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Biomedical subjects

B Foley

Publications and source records attributed to B Foley.

At least 19 recordsLinked to original sources
PubMed2001

Retrieval and on-the-fly alignment of sequence fragments from the HIV database.

MOTIVATION: The amount of HIV-1 sequence data generated (presently around 42000 sequences, of which more than 22000 are from the V3 region of the viral envelope) presents a challenge for anyone working on the analysis of these data. A major problem is obtaining the region of interest from the stored sequences, which often contain but are not limited to that region. In addition, multiple alignment programs generally cannot deal with the large numbers of sequences that are available for many HIV-1 regions. We set out to provide our users with a tool that will retrieve and create an initial alignment of the HIV sequences that are available for a given genomic region. RESULTS: The MPAlign (Multiple Pairwise Alignment) web interface is a collection of Perl scripts that retrieves sequences from the Los Alamos HIV sequence database based on a number of search parameters. All sequences were pairwise-aligned to a model sequence using the Hidden Markov Model-based program HMMER. The HMMER model is general enough to accommodate virtually all HIV-1 sequences stored in the database. To create a multiple sequence alignment, gaps were inserted into the sequences during retrieval, so that they are aligned to one another. Retrieving and aligning the almost 560 gp120 sequences (approximately>1500 nt) stored in the database is at least 1500 times faster than a similar Clustal alignment.

Algorithms↗
PubMed2001

Treatment of exercise-induced muscle injury via hyperbaric oxygen therapy.

PURPOSE: This study examined the role of hyperbaric oxygen therapy (HBO) in the treatment of exercise-induced muscle injury. METHODS: 21 college-aged male volunteers were assigned to three groups: control, immediate HBO (iHBO), and delayed HBO (dHBO). All subjects performed 6 sets (10 repetitions per set) of eccentric repetitions with a load equivalent to 120% of their concentric maximum. HBO treatments consisted of 100-min exposure to 2.5 ATA and 100% oxygen with intermittent breathing of ambient air (30 min at 100% O2, 5 min at 20.93% O2). HBO treatments began either 2 (iHBO) or 24 h (dHBO) postexercise and were administered daily through day 4 postexercise. Forearm flexor cross-sectional area (CSA) and T2 relaxation time via magnetic resonance imaging (MRI) were assessed at baseline, 2, 7, and 15 d postinjury. Isometric strength and rating of perceived soreness of the forearm flexors were assessed at baseline, 1, 2, 3, 4, 7, and 15 d postinjury. Serum creatine kinase (CK) was assessed on day 0 and on days 1, 2, 7, and 15 postinjury. RESULTS: Mean baseline CSA values were: 2016.3, 1888.5, and 1972.2 mm2 for control, iHBO, and dHBO, respectively. All groups showed significant increases in CSA in response to injury (21% at 2 d, 18% at 7 d) (P < 0.0001), but there were no significant differences between groups (P = 0.438). Mean baseline T2 relaxation times were: 26.18, 26.28, and 27.43 msec for control, iHBO, and dHBO, respectively. Significant increases in T2 relaxation time were observed for all groups (64% at 2 d, 66% at 7 d, and 28% at 15 d) (P < 0.0001), but there were no significant differences between groups (P = 0.692). Isometric strength (P < 0.0001), serum CK levels (P = 0.0007), and rating of perceived soreness (P < 0.0001) also indicated significant muscle injury for all groups, but there were no differences between groups (P = 0.459, P = 0.943, and P = 0.448, respectively). CONCLUSION: These results suggest that hyperbaric oxygen therapy was not effective in the treatment of exercise-induced muscle injury as indicated by the markers evaluated.

Adult↗
PubMed2001

Analysis of outbreaks of infectious intestinal disease in Ireland: 1998 and 1999.

