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At least 775 records · Page 43Linked to original sources
PubMed2005

Wheat archive links long-term fungal pathogen population dynamics to air pollution.

We used the PCR to study the presence of two plant pathogens in archived wheat samples from a long-term experiment started in 1843. The data were used to construct a unique 160-yr time-series of the abundance of Phaeosphaeria nodorum and Mycosphaerella graminicola, two important pathogens of wheat. During the period since 1970, the relative abundance of DNA of these two pathogens in the samples has reflected the relative importance of the two wheat diseases they cause in U.K. disease surveys. Unexpectedly, changes in the ratio of the pathogens over the 160-yr period were very strongly correlated with changes in atmospheric pollution, as measured by SO(2) emissions. This finding suggests that long-term, economically important, changes in pathogen populations can be influenced by anthropogenically induced environmental changes.

Air Pollution↗
PubMed1978

Driving offenders and the defensive driving course--an archival study.

Two hundred and seventy-five drivers who had been required by court order to attend a Defensive Driving Course (DDC) were compared on six posttreatment driving measures obtained from archival data with 275 drivers who also had had a court appearance and standard treatment. The DDC group showed greater reductions in serious and accident-promoting convictions but no greater reduction in accidents when compared with the standard treatment comparison group.

Accidents, Traffic↗
PubMed2006

Evaluation of B-cell clonality in archival skin biopsy samples of cutaneous B-cell lymphoma by immunoglobulin heavy chain gene polymerase chain reaction.

Polymerase chain reaction (PCR)-based detection of clonal T- and B-cells is widely used in the diagnosis of various lymphomas, including those of the skin. A large number of corresponding methods have been published. Recently, for the first time, standardized PCR protocols were developed in common by 14 European centers of lymphoma diagnosis and research (Biomed-2 protocols). Here, we have applied Biomed-2 immunoglobulin heavy chain (IgH)-PCR for clonality detection in primary cutaneous B-cell lymphoma (CBCL) and compared it with previously established methods. The DNA of 43 paraffin-embedded lesional skin biopsies of confirmed CBCL cases [27 follicle center cell lymphoma (FCCL), 11 marginal zone B-cell lymphoma/immunocytoma (MZL/IC) and five large CBCL of the lower leg (CBCL-LL)] were amplified by the Biomed-2 IgH-PCR protocols as well as using four other assays, priming also the three IgH framework regions (FR) 1-3. All PCR products were analysed by fluorescence fragment analysis. Twenty-nine of 43 (67%) CBCL samples (5/5, 100% of CBCL-LL; six of 11, 54.5% of IC/MZL; 18 of 27, 66.7% of FCCL) showed monoclonal B-cell presence complementary in all of the IgH-PCR. The three Biomed-2 PCR indicated together clonality in 24 of 43 samples (56%). Considering each method separately, the Biomed-2 FR3-PCR showed the highest rate of clonality detection (20 of 43, 47%). In conclusion, the Biomed-2 FR3-PCR is recommended for detecting B-cell clonality in archival skin samples of CBCL but should be completed by FR1- and/or FR2-PCR.

Biopsy↗
PubMed2006

Ultra-rapid preparation of total genomic DNA from isolates of yeast and mould using Whatman FTA filter paper technology - a reusable DNA archiving system.

Conventional methods for purifying PCR-grade fungal genomic DNA typically require cell disruption (either physical or enzymatic) coupled with laborious organic extraction and precipitation stages, or expensive column-based technologies. Here we present an easy and extremely rapid method of preparing yeast and mould genomic DNAs from living cultures using Whatman FTA filter matrix technology. Aqueous suspensions of yeast cells or hyphal fragments and conidia (in the case of moulds) are applied directly (or after freeze-thawing) to dry FTA filters. Inoculated filters are then subjected to brief microwave treatment, to dry the filters and inactivate the organisms. Filter punches are removed, washed rapidly, dried and placed directly into PCR reactions. We show that this procedure inactivated all of the 38 yeast and 75 mould species tested, and generated PCR-grade DNA preparations in around 15 minutes. A total of 218 out of 226 fungal isolates tested liberated amplifiable DNA after application to FTA filters. Detection limits with yeast cultures were approximately 10 colony-forming units per punch. Moreover, we demonstrate that filter punches can be recovered after PCR, washed and used in fresh PCR reactions without detectable cross-contamination. Whatman FTA technology thus represents a cheap, ultra-rapid method of fungal genomic DNA preparation, and also potentially represents a powerful fungal DNA archiving and storage system.

