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At least 919 records · Page 51Linked to original sources

PubMed2006

Comparison of gene coverage of mouse oligonucleotide microarray platforms.

BACKGROUND: The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. RESULTS: A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis): Affymetrix430 2.0 (75.6%), ABI Genome Survey (81.24%), Agilent (79.33%), Codelink (78.09%), Sentrix (90.47%); and four array-ready oligosets: Sigma (47.95%), Operon v.3 (69.89%), Operon v.4 (84.03%), and MEEBO (84.03%). The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. CONCLUSION: The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here reveals that the commercial microarray Sentrix, which is based on the MEEBO public oligoset, showed the best mouse genome coverage currently available. We also suggest the creation of guidelines to standardize the minimum set of information that vendors should provide to allow researchers to accurately evaluate the advantages and disadvantages of using a given platform.

Animals↗

PubMed2005

Cancer incidence in the south Asian population of California, 1988-2000.

BACKGROUND: Although South Asians (SA) form a large majority of the Asian population of U.S., very little is known about cancer in this immigrant population. SAs comprise people having origins mainly in India, Pakistan, Bangladesh and Sri Lanka. We calculated age-adjusted incidence and time trends of cancer in the SA population of California (state with the largest concentration of SAs) between 1988-2000 and compared these rates to rates in native Asian Indians as well as to those experienced by the Asian/Pacific Islander (API) and White, non-Hispanic population (NHW) population of California. METHODS: Age adjusted incidence rates observed among the SA population of California during the time period 1988-2000 were calculated. To correctly identify the ethnicity of cancer cases, 'Nam Pehchan' (British developed software) was used to identify numerator cases of SA origin from the population-based cancer registry in California (CCR). Denominators were obtained from the U.S. Census Bureau. Incidence rates in SAs were calculated and a time trend analysis was also performed. Comparison data on the API and the NHW population of California were also obtained from CCR and rates from Globocan 2002 were used to determine rates in India. RESULTS: Between 1988-2000, 5192 cancers were diagnosed in SAs of California. Compared to rates in native Asian Indians, rates of cancer in SAs in California were higher for all sites except oropharyngeal, oesophageal and cervical cancers. Compared to APIs of California, SA population experienced more cancers of oesophagus, gall bladder, prostate, breast, ovary and uterus, as well as lymphomas, leukemias and multiple myelomas. Compared to NHW population of California, SAs experienced more cancers of the stomach, liver and bile duct, gall bladder, cervix and multiple myelomas. Significantly increasing time trends were observed in colon and breast cancer incidence. CONCLUSION: SA population of California experiences unique patterns of cancer incidence most likely associated with acculturation, screening and tobacco habits. There is need for early diagnosis of leading cancers in SA. If necessary steps are not taken to curb the growth of breast, colon and lung cancer, rates in SA will soon approximate those of the NHW population of California.

Journal Article↗

PubMed2004

Single nucleotide polymorphism genotyping by two colour melting curve analysis using the MGB Eclipse Probe System in challenging sequence environment.

Probe and primer design for single nucleotide polymorphism (SNP) detection can be very challenging for A-T DNA-rich targets, requiring long sequences with lower specificity and stability, while G-C-rich DNA targets present limited design options to lower GC-content sequences only. We have developed the MGB Eclipse Probe System, which is composed of the following elements: MGB Eclipse probes and primers, specially developed software for the design of probes and primers, a unique set of modified bases and a Microsoft Excel macro for automated genotyping, which ably solves, in large part, this challenge. Fluorogenic MGB Eclipse probes are modified oligonucleotides containing covalently attached duplex-stabilising dihydrocyclopyrroloindole tripeptide (DPI3), the MGB ligand (MGB is a trademark of Epoch Biosciences, Bothell, WA), which has the combined properties of allowing the use of short sequences and providing great mismatch discrimination. The MGB moiety prevents probe degradation during polymerase chain reaction (PCR), allowing the researcher to use real time data; alternatively, hybridisation can be accurately measured by a post-PCR two-colour melt curve analysis. Using MGB Eclipse probes and primers containing modified bases further enhances the analysis of difficult SNP targets. G- or C-rich sequences can be refractory to analysis due to Hoogsteen base pairing. Substitution of normal G with Epoch's modified G prevents Hoogsteen base pairing, allowing both superior PCR and probe-based analysis of GC-rich targets. The use of modified A and T bases allows better stabilisation by significantly increasing the Tm of the oligonucleotides. Modified A creates A-T base pairs that have a stability slightly lower than a G-C base pair, and modified T creates T-A base pairs that have a stability about 30 per cent higher than the unmodified base pair. Together, the modified bases permit the use of short probes, providing good mismatch discrimination and primers that allow PCR of refractory targets. The combination of MGB Eclipse probes and primers enriched with the MGB ligand and modified bases has allowed the analysis of refractory SNPs, where other methods have failed.

