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At least 721 records · Page 40Linked to original sources
PubMed1984

Computer-aided strategies for archive retrieval and sensitivity enhancement in the identification of drugs by photodiode array detection in high-performance liquid chromatography.

An archive retrieval algorithm for high-performance liquid chromatography with UV detection (HPLC-UV) has been developed for the first time for the rapid identification of spectra acquired by rapid-scanning photodiode array detection in HPLC. The algorithm is based on a database of spectra (normalised with respect to area), inverse files of key spectral features, a selective search window, with parabolic weighting factors and least-squares comparison of test and retrieved spectra. The performance of the library search system is demonstrated with respect to a small library of solutes, including: cortisone acetate, ethynyl estradiol, ethisterone, progesterone; caffeine, theobromine, theophylline and 8-chlorotheophylline; morphine and diamorphine; and cycloserine. Since photodiode array detection operates in the domains of both wavelength and time, to generate a matrix of (A, lambda, t) data, the optimum conditions for sensitivity enhancement by ensemble averaging in these domains have been examined. At a given observation wavelength, increase in the detector bandwidth (or "diode bunching") yields a value of delta lambda which gives optimum sensitivity; this value is systematically related to the spectral bandwidth of the analyte. Sensitivity can also be optimised by varying the integration period in the time domain. Sensitivity can be further increased by combination of these instrumental optima, for which there is evidence of dependence on the particular instrument design. Response was found to be linear for detector bandwidths up to twice the optimum value. The comparative sensitivity of some commercially-available photodiode array detectors has been assessed relative to that of conventional detectors under strictly controlled conditions.

Chromatography, High Pressure Liquid↗
PubMed1997

Standardization of a single-cell assay for sensitive detection of multidrug resistance protein expression in normal and malignant cells in archival clinical samples.

Multidrug resistance protein (MRP), like P170, confers multidrug resistance, but its clinical relevance is uncertain, whereas P170 is an accepted cause of chemotherapy failure for which ongoing reversal trials are being conducted. Because such trials have been only modestly successful, we must investigate alternative drug resistance mechanisms such as MRP, which is poorly blocked by P170 inhibitors. The significance of MRP has remained undefined because MRP mRNA is difficult to assay in archival material, does not necessarily reflect MRP levels, and is widely expressed in normal or hematopoietic cells within tumors and bone marrow. Because conventional immunoblot or immunocytochemistry may not be sensitive enough to detect low or heterogeneous MRP expression in clinical samples, we elected to score MRP in single tumor cells by modifying our P170 assays that have proven valuable for correlating P170 expression with the outcome of pediatric cancer chemotherapy. We enhanced the signal-to-noise ratio with several peroxidase-tagged secondary antibody layers and staining refinements, standardizing the assay with MRP-negative and MRP-positive but P170-negative transfected or drug-selected controls in which MRP was quantified by immunoblot. We confirmed sensitivity by staining a very low MRP-expressing revertant line and "mixed" samples containing small numbers of positive cells; we confirmed specificity by applying two antibodies directed against separate MRP epitopes. We examined neuroblastoma, osteosarcoma, rhabdomyosarcoma, and retinoblastoma samples, identifying MRP-positive malignant cells, which were distinguishable from MRP-positive normal cells. This assay may be valuable for early diagnosis of low but potentially important MRP expression, which would allow timely application of alternative therapy, perhaps with MRP-specific blockers.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2003

A database of archived drilling records of the drill cuttings piles at the North West Hutton oil platform.

