Search PubMed⌕ Search

Biomedical subjects

A Bourgeois

Publications and source records attributed to A Bourgeois.

At least 19 recordsLinked to original sources
PubMed2004

Feature extraction and signal processing for nylon DNA microarrays.

BACKGROUND: High-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature location or in signal integration methodology may be a significant contribution to the observed variance in gene expression levels. RESULTS: We explore sources of variability in feature extraction from DNA microarrays on Nylon membrane with radioactive detection. We introduce a mathematical model of the signal emission and derive methods for correcting biases such as overshining, saturation or variation in probe amount. We also provide a quality metric which can be used qualitatively to flag weak or untrusted signals or quantitatively to modulate the weight of each experiment or gene in higher level analyses (clustering or discriminant analysis). CONCLUSIONS: Our novel feature extraction methodology, based on a mathematical model of the radioactive emission, reduces variability due to saturation, neighbourhood effects and variable probe amount. Furthermore, we provide a fully automatic feature extraction software, BZScan, which implements the algorithms described in this paper.

Algorithms↗
PubMed2001

Characterization of a novel simian immunodeficiency virus from guereza colobus monkeys (Colobus guereza) in Cameroon: a new lineage in the nonhuman primate lentivirus family.

Exploration of the diversity among primate lentiviruses is necessary to elucidate the origins and evolution of immunodeficiency viruses. During a serological survey in Cameroon, we screened 25 wild-born guereza colobus monkeys (Colobus guereza) and identified 7 with HIV/SIV cross-reactive antibodies. In this study, we describe a novel lentivirus, named SIVcol, prevalent in guereza colobus monkeys. Genetic analysis revealed that SIVcol was very distinct from all other known SIV/HIV isolates, with average amino acid identities of 40% for Gag, 50% for Pol, 28% for Env, and around 25% for proteins encoded by five other genes. Phylogenetic analyses confirmed that SIVcol is genetically distinct from other previously characterized primate lentiviruses and clusters independently, forming a novel lineage, the sixth in the current classification. Cercopithecidae monkeys (Old World monkeys) are subdivided into two subfamilies, the Colobinae and the Cercopithecinae, and, so far, all Cercopithecidae monkeys from which lentiviruses have been isolated belong to the Cercopithecinae subfamily. Therefore, SIVcol from guereza colobus monkeys (C. guereza) is the first primate lentivirus identified in the Colobinae subfamily and the divergence of SIVcol may reflect divergence of the host lineage.

Amino Acid Sequence↗
PubMed2000

Most env and gag subtype A HIV-1 viruses circulating in West and West Central Africa are similar to the prototype AG recombinant virus IBNG.

The genetic subtype was identified in gag and env of 219 HIV-1-positive samples collected in different African countries, 44 from Senegal, 55 from Cameroon, 82 from Gabon, and 38 from Djibouti. In total, 20 (9.1%) samples had discordant subtypes between gag and env, 6 of 44 (13.9%) in Senegal, 4 of 55 (7.2%) in Cameroon, 1 of 38 (2.6%) in Djibouti, and 10 of 82 (12.1%) in Gabon. Subtypes A and G were predominantly involved in the recombination events. Phylogenetic tree analysis of gag showed that an important number of the A sequences form a distinct subcluster with the AG-IBNG prototype strain (a complex A/G mosaic virus): 27 of 32 (84.3%) in Senegal, 12 of 17 (70.6%) in Nigeria, 24 of 39 (61.5%) in Cameroon, and 38 of 70 (54.3%) in Gabon. Full-length genome analysis of 3 and additional sequences in pol for 10 such strains confirmed that they have a similar complex A/G mosaic genomic structure. These data suggest that in West Africa, most probably between 60% and 84% of the subtype A viruses are recombinant AG-IBNG viruses. This finding has potential implications on future vaccine, diagnostic, and treatment strategies. The actual and future role of these viruses in the global pandemic must be monitored in all new molecular epidemiologic studies, a discrimination between subtype A and AG-IBNG-like viruses is necessary.

Amino Acid Sequence↗
PubMed2000

Near-full-length genome sequencing of divergent African HIV type 1 subtype F viruses leads to the identification of a new HIV type 1 subtype designated K.

We recently reported a high divergence among African subtype F strains. Three well-separated groups (F1, F2, and F3) have been shown based on the phylogenetic analysis of the p24 gag and envelope sequences with genetic distances similar to those observed for known subtypes. In this study, we characterized the near-full-length genomes of two strains from epidemiological unlinked individual belonging to each of the subgroups: F1 (96FR-MP411), F2 (95CM-MP255 and 95CM-MP257), and F3 (96CM-MP535 and 97ZR-EQTB11). Phylogenetic analysis of the near-full-length sequences and for each of the genes separately showed the same three groups, supported by high bootstrap values. Diversity plotting, BLAST subtyping, and bootstrap plotting confirmed that the divergent F strains correspond to nonrecombinant viruses. The divergence between F1 and F2 is consistently lower than that seen in any other intersubtype comparison, with the exception of subtypes B and D. Based on all the different analyses, we propose to divide subtype F into two subclades, with F1 gathering the known subtype F strains from Brazil and Finland, and our African strain (96FR-MP411), and F2 containing the 95CM-MP255 and 95CM-MP257 strains from Cameroon. The F3 strains, 97ZR-EQTB11 from the Democratic Republic of Congo and 96CM-MP535 from Cameroon, meet the criteria of a new subtype designated as K. The equidistance of subtype K to the other subtypes of HIV-1 suggests that this subtype existed as long as the others, the lower distance between B and D, and between F1 and F2 suggest a more recent subdivision for these latter strains.

