PubMed Health⌕ Search

Biomedical subjects

C O'Donovan

Publications and source records attributed to C O'Donovan.

At least 19 recordsLinked to original sources
PubMed2001

The human proteomics initiative (HPI).

The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focussed on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry.

Algorithms↗
PubMed2000

The role SWISS-PROT and TrEMBL play in the genome research environment.

SWISS-PROT, a curated protein sequence data bank, contains not only sequence data but also annotation relevant to a particular sequence. The annotation added to each entry is done by a team of biologists and comes, primarily, from articles in journals reporting the actual sequencing and sometimes characterisation. Review articles and collaboration with external experts also play a role along with the use of secondary databases like PROSITE and Pfam in addition to a variety of feature prediction methods. Annotation added by these methods is checked for relevance and likelihood to a particular sequence. The onset of genome sequencing has led to a dramatic increase in sequence data to be included in SWISS-PROT. This has led to the production of TrEMBL (Translation of the EMBL database). TrEMBL consists of entries in a SWISS-PROT format that are derived from the translation of all coding sequences in the EMBL nucleotide sequence database, that are not in SWISS-PROT. Unlike SWISS-PROT entries those in TrEMBL are awaiting manual annotation. However, rather than just representing basic sequence and source information, steps have been taken to add features and annotation automatically. In taking these steps it is hoped that TrEMBL entries are enhanced with some indication as to what a protein is, could or may be.

Amino Acid Sequence↗
PubMed1999

Removing redundancy in SWISS-PROT and TrEMBL.

SUMMARY: One of the distinguishing criteria of the SWISS-PROT protein sequence data bank is minimal redundancy. The introduction of TrEMBL as a supplementary database ensured the comprehensiveness of SWISS-PROT and TrEMBL but introduced some degree of redundancy. We developed a strategy to identify the redundancy present within and between SWISS-PROT and TrEMBL and its subsequent removal. AVAILABILITY: The tools mentioned in this paper are available on request.

Algorithms↗
PubMed1998

Vancomycin-resistant Enterococcus faecium in a Veterans Affairs Medical Center: association with antibiotic usage.

BACKGROUND: Colonization and infection with vancomycin-resistant Enterococcus faecium (VREF) has been associated with the use of vancomycin and other antibiotics in individual patients. The objective of this study was to determine the association of VREF with the aggregate usage of antibiotics on nursing units in a hospital. METHODS: This was a retrospective correlation study. A usage ratio was calculated for each parenteral antibiotic on each nursing unit as the per-bed usage by weight of that antibiotic divided by its average usage throughout the hospital. An average usage ratio (AUR) for each nursing unit was calculated as the mean of usage ratios of individual antibiotics. The AUR was used to compare the usage of antibiotics among nursing units in the hospital. The incidence of VREF infections on individual nursing units in a Veterans Affairs Medical Center was correlated with the usage of parenteral antibiotics separately and in aggregate in univariate and multivariate regression analyses. RESULTS: The AUR was strongly and positively correlated with the recovery of VREF on individual nursing units. By univariate analyses, increasing use of each antibiotic tested was associated with isolation of VREF but only clindamycin remained significant in the multivariate model. However, usage of various antibiotics was highly interrelated, and only clindamycin usage was significantly correlated with usage of all other antibiotics studied. Intensive care and acute care units and units with fewer patient beds were more likely to have patients with VREF infection than were subacute care units (p < 0.003) or larger units (p < 0.01). CONCLUSIONS: VREF infections were associated with greater aggregate antibiotic use on nursing units. Determination of antibiotic usage ratios may provide a convenient and useful tool for examining the association of antibiotic usage with other nosocomial infections.

Analysis of Variance↗
PubMed1998

Glycosyltransferases in SWISS-PROT.

SWISS-PROT is a curated protein sequence database with a high level of annotation (such as description of the function of a protein, its domain structure, post-translational modification, variants, etc), a minimal level of redundancy and a high level of integration with other databases. An ongoing project is to maintain the glycosyltransferase family of enzymes with comprehensive annotation and documentation in the SWISS-PROT database and to represent the most recent research developments.