Surveillance of general outbreaks of infectious gastroenteritis was introduced in 1998 by the Food Safety Authority of Ireland (FSAI), in co-operation with the eight health boards. A total of 67 general outbreaks of gastroenteritis in Ireland were reported to the FSAI in 1998 and 1999. Over 1900 people were ill as a result of these outbreaks. Four percent required hospitalisation and there were two deaths. The duration of the outbreaks varied between one day and 38 days. Salmonellae (44%) and small round structured viruses (SRSV) (12%) were the most commonly reported pathogens. In 25% of the outbreaks the aetiology was unknown. The commonest settings were restaurants, hotels and take-aways, which accounted for 45% (30/67) of all outbreaks. Sixteen percent of all outbreaks occurred in hospitals and residential institutions. Over half of the outbreaks were reported to be foodborne, 63% of which were due to various serotypes of Salmonella enterica. Eggs were implicated as the vehicle of infection in 13% of all outbreaks. An infected food handler was identified in almost one third of outbreaks, although it could not be established if this had contributed directly to the outbreak.

Cross Infection↗
PubMed2000

Apparent founder effect during the early years of the San Francisco HIV type 1 epidemic (1978-1979).

HIV-1 envelope sequence variants were RT-PCR amplified from serum samples cryopreserved in San Francisco in 1978-1979. The HIV-1 subtype B env V3-V5 sequences from four homosexual men clustered phylogenetically, with a median nucleotide distance of 2.8%, reflecting a recent common origin. These early U.S. HIV-1 env variants mapped close to the phylogenetic root of the subtype B tree while env variants collected in the United States throughout the 1980s and 1990s showed, on average, increasing genetic diversity and divergence from the subtype B consensus sequence. These results indicate that the majority of HIV-1 currently circulating in the United States may be descended from an initial introduction and rapid spread during the mid- to late 1970s of subtype B viruses with limited variability (i.e., a founder effect). As expected from the starburst-shaped phylogeny of HIV-1 subtype B, contemporary U.S. strains were, on average, more closely related at the nucleic acid and amino acid levels to the earlier 1978-1979 env variants than to each other. The growing levels of HIV-1 genetic diversity, one of multiple obstacles in designing a protective vaccine, may therefore be mitigated by using epidemic founding variants as antigenic strains for protection against contemporary strains.

AIDS Vaccines↗
PubMed2000

Hyponatremia and seizures in an ultradistance triathlete.

Hyponatremia is being increasingly recognized as a complication of participation in ultra-endurance sports. Reported is the case of an Ironman triathlete who collapsed at the end of the race, having gained 5% in body weight. His serum sodium concentration at the finish was 116 mmol/L. After an Intensive Care Unit course complicated by recurrent seizures, he eventually made a complete neurologic recovery. The pathogenesis of hyponatremia and its management in such cases is discussed.

Adult↗
PubMed2000

Detection of sporadic cases of Norwalk-like virus (NLV) and astrovirus infection in a single Irish hospital from 1996 to 1998.

BACKGROUND: 'Norwalk-like viruses' (NLV) and astroviruses are recognised as the most important etiologic agents of viral gastroenteritis, excluding rotaviruses. However, neither of these two groups of viruses is routinely screened for in Irish hospital laboratories. OBJECTIVE: The objective of this study was to examine faeces collected from patients with non-bacterial, non-rotaviral gastroenteritis and examine if NLVs and astroviruses could be identified as the causative agents of the illness. STUDY DESIGN: Faecal specimens were collected from a single Irish hospital from February 1996 to June 1998. Three hundred and sixty samples were tested for the presence of NLVs using newly designed inosine-containing degenerate primers. Two hundred and three faecal specimens from paediatric patients were screened for the presence of astroviruses. RESULTS: the results of the screening study were that 29 (8%) specimens were found to be positive for NLV by reverse transcription polymerase chain reaction (RT-PCR) and 15 (7%) specimens from paediatric patients were found to be positive for astroviruses. Genotyping of the NLV-positive samples determined that four of the isolates were from genotype I (G1) and 25 were G2. The G2 positive specimens were further subtyped by oligonucleotide probing and the majority (n = 21) were found to be subtype P2-B, with four isolates being typed as P2-A. No P1-B isolates were found. CONCLUSIONS: This is the first report of detection of sporadic cases of NLV and astrovirus in Ireland. The results obtained highlight the need for continued surveillance of these viruses and the development of rapid detection systems for use in clinical laboratories.

