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Biomedical subjects

J Clarke

Publications and source records attributed to J Clarke.

At least 91 records · Page 5Linked to original sources
PubMed2000

Alcohol use patterns predict high-risk HIV behaviors among active injection drug users.

The purpose of this study was to determine if alcohol use is independently associated with needle-sharing behavior. Participants were 196 active injection drug users recruited into the Providence, Rhode Island Needle Exchange program between July 1997 and March 1998. All subjects were administered a 45-minute questionnaire that included questions on quantity/frequency of alcohol use and the alcohol abuse section of the Structured Clinical Interview for DSM-III-R (SCID; Spitzer, Williams, Gibbon, & First, 1992). Drug risk behaviors, including needle sharing were assessed using the HIV Risk Assessment Battery (RAB; Navaline et al., 1994). Of 196 IDUs, 60% had used alcohol in the last month. Twenty-eight percent met criteria from the Diagnostic and Statistical Manual for Mental Disorders, 3rd ed., rev. (DSM-III-R; American Psychiatric Association, 1987) for alcohol abuse over the last 6 months. One half of IDUs had shared needles in the last 6 months. Increasing levels of alcohol ingestion were associated with greater RAB drug risk scores and greater needle sharing. Using multiple logistic regression, high-level "at-risk" alcohol use (odds ratio [OR], 2.5) and alcohol abuse (OR, 2.3) were significantly associated with needle sharing when controlling for other demographic and behavioral factors previously found to be associated with sharing. The results of this study showed that prevalence of alcohol abuse is high in this population and is associated with needle sharing. HIV prevention effects in needle exchange programs should address alcohol use.

Adult↗
PubMed2000

Depression among needle exchange program and methadone maintenance clients.

The objective of this study was to compare the prevalence of major depression in two cohorts of injection drug users, those enrolled in a Rhode Island Methadone Maintenance Treatment Program (MMTP) and those enrolled in a Rhode Island Needle Exchange Program (NEP) using cross-sectional interviews. Symptomatic and duration criteria for major depression in the last 6 months were identified using the Structured Clinical Interview for DSM-III-R (SCID). Among 528 persons interviewed, 54% of those in NEP and 42% of those in MMTP met criteria for major depression. Using multivariate logistic regression, women (odds ratio [OR] 2.5; 95% confidence interval [CI] 1.7-3.7), persons with alcohol use disorders (OR 1.7; 95% CI 1.1-2. 7), and persons without a current partner (OR 1.8; 95% CI 1.2-2.6) were more likely to be depressed controlling for age, race, education and HIV status. Persons enrolled in MMTP were less likely to be depressed (OR 0.6; 95% CI 0.4-0.8) than NEP. Higher rates of depression were found among NEP attendees than among those enrolled in MMTP. Mental health referrals should be part of the growing number of needle exchanges in the United States.

Adult↗
PubMed2000

Developing senior doctors as mentors: a form of continuing professional development. Report Of an initiative to develop a network of senior doctors as mentors: 1994-99.

BACKGROUND: Senior doctors report that mentoring skills are transferable to everyday medical practice and managing juniors. An analysis of views from consultants and general practitioners, who had trained together on a regional mentoring scheme, reveals significant potential for personal and professional development in such networks. CONTEXT: The Northern and Yorkshire Region Doctors' Development and Mentoring Network was set up in 1994. Since then there have been six programmes with 116 senior doctors participating. In 1997 there was an evaluation of the first four programmes. METHOD: Focus groups and postal questionnaire. RESULTS: There were responses from 71 senior doctors, giving a response rate of 86%, and responses from 78 professional stakeholders in 49 NHS organizations, a response rate of 54%. Results indicate that the programmes were highly valued by the participants, particularly with regard to: being part of a network of senior doctors; developing mentoring skills, and engaging in personal and professional development. The most difficult part of the programme was setting up mentoring networks for junior doctors, and reasons included: personal factors, such as levels of confidence in providing mentoring; cultural factors, such as juniors not wishing to be seen to need help, and organizational factors, such as lack of time allocated for mentoring. RECOMMENDATIONS AND ISSUES FOR FURTHER DEBATE: The positive benefits from the scheme raise questions about how to develop mentoring training for senior doctors. Issues include: developing mentors; who needs mentoring; mentoring and the organization; transferability of mentoring skills, and widening the network.

Clinical Competence↗
PubMed2000

Detection of Mycoplasma fermentans in broncho-alveolar lavage fluid specimens from AIDS patients with lower respiratory tract infection.

