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PubMed1992

The development of a virtual database to provide on-line access to a large archive of clinical data.

The archival database of the HELP Hospital Information System at LDS Hospital is too large to be stored on line. The archival data are important for clinical and research applications. Demountable disk packs have been used to store the archival database. This method of storage has four significant disadvantages. A virtual database was developed to overcome the limitations of this data-management scheme. This virtual database enables the transparent use of appropriate low-cost network-based storage technology to provide on-line availability of the entire archive of clinical data. The virtual database successfully resolves the problems associated with disk packs, and opens the door to enhanced use of the data for clinical and research applications.

Computer Storage Devices↗
PubMed1998

[Minimally invasive surgery with the Port-Access method. Preliminary experience].

METHODS: Data from the initial experience of 40 patients operated on with the Port-Access technique are reported. Indication to surgery was mitral disease in 24 patients and coronary stenosis in 16 patients. Mean age was 52 years (range 32-75). Operations performed were: 8 mitral valvuloplasties, 16 valve replacements, 9 single CABG (associated with an MVR in one case), 1 double CABG, 6 triple CABG and one quadruple CABG. Coronary endarterectomy was performed in 5 patients and left atrial isolation was associated with MV surgery in 5 cases. RESULTS: There were no operative deaths and every patient was discharged after a mean postoperative stay of 5.5 days (range 3-30). Postoperative course was complicated in 7 patients: surgical revision was necessary in 4 patients due to bleeding (through the mini-thoracotomy incision in 3 cases), 1 pacemaker was implanted for A-V block, one retained pulmonary catheter was removed through the mini-thoracotomy without the aid of cardiopulmonary bypass and in one case, there was an emergency conversion to median sternotomy due to a ventricular fibrillation unresponsive to usual resuscitative maneuvers a few hours after surgery. Some of these complications can be ascribed to the learning phase of this new technique and should disappear as experience is increased. CONCLUSIONS: Port-Access surgery is a new minimally invasive technique that utilizes a cardiopulmonary bypass with femoral access and a specialized catheter system that provides endoaortic clamping, pulmonary artery venting and myocardial preservation with infusion of cardioplegic solution in the aortic bulb or in the coronary sinus. Major contraindications to this technique are iliac-femoral disease or severe dilatation of ascending aorta. The aim of the Port-Access technique is to combine the aesthetic and functional advantages of the minimally invasive surgery with the wide range of surgical options that cardiopulmonary bypass can afford (to operate on atrioventricular valves and perform all the CABG that the patient need), without the limitations characteristic of the classic minimally invasive direct coronary artery bypass (MIDCAB) technique.

Adult↗
PubMed2003

Measuring access to primary care appointments: a review of methods.

BACKGROUND: Patient access to primary care appointments is not routinely measured despite the increasing interest in this aspect of practice activity. The generation of standardised data (or benchmarks) for access could inform developments within primary care organisations and act as a quality marker for clinical governance. Logically the setting of targets should be based on a sound system of measurement. The practicalities of developing appropriate measures need debate. Therefore we aimed to search for and compare methods that have been published or are being developed to measure patient access to primary care appointments, with particular focus on finding methods using appointment system data. METHOD: A search and review was made of the primary care literature from 1990 to 2001, which included an assessment of online resources (websites) and communication with recognised experts. The identified methods were assessed. RESULTS: The published literature in this specific area was not extensive but revealed emerging interest in the late 1990s. Two broad approaches to the measurement of waiting times to GP appointments were identified. Firstly, appointment systems in primary care organisations were analysed in differing ways to provide numerical data and, secondly, patient perceptions (reports) of access were evaluated using survey techniques. Six different methods were found which were based on appointment systems data. CONCLUSION: The two approaches of either using patient questionnaires or appointment system data are methods that represent entirely different aims. The latter method when used to represent patient waiting times for 'routine' elective appointments seems to hold promise as a useful tool and this avoids the definitional problems that surround 'urgent' appointments. The purpose for which the data is being collected needs to be borne in mind and will determine the chosen methods of data retrieval and representation.

Appointments and Schedules↗
PubMed2003

STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and Calpha-Calpha and Cbeta-Cbeta distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)-amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS.

Chymotrypsin↗
PubMed2000

MouseNet database: digital management of a large-scale mutagenesis project.