Base Sequence↗

PubMed2006

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.

We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.

Codon↗

PubMed2000

Drug interactions in palliative care.

PURPOSE: This review of drug interactions in palliative care examines the relevant literature in this area and summarizes the information on interactions of drugs, nutrients, and natural products that are used in the palliative care setting. Particular emphasis is placed on describing the newer information on the cytochrome P450 (CYP) system and the interactions of opioids, antidepressants, and the antitussive, dextromethorphan. METHODS: We performed a search of the MEDLINE database of the time period from 1966 until April 1998, using medical subject headings such as the names of selective serotonin reuptake inhibitors and other relevant medications in palliative care. Literature reviewed included both human and animal articles as well as non-English literature. Bibliographies of these articles and the personal libraries of several palliative care specialists were reviewed. Software developed by The Medical Letter-The Drug Interaction Program was also used. RESULTS: Drug interactions can be categorized in several ways. Drug-drug interactions are the most well known and can be kinetic, dynamic, or pharmaceutical. Pharmacokinetic interactions can involve CYP 2D6, which acts on drugs such as codeine and is responsible for its conversion to morphine. Poor metabolizers, either genotypic or due to phenocopying, are at risk for undertreatment if not recognized. Pharmacodynamic interactions with dextromethorphan may produce serotonin syndrome. CONCLUSION: Drug interactions are important in palliative care as in other aspects of medicine. These interactions are similar to those seen in other areas of medical care but have significant consequences in pain management. Failure to recognize these interactions can lead to either overdosing or undertreatment.

Drug Interactions↗

PubMed2004

Development and application of a rat ovarian gene expression database.

The pituitary gonadotropins play a key role in follicular development and ovulation through the induction of specific genes. To identify these genes, we have constructed a genome-wide rat ovarian gene expression database (rOGED). The database was constructed from total RNA isolated from intact ovaries, granulosa cells, or residual ovarian tissues collected from immature pregnant mare serum gonadotropin (PMSG)/human chorionic gonadotropin-treated rats at 0 h (no PMSG), 12 h, and 48 h post PMSG, as well as 6 and 12 h post human chorionic gonadotropin. The total RNA was used for DNA microarray analysis using Affymetrix Rat Expression Arrays 230A and 230B (Affymetrix, Santa Clara, CA). The microarray data were compiled and used for display of individual gene expression profiles through specially developed software. The final rOGED provides immediate analysis of temporal gene expression profiles for over 28,000 genes in intact ovaries, granulosa cells, and residual ovarian tissue during follicular growth and the preovulatory period. The accuracy of the rOGED was validated against the gene profiles for over 20 known genes. The utility of the rOGED was demonstrated by identifying six genes that have not been described in the rat periovulatory ovary. The mRNA expression patterns and cellular localization for each of these six genes (estrogen sulfotransferase, synaptosomal-associated protein 25 kDa, runt-related transcription factor, calgranulin B, alpha1-macroglobulin, and MAPK phosphotase-3) were confirmed by Northern blot analyses and in situ hybridization, respectively. The current findings demonstrate that the rOGED can be used as an instant reference for ovarian gene expression profiles, as well as a reliable resource for identifying important yet, to date, unknown ovarian genes.

Amphiregulin↗

PubMed2005

A quantitative model of tumor-induced angiogenesis in the nude mouse.