OBJECTIVE: To investigate the role of Mycoplasma fermentans in lower respiratory tract disease of HIV-positive patients. METHODS: A polymerase chain reaction (PCR) assay was used to detect M. fermentans in broncho-alveolar lavage (BAL) fluid and peripheral blood mononuclear cells (PBMCs) collected from 78 hospitalized HIV-positive patients with lower respiratory tract disease (the index group). BAL specimens were also assessed from two control groups; 25 HIV-positive patients without respiratory symptoms and 46 patients with a respiratory illness who did not have risk factors for HIV. RESULTS: Seventy-one (91%) of the 78 patients who comprised the index group had AIDS. Sixty-one patients provided BAL and PBMC specimens; 16 provided a BAL specimen and one only a PBMC specimen; 15 (25%) of the 61 patients had M. fermentans positive BAL fluid, of whom 10 (67%) also had a positive PBMC specimen. In contrast, of the 46 patients who had a negative BAL fluid, only three (6.4%) had a positive PBMC sample (P < 0.00001 Fisher's exact test). Overall, 21 (27%) of 77 patients had M. fermentans positive BAL fluid. Of these positive patients, 16 also had another microorganism in the BAL fluid and for five patients M. fermentans was detected alone. Compared with patients in the index group, none of the 46 BAL fluid specimens from patients at low risk of HIV infection was M. fermentans positive (P < 0.001, chi2 15.13). Two (8%) of the 25 HIV-positive patients without respiratory symptoms had a M. fermentans positive BAL fluid, positivity that was also statistically different from the index group (P = 0.045, chi2 4.01). CONCLUSIONS: M. fermentans frequently invades the lower respiratory tract of AIDS patients as an opportunist and may cause disease in some.

AIDS-Related Opportunistic Infections↗
PubMed2000

Adherence to antiretroviral therapy among HIV-infected methadone patients: effect of ongoing illicit drug use.

Methadone maintenance patients infected with human immunodeficiency virus (HIV) currently receiving antiretroviral therapy had HIV RNA testing and were surveyed regarding their adherence to their treatment regimens. Adherence was measured using self-report on four questions relating to medication use in the last day and last month and whether the patient took "drug holidays." Of the patients (N = 42), 52% were receiving two-drug antiretroviral therapy and 48% were receiving triple therapy that included a protease inhibitor. Persons on triple therapy reported higher rates of adherence on all measures and were more likely to have undetectable HIV RNA levels than persons on dual therapy (60% vs. 50%). Ongoing illicit drug injection was the only factor significantly associated (p < .05) with multiple measure nonadherence; however, it was not associated with undetectable HIV RNA level. Levels of nonadherence were comparable to estimates from other chronic diseases, but this finding has important implications for patients receiving highly active antiretroviral therapy.

Antiretroviral Therapy, Highly Active↗
PubMed2000

Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module.

An analysis of the folding of the 94 residue tenth fibronectin type III (fnIII) domain of human fibronectin (FNfn10) is presented. Use of guanidine isothiocyanate as a denaturant allows us to obtain equilibrium and kinetic data across a broad range of denaturant concentrations that are unavailable in guanidine hydrochloride. Equilibrium unfolding experiments show that FNfn10 is significantly more stable than has been reported previously. Comparison of equilibrium and kinetic parameters reveals the presence of an intermediate that accumulates at low denaturant concentrations. This is the first demonstration of three-state folding kinetics for a fnIII domain. We have previously shown that a homologous domain from human tenascin (TNfn3) folds by a two-state mechanism, but this does not necessarily indicate that the two proteins fold by different folding pathways.

Fibronectins↗
PubMed2000

The effects of disulfide bonds on the denatured state of barnase.

The effects of engineered disulfide bonds on protein stability are poorly understood because they can influence the structure, dynamics, and energetics of both the native and denatured states. To explore the effects of two engineered disulfide bonds on the stability of barnase, we have conducted a combined molecular dynamics and NMR study of the denatured state of the two mutants. As expected, the disulfide bonds constrain the denatured state. However, specific extended beta-sheet structure can also be detected in one of the mutant proteins. This mutant is also more stable than would be predicted. Our study suggests a possible cause of the very high stability conferred by this disulfide bond: the wild-type denatured ensemble is stabilized by a nonnative hydrophobic cluster, which is constrained from occurring in the mutant due to the formation of secondary structure.

Bacterial Proteins↗
PubMed2000

Drug resistance and drug combination features of the human immunodeficiency virus inhibitor, BCH-10652 [(+/-)-2'-deoxy-3'-oxa-4'-thiocytidine, dOTC].