Adolescent↗
PubMed1999

Quantifying GPIIb/IIIa receptor binding using 2 monoclonal antibodies: discriminating abciximab and small molecular weight antagonists.

BACKGROUND: Dosing of glycoprotein (GP) IIb/IIIa receptor antagonists is frequently based on the inhibition of platelet aggregation, which may be influenced by the agonist used or concurrent medications. Here we describe a monoclonal antibody-based technique to quantify total and ligand-occupied GPIIb/IIIa receptors. METHODS AND RESULTS: In vitro binding of monoclonal antibodies, LYP18 (Mab1) and 4F8 (Mab2), to the GPIIb/IIIa complex, was characterized using purified receptor and to platelets by flow cytometry. Patients undergoing coronary angioplasty received a single 20 mg dose of the oral GPIIb/IIIa antagonist, xemilofiban, or matching placebo, and antibody binding was compared with inhibition of platelet aggregation. Mab1 and Mab2 were bound to purified GPIIb/IIIa and to unoccupied, inactivated receptor on platelets. Mab2 identified the beta3 subunit, whereas Mab1 was complex-specific. Neither antibody interfered with the other's binding, suggesting that they identified distinct sites. Mab1 identified 53 300+/-5423 GPIIb/IIIa sites per platelet, whereas Mab2 identified 50 120+/-5066 sites per platelet. Mab1 binding was inhibited by abciximab in a dose dependent manner (IC50, 0.85+/-0.1 microg/mL), whereas Mab2 binding was unaffected. In contrast, the 2 small molecular weight antagonists, SC-57101A (IC50, 0.22+/-0.06 micromol/L) and eptifibatide (IC50, 0.35+/-0.14 micromol/L) inhibited Mab2 but not Mab1 binding. In patients treated with xemilofiban, Mab1 binding was unaltered but Mab2 binding decreased from 37 930+/-2061 sites per platelet at baseline to 8318+/-870 sites per platelet 6 hours after dosing (P<0.0001). Platelet aggregation to adenosine diphosphate (20 micromol/L) fell to 3+/-3% of baseline in line with the inhibition of Mab2 binding (correlation coefficient 0.8, P<0.0001). CONCLUSIONS: Mab1 and Mab2 bind to GPIIb/IIIa and are differentially displaced by abciximab and small molecular weight antagonists. These antibodies may be used to monitor receptor number and occupancy during administration of a GPIIb/IIIa antagonist.

Abciximab↗
PubMed1999

Percutaneous catheter and guidewire fragmentation with local administration of recombinant tissue plasminogen activator as a treatment for massive pulmonary embolism.

The purpose of this article is to report four patients with massive pulmonary embolism treated with percutaneous catheter and guidewire fragmentation and local administration of recombinant tissue plasminogen activator (r-TPA). Four patients with massive pulmonary embolism initially underwent pulmonary angiography. Thrombus fragmentation was performed with both standard angiographic guidewires and catheters followed by local infusion of 41-200 mg of r-TPA. Pulmonary angiography was repeated after treatment. All patients survived with improvement in their clinical status and eventual discharge from hospital. Angiography in all patients post treatment demonstrated improvement in pulmonary perfusion (mean Miller score before treatment 22.5; mean Miller score after treatment 5.75). No patient had a significant complication. Mechanical fragmentation of the thrombus followed by local infusion of r-TPA was an effective treatment for massive pulmonary embolism in these four patients with no significant complications.

Aged↗
PubMed1999

Passivity vs. militancy: a Q methodological study of nurses' industrial relations on Merseyside (England).