OBJECTIVE: Novel animal models allowing for the quantification of tumor-induced angiogenesis and cell migration may offer significant insight into the characterization and multidisciplinary treatment of brain tumors. In this study, we seek to establish such a model in tumor-bearing brain, allowing for a clear demarcation of primary and satellite tumor tissue in conjunction with precise quantification of cerebral microvasculature. METHODS: We used green fluorescent protein-transfected 9L-gliosarcoma cells stereotactically injected into the brain parenchyma of nude mice perfused with tetramethylrhodamine-dextran immediately before they were killed. New three-dimensional analytical software developed in our laboratory provided a quantitative analysis of laser-scanning confocal microscopy images of dextran-labeled cerebral microvessels. RESULTS: Our data confirm significant angiogenesis in tumor and brain adjacent to tumor. CONCLUSION: Because these highly infiltrative malignant brain tumors interdigitate with normal brain parenchyma through finger-like projections at the periphery of the solid tumor boundary, therapeutic options targeting tumor blood flow--combined with novel three-dimensional imaging to localize and track such interventions--may offer new hope for glioma management. To our knowledge, this system represents the first animal brain tumor model allowing for the precise colocalization and quantification of angiogenesis and tumor cell invasion, which may play an important role in the development of future therapy for brain tumors.

Animals↗

PubMed1997

Application of numerical descriptors to the characterization of wear particles obtained from joint replacements.

The application of image analysis techniques to the characterization of wear particles from failed joint replacements has been described. Wear particles were extracted from periprosthetic tissues collected during revision surgery. Chemical digestive methods were used to separate the wear particles from the biological soft material. The particles isolated were examined by optical and scanning electron microscopy. Digitized particle images were analysed on a Macintosh computer by a specially developed software and by the image analysis program 'Prism'. The following numerical descriptors were used to characterize the particles: particle size, boundary fractal dimension and shape parameters such as form factor, roundness, convexity and aspect ratio. Elemental composition of the particles was determined by energy dispersive X-ray spectroscopy. Three selected types of wear particles were analysed and compared: titanium (Ti)-based and calcium (Ca)-based particles from a hip prosthesis and ultra-high molecular weight polyethylene (UHMWPE) particles from a knee prosthesis. The particles exhibited significantly different sizes and their shape numerical descriptors were also different. From the results obtained it appears that computer image analysis of wear particle morphology can be employed to determine the wear processes occurring in the joints. In some cases, the condition of the joint can also be assessed based on this analysis.

Fractals↗

PubMed2003

Power Doppler ultrasound of rheumatoid synovitis: quantification of therapeutic response.

The aim of this study is to quantify power Doppler assessment of therapeutic response in rheumatoid synovitis. 13 patients (6 male, 7 female) with rheumatoid arthritis, who had an acute exacerbation of small joint synovitis in the hands, were examined with quantitative power Doppler, before and after intravenous corticosteroid treatment. All patients were examined by a single radiologist, using an ATL HDI 5000 ultrasound machine (ATL, Boswell). The images were analysed using a specially developed software package (HDI Lab), which quantifies power Doppler signal. All patients improved clinically following treatment, which was reflected in functional disability scores, and in the C-reactive protein levels and erythrocyte sedimentation rate. In all cases, there was a significant decrease in synovial vascularity as measured by the mean amplitude of signal on quantitative power Doppler. Quantitative power Doppler may allow objective assessment of treatment in small joint synovitis.

Aged↗

PubMed2006

Quantitative assessment of hip osteoarthritis based on image texture analysis.

A non-invasive method was developed to investigate the potential capacity of digital image texture analysis in evaluating the severity of hip osteoarthritis (OA) and in monitoring its progression. 19 textural features evaluating patterns of pixel intensity fluctuations were extracted from 64 images of radiographic hip joint spaces (HJS), corresponding to 32 patients with verified unilateral or bilateral OA. Images were enhanced employing custom developed software for the delineation of the articular margins on digitized pelvic radiographs. The severity of OA for each patient was assessed by expert orthopaedists employing the Kellgren and Lawrence (KL) scale. Additionally, an index expressing HJS-narrowing was computed considering patients from the unilateral OA-group. A textural feature that quantified pixel distribution non-uniformity (grey level non-uniformity, GLNU) demonstrated the strongest correlation with the HJS-narrowing index among all extracted features and utilized in further analysis. Classification rules employing GLNU feature were introduced to characterize a hip as normal or osteoarthritic and to assign it to one of three severity categories, formed in accordance with the KL scale. Application of the proposed rules resulted in relatively high classification accuracies in characterizing a hip as normal or osteoarthritic (90.6%) and in assigning it to the correct KL scale category (88.9%). Furthermore, the strong correlation between the HJS-narrowing index and the pathological GLNU (r = -0.9, p<0.001) was utilized to provide percentages quantifying hip OA-severity. Texture analysis may contribute in the quantitative assessment of OA-severity, in the monitoring of OA-progression and in the evaluation of a chondroprotective therapy.