Drill cuttings piles are found underneath several hundred oil platforms in the North Sea, and are contaminated with hydrocarbons and chemical products. This study characterised the environmental risk posed by the cuttings pile at the North West Hutton (NWH) oil platform. Data on the drilling fluids and chemical products used over the platform's drilling history were transferred from archived well reports into a custom database, to which were added toxicological and safety data. Although the database contained many gaps, it established that only seven chemical products used at NWH were not in the lowest category of the Offshore Chemicals Notification Scheme, and were used in only small quantities. The study therefore supports the view that the main environmental risk posed by cuttings piles comes from hydrocarbon contamination. The (dated) well records could help future core sampling to be targeted at specific locations in the cuttings piles. Data from many platforms could also be pooled to determine generic 'discharge profiles.' Future study would benefit from the existence, in the public domain, of a standardised, 'legacy' database of chemical products.

Databases, Factual↗
PubMed1998

Numerical abnormalities of chromosomes 1 and 10 in endometrial adenocarcinoma: fluorescence in situ hybridization analysis of 23 archival paraffin-embedded samples.

Retrospective analysis of chromosomal changes in endometrial carcinoma was performed by fluorescence in situ hybridization on free nuclei isolated from formalin-fixed paraffin-embedded tissue. We examined 23 archival samples for numerical aberrations of chromosomes 1 and 10 with the use of specific DNA probes for the pericentromeric and centromeric regions of these two chromosomes. Numerical aberrations of chromosomes 1 and 10 were detected in 39% of the case analyzed, and the frequency of trisomy 10 tended to increase as the histological grade worsened. Our findings confirm the association of cytogenetic anomalies involving chromosomes 1 and 10 with endometrial carcinoma, as reported by other studies, and suggest that changes in centromere 10 copy number may correlate with the degree of tumor differentiation.

Adult↗
PubMed2004

HeiDATAProVIT-Heidelberg data archiving, tag assembling, processing and visualization tool.

The demands that have to be met by software tools for biomedical data evaluation strongly differ depending on the background of their application. In clinical routine emphasis is placed on ease of handling and application of standardized procedures, whereas in biomedical research the main focus lies on flexibility and extensibility. These contradictory requirements are reflected by the design principles of existing software solutions: programs for routine application are barely extensible or modifiable by the user and the complexity of highly flexible data processing tools for research purposes hampers the application of new methods to larger data volumes. This gap poses technical difficulties to the transfer of methods from research into clinical routine. The software we present in this paper bridges this discrepancy by incorporating two different levels of application. The lower level offers options to integrate custom written MATLAB((R)) processing routines and to add new evaluation schemes to a pool of existing procedures. The higher level allows for performing standard evaluations by accessing and applying these previously defined procedures. Four basic concepts were introduced to ensure that the program is both maximally flexible on a lower level and readily applicable on a higher level: the tag concept, the concept of modularized visualization, the dummy file concept, and the batchjob concept. These concepts are the key to flexibly assemble and apply the three universal stages of data evaluation: (1) archiving of acquired data, (2) processing the data using signal processing algorithms and (3) visualizing the results in appropriate graphical formats. The present paper illustrates the four concepts within the two levels of the software architecture. The basic functionality and usefulness of the program are demonstrated using an evaluation of gait analysis data as sample application. In summary, this software tool closely integrates a database for biomedical datasets and an extensible pool of evaluation and visualization procedures realized using MATLAB((R)). It is well suited both for data processing in clinical routine and for evaluation of measurement data in any medical research project.

Information Storage and Retrieval↗
PubMed1999

Novel somatic mutations in the VHL gene in Swedish archived sporadic renal cell carcinomas.

Frequent loss-of-function somatic mutations of the VHL gene have been detected in sporadic renal cell carcinoma (RCC), indicating that inactivation of the VHL gene plays a critical role in RCC. In this study, we collected 35 archived Swedish sporadic RCCs identified from an epidemiological study on occupational exposure and kidney cancer to test how well stored pathological specimens could be retrieved and analyzed for VHL mutations. Thirty specimens were successfully analyzed with PCR-SSCP and sequencing. Aberrant SSCP bands were detected in 16 out of the 30 samples (53%). Sequencing analysis of the aberrant bands revealed seven deletions, one insertion, one base substitution on a splicing site, six missense mutations, one silent mutation and several base substitutions in the 5' non-coding region and intron 1. Most were novel somatic mutations that have not been reported in sporadic RCC. The mutations were found in three types of non-papillary RCC cases, i.e. 14 clear cells, one granular chromophilic and one sarcomatoid RCC. Interesting multiple mutations were found in three cases (5, 3, 2 mutations, respectively).