The heterosubstituted nucleoside analogue dOTC [( )-2'-deoxy-3'-oxa-4'-thiocytidine, BCH-10652] is a racemic compound structurally related to 3TC (lamivudine), but has the oxygen and sulphur in the furanosyl ring transposed. Both the enantiomers (-)dOTC (BCH-10618) and (+)dOTC (BCH-10619) had equivalent activity against wild-type strains of HIV-1 in C8166 T-cells (EC50 1.0-10.0 microM) and in PBMCs (EC50 0.1-3.0 microM). Investigation of the activity of dOTC and its enantiomers against laboratory strains of HIV-1 with defined resistance to 3TC, AZT (zidovudine), ddl (didanosine), PMEA (adefovir), nevirapine and saquinavir indicated that sensitivity was maintained (<3-fold change in EC50) in all cases, with the exception of HIV-1RF 3TC-resistant viruses. The degree of resistance recorded for dOTC (four- to sevenfold), (-)dOTC (five- to eightfold) and (+)dOTC (five- to >18-fold) against these M1841 or M184V mutants, was significantly less than that recorded for 3TC (>100-fold). In addition, the inhibitory effect of the compounds against clinical isolates of HIV-1 recovered from patients with suspected resistance to 3TC and AZT was investigated. Clinical isolates were genotyped using the Murex Line Probe Assay (LiPA) and subgrouped into wild-type, 3TC-resistant and dual 3TC/AZT-resistant, as well as undefined or mixed genotype populations. Compared with the mean EC50 values obtained with genotypically and phenotypically wild-type clinical isolates, the mean EC50 values calculated for isolates phenotypically resistant to 3TC or 3TC and AZT were only 2.6-, 1.6- and 8.2-fold higher for dOTC, (-)dOTC and (+)dOTC, respectively. When the rate of emergence of virus resistant to dOTC and its enantiomers in vitro was investigated, virus resistant to (+)dOTC was readily selected for (<10 passages), and a methionine (ATG) to isoleucine (ATA) amino acid change at codon 184 was identified. In contrast, virus resistant to dOTC and (-)dOTC took longer to appear (15-20 passages), with a methionine (ATG) to valine (GTG) amino acid change at position 184 identified in both cases. In addition, virus passaged 20 times in the presence of dOTC also had a partial lysine (AAA) to arginine (AGA) exchange at position 65. These viruses showed only low-level resistance to dOTC and its enantiomers, but were highly resistant to 3TC. The antiviral effects of dOTC in combination with the nucleoside RT inhibitors AZT, 3TC, d4T (stavudine) and ddl, the non-nucleoside RT inhibitor nevirapine and the protease inhibitors saquinavir, ritonavir and indinavir was investigated. Two-way drug combination assays were carried out in peripheral blood mononuclear cell (PBMC) cultures by measuring the reduction in p24 viral antigen levels, and data was analysed using the MacSynergy II program. dOTC in combination with 3TC or d4T showed a moderate synergistic effect while all other combinations had an additive interaction.

Anti-HIV Agents↗
PubMed2000

Disseminated Mycoplasma fermentans in AIDS patients: several case reports.

We describe the clinical course of 2 HIV-positive patients in whom Mycoplasma fermentans was disseminated and persistent. We identified individuals in whom M. fermentans had been detected in a peripheral blood mononuclear cell (PBMC) or bronchoalveolar lavage (BAL) specimen. Of this group a number had archival specimens of interest: liver and/or bone marrow, taken to investigate a systemic illness, and a few had M. fermentans positive tissues. Two patients, NC and DP, had recurrent episodes of lower respiratory tract infection and fever and both had been investigated by bronchoscopy on 4 occasions. M. fermentans was detected in specimens taken 18 and 27 months apart for NC and DP respectively, and in between, and repeatedly in respiratory tract tissues of DP. Granuloma were identified in the liver of NC that was M. fermentans positive but no further evidence of opportunistic infection was found during his illness. Both patients had M. fermentans positive bone marrow specimens. Assessment of the patients' records suggested that in one patient M. fermentans may have contributed to the respiratory disease and in the other to the systemic disease.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Application of draft European Commission reference levels to a regional CT dose survey.

