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Biomedical subjects

P McNeil

Publications and source records attributed to P McNeil.

16 recordsLinked to original sources
PubMed2003

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

Animals↗
PubMed2000

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

BACKGROUND: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. RESULTS: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. CONCLUSIONS: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Computational Biology↗
PubMed2000

The impact of the Women's Centre of Jamaica Foundation programme for adolescent mothers on repeat pregnancies.

A random sample (n = 260) of primiparous Jamaican adolescent mothers (12-16 years old) who gave birth in 1994 in the parishes of Kingston and St Andrew, St Catherine and Manchester was selected from vital records and interviewed in 1998 for this historical cohort study. Among programme participants, the incidence of repeat pregnancy was 37 per cent compared with 60 percent among non-participants. Programme participation reduced the risk of one or more repeat pregnancies by 45 per cent with 95% confidence interval (0.22, 0.91). Programme participants were also 1.5 times (1.005, 2.347) more likely to complete high school than non-participants; however, this effect did not achieve statistical significance. The results confirmed that the WCJF Programme exerts a considerable effect on the incidence of repeat pregnancy among participants. The benefits of programme participation were greatest among residents of the Kingston Metropolitan Area from single-parent, female-headed households with average monthly incomes below J$10,000, who wanted to continue their education after the first live birth.

Adolescent↗
PubMed1999

Organising multi-dimensional biological image information: the BioImage Database.

Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. At the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on BioImage started two years ago, and that its first version is now presented here. In essence, BioImage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of BioImage can be accessed at http://www. bioimage.org and http://www-embl.bioimage.org

Bacterial Proteins↗
PubMed1998

Deposition of macromolecular structures.

Macromolecular structures are being determined at an increasing rate, and are of interest to a wide diversity of researchers. Depositing a macromolecular structure with the Protein Data Bank makes it readily available to the community. Accuracy, consistency and machine-readability of the data are essential, as are clear indications of quality, and sufficient information to allow non-experimentalists to interpret the data. Good-quality depositions are necessary to allow this to be achieved. The PDB's AutoDep system allows deposition and some preliminary automatic checking to take place at multiple sites, prior to full processing and release of the structure by the PDB. However, depositing a structure currently requires the manual entry of a large amount of information at the time of deposition. The data-harvesting approach will allow much more information to be deposited, without placing an additional burden on the depositor. Deposition-ready files will be generated automatically during the course of a structure-determination experiment. The additional information will allow improved validation procedures to be applied to the structures, and the data to be made more useful to the wider scientific community.

Database Management Systems↗
PubMed1998

Outbreak of Acinetobacter spp. bloodstream infections in a nursery associated with contaminated aerosols and air conditioners.

BACKGROUND: Acinetobacter spp. are multidrug-resistant bacteria that grow well in water and cause infections with unexplained, increased summer prevalence. In August, 1996, eight infants acquired Acinetobacter spp. bloodstream infection (A-BSI) while in a nursery in the Bahamas; three infants died and an investigation was initiated. METHODS: A case patient was defined as any newborn in the nursery during August 6 to 13, 1996, with A-BSI. To identify risk factors for A-BSI we conducted a retrospective cohort study and performed environmental cultures and air sampling using settle plates. The genetic relatedness of environmental isolates was assessed by pulsed field gel electrophoresis. RESULTS: Of 33 patients in the nursery 8 (24%) met the case definition. Patients with peripheral iv catheters were more likely to develop A-BSI (8 of 21 vs. O of 10, P < 0.05). Multivariate analysis among patients with iv catheters indicated that only exposure to one nurse was an independent risk factor for developing A-BSI (P < 0.005). Nursery settle plates were more likely to grow Acinetobacter spp. than were settle plates from other hospital areas (8 of 9 vs. 0 of 5, P < 0.005); cultures from nursery air conditioners also grew Acinetobacter spp. Environmental isolates were genetically diverse. After installation of a new air conditioner in May, 1995, A-BSIs occurred more frequently during months of increased absolute humidity or environmental dew point. CONCLUSIONS: Acinetobacter spp. may cause nosocomial BSI and death among infants during periods of polyclonal airborne dissemination; breaks in aseptic technique during i.v. medication administration may facilitate transmission from the environment to the patient. Environmental conditions that increase air conditioner condensate may predispose to airborne dissemination via contaminated aerosols and increase the risk of nosocomial A-BSI.

Acinetobacter↗
PubMed1991

Duodenal ulcer. Discovery of a new mechanism and development of angiogenic therapy that accelerates healing.

The complete purification of the first angiogenic molecule, basic fibroblast growth factor (bFGF), was carried out in the authors' laboratory in 1983. Application of this peptide to chronic wounds enhances angiogenesis and accelerates wound healing. The authors showed that an acid-stable form of bFGF (i.e., bFGF-CS23) could be administered orally to rats with duodenal ulcers. The peptide promoted a ninefold increase of angiogenesis in the ulcer bed and accelerated ulcer healing more potently than cimetidine. Basic fibroblast growth factor did not reduce gastric acid. The authors now show that bFGF exists as a naturally occurring peptide in rat and human gastric and duodenal mucosa. This endogenous bFGF is present also in the bed of chronic ulcers in rats. Sucralfate binds bFGF and protects it from acid degradation. The sucralfate is angiogenic, based on its affinity for bFGF. When sucralfate is administered orally to rats, it significantly elevates the level of bFGF in the ulcer bed. Cimetidine, by its capacity to reduce gastric acid, also elevates bFGF in the ulcer bed. A hypothetical model is proposed in which prevention of ulcer formation or accelerated healing of ulcers by conventional therapies may be FGF dependent. Acid-stable bFGF-CS23 may be considered as a form of replacement therapy in the treatment of duodenal ulcers.