Adult↗
PubMed1994

DNA ploidy in carcinoma of the gallbladder. Prognostic significance and comparison of flow and image cytometry on archival tumor material.

The aim of this investigation was to determine whether the cytometrically assessed DNA ploidy is a parameter of prognostic significance in gallbladder carcinomas. For this purpose the DNA content of tumor cells from archival tumor material from 80 patients with cholecystic cancer was analysed retrospectively by using comparatively different cytometrical methods, namely flow cytometry (FCM) and image cytometry, using tissue sections (ICM-S) and nuclear suspensions (ICM-N). Conventional tumor classifications (according to pTNM and Nevin) were able to predict the further clinical course. DNA ploidy showed a statistically significant correlation only to histological grade (P < 0.001), but not to tumor stage and survival. Only a trend towards a poorer outcome for patients harboring non-diploid tumors became evident especially when no residual tumor was present postoperatively (R 0-stage; P = 0.08). The different cytometrical methods discussed in detail, showed a highly significant concordance in the determination of DNA index values (DI) and in the classification of the tumors as either diploid or non-diploid. In conclusion, our results indicate that cytometrical determination of DNA ploidy provides no further prognostic informations in gallbladder carcinomas as compared to conventional tumor staging.

Aged↗
PubMed2002

Archived or directly swabbed latent fingerprints as a DNA source for STR typing.

Former studies [Nature (1997) 387, Electrophoresis 20 (1999) 2870, P. Van Renterghem, D. Leonard, C. De Greef, Progress in Forensic Genetics, Vol. 8, 2000, p. 501, J. Forensic Sci. 45 (3) (2000) 687] have shown that even a single skin contact, documented by a latent fingerprint, can transfer enough DNA for a genetic analysis. It was proven in these studies that it is possible to swab fingerprints from surfaces [Nature (1997) 387, Electrophoresis 20 (1999) 2870, P. Van Renterghem, D. Leonard, C. De Greef, Progress in Forensic Genetics, Vol. 8, 2000, p. 501] and use them as a DNA source. Usually, however, discovered fingerprints are removed with scotch tape and placed on evidence cards for further investigation.In this study, we tried to assess the potential use of latent fingerprints as a DNA source for STR typing. The materials (magnetic powder, soot powder and scotch tape) used for visualization and archiving fingerprints in Germany were tested for their PCR inhibitory characteristics. Then, fingerprints were placed on clean glass surfaces, visualized and tested for their usefulness as a DNA source. Obtained DNA was quantified and tested in an STR system. Partly it proved possible to type fingerprints taken directly from the surface as well as fingerprints removed from the surface with scotch tape.

DNA Fingerprinting↗
PubMed2000

The impact of a picture archiving and communication system (PACS) upon an intensive care unit.

OBJECTIVE: The aim of the study was to assess the effect of the introduction of PACS (Picture Archiving and Communication System) upon image availability in an Intensive Care Unit (ICU) and the consequent impact upon the behaviour of the ICU physicians, in terms of the initiation of image-based clinical actions. DESIGN: A before and after study was used to compare the speed of image availability prior to, and following, the implementation of a hospital-wide PACS. SETTING: The research was part of an economic evaluation of PACS at Hammersmith Hospital, West London. PATIENTS AND PARTICIPANTS: All ICU patients who were X-rayed during two pre-PACS and one post-PACS data collection periods were included within the study. MEASUREMENTS: The times of: the X-ray request; acquisition; availability on ICU; and of any image-based clinical action taken by the ICU physician were recorded by radiographers and ICU physicians. RESULTS: PACS significantly reduced the time between request and image availability on ICU for routine X-rays but did not have any measurable impact upon the time clinical actions were initiated by ICU physicians. The data on non-routine images were statistically inconclusive. CONCLUSIONS: This study shows that PACS significantly improves the speed of delivery of routine images to the ICU, but it appears that the instigation of image-based clinical actions is determined by other organisational factors in ICU, such as ward rounds, rather than the availability of the image for viewing. Further work is required on non-routine X-rays to clarify the impact of PACS on physician behaviour in clinically urgent situations.