A survey of CT doses in Northern Ireland in the period between October 1995 and March 1997 was carried out. The survey included all but one of the 10 scanners in use at the time, and, additionally, two others that were replacement machines. The method used was to study standard protocols and calculate doses to the NRPB mathematical phantom, so that a direct comparison could be made with other surveys carried out in a similar fashion elsewhere. The survey addressed the patient radiation dose but not image quality or clinical outcomes. It is estimated that in Northern Ireland the contribution to collective dose to the population from CT is about 40% of that from all medical X-rays. The proposed European Commission reference quantities, weighted CT dose index and dose-length product were computed and their potential use evaluated. A full study of mean values of effective dose per examination revealed the average dose per examination was not significantly different from that found in the 1989 UK survey, although several procedures gave rise to doses that were high enough to be investigated with a view to justification or reduction. One of the scanners was found to give consistently high doses. It is likely that a revision of the mAs values used on this scanner will produce a significant reduction in patient doses without compromising image quality. When compared with the draft EC reference levels, fewer procedures were found to have excessively high dose values. The proposed EC reference levels would therefore be useful for continual monitoring of CT dose status, but do not appear to provide as comprehensive an assessment of patient exposure as that given by consideration of effective doses.

Clinical Protocols↗
PubMed2000

Use of antiretroviral therapies by HIV-infected persons receiving methadone maintenance.

HIV-infected persons receiving methadone maintenance must often seek their medical care at a separate site. However, little data is available on the receipt of antiretroviral therapy (ART), beliefs about ART, and influences on the decision to initiate ART among those referred off-site. HIV-infected injection drug users (n = 72) were interviewed at three methadone maintenance programs; 83% with CD4 cell counts under 500 reported that they had received ART. Of these persons, 56% had used three drug combination therapy. Beliefs about the benefits of ART included: increased survival, 96%; decreased viral load 87%; decreased HIV-related infections 87%; could cure HIV, 29%. For those receiving ART, physician input, CD4 count, and possible side effects were more important than friends, family or mass media in deciding to start ART. We conclude that the model of referral for HIV care off-site does not appear to impede access to ART for HIV-infected IDUs in methadone maintenance.

Adult↗
PubMed1999

The stratum corneum chymotryptic enzyme that mediates shedding and desquamation of skin cells is highly overexpressed in ovarian tumor cells.

BACKGROUND: Proteases play essential roles in the process of tumor invasion and metastasis. The serine protease stratum corneum chymotryptic enzyme (SCCE) has been purified from human stratum corneum and is known to contribute to the cell shedding process by catalyzing the degradation of intercellular cohesive structures at the skin surface. The presence of SCCE on the surface of tumor cells suggests it also may contribute to the process of tumor cell shedding, resulting in early metastasis of carcinoma. METHODS: Gene expression of SCCE was investigated in 44 ovarian tumors (12 low malignant potential tumors and 32 carcinomas) and 10 normal ovaries by quantitative polymerase chain reaction (PCR). The PCR product was labeled with (32)P and a phosphoimager was used to determine the relative expression of SCCE compared with an internal control Beta-tubulin. mRNA transcripts were studied by Northern blot hybridization and protein expression and localization was examined by Western blot analysis and immunohistochemistry. RESULTS: mRNA expression levels of SCCE were elevated significantly in 66.7% of 12 low malignant potential tumors and 78.1% of 32 carcinomas. Furthermore, SCCE protein was abundant in tumor cells and tumor cell lines that overexpressed the mRNA transcript. CONCLUSIONS: The results of the current study suggest that SCCE frequently is overexpressed in ovarian tumors and therefore may contribute to tumor cell growth, tumor spread, and the metastatic potential of ovarian tumor cells.

Blotting, Northern↗
PubMed1999

Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway.

BACKGROUND: Are folding pathways conserved in protein families? To test this explicitly and ask to what extent structure specifies folding pathways requires comparison of proteins with a common fold. Our strategy is to choose members of a highly diverse protein family with no conservation of function and little or no sequence identity, but with structures that are essentially the same. The immunoglobulin-like fold is one of the most common structural families, and is subdivided into superfamilies with no detectable evolutionary or functional relationship. RESULTS: We compared the folding of a number of immunoglobulin-like proteins that have a common structural core and found a strong correlation between folding rate and stability. The results suggest that the folding pathways of these immunoglobulin-like proteins share common features. CONCLUSIONS: This study is the first to compare the folding of structurally related proteins that are members of different superfamilies. The most likely explanation for the results is that interactions that are important in defining the structure of immunoglobulin-like proteins are also used to guide folding.

Amino Acid Motifs↗
PubMed1999

Victims as victimizers: physical aggression by persons with a history of childhood abuse.