This paper describes a Q methodological study of accounts of nurses' industrial relations expressed by a sample of nurses (n = 60) drawn from the geographical area of Merseyside, United Kingdom (UK). The participants completed a 65-item Q sort made up of statements which could be ranked in terms of their relevance to an understanding of their industrial relations situation. Of interest was the importance of the narrative accounts which nurses draw upon in making sense of their employment relations, having the potential to underpin or delimit their actions. The notion of industrial action was an important focus of this research. Q methodology was chosen to allow the meaningful investigation of such subjectivity, with interesting tensions between differing notions of professionalism and militancy apparent from the analysis. Six accounts of industrial relations, which are available to be drawn on by nurses, are described and interpreted within a social constructionist framework. Some implications for the conduct of nurses' industrial relations in the UK are contemplated.

England↗
PubMed1999

Surviving cancer competently intervention program (SCCIP): a cognitive-behavioral and family therapy intervention for adolescent survivors of childhood cancer and their families.

Psychological reactions to having had childhood cancer often continue after treatment ends, for survivors and their parents. Based on our previous research, we developed an intervention program for adolescent survivors of childhood cancer, their parents, and siblings. Surviving Cancer Competently: An Intervention Program--SCCIP--is a one-day family group intervention that combines cognitive-behavioral and family therapy approaches. The goals of SCCIP are to reduce symptoms of distress and to improve family functioning and development. SCCIP is described and data from a pilot study of 19 families are presented. Program evaluation data indicated that all family members found SCCIP helpful. Standardized measures administered before the intervention and again at 6 months after SCCIP showed that symptoms of posttraumatic stress and anxiety decreased. Changes in family functioning were more difficult to discern. Overall, the results were promising with regard to the feasibility of the program and its potential for reducing symptoms of distress for all family members.

Adaptation, Psychological↗
PubMed1999

VP4 and VP7 genotyping of rotavirus samples recovered from infected children in Ireland over a 3-year period.

Between September 1995 and August 1998, the incidence and diversity of the main human rotavirus genotypes (G1, G2, G3, and G4 and P[8], P[4], P[6], and P[9]) among Irish children were determined by using established and adapted reverse transcriptase PCR-based genotyping methods. From a total of 193 rotavirus-positive specimens collected from nine hospitals we successfully identified the P type in 182 (94%) of the samples and the G type in 165 (85.5%) of the samples. Only four samples could not be assigned a G or P type. Two P types existed in Ireland, P[8] (78%) and P[4] (16%), and their relative incidence varied over the 3 years of this study. No P[6] or P[9] types were detected. G1 was the most predominant G type (55%), and the incidences of G2, G3, and G4 isolates were 15.5, 1, and 11%, respectively. Three percent of the samples tested had a mixed G type. A P and G type was assigned to 158 (81.8%) of samples. Of the typeable samples, G1 P[8] was the most prevalent (65%), whereas G2 P[4] (17%), G3 P[8] (1%), G4 P[8] (12%), and mixed types (all G1/ G4 P[8]) (4%) were detected less frequently. In the third year a significant genotypic shift from G1 P[8] to G2 P[4] and G4 P[8] was observed. During the study, we noticed that the inclusion of random primers during cDNA synthesis greatly increased the specificity of the PCR typing assays. No correlation was seen between the contributing hospitals and a specific genotype. In conclusion, the coverage of infection given by the recently licensed tetravalent vaccine would be significantly high in Ireland, although future monitoring of genotypic changes among Irish isolates should be encouraged.

Antigens, Viral↗
PubMed1998

Impact of intravenous nitroglycerin on pulsed Doppler indexes of left ventricular filling in acute anterior myocardial infarction.