Humans↗
PubMed1999

A hospital-wide picture archiving and communication system (PACS): the views of users and providers of the radiology service at Hammersmith Hospital.

OBJECTIVE: To obtain users' views of the new picture archiving and communication system (PACS) from clinical and radiological staff at Hammersmith Hospital, UK. METHODS: Semi-structured interviews were used to ascertain the views of staff, following an interview schedule which covered aspects of: (1) their use of PACS, (2) facilities available, (3) the perceived quality of images, (4) reporting, (5) image availability, (6) image accessibility, (7) training, and (8) ease of use of PACS. RESULTS: Interviews were carried out with 34 key users and providers of the radiological service at Hammersmith Hospital. Overall, staff were very satisfied with PACS particularly in terms of image availability. All staff said that they preferred PACS to the previous, conventional radiology service. CONCLUSIONS: The key implications of issues raised by staff were: the impact of 'down-time' and the importance of an efficient back-up system, the requirement for sufficient short-term storage to prevent images being off-line during clinical situations, the usefulness of the folder system for management of the images, the need to access images for teaching purposes, the advantage of having a default display protocol to facilitate radiological reporting, and the requirement for flexible, yet effective, training to ensure that the system is utilised to its full potential by users.

Attitude of Health Personnel↗
PubMedDate not supplied

Fast image accessing based on an analysis of the picture archiving and communications system in Kochi Medical School.

A large-scale picture archiving and communication system was developed by Kochi Medical School. Using JPEG to achieve 90% compression, this system was capable of storing several years worth of CT and MR examination records and eliminated the bottleneck in conventional systems caused by slow data access in the filing system. Under the new system, access of image files from client PCs was checked for bottlenecks. The image file retrieval from the image database on the server was found to require the longest time. Two methods were considered to eliminate this bottleneck. One was a multiimages filing into a file. Another was an image transmission with multiparallel transmission sessions, which is proposed in this article. By adopting the latter method, the system can transmit 50 CT images from the image database server to a client PC in about 10 s.

Humans↗
PubMedDate not supplied

Prevalence of HPV in premalignant and malignant cervical lesions in Greenland and Denmark: PCR and in situ hybridization analysis on archival material.

Archival formalin-fixed paraffin-embedded cervical specimens from 125 women in Greenland and 139 women in Denmark who had CIN I-III or cervical cancer diagnosed between 1983 and 1987 were analysed for human papillomavirus type 16 (HPV-16) by in situ hybridization and for HPV-16, 18, 31, 33, 35 and 45 by PCR. In situ hybridization analysis showed an HPV-16 prevalence of 17% (16/95) and 23% (24/105) in the premalignant lesions from Greenland and Denmark, respectively. The HPV-16 prevalence rate in the cancer specimens was 10% (3/30) in the samples from Greenland and 29% (10/34) in the Danish specimens. A total of 82 Greenlandic and 107 Danish specimens were beta-globin-positive by PCR reaction. HPV-16-specific PCR on these samples showed 63% (34/54) of the Greenlandic and 68% (50/74) of the Danish preinvasive lesions to be positive. The corresponding HPV-16-positive rates for the invasive cancers were 82% (23/28) for Greenland and 70% (23/33) for Denmark. This study of patient samples supports our previous population-based studies in which similar HPV-detection rates were found among random samples of women from Greenland and Denmark, although Greenland has a 4-5-fold higher cervical cancer incidence.