DNA, Fungal↗
PubMed2004

HIV type 1 pol gene diversity and archived nevirapine resistance mutation in pregnant women in Rwanda.

This study aimed to find out whether genetic polymorphisms were present in positions potentially affecting susceptibility to antiretrovirals in non-B subtypes from HIV-1-infected patients in Rwanda. Viral pol gene diversity was investigated by direct sequencing in 43 treatment-naive women. In addition, 10 DNA sequences from uncultured peripheral blood mononuclear cells were analyzed 6 weeks after a single dose of nevirapine (prevention of mother-to-child transmission program). Phylogenetic analyses have shown 34 subtype A1, 6 subtype C, and 2 subtype D strains. In addition, an A/C recombinant between the protease (PR) (subtype A1) and the reverse transcriptase (RT) (subtype C) was identified. In the PR coding region, high numbers of polymorphisms were found, including substitutions in secondary PR resistance sites. PR 35D, 36I, and 37N were always present within subtype A as were PR 93L in subtype C strains. PR 10I/V, 20R, 33F, and 77V were found in subtype A whereas PR 36I was highly prevalent in subtype C strains. The A/C recombinant displayed substitutions related to resistance (PR 10, 33, 36 and RT 118). One nevirapine resistance mutation (RT 181Y/C) was found in proviral DNA after 6 weeks. In conclusion, subtypes A and C are predominant in this cohort in Rwanda. Substitutions similar to secondary protease inhibitor resistance mutations are common before treatment whereas major resistance mutation may be archived after a single dose of nevirapine. Accordingly, the hypothesis of a genetic background effect in non-B strains has to be further addressed in programs of introduction of antivirals in Africa.

Drug Resistance, Viral↗
PubMed2003

Next generation pharmaceutical impactor (a new impactor for pharmaceutical inhaler testing). Part II: Archival calibration.

A new seven-stage cascade impactor, the Next Generation Pharmaceutical Impactor (NGI), has been developed for the pharmaceutical industry. A calibration following "good laboratory practice (GLP)" procedures has been performed on a specific archival NGI, deemed to be representative of all NGIs. Thus, this impactor had nozzle dimensions for each stage manufactured close to the middle of the tolerance band for the design specification, and therefore the average nozzle diameter was equal to the nominal value for that stage. An essential feature of the NGI is that it is designed to operate at any flow rate between 30 and 100 L/min. Thus, the calibration was made at inlet flow rates of 30, 60 and 100 L/min representing the lower bound, mid-region and upper bound of the specified range of operation for the impactor. The calibration data were then used to develop equations that predict the particle cut size for all components of the impactor at any flow rate from 30 to 100 L/min.

Administration, Inhalation↗
PubMed2006

Recovery of genomic DNA from residual frozen archival blood clots suitable for amplification and use in genotyping assays.