The Munich ENU Mouse Mutagenesis Screen is a large-scale mutant production, phenotyping, and mapping project. It encompasses two animal breeding facilities and a number of screening groups located in the general area of Munich. A central database is required to manage and process the immense amount of data generated by the mutagenesis project. This database, which we named MouseNet(c), runs on a Sybase platform and will finally store and process all data from the entire project. In addition, the system comprises a portfolio of functions needed to support the workflow management of the core facility and the screening groups. MouseNet(c) will make all of the data available to the participating screening groups, and later to the international scientific community. MouseNet(c) will consist of three major software components:* Animal Management System (AMS)* Sample Tracking System (STS)* Result Documentation System (RDS)MouseNet(c) provides the following major advantages:* being accessible from different client platforms via the Internet* being a full-featured multi-user system (including access restriction and data locking mechanisms)* relying on a professional RDBMS (relational database management system) which runs on a UNIX server platform* supplying workflow functions and a variety of plausibility checks.

Animals↗
PubMed2003

The relation between anti-hepatitis A virus antibodies and residence water access in Rio de Janeiro, Brazil.

OBJECTIVES: The objective of this study was to analyse the relation between residence water access (water taps) and hepatitis A virus (HAV) antibodies, associated with socio-economic, environmental and demographic factors. METHODS: A logistic regression model was used for estimating the relation between residential water access (presence of water taps inside the house) and HAV antibodies, related to confounding effects of selected variables. The odds ratios estimated by the model were used as incidence density ratios (IDR) for the analysis of the water access-antibody association. Data were obtained from a cross-sectional study on the seroprevalence of hepatitis A in 3779 volunteers from Duque de Caxias city, greater Rio de Janeiro, Brazil. Participants were selected according to an age-specified random sampling survey. RESULTS: Besides water access (main variable of interest), age, monthly family income, housewife schooling, persons per room, proximity to open sewage channels and consumption water treatment were statistically associated to hepatitis A seroprevalences. An interaction between water access and proximity to open sewage channels was detected. Persons living in residences distant from an open sewage channel had a water access-antibody IDR of 2.5 (95% CI [1.4; 4.3]), in contrast to 1.1 for those living close to such channels. CONCLUSIONS: Although indirectly measured through the proxy variable water access, personal hygiene, in conjunction with the absence of open sewage channels in the proximity of the residence, was an important factor for low HAV seroprevalence study population.

Adolescent↗
PubMed1998

The uracil permease of Schizosaccharomyces pombe: a representative of a family of 10 transmembrane helix transporter proteins of yeasts.

The uracil permease gene of Schizosaccharomyces pombe was cloned and sequenced. The deduced protein sequence shares strong similarities with five open reading frames from Saccharomyces cerevisiae, namely the uracil permease encoded by the FUR4 gene, the allantoin permease encoded by DAL4, a putative uridine permease (YBL042C) and two unknown ORFs YOR071c and YLR237w. A topological model retaining ten transmembrane helices, based on predictions and on experimental data established for the uracil permease of S. cerevisiae by Galan and coworkers (1996), is discussed for the four closest proteins of this family of transporters. The sequence of the uracil permease gene of S. pombe has been deposited in the EMBL data bank under Accession Number X98696.

Amino Acid Sequence↗
PubMed2003

The ICL1 gene of Pichia pastoris, transcriptional regulation and use of its promoter.

We cloned and characterized a gene encoding isocitrate lyase from the methylotrophic yeast Pichia pastoris. This gene was isolated from a P. pastoris genomic library using a homologous PCR hybridization probe, amplified with two sets of degenerate primers designed from conserved regions in yeast isocitrate lyases. The cloned gene was sequenced and consists of an open reading frame of 1563 bp encoding a protein of 551 amino acids. The molecular mass of the protein is calculated to be 60.6 kDa with high sequence similarity to isocitrate lyase from other organisms. There is a 64% identity between amino acid sequences of P. pastoris Icl and Saccharomyces cerevisiae Icl. Northern blot analyses showed that, as in S. cerevisiae, the steady-state ICL1 mRNA levels depend on the carbon source used for cell growth. Expression in P. pastoris of the dextranase gene (dexA) from Penicillium minioluteum under control of the ICL1 promoter proved that P(ICL1) is a good alternative for the expression of heterologous proteins in this methylotrophic yeast. The sequence presented here has been deposited in the EMBL data library under Accession No. AJ272040.