Adult↗
PubMed1997

BRCA1 mutations found in archived early onset breast tumours.

Inherited mutations in the BRCA1 gene are thought to account for approximately 5% of breast cancers in women under the age of 45 years. In order to determine whether mutations could be found at the expected frequency, 60% of the protein coding region of BRCA1 was screened in 75 archived early-onset breast tumours, taken from women under 45 years of age. Two of the 75 tumours (2.7%) had detectable mutations, in close agreement to that predicted. Since BRCA1 mutations found in breast tumours are invariably germline, two immediate consequences are apparent. Firstly, family members of affected patients are likely to carry mutations as well, and should be considered for BRCA1 screening; and secondly, persons harbouring a germline BRCA1 mutation should be examined frequently and indefinitely for new primary tumours in remaining breast tissue.

Adult↗
PubMed1998

Expression of MDR1 mRNA and encoding P-glycoprotein in archival formalin-fixed paraffin-embedded gall bladder cancer tissues.

The aim of this study was to examine the expression of P-glycoprotein (Pgp) and MDR1 mRNA, in gall bladder carcinoma, a chemo-resistant tumour. 26 cases of gall bladder cancer and nine samples of normal gall bladder archival paraffin blocks were investigated for the presence of Pgp protein with immunohistochemistry (IHC) and MDR1 RNA by reverse transcription-polymerase chain reaction (RT-PCR). Monoclonal antibodies JSB-1 and UIC-2, recognising separate epitopes of Pgp, were used for IHC. For RT-PCR, total RNA was extracted from paraffin-embedded tissue. After RT, the samples were subjected to nested PCR (NPCR) using primers specific for the MDR1 gene, and evaluated by electrophoresis. In gall bladder carcinoma, the percentage of positive cases expressing Pgp (77% for JSB-1, 69% for UIC-2) and MDR1 mRNA (52%) was significantly higher than those in normal gall bladder. In earlier TNM stages Pgp and MDR1 mRNA were more frequently expressed (non-significant) than in advanced stages. The results of this study suggested that overexpression of MDR1 mRNA and Pgp in gall bladder carcinoma tissue probably is a very important reason why gall bladder cancer is generally not responsive to chemotherapy.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2001

Photosensitizer initiated attacks on DNA under dry conditions and their inhibition: a DNA archiving issue.

Long-term aging of dry DNA is thought to be due to the attack of diverse cascades of reactive species with probably, no one single initiator of the cascades explaining all circumstances. Photosensitizer-initiated reactions from methylene blue and riboflavin were used to generate two model systems of reactive species around dry DNA in order to understand such systems and how to block them. Damage was assessed using plasmid DNA as a substrate with an in-situ microgel electrophoretic technique. Photodynamic methylene blue damage to DNA was very oxygen dependent but not that of riboflavin. This indicates that indirect type II pathways, probably via singlet oxygen were important for methylene blue but not for riboflavin. In both the absence and presence of oxygen, the DNA protection offered by dry caffeine and urate to both photodynamic agents indicated that most DNA attack was via electrophilic species. Overall, protection of dry archived DNA from spontaneously reactive species such as free radicals appears to be a real issue and, as expected, the predominant species in air appear to involve oxygen but not exclusively or necessarily so.

DNA↗
PubMed2004

Financing a large-scale picture archival and communication system.