Aged↗

PubMed1990

Three-dimensional reconstruction of the temporal bone.

Study of the complex anatomy and pathology of the temporal bone has traditionally used microscopy which permits analysis in only two dimensions. Recent advances in bioimaging technology have permitted visualization and reconstruction of computed tomography images in three dimensions. We have developed a technique that applies this technology in the imaging and reconstruction of human temporal bones. Data taken from serial histologic sections of the temporal bone are entered into a computer. The sections are edited and, through the use of specially developed software, a realistic three-dimensional reconstruction is produced. The reconstructed image can be rotated along any of three axes, and structures within the temporal bone can be isolated for more detailed analysis. Applications for the study of pathologic conditions of the temporal bone will be discussed.

Adult↗

PubMed1998

Trabecular bone mineral and calculated structure of human bone specimens scanned by peripheral quantitative computed tomography: relation to biomechanical properties.

The relationship of cortical bone mineral density (BMD), and geometry to bone strength has been well documented. In this study, we used peripheral quantitative computerized tomography (pQCT) to acquire trabecular BMD and high-resolution images of trabeculae from specimens to determine their relationship with biomechanical properties. Fifty-eight human cubic trabecular bone specimens, including 26 from the vertebral bodies, were scanned in water and air. Trabecular structure was quantitated using software developed with Advanced Visual Systems interfaced on a Sun/Sparc Workstation. BMD was also obtained using a whole-body computerized tomography scanner (QCT). Nondestructive testing of the specimens was performed to assess their elastic modulus. QCT and pQCT measurements of BMD of specimens in water were strongly correlated (r2 = 0.95, p < 0.0001), with a slope (0.96) statistically not significantly different from 1. Strong correlations were found between pQCT measurements of specimens in water and in air, for BMD (r2 = 0.96, p < 0.0001), and for apparent trabecular structural parameters (r2 = 0.89-0.93, p < 0.0001). Correlations were moderate between BMD and apparent trabecular structural parameters (r2 = 0.37-0.64, p < 0.0001). Precision as coefficient of variation (CV) and standardized coefficient of variation (SCV) for these measurements was < 5%. For the vertebral specimens, the correlation was higher between elastic modulus and BMD (r2 = 0.76,p < 0.0001) than between elastic modulus and apparent trabecular structural parameters (r2 = 0.58-0.72, p < 0.0001), while the addition of apparent trabecular nodes and branches to BMD in a multivariate regression model significantly increased the correlation with the elastic modulus (r2 = 0.86, p < 0.01). Thus, pQCT can comparably and reproducibly measure trabecular bone mineral in water or air, and trabecular structure can be quantitated from pQCT images. The combination of volumetric BMD with trabecular structural parameters rather than either alone improves the prediction of biomechanical properties. Such a noninvasive approach may be useful for the preclinical study of osteoporosis.

Adult↗

PubMed2006

Interactive approach to optical tweezers control.

We have developed software with an interactive user interface that can be used to generate phase holograms for use with spatial light modulators. The program utilizes different hologram design techniques, allowing the user to select an appropriate algorithm. The program can be used to generate multiple beams and can be used for beam steering. We see a major application of the program to be in optical tweezers to control the position, number, and type of optical traps.

Algorithms↗

PubMed2006

Diffusivity studies of transparent liquid solutions by use of digital holographic interferometry.

Real-time digital holography is used to study the diffusion process in transparent liquid solutions. Holograms of an object diffusively reflecting through an experimental cell containing diffusing solutions are recorded at different time instances. The recording medium is a CCD chip. The holographic interference of the object at two time instances is carried out numerically in a PC and is used to determine the diffusion coefficient. Holographic interferometric fringes can be displayed on a PC monitor in near real time. The software developed for this method determines the diffusion coefficients automatically. The calculated diffusion coefficients obtained with this method matched well with literature values.

Journal Article↗

PubMed2003

Spectral code index (SPECOIND): a general infrared spectral database search method.

A new spectral code that can be used by Relational Database Management Systems (RDBMS) as an index for infrared (IR) spectra searches in Relational Database (RDB) is presented and its suitability is evaluated. Spectral codes are constructed for all spectra in the database as the spectral indexes and three query strings are created with the same theory used for the creation of the index code for the query spectrum. Some effects of parameters used to create index strings and query strings are discussed. All spectral searches are accomplished in structured query language (SQL) approach and the utilization examples of SQL have been shown. The sequential application of this procedure can reduce the original library of about 18000 spectra to a few spectra that can be used as references for subsequent detailed comparison. The software developed for the proposed system is particularly suitable for spectral search and structure interpretation.