Amino Acid Sequence↗
PubMed1997

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Ongoing genome sequencing projects have dramatically increased the number of protein sequences to be incorporated into SWISS-PROT. Since we do not want to dilute the quality standards of SWISS-PROT by incorporating sequences without proper sequence analysis and annotation, we cannot speed up the incorporation of new incoming data indefinitely. However, as we also want to make the sequences available as fast as possible, we introduced TREMBL (TRanslation of EMBL nucleotide sequence database), a supplement to SWISS-PROT. TREMBL consists of computer-annotated entries in SWISS-PROT format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in SWISS-PROT. While TREMBL is already of immense value, its computer-generated annotation does not match the quality of SWISS-PROTs. The main difference is in the protein functional information attached to sequences. With this in mind, we are dedicating substantial effort to develop and apply computer methods to enhance the functional information attached to TREMBL entries.

Amino Acid Sequence↗
PubMed1996

Usefulness of prolonged video-EEG monitoring in the elderly.

The diagnosis of epilepsy in the elderly can be difficult. We sought to determine whether video-EEG monitoring (VEEG) is useful in the diagnosis and management of elderly patients with epilepsy. We reviewed the medical records of 20 consecutive patients, over 60 years of age, selected from a total of 1423 patients referred over a five year period for VEEG evaluation for epilepsy. The usefulness of VEEG was assessed by comparing changes in (a) the diagnosis and treatment of these patients before and after VEEG, and (b) the assessments made by an epileptologist who reviewed medical records before and after receiving results of VEEG. Compared to the initial diagnosis by the referring physician, VEEG resulted in changes in either the diagnosis or treatment in 11/20 patients based on the results of VEEG. The epileptologist was able to correctly assess the diagnosis and treatment of 16/20 patients without knowledge of the VEEG results. In 4/20 cases, the VEEG provided additional information to the epileptologist. In selected elderly patients, VEEG is useful in establishing the diagnosis of epilepsy, and may change the management of these patients.

Aged↗
PubMed1995

Oral fluconazole versus amphotericin B bladder irrigation for treatment of candidal funguria.

A randomized trial was conducted to compare amphotericin B bladder irrigation (AmBBI) with oral fluconazole in terms of efficacy and safety in the treatment of candidal funguria. Fifty-three patients with two consecutive positive funal cultures of urine were randomized to undergo AmBBI (50 mg/L over 24 hours or 50 mg/L for 7 days) or to receive fluconazole (200 mg/d for 7 days). Urinary catheters were changed upon entry into the study and following therapy. Blood and urine specimens were obtained throughout the study. Candida albicans was the species isolated most frequently from urine cultures. Eradication rates for funguria at 24 hours and 5-9 days after therapy were 82.4% and 75%, respectively, with the 7-day AmBBI regimen; and 83.3% and 76.9%, respectively, with fluconazole. There were no differences in the posttherapy eradication rates between the regimens at 24 hours (P = .597) and at 5-9 days (P = .66). Candida glabrata was the predominant organism recovered from patients in the fluconazole group 5-9 days after the completion of therapy. Adverse events were limited to bladder fullness in a patient who underwent AmBBI and hypoglycemia in a patient who received concomitant therapy with fluconazole and glyburide. AmBBI (once or for 7 days) and fluconazole appear to be equally efficacious in the treatment of candidal funguria.

Administration, Oral↗
PubMed1994

Phenelzine reduces plasma vitamin B6.

Plasma levels of the active form of vitamin B6 (pyridoxal phosphate) in 19 patients taking phenelzine were found to be reduced on the average to approximately 54% of the value in a control group. There was no correlation of pyridoxal phosphate level with phenelzine daily dosage over the range of 30 mg to 90 mg. No symptoms of vitamin B6 deficiency peripheral neuropathy were found.

Adolescent↗
PubMed1993

Effect of lithium dosing schedule on urinary output.

