1 caused a significant decrease in total movement time without affecting end-point accuracy. Our data provide evidence that 5 Hz rTMS over M1 can improve bradykinesia in PD patients beyond the time of magnetic stimulation.

Adult↗
PubMed1996

Economic evaluation of alternative adjuvant chemotherapy modalities for colorectal carcinoma.

Concerns regarding quality of care, combined with financial constraints, have fostered the growth of health economic analyses. The accompanying cost-effectiveness analysis of intraportal adjuvant chemotherapy by Messori et al. illustrates the strengths and limitations of health economic investigations. The reader of cost-effectiveness studies must examine the relevance and perspective of the cost data, the accuracy and generalizability of the assumed clinical benefits, and the relationship of the investigated treatment strategies to standard clinical practice. As clinicians learn to interpret health economic analyses and other forms of outcomes-based research, unnecessary expenditures will be avoided and the quality of care will improve.

Chemotherapy, Adjuvant↗
PubMed2005

Prognosis or "curabo effect?": physician prediction and patient outcome of surgery for low back pain and sciatica.

STUDY DESIGN: Prospective study with patient and physician questionnaires, clinical records, and imaging. OBJECTIVE: To compare physician expectations of surgery for sciatica and patient outcome. SUMMARY OF BACKGROUND DATA: Physician accuracy in identifying individual patient prognosis is important for therapeutic decisions. METHODS: A total of 197 consecutive patients with low back pain and/or sciatica who underwent low back surgery in the University Hospital of Lausanne, Switzerland. RESULTS: Physicians predicted "a great improvement" of quality of life after surgery for 79% and "moderate improvement" for 20% (1% others); 39% of patients had no "minimal clinically important difference" in back pain after surgery, despite physician prediction of "great improvement." Correlations between physician expectation and various dimensions of patient outcome were not significant, and agreement with patient global judgment of 1-year outcome was poor (kappa = 0.03). However, in a subgroup where the indication for treatment was not considered appropriate, physician prediction of "great improvement" was followed by greater improvement outcome on SF-36 mental component score (P = 0.05), mental health (0.02), and general health (0.03) compared with patients where the physician did not predict "great improvement." CONCLUSION: Despite clear average improvement, surgeons tended to give overly optimistic predictions that were not correlated with patient outcome. For patients receiving a treatment not meeting explicit criteria of appropriateness, more optimistic physician expectation was associated with better improvement of psychological dimensions. Besides prognostic ability, the influence of physician expectation on patient outcome is discussed and the concept of "curabo effect" (differentiated from "placebo effect") proposed.

Adolescent↗
PubMed2003

Is sentinel lymph node mapping indicated for isolated local and in-transit recurrent melanoma?

OBJECTIVE: To determine the feasibility of sentinel lymph node mapping in local and in-transit recurrent melanoma. SUMMARY BACKGROUND DATA: The accuracy of intraoperative lymphatic mapping and sentinel lymphadenectomy (LM/SL) for identification of occult lymph node metastases is well established in primary melanoma. We hypothesized that LM/SL could be useful to detect regional node metastases in patients with isolated local and in-transit recurrent melanoma (RM). METHODS: Review of our prospective melanoma database of 1600 LM/SL patients identified 30 patients who underwent LM/SL for RM. Patients with tumor-positive sentinel nodes (SNs) were considered for completion lymph node dissection. RESULTS: Of the 30 patients, 17 were men and 13 were women; their median age was 57 years (range, 29-86 years). Primary lesions were more often on the extremities (40%) than the head and neck (33%) or the trunk (8%). At least 1 SN was identified in each lymph node basin that drained an RM. Of the 14 (47%) patients with tumor-positive SNs, 11 (78%) underwent complete lymph node dissection; 4 had tumor-positive non-SNs. The median disease-free survival after LM/SL was 16 months (range, 1-108 months) when an SN was positive and 36 months (range, 6-132 months) when SNs were negative. At a median follow-up of 20 months (range, 2-48 months), there were no dissected basin recurrences after a tumor-negative SNs. CONCLUSIONS: LM/SL can accurately identify SNs draining an RM, and the high rate of SN metastases and associated poor disease-free survival for patients with tumor-positive SN suggests that LM/SL should be routinely considered in the management of patients with isolated RM.

Adult↗
PubMed2002

Evaluation of effective ion-ion potentials in aqueous electrolytes.

We present high-accuracy simulation data for ion-ion radial distribution functions in NaCl aqueous electrolyte. From the data we evaluate ion-ion effective potentials via inverse Monte Carlo simulation procedure. Alternatively, we first evaluate effective direct correlation functions and then obtain effective potentials using the hypernetted-chain (HNC) approximation. Both methods are in excellent agreement, indicating that HNC approximation performs well with effective ion-ion potentials in aqueous solutions.