RATIONALE AND OBJECTIVES: An attempt to finance a large-scale multi-hospital picture archival and communication system (PACS) solely based on cost savings from current film operations is reported. MATERIALS AND METHODS: A modified Request for Proposal described the technical requirements, PACS architecture, and performance targets. The Request for Proposal was complemented by a set of desired financial goals-the main one being the ability to use film savings to pay for the implementation and operation of the PACS. RESULTS: Financing of the enterprise-wide PACS was completed through an operating lease agreement including all PACS equipment, implementation, service, and support for an 8-year term, much like a complete outsourcing. Equipment refreshes, both hardware and software, are included. Our agreement also linked the management of the digital imaging operation (PACS) and the traditional film printing, shifting the operational risks of continued printing and costs related to implementation delays to the PACS vendor. An additional optimization step provided the elimination of the negative film budget variances in the beginning of the project when PACS costs tend to be higher than film and film-related expenses. CONCLUSION: An enterprise-wide PACS has been adopted to achieve clinical workflow improvements and cost savings. PACS financing was solely based on film savings, which included the entire digital solution (PACS) and any residual film printing. These goals were achieved with simultaneous elimination of any over-budget scenarios providing a non-negative cash flow in each year of an 8-year term.

Academic Medical Centers↗
PubMed2000

Comparison of human papillomavirus genotypes in archival cervical cancer specimens from Alaska natives, Greenland natives and Danish Caucasians.

Archival, formalin-fixed, paraffin-embedded cervical cancer specimens from 53 Alaska natives, 32 Greenland natives and 34 Danish Caucasians were analyzed for human papillomavirus (HPV) genotypes 16, 18, 31, 33, 35 and 45 and unidentified genotypes (HPV X) using PCR. The specimens were from the time period 1980-1989. No significant differences were observed in the overall HPV detection rates among cases from Alaska (98.1%), Greenland (84.4%) and Denmark (85.3%). HPV genotype 16 was the most prevalent type: 78.8% in Alaska natives, 96.3% in Greenland natives and 82.8% in Danish Caucasians. A prevalence of 21.2% HPV 31 and 30.8% HPV 33 was found in Alaska natives, of which most were coinfections with HPV 16. Only 3.7% HPV 31 and 3.7% HPV 33 were found in Greenland natives and no HPV 31 and 6.9% HPV 33 were found in Danish Caucasians. HPV 18 was only detected in Alaska natives and HPV 35 and 45 were not detected in any of the three populations. Infections with multiple genotypes were prevalent in Alaskan (36.5%) but not in Greenland natives (3. 7%) and Danish Caucasians (6.9%). The Eskimo subgroup of the Alaska native population has a significantly higher prevalence of HPV genotypes 31 and 33 associated with mixed infections in invasive cancer than the two other native subgroups (P = 0.04) and Greenland and Danish populations, reflecting genotype distributions in dysplasia and normal cervical cytology. The reason for HPV genotype diversity, although unknown, may be relevant to the current development of HPV vaccines.

Adolescent↗
PubMed2003

The detection of t(14;18) in archival lymph nodes: development of a fluorescence in situ hybridization (FISH)-based method and evaluation by comparison with polymerase chain reaction.

Fluorescence in situ hybridization (FISH) has been used to demonstrate the t(14;18) in up to 100% of follicular lymphoma (FL) cases, however, there is little reproducible data using fixed tissue. The aim was therefore to develop a robust FISH method for the demonstration of translocations in archival tissue. The technique was evaluated by comparison with multiplex polymerase chain reaction (PCR), capable of detecting the majority of known breakpoints. Twenty-eight paired frozen and fixed cases of FL and 20 reactive controls were analyzed. The t(14;18) was detected in 23 of 28 cases using PCR on frozen material and 8 of 20 in paraffin. Using FISH, 24 of 26 frozen and 26 of 28 paraffin cases had a demonstrable translocation. All 20 reactive nodes were negative for the t(14;18) by PCR. Using FISH, one of the reactive cases had occasional cells with a translocation FISH pattern, demonstrable in frozen and paraffin samples. This is consistent with the presence of the t(14;18), which is well described in normal individuals. Both PCR and FISH are highly effective for t(14;18) analysis in unfixed tissue. When only paraffin blocks are available, FISH is the method of choice, and a result was achieved in 100% of cases. The method is applicable to the retrospective analysis of a range of translocations.

Chromosomes, Human, Pair 14↗