Amino Acid Sequence↗
PubMed2001

Isolation and sequence of the MIG1 homologue from the yeast Candida utilis.

The Mig1p repressor from the food yeast Candida utilis has been isolated using a homologous PCR hybridization probe. This probe was amplified with two sets of degenerate primers designed on the basis of highly conserved motifs in the DNA-binding region (zinc-finger domain) from yeast Mig1p and fungi CreA repressors. The cloned gene was sequenced and found to encode a polypeptide of 345 amino acids which shows significant identity with other yeast and fungus repressors in the DNA-binding domain and also with the yeast Mig1 proteins in the C-terminal region (effector domain). The MIG1 repressor gene from C. utilis was able to complement functionally the mig1 mutation of S. cerevisiae. The sequence presented here has been deposited in the EMBL data library under Accession No. AJ277830.

Amino Acid Sequence↗
PubMed1999

Ethical issues in computerized medical records.

Greater use of computer technology has permitted rapid access to many forms of data. Hospitals have traditionally been slower to accept this technology for patient medical records. With the rapid approach of the new millennium, hospitals are being forced into re-evaluating many processes, including the volumes of data collected on paper. Electronic medical records are one approach to reducing storage and streamlining care across the health care continuum. This article examines the ethical impact of computerized medical records, including access to data, ownership of data, confidentiality, and medical record brokering.

Computer Security↗
PubMed2004

Searching the medical literature.

Medical literature searches have become more complex because of the increasing amount of published material and the multiple available databases indexing those publications. Although newly graduated physicians may have received some training in literature searching as part of a medical school curriculum, most clinicians have received no formal training in this skill. In today's world of evidence-based medicine, access to published data is crucial, and the importance of a systematic approach to searching cannot be overemphasized. A brief review of searching techniques can greatly increase productivity while using the MEDLINE, Excerpta Medica, Science Citation Index, and other databases. Similarly, knowing the options available for remote access to databases and electronic delivery of articles can expedite the task of accessing publications.

Databases, Bibliographic↗
PubMed2002

Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes.

Access to the complete gene inventory of an organism is crucial to understanding physiological processes like development, differentiation, pathogenesis, or adaptation to the environment. Transcripts from many active genes are present at low copy numbers. Therefore, procedures that rely on random EST sequencing or on normalisation and subtraction methods have to produce massively redundant data to get access to low-abundance genes. Here, we present an improved oligonucleotide fingerprinting (ofp) approach to the genome of sugar beet (Beta vulgaris), a plant for which practically no molecular information has been available. To identify distinct genes and to provide a representative 'unigene' cDNA set for sugar beet, 159 936 cDNA clones were processed utilizing large-scale, high-throughput data generation and analysis methods. Data analysis yielded 30 444 ofp clusters reflecting the number of different genes in the original cDNA sample. A sample of 10 961 cDNA clones, each representing a different cluster, were selected for sequencing. Standard sequence analysis confirmed that 89% of these EST sequences did represent different genes. These results indicate that the full set of 30 444 ofp clusters represent up to 25 000 genes. We conclude that the ofp analysis pipeline is an accurate and effective way to construct large representative 'unigene' sets for any plant of interest with no requirement for prior molecular sequence data.

Arabidopsis↗
PubMed1996

Analysis of a 26 kb region on the left arm of yeast chromosome XV.

In the framework of the EC programme for sequencing yeast chromosome XV, we have determined the nucleotide sequence of a 26 kb region. Subsequent analysis revealed 13 non-overlapping open reading frames, three of which correspond to known yeast genes. A pair of tRNA genes associated with remnant Ty elements were localized in this region. From structural parameters and/or similarity searches with entries in the current data libraries, a preliminary functional assessment of several of the putative novel gene products can be made. The gene density in this region amounts to one gene in 2 kb. Protein coding regions occupy 61% of the total DNA sequence. Within the intergenic regions, potential regulatory elements can be predicted. The data obtained here may serve as a basis for a more detailed biochemical analysis of the novel genes. The complete nucleotide sequence of the 26 kb segment as depicted in Figure 1 has been deposited at the EBI data library under Accession Number X91067.

Amino Acid Sequence↗