A greatly neglected source of DNA potentially useful for genetic or forensic studies is the clot remaining from blood samples collected for serum chemistry measurements. We have investigated the utility of residual clots remaining from venipunctures collected for California's Expanded Maternal Serum Alpha-Fetoprotein Screening Program. We report a protocol based on the salting out method for the extraction of DNA from samples which have been archived and frozen for up to 2.5 years. As much as 57 microg of high-quality DNA can be obtained from a 2-ml clot as determined by PicoGreen (Molecular Probes, Inc., Eugene, OR) fluorescence measurements. Quality of the purified DNA was evaluated by its ability to serve as template in polymerase chain reaction (PCR) amplifications, using primers that flank the polymorphic regions of six genes of pharmacogenetic interest distributed throughout the human genome. Sizes of the gene regions successfully amplified range from 215 bp to 2064 bp, using as little as 10 ng of template DNA. Because many genotyping protocols routinely recommend the design of amplicons in the 100-200 bp range, and 10-50 ng of template, we conclude that the clot remaining after serum has been removed from blood collected for serum chemistry measurements can serve as a reliable source of DNA for genotyping studies.

Biological Specimen Banks↗
PubMed2004

Next generation pharmaceutical impactor: a new impactor for pharmaceutical inhaler testing. Part III. extension of archival calibration to 15 L/min.

An extension of the archival calibration of the recently developed 30-100-L/min seven-stage impactor, the Next Generation Pharmaceutical Impactor (NGI), has been undertaken at 15 L/min. The NGI stage cut sizes are 0.98-14.1 microm aerodynamic diameter at this flow rate. This 15-L/min calibration was motivated by the desire to sample the entire aerosol produced by a nebulizer when tested in accordance with a new international standard developed by the Comite Européen de Normalisation (CEN), as well as the need to test various types of inhalers at flow rates lower than 30 L/min for pediatric applications. Measurements were undertaken with monodisperse oleic acid droplets in the range of 0.7-22 microm aerodynamic diameter following a procedure established in the original 30-100-L/min calibration study. The NGI was found to be effective for particle size separation at 15 L/min. Users should decide the most applicable configuration that meets their needs, based on the following recommendations: (1) the pre-separator should not normally be used, as its performance is significantly degraded by the influence of gravity, resulting in interference with stage 1; and (2) a filter should be inserted below the micro-orifice collector (MOC), as the size corresponding to 80% collection efficiency of the MOC becomes excessively large with decreasing flow rate, so that this component becomes ineffective as a means of collecting fine particles that penetrate beyond stage 7.

Administration, Inhalation↗
PubMed1997

Interphase cytogenetic (in situ hybridization) analysis of astrocytomas using archival, formalin-fixed, paraffin-embedded tissue and nonfluorescent light microscopy.

Astrocytomas contain nonrandom chromosomal abnormalities that recently have been correlated with shortened patient survival. Two frequently reported aberrations are trisomy 7 and monosomy 10. We assessed the numerical complement of chromosomes 7 and 10 in formalin-fixed, paraffin-embedded brain biopsy tissue from 28 diffuse astrocytomas by in situ hybridization using a nonfluorescent enzymatic detection system. Clinical follow-up of at least 5 years was available in 26 cases (93%). Monosomy 10 was identified in 7 cases (25%): astrocytoma, 1 case; anaplastic astrocytoma, 1 case; and glioblastoma, 5 cases. Trisomy 7 was identified in 11 cases (39%): astrocytoma, 5 cases; glioblastoma, 6 cases. Multivariate analysis revealed that monosomy 10 was the most statistically significant negative predictor of patient survival. Numerical chromosomal abnormalities are detectable in astrocytomas in archival tissue using interphase cytogenetics and nonfluorescent light microscopy. Although larger studies are required, our data suggest that potentially useful prognostic information may be obtained with this approach.

Adult↗
PubMed1999

Detection of SYT-SSX fusion transcript in synovial sarcoma using archival cytologic specimens.

Identification of the SYT-SSX fusion transcript can be a useful diagnostic aid for synovial sarcoma. However, there is no report on the detection of the specific transcript in archival cytologic specimens. We performed a rapid reverse transcription-polymerase chain reaction assay to detect the fusion transcript using such specimens as RNA sources and compared its usefulness with the assay using formalin-fixed paraffin-embedded histologic specimens. Eleven cytologic and 12 histologic specimens stored for 0.1 to 20 years were selected from 9 patients. The SYT-SSX transcript was identified in 10 (91%) of 11 of cytologic and 9 (75%) of 12 histologic cases. One of the transcript-positive cytologic cases was obtained by fine-needle aspiration. SYT-SSX1 fusion was found in 4 patients and SYT-SSX2 in 5. Cytologic specimens will be an excellent RNA source for the reverse transcription-polymerase chain reaction diagnosis of synovial sarcoma with a sensitivity of more than 90%, comparable to that in frozen materials. Histologic materials also may be useful when cytologic or frozen materials are not available.