Lithium has been reported to induce polyuria in up to 35% of patients receiving it. It has been suggested that polyuria may be reduced by using single rather than multiple daily dosing. However, this information is based on non-randomized studies, which used higher serum lithium levels than are currently used. In fact, the incidence of polyuria may be lower at currently used lithium levels, and the benefits of a single daily dose regimen on urine volume at these levels have not been assessed. We conducted a prospective randomized study to test the hypothesis that switching patients from multiple daily dose lithium to single daily dose lithium would significantly lower urine volume. Twenty-four patients previously stabilized on multiple daily dosing were randomly allocated to either single or multiple daily dose lithium. Twenty-four-hour urine volume, serum creatinine, creatinine clearance and serum lithium were measured at study entry and completion. Switching to single daily dose lithium did not significantly reduce the 24-h urine volume.

Adolescent↗
PubMed1991

Granulomatous gastritis: part of a vasculitic syndrome.

The previously unreported association of granulomatous gastritis and mononeuritis multiplex occurring in the setting of a vasculitic syndrome is described. The two conditions are considered to be associated and to be immune mediated. The previously accepted concept of isolated granulomatous gastritis is disputed.

Female↗
PubMed1991

Eradication of methicillin-resistant Staphylococcus aureus vaginitis with mupirocin.

We report the case of a 54-year-old, quadriplegic woman with a methicillin-resistant Staphylococcus aureus (MRSA) vaginal infection. After failing a five-day course of intravenous vancomycin therapy, the patient was treated for ten days with mupirocin ointment applied intravaginally twice daily, which resulted in eradication of the infection. This report details a novel approach in treating MRSA vaginal infections.

Administration, Intravaginal↗
PubMed1991

Role of a soy-based lactose-free formula in the outpatient management of diarrhea.

The introduction of a soy-based, lactose-free formula during the acute phase of diarrheal illness in infants has been shown to reduce stool output and duration of diarrhea in hospitalized patients. In the United States, most infants with acute diarrhea are treated as outpatients. In the present study, infants with diarrhea who were treated as outpatients were randomly assigned to receive either a soy-based, lactose-free formula alternating with oral rehydration solution from the beginning of therapy ("early feeding") or oral rehydration solution alone for the first 24 hours of therapy, followed by a soy-based, lactose-free formula alternating with oral rehydration solution (control group). Twenty-nine infants were randomly assigned to the early-feeding group and 27 to the control group. Twenty-one (72%) of 29 in the early-feeding group resolved their diarrhea at the end of 48 hours of therapy compared with 12 (44%) of 27 in the group fed oral rehydration solution only (P = .02). It is concluded that the introduction of a soy-based, lactose-free formula from the beginning of therapy for acute diarrhea in children treated as outpatients is safe and may shorten duration of diarrhea while maintaining adequate caloric intake.

Ambulatory Care↗
PubMed1989

Effects of low- and high-intensity exercise on plasma and cerebrospinal fluid levels of ir-beta-endorphin, ACTH, cortisol, norepinephrine and glucose in the conscious dog.

This study was designed to assess effects of exercise on plasma and cerebrospinal fluid (CSF) levels of immunoreactive (ir) beta-endorphin, ACTH, cortisol, norepinephrine, and glucose in the conscious dog. Dogs were exercised on a treadmill at low or high intensity (4.2 miles/h and a 6% or 20% incline) for 90 min, and were allowed to recover for 90 additional min. Neither intensity of exercise changed plasma glucose levels, but dose-related changes in glucose kinetics did occur. CSF glucose declined in both groups. During low intensity exercise, plasma levels of ir-beta-endorphin, ACTH, and cortisol increased with duration of exercise. During high intensity exercise, ACTH, ir-beta-endorphin and cortisol increased faster, and the integrated plasma response of these hormones was greater. Thus, peripheral release of ir-beta-endorphin, ACTH, and cortisol during exercise is dose-related with respect to time and intensity. CSF ir-beta-endorphin and ACTH both increased during low- but not high-intensity exercise. CSF cortisol rose markedly in both exercise groups. During high-intensity exercise there was a 50% increase in CSF norepinephrine, indicating that exercise induces alterations in central noradrenergic turnover. We conclude that exercise is a physiologic regulator of both peripheral and central neuroendocrine systems.

Adrenocorticotropic Hormone↗