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At least 739 records · Page 41Linked to original sources
PubMed2002

Loss of heterozygosity studies revisited: prior quantification of the amplifiable DNA content of archival samples improves efficiency and reliability.

Polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) studies of archival formalin-fixed, paraffin-embedded (FFPE) tumor tissues have become an important tool in the search for tumor suppressor genes and oncogenes and are also used increasingly in clinical practice. However, FFPE tissue samples may contain little amplifiable DNA, resulting in frequent reaction failures and unreliable LOH data. Using pairs of serial dilutions of reference DNA, we determined the minimum amplifiable DNA concentration necessary for reliable microsatellite-PCR LOH analysis. We then measured the amplifiable DNA content of a selection of frozen and FFPE-derived tumor specimens by real-time quantitative PCR. A minimum input of 600 pg of 100% amplifiable DNA per PCR was required for reliable LOH analysis. While the total DNA concentrations of all samples exceeded this figure, most FFPE-sample-derived DNA was non-amplifiable, with ratios of actually amplifiable DNA to total DNA as low as 1 to 3625. Many FFPE samples therefore contained substantially less than 600 pg/microl of actually amplifiable DNA, making them potentially unsuitable for LOH studies. Real-time quantitative PCR before LOH studies of FFPE tissues allows: identification of samples, which will fail microsatellite-PCR; exclusion of samples, which will yield unreliable results; and optimal adjustment of template input for the remainder. Amplification reactions undertaken without this precaution can result in unreliable LOH data.

DNA↗
PubMed2003

Effect of filmless imaging on utilization of radiologic services with a two-stage, hospital-wide implementation of a picture archiving and communication system: initial experience of a fee-for-service model.

A medium-sized general hospital using a fee-for-service model implemented a hospital-wide picture archiving and communication system (PACS) in two stages. This study evaluated the reporting time with filmless operation and the effect of filmless imaging on referring physicians' use of the radiologic service before and after completion of the second stage of PACS implementation. The relationship between the total number of hospital patients and the number of radiologic department patients was also evaluated. All sample images were retrieved from the PACS. All corresponding reports except for one for a computerized tomography study were available. The median reporting time for different studies performed during working hours was less than 2 hours. There was a significantly positive and linear relationship (p < 0.01) between the total number of hospital patients and the number of radiologic department patients after hospital-wide implementation of PACS. We conclude that the fee-for-service model had no negative impact on referring physicians' use of radiologic services in a filmless hospital.

Data Interpretation, Statistical↗
PubMed2006

Construction of gender-enriched cDNA archives for adult Oesophagostomum dentatum by suppressive-subtractive hybridization and a microarray analysis of expressed sequence tags.

In the present study, we constructed gender-enriched cDNA libraries for the adult stage of the parasitic nematode Oesophagostomum dentatum (order Strongylida) using suppressive-subtractive hybridization (SSH), sequenced clones from the female-library and male-library (480 from each) and conducted bioinformatic and microarray analyses of the expressed sequence tags (ESTs). In total, 873 ESTs (440 male and 433 female) were obtained, achieving a sequencing success of 91%The nucleotide sequences reported in this article (Tables 1-5) have been deposited in the EMBL, GenBank and DDJB databases under the Accession nos. AM157797-AM158083. Microarray analyses of 516 unique ESTs representing both gender-enriched libraries revealed differential hybridization for 391 of them (75.8%). Of these, 220 (56.3%) had significantly greater signal intensities in the female than in the male, and 154 (70%) of these were predicted to have homologues in C. elegans. These homologues were predicted to be involved in key biological processes, including embryonic nutrition, gametogenesis, molecular binding/transport or metabolism, nucleic acid synthesis and function, and signal transduction. Of the 171 ESTs with statistically higher signal intensities in male O. dentatum, 43.8% had homologues in C. elegans. These homologues included major sperm proteins (MSPs) or MSP-like molecules, keratin-like molecules, molecules involved in metabolism, PDZ domain-containing proteins, sugar binding proteins, protein kinases, serine proteases or protease inhibitors, molecules involved in proteolysis and other proteins, such as enzymes and various putative proteins. Of the 287 ESTs (from both gender-enriched cDNA libraries) with no known homologues in C. elegans, 50 (17.4%) had homologues in other nematodes, 8 had homologues in various other organisms and 104 (36.2%) had no homology to any sequence in current gene databases. The present study lays a foundation for the isolation and molecular, biochemical and functional characterization of selected genes from the gender-enriched cDNA archives established for O. dentatum.