Algorithms↗

PubMed2005

Factors influencing survival following surgical treatment of obesity.

BACKGROUND: The prevalence of obesity in the United States and the surgical treatment of obesity have increased since 1999. An important measure of outcome following surgical treatment is survival. METHODS: This study began with data prospectively collected from Jan 1, 1986 to Dec 31, 1999 by 55 data collection sites, representing 77 surgeons who used standardized data collection software developed by the International Bariatric Surgery Registry (IBSR). A subset of 18,972 subjects was submitted to the National Death Index (NDI) for search of death occurring from Jan 1, 1986 to Dec 31, 2001. The univariate survival analysis included Kaplan-Meier plots and log-rank tests. Cox proportional-hazards (PH) frailty model was used to identify risk factors and estimate hazard ratios in a multi-factor survival analysis. Covariates included gender, operative age, body mass index, operation category (simple and complex), operation year, diabetes, smoking and hypertension as recorded prior to operation. RESULTS: Deaths were found for 3.45% of the patients (654/18,972). Average follow-up was 8.3 years. Age, gender, BMI, history of smoking, diabetes, and hypertension were significant predictors of survival. Operation category (P=0.13) and operation year (P=0.89) were not significant predictors of survival. CONCLUSION: Simple and complex operations were equally effective in keeping patients alive in this cohort of patients operated on for severe obesity from 1986 to 1999. Young, female, non-smoking patients with low BMI at operation and no history of diabetes or hypertension had the longest survival. Longer follow-up for death is needed before any recommendations can be made for operation category based on survival.

Adult↗

PubMed2003

In vivo measurement of apparent trabecular bone structure of the radius in women with low bone density discriminates patients with recent wrist fracture from those without fracture.

The purpose of this cross-sectional case-control study was to determine whether indices of bone structure at the 4% site of the radius discriminate women who have sustained a recent low-energy fracture of the contralateral distal radius (n = 21) from women with similar bone density and no history of fracture (n = 21). Images of the distal forearm were acquired using peripheral quantitative computed tomography (pQCT) and were analyzed using in-house-developed software to determine indices of trabecular bone structure (average hole size [H(A)], maximum hole size, and connectivity index). The same images were analyzed using commercial software to determine bone density, mass, geometry, and torsional strength. The fracture group had significantly larger H(A) (p = 0.03). No other bone variable differed between groups. Individual H(A) values were compared to the mean value for young adult women (n = 42). The odds ratio (95% confidence interval) associated with an H(A) >2 SDs above the young adult mean was 5.4 (1.2-24.3). Thus, estimation of in vivo trabecular bone porosity by measuring the average diameter of the pQCT-imaged marrow spaces in the ultradistal radius identifies individuals with low bone mass most at risk for osteoporotic fracture.

Bone Density↗

PubMed2005

Analysis of fetal breathing movements at 30-38 weeks of gestation.

AIMS: This study reports the changes in patterns of fetal breathing movements recorded with a photogrammetric method in three successive periods of gestation. METHODS: Respiratory movements were studied in fetuses of 28 healthy women with uncomplicated pregnancies of 30-38 weeks of gestation. Women were divided into three groups according to gestational age of the fetus: 30-32 weeks, 7 fetuses; 33-36 weeks, 9 fetuses; and 37-38 weeks, 12 fetuses. Sonographic images of the fetuses were recorded on videotape, digitized (1 image per 0.12 s) and analyzed with specially developed software. RESULTS: The proportion of fetuses in each age group for which movements were detectable was similar in all three groups, as was the frequency of movements. Duration of a complete respiratory cycle, the inspiratory phase and the expiratory phase tended to be shorter at 33-36 weeks of gestation than in younger and older fetuses. Fetuses in the 30-32-week group had slower breathing rates than fetuses in the two older groups. CONCLUSIONS: The photogrammetric technique revealed differences in some patterns of fetal breathing movements between weeks 30-32, 33-36 and 37-38 of gestation. The data provide a sound basis for relating changes in fetal breathing movements with physiological and anatomical changes that occur as the respiratory system matures.

Adolescent↗