Adolescent↗
PubMed1994

A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology.

The paper describes a digital image archiving system for time-lapse microscopy. The system uses an MS-DOS compatible computer to store video images while simultaneously controlling a stepping motor. In a typical experiment, images might be taken at 30 s intervals in each of 25 consecutive focal planes. A system with 2.5 Gbyte disk capacity can store approximately 18,000 full frame images: 6 h recording at maximum resolution. Once recorded, images series stored on disk can be 'played back' in any order. Generally, images from a single focal plane are displayed consecutively in either forward or reverse time. The focal plane can be shifted during playback, allowing individual cells to be followed as they move between focal planes. To facilitate the annotation and interpretation of the real-time images, a mouse-driven interface allows users to define and follow individual objects (e.g. cells). The recorded image series can be achieved inexpensively using standard digital tape backup hardware. In this laboratory, the system has been particularly useful for tracing embryonic cell lineages and cell migrations. Detailed system specifications, including source code, compiled programs, hardware requirements and users manual are available directly from the author or by anonymous FTP (ciw1.ciwemb.edu).

Algorithms↗
PubMed2004

UniProt archive.

UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant, publicly accessible resources. All new and updated protein sequences are collected and loaded daily into UniParc for full coverage. To avoid redundancy, each unique sequence is stored only once with a stable protein identifier, which can be used later in UniParc to identify the same protein in all source databases. When proteins are loaded into the database, database cross-references are created to link them to the origins of the sequences. As a result, performing a sequence search against UniParc is equivalent to performing the same search against all databases cross-referenced by UniParc. UniParc contains only protein sequences and database cross-references; all other information must be retrieved from the source databases.

Amino Acid Sequence↗
PubMed2004

PDBML: the representation of archival macromolecular structure data in XML.

SUMMARY: The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.

Amino Acid Sequence↗
PubMed1992

Genetic alterations in the 61st codon of the H-ras oncogene isolated from archival sections of hepatic hyperplasias, adenomas and carcinomas in control groups of B6C3F1 mouse bioassay studies conducted from 1979 to 1986.

In order to better understand the molecular events in murine hepatocarcinogenesis, the frequency and types of mutations in the murine H-ras proto-oncogene isolated from 184 independent, spontaneously occurring hepatic lesions were determined. Hepatocellular foci, hyperplasias, adenomas and carcinomas were obtained from archival samples of control male (134 samples) and female (50 samples) B6C3F1 mice used in oncogenicity studies that were conducted at Lilly Research Laboratories from 1979 to 1986. The 61st codon region of the H-ras oncogene from these sections was amplified using the polymerase chain reaction. Mutation frequencies were determined by restriction fragment length polymorphism analysis. The types of mutations were characterized by allele-specific oligonucleotide hybridization and confirmed by DNA sequencing. Forty-two per cent of the carcinomas, 44% of the adenomas, 42% of the hyperplasias and 29% of the foci contained mutations at the 61 codon. The mutation spectra for the carcinomas, adenomas and hyperplasias consisted of mostly CAA-AAA transversions, followed by CAA-CGA transitions, followed by CAA-CTA transversions. These results demonstrate that: (i) the frequency of spontaneous mutations in the H-ras 61st codon is equivalent in murine hyperplasias, adenomas and carcinomas, and (ii) sex was not a determining factor in either the mutation frequency or mutation spectrum for the spontaneous lesions. If these lesions represent successive stages in the carcinogenic process, then these results suggest that mutations in the 61st codon of H-ras are early events in spontaneous murine hepatocarcinogenesis.