Animals↗
PubMed1998

An assessment of picture archiving and communication systems (PACS). The case study of the SMZO Project. Socialmedizinischenes Zentrum Ost.

In order to make rational decisions for further implementation of picture archiving and communication systems (PACS) in Viennese community hospitals, an assessment of the Sozialmedizinisches Zentrum Ost (SMZO) project was launched by the Viennese community hospital financing body. The aim of the technology assessment was to look at the experiences of day-to-day practice, organizational aspects of, and obstacles to developing the full potential of the PACS installation. The study analyzes the conditions for employment of digital radiology, gathers the experiences of national and international projects, and presents a view on critical points, from which options for further implementation can be derived. In the center of interest stood work organization, handling and user attitudes, perceptions of radiologists and clinicians, realism of expectations regarding economic efficiency, technical aspects, and influence of quality of medical care.

Austria↗
PubMed2000

Estimating the impact of a diffuse technology on the running costs of a hospital. A case study of a picture archiving and communication system.

OBJECTIVES: This paper considers the methodological problems that arise in conducting cost analyses in economic evaluations where only observational (rather than experimental) data are available and where the technology being evaluated is diffuse, such that the unit of analysis has to be the institution rather than the patient. METHODS: A case study is reported that concerns the application of computer technology in radiology: picture archiving and communication systems (PACS). A range of different approaches were used to estimate changes in running costs, including time series analyses of routine data and direct observation of resource use. RESULTS: The analysis illustrates some of the difficulties involved in costing the introduction of a diffuse technology. Nevertheless, it provides a firm indication that, overall, the introduction of PACS was found to be associated with a significant increase in hospital costs, suggesting that the initial expectations of financial savings were unduly optimistic. CONCLUSIONS: The research demonstrates that, using multiple methods, it is possible to estimate cost changes within a single hospital. In addition, the paper discusses the nature of the uncertainties in such analyses and possible ways of representing such uncertainty in terms of confidence intervals.

Budgets↗
PubMed2005

Toward a multidimensional assessment of picture archiving and communication system success.

OBJECTIVES: Based on a prevalent framework in the information systems field, this study proposes and describes an integrated model for evaluating picture archiving and communication system (PACS) success from multiple users' perspectives. METHODS: Our study details the validation process of the proposed model at a large tertiary-care teaching hospital in Canada. Both qualitative and quantitative data were collected to assess the psychometric properties of the measurement instrument and test the research hypotheses. RESULTS: Our findings clearly reveal that radiologists, technologists, and clinicians have different views regarding the factors influencing PACS success. For instance, the results for radiologists show that their concern with efficiency and productivity is best guaranteed by a system that is reliable and easy to use. Furthermore, that only perceived system usefulness influenced clinicians' satisfaction with PACS is a reflection of the primary impact that technology has on their work, namely, the ability to have instant access to images from any point in the hospital. Even though, overall, all three groups view the adoption of PACS positively, the mean scores indicate that radiologists and technologists seem to be more satisfied and their expectations to be met at a higher level than clinicians. CONCLUSIONS: We believe the measurement instruments developed in this study can be used as a diagnostic tool by project managers interested in better understanding the extent to which different groups of stakeholders perceive the deployment of PACS as being successful and how factors influencing perceptions of PACS success vary across user types.

Data Collection↗
PubMed1998

Detection of Giardia Trophozoites in Archival Pathology Specimens of Human Small Intestine.

: The examination of archival pathology specimens of human small intestine by light microscopy, field emission scanning electron microscopy (FESEM), and confocal scanning laser microscopy using fluorescent in situ hybridization (FISH) techniques was undertaken to better understand the epidemiology of Giardia. Giardia trophozoites were tentatively identified in the light microscope after hematoxylin and eosin (H&E) staining. The organisms were adherent to the intestinal epithelium where they were also associated with strands of mucus within the lumen. Fluorochrome-conjugated antisense oligonucleotide probes, developed for the 16S rRNA of Giardia lamblia and Giardia muris, were used in FISH experiments with confocal scanning laser microscopy. Positive identification of trophozoites could be obtained with the G. lamblia probe, but not with the G. muris probe. FESEM examination of serial sections adjacent to FISH-stained sections revealed trophozoites characterized by their morphological features. The 16S rDNA probes specifically distinguished different species of Giardia, but whether multiple infections can occur within an individual host could not be determined.

Journal Article↗
PubMed2002

Polymerase chain reaction amplification of DNA from aged blood stains: quantitative evaluation of the "suitability for purpose" of four filter papers as archival media.