Aluminum Hydroxide↗
PubMed1989

Randomized, double-blind comparative study of intravenous ciprofloxacin versus ceftazidime in the treatment of serious infections.

We compared intravenously administered ciprofloxacin with ceftazidime in a randomized, double-blind study. Patients received ciprofloxacin 200 mg intravenously every 12 hours or ceftazidime 2 g intravenously every eight hours, with placebo infusions to maintain blinding. Therapy with metronidazole was added for suspected or documented intra-abdominal infection. Thirty-two of the 57 ciprofloxacin-treated patients were evaluable for determination of efficacy and had 41 bacterial isolates from 34 sites. Thirty-six of the 56 ceftazidime patients were evaluable for determination of efficacy and had 41 bacterial isolates from 38 sites. Seven of 35 bacteremic patients had no identifiable primary focus. The most commonly isolated pathogens were Escherichia coli, Streptococcus pneumoniae, Staphylococcus aureus, and Klebsiella pneumoniae. Cure rates and bacteriologic eradication rates were comparable. Nine patients did not improve. Patients with treatment failures in the ciprofloxacin group included a quadriplegic patient with relapse of urinary tract infection with bacteremia (K. pneumoniae). Another patient with bacteremia (Pseudomonas aeruginosa), pneumonia (Proteus vulgaris), and urinary tract infection (P. vulgaris, Providencia sp.) died on the first treatment day. The third patient (S. aureus and Streptococcus pneumoniae pneumonia) had a new aspiration pneumonia develop on the third day; the pneumococcus also persisted. Undrained S. pneumoniae empyema caused the fourth ciprofloxacin treatment failure, and the fifth patient had a relapse of S. aureus pneumonia with bacteremia. One ceftazidime-treated patient died of pneumococcal pneumonia on the first day. Another had persistent Staphylococcus epidermidis and Listeria bacteremia despite 48 hours of treatment. Two other patients had pneumonia (S. aureus and P. aeruginosa, respectively) and completed full courses of ceftazidime therapy without improvement. Five patients had pneumococcal bacteremia; four patients were cured: one of two patients in the ciprofloxacin group and three of three patients in the ceftazidime group. Significant increases in the number of platelets (four patients with ciprofloxacin treatment, one patient with ceftazidime treatment) and declines in the number of platelets (one patient with ciprofloxacin treatment, one patient with ceftazidime treatment) were observed. Intravenously administered ciprofloxacin is comparable with ceftazidime and is a safe and effective antibiotic for the treatment of patients with serious infections, including bacteremia.

Bacterial Infections↗
PubMed1985

Anti-Ro (SS-A) antibodies and congenital complete heart block.

Maternal anti-Ro (SS-A) antibodies have been implicated in the pathogenesis of congenital complete heart block. When congenital complete heart block occurs, SS-A antibodies are almost always present in maternal and fetal serum, although not all infants of SS-A antibody positive mothers are affected. We describe a situation in which antibodies to SS-A were present in high titre in both maternal and fetal serum, although there was no evidence of heart block in the infant. This is the first report of a normal infant in whom maternally derived SS-A antibodies have been documented in high titre.

Adult↗
PubMed1984

Microspectrofluorometry by digital image processing: measurement of cytoplasmic pH.

An interface of our microspectrofluorometer with an image processing system performs microspectrofluorometric measurements in living cells by digital image processing. Fluorescence spectroscopic parameters can be measured by digital image processing directly from microscopic images of cells, and are automatically normalized for pathlength and accessible volume. Thus, an accurate cytoplasmic "map" of various spectroscopic parameters can be produced. The resting cytoplasmic pH of fibroblasts (3T3 cells) has been determined by measuring the ratio of fluorescein fluorescence exited by two successive wavelengths (489 and 452 nm). Fluorescein-labeled dextran microinjected into the cells is used as a pH indicator, since it is trapped in the cytoplasm but is excluded from the nucleus and other organelles. The average cytoplasmic pH is 6.83 (+/- 0.38). However, cytoplasmic pH exhibits a nonunimodal distribution, the lower mean pH being 6.74 (+/- 0.23). When 3T3 cells pinocytose medium containing fluorescein dextran, pinosomes peripheral to the nucleus exhibit a lower pH than those closer to the ruffling edge of the cell. The present image processing system is analyzed for linearity of detection, light scattering artifacts, signal to noise ratio, standard curves, and spatial resolution. The results obtained from digital image analysis are shown to be comparable to the results from standard microspectrofluorometry. We also discuss several other applications of this ratio imaging technique in cell biology.

Animals↗
PubMed1983

The Women's Centre in Jamaica: an innovative project for adolescent mothers.

In 1978 the Jamaican Women's Bureau established the Women's Centre, the first project in the developing world to help pregnant teenagers avoid the usual hardships of poverty and dependence. The women take courses in academic subjects and prenatal and postnatal health, and receive good medical care. Fathers and parents are involved in counseling sessions where practical life skills, including family planning, are emphasized. The young mothers improve dramatically in self-confidence, self-esteem, and in their ability to take care of their babies. The Centre's success has helped to loosen the policies of the Jamaican government on the education of pregnant school-age women.

Adolescent↗