Adenoma↗
PubMed1992

An analysis of physician utilization by elderly persons: systematic differences between self-report and archival information.

Elderly persons may over- or underreport their utilization of services, and systematic variance in this discrepancy may bias research findings. Therefore, this study analyzed the discrepancy between archival and self-report measures of physician utilization and examined the association of that discrepancy with health status and sociodemographic variables. Each older person underreported physician utilization by a net of .35 visits, but the total discrepancy was nearly two visits per person, or 65 percent of the number of self-reported visits. The multivariate findings indicate that underreports of utilization are smaller for those elderly persons with lower health status (as measured by disease history) and larger for those with higher levels of utilization. Those in poor health tend to overreport physician visits, and those with greater levels of utilization tend to have greater proportional reporting error. Self-reported measures of physician utilization should be considered in the context of the net error and the systematic nature of that error.

Activities of Daily Living↗
PubMed2005

The latent HIV-1 reservoir in patients undergoing HAART: an archive of pre-HAART drug resistance.

Recent studies on patients with a history of pre-HAART drug resistance, but currently on a successful regimen, provided new insights into the dynamics of the latent cellular viral reservoir. Results indicated that the latent reservoir is an archive, composed of a mixture of wild-type and drug-resistant strains. The studies showed that, even after years of successful HAART, the wild-type viral strains that circulated before the initiation of the therapy as well as all the different drug-resistant viral strains that evolved over time during eventual periods of non-suppressive treatment, remain detectable in the proviral reservoir. These findings support the hypothesis that during active viral replication, new variants, including drug-resistant ones, continuously enter the latent viral reservoir. It can be concluded that, as a consequence of the lifelong conservation of this latent reservoir, the potency of drugs for which resistance once developed will remain reduced, even after years of withdrawal of the drug.

Antiretroviral Therapy, Highly Active↗
PubMed2004

Picture archiving and communication system introduced to a new Japanese cancer center hospital.

Picture archiving and communication systems (PACS) have been widely introduced as a credible alternative to the traditional film-based radiological service. Shizuoka Cancer Center Hospital (SCCH) introduced PACS and hospital information systems as an alternative to the film- and traditional paper-based hospital system at the opening of the hospital. Using PACS, whole images and their reports can be available at any nearby terminal. Users can select the display format for monitor viewing on the bases of individual preference and navigate through cases by buttons and rollerballs on the mouse with easy handling and quick response. Most clinicians in SCCH evaluated such medical circumstances well. Filmless image management systems will become popular in all hospitals in the near feature. All staff in each hospital should investigate the merits and demerits of this system and how to introduce it effectively.

Cancer Care Facilities↗
PubMed1994

Differential synaptic loss in the cortex in Alzheimer's disease: a study using archival material.

We have developed techniques to utilize immunocytochemical localization of synaptic protein (SNAP-25) in conjunction with image analysis to investigate synaptic loss in readily available archival material. Sections from 5 cortical regions were examined in cases of Alzheimer's disease (n = 7) and controls (n = 5). Image analysis was used to determine a relative synaptic index (RSI) and probe for changes in synaptic integrity. RSI value for cortical regions did not differ in controls. RSIs from sulci and gyri were significantly correlated in Brodmann areas 6, 9 and 18 (40 and 52 approached significance). Cases with Alzheimer's disease showed decreases in sulcal and gyral RSI values of between 60% (Brodmann area 6 < 0.01) and 10% (Brodmann area 18 > 0.4) and a lack of correlation in sulco-gyral values except in Brodmann area 18. We have demonstrated that synaptic pathology is heterogeneous with frontal cortex most and occipital cortex least affected. Sulci and gyri are affected to different degrees. The underlying cytoarchitecture of the cortex and its pattern of connectivity appears to have a considerable influence on the degree and extent of synaptic pathology.

Aged↗