In collaboration with the Armed Forces Institute of Pathology's Department of Defense DNA Registry, the National Institute of Standards and Technology recently evaluated the performance of a short tandem repeat multiplex with dried whole blood stains on four different commercially available identification card matrixes. DNA from 70 stains that had been stored for 19 months at ambient temperature was extracted or directly amplified and then processed using routine methods. All four storage media provided fully typeable (qualitatively identical) samples. After standardization, the average among-locus fluorescence intensity (electropherographic peak height or area) provided a suitable metric for quantitative analysis of the relative amounts of amplifiable DNA in an archived sample. The amounts of DNA in Chelex extracts from stains on two untreated high-purity cotton linter pulp papers and a paper treated with a DNA-binding coating were essentially identical. Average intensities for the aqueous extracts from a paper treated with a DNA-releasing coating were somewhat lower but also somewhat less variable than for the Chelex extracts. Average intensities of directly amplified punches of the DNA-binding paper were much larger but somewhat more variable than the Chelex extracts. Approximately 25% of the observed variation among the intensity measurements is shared among the four media and thus can be attributed to intrinsic variation in white blood count among the donors. All of the evaluated media adequately "bank" forensically useful DNA in well-dried whole blood stains for at least 19 months at ambient temperature.

Blood Stains↗
PubMed2005

Archiving and absolute quantitation of solutes separated by single charged droplet coulomb explosion.

The electrospray (ES) ion source relies on the transfer of low-volatility solutes to the gas phase as an outcome of coulomb explosion events of charged droplets generated by electrical atomization. Introduced here are two methods for archiving compounds separated by coulomb explosion of single droplets having net charge that had been levitated in an electrodynamic balance. We categorized compounds separated by the explosion as either material ejected, including progeny droplets, or the material retained in the main residue. The potential for this methodology is illustrated by (i) qualitative characterization of solute states, aqueous versus precipitated in the separated material, and (ii) absolute quantitation of solutes separated by such an event. For a droplet containing 5 x 10(7) 20-nm-diameter fluospheres, its first encountered coulomb explosion event resulted in the ejection of 1.70% of them. The capability to acquire such detailed information regarding the individual steps in the process of transferring low-volatility solutes to the gas phase in an ES ion source is essential to develop strategies for absolute quantitation in applications of ES mass spectrometry.

Journal Article↗
PubMed2004

Determination of hereditary mutations in the BRCA1 gene using archived serum samples and capillary electrophoresis.

Analysis of DNA variation in biological samples most frequently utilizes the polymerase chain reaction (PCR) performed on extracted genomic DNA, followed by visualization of alleles using various methodologies. Few reports have demonstrated that amplification of DNA from plasma and serum samples is possible. We have performed DNA amplification on a large set of serum samples (n = 2955). Here, we report that known hereditary mutations in the BRCA gene can efficiently be analyzed in serum samples collected and stored over several decades. Fragments were PCR-amplified following a short initial denaturation of the serum sample in a standard microwave oven. Fragment analysis was subsequently performed using a DNA capillary-sequencing instrument. The PCR success rates were fragment- and size-dependent ranging from 83.2% to 97.9%. Of the 11,820 polymerase chain reactions performed, the overall PCR success rate was 91.3% (10,796/11,820), which is comparable to PCR performed on genomic DNA. The advantage of the method described herein is its ability to utilize archival material stored in serum biobanks for long periods of time.

Base Sequence↗
PubMed2006

Antigen-epitope retrieval to facilitate proteomic analysis of formalin-fixed archival brain tissue.

Formalin is a routine fixative facilitating tissue preservation and histopathology. Proteomic techniques require freshly frozen specimens, which are often difficult to procure, and methods facilitating proteomic analysis of archival formalin-fixed brain tissue are lacking. We employed antigen-epitope-retrieval principles to facilitate proteomic analysis of brain tissue that had been fixed and stored in formalin for 3-7 years. Twenty-micrometer-thick cryopreserved OCT-embedded sections from inferior temporal cortex of human (7 years in formalin) or mouse brain specimens (3 years in formalin) were hematoxylin-/eosin-stained. Approximately 16-64-mm2 areas of the tissue sections were manually scraped off slides, or approximately 2 mm2 of human brain cortex was captured off membrane-coated slides using laser microdissection. Tissue was treated using various pH and temperature conditions prior to trypsin digestion and nano-LC-MS/MS. The largest number of proteins were retrieved by solubilization at pH 9 at 95 degrees C for 1 h; treatments at pH 4 or 6 at 25 or 65 degrees C were generally ineffective. Three-year formalin-fixed murine tissue did not yield more proteins compared to human tissue. Use of formalin-fixed tissue for proteomics is an invaluable tool for medical research. The combination of proteomics and microdissection enables selective enrichment and identification of novel, unique, or abundant proteins that may be important in pathogenesis.