BACKGROUND: Restrictive transmitral Doppler flow patterns are associated with heart failure in acute myocardial infarction (AMI). METHODS AND RESULTS: The objective of this study was to evaluate the effect of intravenous nitroglycerin on the transmitral pulsed Doppler patterns in patients with anterior AMI. Twenty-four patients with anterior AMI were randomly assigned to receive incremental intravenous nitroglycerin or placebo over a 16-minute period with change to the other arm after a washout period. Left ventricular filling was assessed with transmitral pulsed Doppler echocardiography. According to the baseline E/A ratio, patients were divided into a restrictive group (n = 17, E/A ratio > or =21.4) and a nonrestrictive group (n = 7, E/A <1.4). In the restrictive group after administration of nitroglycerin the E/A ratio decreased (1.9+/-0.7 to 1.1+/-0.2, P < .001), E-wave peak velocity decreased (71+/-10 to 60+/-9 cm/s, P < .01), and A-wave peak velocity increased (39+/-9 to 58+/-8 cm/s, P < .01 ). In the nonrestrictive group there were no significant changes after nitroglycerin infusion in the E/A ratio (1.1+/-0.2 to 0.8+/-0.1, not significant), peak E-wave velocity (55+/-4 to 47+/-6 cm/s), and peak A-wave velocity (49+/-8 to 52+/-8 cm/s). Deceleration time increased significantly in both groups after administration of nitroglycerin. Placebo did not result in significant changes in hemodynamic or Doppler parameters in either group. CONCLUSIONS: Intravenous nitroglycerin administration was associated with reversal of restrictive left ventricular diastolic filling pattern on pulsed wave Doppler in patients with anterior AMI.

Aged↗
PubMed1997

Evidence for copurification of HERV-K-related transcripts and a reverse transcriptase activity in human platelets from patients with essential thrombocythemia.

We have previously reported that particles resembling retroviral particles and possessing an RNA-directed DNA polymerase activity can be prepared from platelets. Furthermore, we and others have shown that these particles are present at higher levels in patients with essential thrombocythemia and polycythemia vera. We show here that these particles package RNA molecules that encode HERV-K-related pol genes. A subset of the RNA molecules that are packaged are likely to encode the RNA directed DNA polymerase activity and, because these RNAs possess long/full-length open reading frames for the reverse transcriptase and RNaseH (also for part of the integrase domains in genomic clones) of HERV-K, we propose that these transcripts are indeed strong candidates for encoding the enzyme activity found in these particles. Moreover, by using a modification of the polymerase chain reaction-based reverse transcriptase assay in which activated DNA is added during cDNA synthesis to suppress DNA polymerase-mediated RNA-directed DNA synthesis, we have found that the particle-associated enzyme behaves like a retroviral reverse transcriptase, further supporting the conclusion that retrovirus-like, perhaps HERV-K sequences, encode this enzyme activity.

Adult↗
PubMed1997

Elevated levels of circulating soluble adhesion molecules in peripheral blood of patients with unstable angina.

We have demonstrated increased levels of the circulating soluble adhesion molecules (sCAMs), ICAM-1, VCAM-1, and E-selectin in patients with unstable angina compared with healthy controls. Our findings support the role of inflammation in clinically unstable coronary disease, and may indicate a potential role for measurement of peripheral sICAM levels as a marker for inflammatory activity in atherosclerotic plaque.

Adult↗
PubMed1997

Elevated levels of circulating soluble adhesion molecules in patients with nonrheumatic aortic stenosis.

Increased serum levels of soluble adhesion molecules are found in various disorders of inflammatory or immunologic etiology. We found elevated levels of the soluble adhesion molecules ICAM-1, VCAM-1, and E-selectin in patients with nonrheumatic aortic stenosis, suggesting that inflammation may be important in the pathogenesis of this condition, which is generally believed to be degenerative.

Aortic Valve Stenosis↗
PubMed1996

Emotional distress among males with "syndrome X".

The present study examined traditional risk factors and various indices of emotional distress in males with positive angiograms (N = 122), "syndrome X" males with negative or nominal results on angiogram (N = 53), and age- and socioeconomic status-matched males with no manifest history of otherosclerotic disease (N = 56). Syndrome X patients reported more depression on the Ketterer Stress Symptom Frequency Checklist (KSSFC) than positive angiographic patients. And compared with healthy controls, they were more likely to be perceived by a spouse/friend as depressed and anxious on the KSSFC, scored higher on the Framingham Type A Scale, and reported more unprovoked nocturnal awakening. Syndrome X patients generally appear to be similar to patients with positive angiograms with regard to traditional risk factor history but are more distressed than healthy controls. This becomes most evident when denial is circumvented by discussion with significant others or inquiries are "framed" appropriately.

Analysis of Variance↗