Journal Article↗
PubMed1995

Functional design features and initial performance characteristics of a magnetic-implant guidance system for stereotactic neurosurgery.

A helmet with a roughly cubic array of six super-conducting coils is used to apply force on a small permanent magnet pellet in brain or in brain phantom material. This apparatus, called the Magnetic Stereotaxis System, will be used to deliver drugs and other therapies directly into deep brain tissues, under control of a computer and fluoroscopic imaging system. This paper considers only the force application aspects of the instrument. The primary design features of the helmet and power supply controls are presented, along with field plot data and single-axis motion results. The field plot data show that agreement with the finite-element iron-free field calculations is sufficiently high (> 1%) for the instrument. These preliminary motion data indicate accuracy better than 2 mm for the impulsive pellet motion, even though the visual position observations had significantly greater error than the completed imaging system will have. The companion paper will take up analysis of the control aspects of the motion, and our recent solutions to difficulties found in the experimental work described here.

Brain↗
PubMed2006

Image segmentation based on fuzzy connectedness using dynamic weights.

Traditional segmentation techniques do not quite meet the challenges posed by inherently fuzzy medical images. Image segmentation based on fuzzy connectedness addresses this problem by attempting to capture both closeness, based on characteristic intensity, and "hanging togetherness," based on intensity homogeneity, of image elements to the target object. This paper presents a modification and extension of previously published image segmentation algorithms based on fuzzy connectedness, which is computed as a linear combination of an object-feature-based and a homogeneity-based component using fixed weights. We provide a method, called fuzzy connectedness using dynamic weights (DyW), to introduce directional sensitivity to the homogeneity-based component and to dynamically adjust the linear weights in the functional form of fuzzy connectedness. Dynamic computation of the weights relieves the user of the exhaustive search process to find the best combination of weights suited to a particular application. This is critical in applications such as analysis of cardiac cine magnetic resonance (MR) images, where the optimal combination of affinity component weights can vary for each slice, each phase, and each subject, in spite of data being acquired from the same MR scanner with identical protocols. We present selected results of applying DyW to segment phantom images and actual MR, computed tomography, and infrared data. The accuracy of DyW is assessed by comparing it to two different formulations of fuzzy connectedness. Our method consistently achieves accuracy of more than 99.15% for a range of image complexities: contrast 5%-65%, noise-to-contrast ratio of 6%-18%, and bias field of four types with maximum gain factor of up to 10%.

Algorithms↗
PubMed2006

The management of skin malignancy: to what extent should we rely on clinical diagnosis?

BACKGROUND: Cutaneous malignancy forms a major part of the dermatologist's workload. Clinical diagnosis is an important factor in facilitating the urgent excision of squamous cell carcinomas (SCC) and malignant melanomas. OBJECTIVES: To identify the numbers and types of malignant skin tumours managed in an NHS teaching hospital and to assess the diagnostic accuracy. METHODS: Data were collected on every histologically proven malignant skin lesion over a 6-month period. RESULTS: One thousand one hundred and ninety-five malignant skin tumours were identified: 78% were basal cell carcinomas, 14% were SCC, 6% were malignant melanomas and the remaining 2% included Merkel cell tumours, malignant adnexal tumours and lentigo maligna. Eighty-one per cent of the tumours were managed by dermatologists. The correct clinical diagnosis had been made by the secondary care clinician in 84% of cases but an incorrect clinical diagnosis was given in 32% of SCC. Of the 1195 tumours, 916 (77%) had a primary excision and 92% (843 of 916) of these were completely excised. CONCLUSIONS: The majority of skin malignancies (968 of 1195, 81%) were managed by dermatologists. Where primary excision was attempted, this was complete in 91% (767 of 916) of cases. The correct clinical diagnosis was made in 84% of all tumours, but 32% of SCC were not correctly diagnosed prior to surgery.

Biopsy↗
PubMed1988

Inheritance and bleeding in factor XI deficiency.

A study of 20 Jewish and four non-Jewish kindreds transmitting factor XI deficiency (164 individuals) confirmed inheritance to be autosomal with severe deficiency in homozygotes (mean factor XI level 3.8 u/dl, SD 2.91) and partial deficiency in heterozygotes (mean factor XI level 57 u/dl, SD 10.42; normal mean factor XI level 96 u/dl, SD 11.6). The probability of an individual being heterozygous can be predicted from the factor XI level using a graph derived from this data. The accuracy is increased by including the prior probability derived from the pedigree. A high frequency of heterozygote to heterozygote mating was observed in the Jewish families consistent with an estimated gene frequency of 13.4% in this racial group. The relationship between factor XI level and bleeding tendency is poor; a third of heterozygotes had bled excessively after surgery, including six with factor XI levels above 50 u/dl, showing this condition to have clear signs of expression in heterozygotes. The lower limit of the normal range (2 SDs from the mean) was found to be 72 u/dl.

Adolescent↗