Animals↗
PubMedDate not supplied

From knowledge generation to knowledge archive. A general strategy using TOPS-MODE with DEREK to formulate new alerts for skin sensitization.

A general strategy for knowledge flow concerning skin sensitization based on the combined use of TOPS-MODE and DEREK expert system is proposed. TOPS-MODE is used as a knowledge generator, while DEREK represents the knowledge archive. A TOPS-MODE classification model allows the identification of structural fragments and groups responsible for strong/moderate skin sensitization. These structural contributions are sorted, analyzed, and graphically displayed in an appropriate way allowing the identification of several structural alerts for skin sensitization. Nine structural alerts already implemented in DEREK are identified using this strategy. They comprise, among others, alkyl halides, aldehydes, alpha,beta-unsaturated compounds, aromatic amines, phenols, hydroquinone, isothiazolinone, and alkyl sulfonates. Four new hypotheses are generated using TOPS-MODE structural contributions to skin sensitization, which are not recognized as structural alerts by DEREK. They include the reduction of aromatic nitro groups and epoxidation reaction of double bonds as metabolic activation steps that can lead to reactive haptens which can trigger the skin sensitization mechanism. Another new alert is based on 1,2,5-thiadiazole-1,1-dioxide for which we have identified a possible mechanism explaining its strong skin sensitization profile. It is based on the existence of a tautomeric equilibrium and further reaction with nucleophiles, which are both supported by experimental evidence. Finally, we have identified a possible new mechanism for the skin sensitization of nonreactive compounds, which involves the formation of noncovalent complexes with proteins in a processing- and metabolism-independent way.

Journal Article↗
PubMed2001

Organochlorine pesticide residues in archived UK soil.

Archived background soils ("Broadbalk', 1944-1986) and sludge-amended soils ("Luddington", 1968-1990), collected from long-term agricultural experiments in the UK, were analyzed for a range of organochlorine (OC) pesticides to establish trends over time. Concentrations typically ranged from 0.1 to 10 ng/g of soil (dry weight), with gamma-hexachlorocyclohexane (gamma-HCH), dieldrin, and p,p'-DDE consistently having the highest concentrations. The trends in the Broadbalk background soils are largely consistent with usage patterns, with peak concentrations occurring in the 1960s for DDTs and between the 1960s and the 1980s for the other OCs. In the Luddington control and sludge-amended soils, several of the OCs show a significant decline in concentrations from the late 1960s to 1990, with half-lives ranging from approximately 7 years (alpha-HCH) to approximately 25 years (dieldrin). The sludge-amended plot received 125 tonnes of sludge per ha in 1968, which was mixed in to a depth of 15 cm. It appears that the sludge treatment had little effect on concentrations in the soil, with no significant difference between control soil and sludge-amended soil for most compounds, except for HCB, p,p'-DDE, and dieldrin. Enantiomeric fractions (EFs) of some chiral pesticides (alpha-HCH, cis- and trans-chlordane, and o,p'-DDT) were determined in the Luddington soils. Results reveal that enantioselective degradation of OC pesticides is occurring in these soils for trans-chlordane (TC) and cis-chlordane (CC). However, the depletion over time is not statistically significant, and there is no statistically significant difference between EFs in the control soil and sludge-amended soil. This indicates that enantioselective microbial degradation was not consistent over time and that the addition of sludge to soil did not significantly alter the enantiomeric preference of the microbial community.

Agriculture↗
PubMed2002

Historical trends in the lead isotopic composition of archival Sphagnum mosses from Scotland (1838-2000).

The analysis of almost 200 Scottish Sphagnum moss samples collected over the past 170 years has revealed trends in the isotopic composition of lead similar to those previously established for dated Scottish lake sediments and peat bogs, lending credibility to these proxy records of atmospheric lead contamination and deposition. The effect of temporal variations in contributions from sources such as smelting of indigenous lead ores (206Pb/207Pb approximately 1.16-1.18), coal combustion (206Pb/207Pb approximately 1.17-1.19), and the use of imported Australian lead (206Pb/207Pb approximately 1.04) was clearly seen in the Scottish moss 206Pb/207Pb record. This showed some differences from the corresponding archival herbage record for the south of England, where the initial influence of Australian lead occurred earlier, at the end of the 19th century. A significant decline from a 206Pb/ 207Pb value of approximately 1.17 in the Scottish moss record began in the 1920s and continued until the 1980s (206Pb/207Pb approximately 1.12). The success of measures to reduce lead emissions to the atmosphere over the past 20 years in the U.K., in particular from petrol-engined vehicles using alkyl lead additives manufactured primarily from Australian lead, is evident in both the increasing 206Pb/207Pb ratio and falling lead concentration data for Scottish moss.