BACKGROUND: Substance abuse has been called the dominant characteristic of families involved in child abuse cases, but the frequency with which childhood victims become adult victimizers remains uncertain. OBJECTIVE: To examine whether a history of childhood sexual or physical abuse is associated with becoming a victimizer (ie, abusing or assaulting others) as an adult. METHODS: Interview data were collected from 439 persons in Providence, RI, from July 1997 through March 1998 who had a history of intravenous drug use. Victimizers were defined as adults who had ever physically abused or assaulted a family member or sexual partner (eg, kicked, hit, choked, shot, stabbed, burned, or held at gunpoint). We compared persons who had a history of victimizing others with those who did not have such a history by bivariate and multivariate analyses. Variables included demographic factors as well as a history of sexual or physical abuse before the age of 16 years. abuse was 51% for women and 31% for men. Seventeen percent of our subjects reported being victimizers. Among persons who reported being victims of either physical or sexual childhood abuse, 28% victimized others; among those who denied a history of childhood abuse, 10% victimized others. Two thirds of victimizers reported being intoxicated while assaulting others. When we used logistic regression to control for sex, having children, education, race, and history of incarceration, childhood abuse was significantly and independently associated with becoming a victimizer (odds ratio, 3.6; 95% confidence interval, 2.1-6.1). CONCLUSIONS: Large numbers of intravenous drug users, both men and women, have victimized family members or sexual partners. We confirm a high rate of childhood abuse among this population and demonstrate that among intravenous drug users past abuse is associated with becoming a victimizer as an adult. Primary care providers should be alert to this cycle of violence.

Adult↗
PubMed1999

Regulation of the photosynthetic electron transport chain.

The regulation of electron transport between photosystems II and I was investigated in the plant Silene dioica L. by means of measurement of the kinetics of reduction of P(700) following a light-to-dark transition. It was found that, in this species, the rate constant for P(700) reduction is sensitive to light intensity and to the availability of CO(2). The results indicated that at 25 degrees C the rate of electron transport is down-regulated by approximately 40-50% relative to the maximum rate achievable in saturating CO(2) and that this down-regulation can be explained by regulation of the electron transport chain itself. Measurements of the temperature sensitivity of this rate constant indicated that there is a switch in the rate-limiting step that controls electron transport at around 20 degrees C: at higher temperatures, CO(2) availability is limiting; at lower temperatures some other process regulates electron transport, possibly a diffusion step within the electron transport chain itself. Regulation of electron transport also occurred in response to drought stress and sucrose feeding. Measurements of non-photochemical quenching of chlorophyll fluorescence did not support the idea that electron transport is regulated by the pH gradient across the thylakoid membrane, and the possibility is discussed that the redox potential of a stromal component may regulate electron transport.Keywords: DeltapH. Electron transport. Photosynthesis. Photosynthetic control. Redox regulation. Silene (photosynthesis)

Journal Article↗
PubMed1999

Mechanical and chemical unfolding of a single protein: a comparison.

Is the mechanical unraveling of protein domains by atomic force microscopy (AFM) just a technological feat or a true measurement of their unfolding? By engineering a protein made of tandem repeats of identical Ig modules, we were able to get explicit AFM data on the unfolding rate of a single protein domain that can be accurately extrapolated to zero force. We compare this with chemical unfolding rates for untethered modules extrapolated to 0 M denaturant. The unfolding rates obtained by the two methods are the same. Furthermore, the transition state for unfolding appears at the same position on the folding pathway when assessed by either method. These results indicate that mechanical unfolding of a single protein by AFM does indeed reflect the same event that is observed in traditional unfolding experiments. The way is now open for the extensive use of AFM to measure folding reactions at the single-molecule level. Single-molecule AFM recordings have the added advantage that they define the reaction coordinate and expose rare unfolding events that cannot be observed in the absence of chemical denaturants.

Calmodulin-Binding Proteins↗
PubMed1999

The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.

Most cases of autosomal dominant polycystic kidney disease (ADPKD) are the result of mutations in the PKD1 gene. The PKD1 gene codes for a large cell-surface glycoprotein, polycystin-1, of unknown function, which, based on its predicted domain structure, may be involved in protein-protein and protein-carbohydrate interactions. Approximately 30% of polycystin-1 consists of 16 copies of a novel protein module called the PKD domain. Here we show that this domain has a beta-sandwich fold. Although this fold is common to a number of cell-surface modules, the PKD domain represents a distinct protein family. The tenth PKD domain of human and Fugu polycystin-1 show extensive conservation of surface residues suggesting that this region could be a ligand-binding site. This structure will allow the likely effects of missense mutations in a large part of the PKD1 gene to be determined.

Amino Acid Sequence↗