Bryopsida↗
PubMed2002

Brominated flame retardants in archived serum samples from Norway: a study on temporal trends and the role of age.

The temporal trends and influence of age and gender on levels of selected brominated flame retardants (BFRs) in human serum have been assessed by analyzing archived samples from Norway. Serum from 40 to 50 year old men collected at six time periods during 1977 to 1999 and from eight groups of differing age and gender sampled in 1998 were pooled into six and eight samples, respectively. The BFRs were isolated using solid-phase extraction (SPE) and the serum lipids decomposed bytreatmentwith concentrated sulfuric acid directly on the polystyrene-divinylbenzene SPE column, prior to elution of the BFRs. Following diazomethane derivatization, the samples were analyzed by gas chromatography-electron capture mass spectrometry. Eight BFRs were quantified in the serum samples: 2,4,4'-tribromodiphenyl ether (BDE-28), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), 2,2',4,4',5-pentabromodiphenyl ether (BDE-99), 2,2',4,4',6-pentabromodiphenyl ether (BDE-100), 2,2',4,4',5,5'-hexabromodiphenyl ether (BDE-153), 2,2',4,4',5,6'-hexabromodiphenyl ether (BDE-154), 2,4,6-tribromophenol (TriBP), and tetrabromobisphenol A (TBBP-A). The serum concentrations of all the BFRs, increased during the entire period with the exception of TriBP, and the sum of the six polybrominated diphenyl ethers increased from 0.44 ng/g lipids in 1977 to 3.3 ng/g lipids in 1999. The BFR concentrations in the serum from the different age groups were relatively similar, except for the age group 0-4 years, which had 1.6-3.5 times higher serum concentrations. Women older than 25 years had lower serum concentrations of BFRs compared to the corresponding group of men. No trend related to age or gender, nor time during the period 1977 to 1999 was observed for TriBP. The present study indicates an ongoing increase in human exposure to BFRs, and the current body burden appears to be independent of age, except for infants (0-4 years old), who seem to experience elevated exposure.

Adolescent↗
PubMed2005

Time trends of atmospheric PBDEs inferred from archived U.K. herbage.

Aerial portions of vegetation receive the bulk of their burden of persistent organic pollutants (POPs) from the atmosphere. Vegetation can therefore be a useful indicator of the changing atmospheric burden of POPs. Samples of archived pasture, collected from Rothamsted Experimental Station in the United Kingdom between 1930 and 2004, were analyzed for a range of polybrominated diphenyl ethers (PBDEs). PBDEs could not be routinely detected in the pre-1970 samples. Thereafter, the dominant congeners BDE 28, 47, 49, 99, 100, 153, 154, and 183 were frequently detected. The general trend was (a) a rise through the 1970s; (b) a minipeak in the mid-1980s, strongly influenced by one particularly high sample for 1984; (c) values remaining high through the late 1980s/1990s; (d) an indication of a more recent decline for all congeners (except BDE-28), consistent with recent restrictions on PBDE usage in Europe. These trends were compared to recent modeled estimates of U.K. PBDE emissions. The congener profiles of technical mixtures, U.K. air, soil, and pasture were compared and shown to be broadly similar. The implications for environmental release mechanisms are discussed.

Air Pollutants↗
PubMed1998

Replacement of cinefilm with a digital archive and review network.

The replacement of cinefilm with digital cardiac angiography has accelerated significantly in recent years with the development and widespread adoption of the DICOM standard for interchange of procedure image data. While the acceptance of the Compact Disk-Recordable (CD-R) media has provided the opportunity for numerous laboratories to eliminate cinefilm in all its functions, the task is more complex for larger catheterization laboratories which require the use of high speed networks and automated libraries. The Cardiac Laboratory at the Mayo Clinic has implemented the final stages of a large-scale network and archive which meets a large institution's demanding requirements for access, speed, and storage for high volumes of digital cardiac angiographic images. Initial experience with the system demonstrates that this approach will be a successful one for the elimination of cinefilm and the employment of digital imaging and networking technology. In addition, direct access to digital image records will also facilitate the integration of image data with other clinical information acquired and stored in a digital format.

Cardiac Catheterization↗