Africa↗
PubMed2000

Genetic diversity of protease and reverse transcriptase sequences in non-subtype-B human immunodeficiency virus type 1 strains: evidence of many minor drug resistance mutations in treatment-naive patients.

Most human immunodeficiency virus (HIV) drug susceptibility studies have involved subtype B strains. Little information on the impact of viral diversity on natural susceptibility to antiretroviral drugs has been reported. However, the prevalence of non-subtype-B (non-B) HIV type 1 (HIV-1) strains continues to increase in industrialized countries, and antiretroviral treatments have recently become available in certain developing countries where non-B subtypes predominate. We sequenced the protease and reverse transcriptase (RT) genes of 142 HIV-1 isolates from antiretroviral-naive patients: 4 belonged to group O and 138 belonged to group M (9 subtype A, 13 subtype B, 2 subtype C, 5 subtype D, 2 subtype F1, 9 subtype F2, 4 subtype G, 5 subtype J, 2 subtype K, 3 subtype CRF01-AE, 67 subtype CRF02-AG, and 17 unclassified isolates). No major mutations associated with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) or protease inhibitors were detected. Major mutations linked to resistance to non-NRTI agents were detected in all group O isolates (A98G and Y181C) and in one subtype J virus (V108I). In contrast, many accessory mutations were found, especially in the protease gene. Only 5.6% of the 142 strains, all belonging to subtype B or D, had no mutations in the protease gene. Sixty percent had one mutation, 22.5% had two mutations, 9.8% had three mutations, and 2.1% (all group O strains) had four mutations. In order of decreasing frequency, the following mutations were identified in the protease gene: M36I (86.6%), L10I/V (26%), L63P (12.6%), K20M/R (11.2%), V77I (5.6%), A71V (2.8%), L33F (0.7%), and M46I (0.7%). R211K, an accessory mutation associated with NRTI resistance, was also observed in 43.6% of the samples. Phenotypic and clinical studies are now required to determine whether multidrug-resistant viruses emerge more rapidly during antiretroviral therapy when minor resistance-conferring mutations are present before treatment initiation.

Amino Acid Sequence↗
PubMed1999

High diversity of HIV-1 subtype F strains in Central Africa.

In this paper, we studied the variability of HIV-1 subtype F strains in Africa. For 11 viruses, mainly of Central African origin, different parts of the genome were genetically characterized. For all strains the V3-V5 region of the envelope gene was sequenced, and for 7 strains, the entire envelope gene was studied. For 10 strains, the p24 region of the gag gene was also sequenced. For each region studied, three subgroups in the F subtype were identified, F1, F2, and F3. These three subgroups were supported by high bootstrap values and the intra- and inter-subgroup F distances were comparable to those obtained for the known subtypes A, B, C, D, E, G, and H. In subgroup F1, some African strains clustered with previously described strains from Brazil and Romania, suggesting an African origin of the HIV-1 epidemic in these countries. A more detailed analysis of the gag and the envelope sequences allowed the identification of four recombinant viruses. Our data show a high diversity among subtype F strains, suggesting the presence of new subtypes in the regions studied. If biological differences exist among subtypes, it is important that these subtypes be well defined. The data from our study show that there is a need to clearly identify the different subgroups within the F subtype.

Acquired Immunodeficiency Syndrome↗
PubMed1999

Characterization of a highly replicative intergroup M/O human immunodeficiency virus type 1 recombinant isolated from a Cameroonian patient.

A Cameroonian patient with antibodies reacting simultaneously to human immunodeficiency virus type 1 (HIV-1) group O- and group M-specific V3-loop peptides was identified. In order to confirm that this patient was coinfected with both viruses, PCRs with O- and M-specific discriminating primers corresponding to different regions of the genome were carried out with both primary lymphocyte DNA and the corresponding viral strains isolated from three consecutive patient samples. The PCR data suggested that this patient is coinfected with a group M virus and a recombinant M/O virus. Indeed, only type M gag sequences could be amplified, while for the env region, both type M and O sequences were amplified, from plasma or from DNA extracted from primary lymphocytes. Sequence analysis of a complete recombinant genome isolated from the second sample (97CA-MP645 virus isolate) revealed two intergroup breakpoints, one in the vpr gene and the second in the long terminal repeat region around the TATA box. Comparison of the type M sequences shared by the group M and the recombinant M/O viruses showed that these sequences were closely related, with only 3% genetic distance, suggesting that the M virus was one of the parental viruses. In this report we describe for the first time a recombination event in vivo between viruses belonging to two different groups, leading to a replicative virus. Recombination between strains with such distant lineages (65% overall homology) may contribute substantially to the emergence of new HIV-1 variants. We documented that this virus replicates well and became predominant in vitro. At this time, group O viruses represent a minority of the strains responsible for the HIV-1 pandemic. If such recombinant intergroup viruses gained better fitness, inducing changes in their biological properties compared to the parental group O virus, the prevalences of group O sequences could increase rapidly. This will have important implications for diagnosis of HIV-1 infections by serological and molecular tests, as well as for antiviral treatment.

Adult↗
PubMed1998

Clinical algorithms for the screening of pregnant women for STDs in Libreville, Gabon: which alternatives?

OBJECTIVE: Sexually transmitted diseases (STDs) remain one of the major public health problems in the developing world. To implement a systematic screening of STDs among pregnant women in Libreville, Gabon, a preliminary cross sectional study on STD prevalence and risk factors was performed in antenatal clinics. A score, integrating risk factors and elementary clinical signs for the screening of STDs, showed higher performances compared with hierarchical algorithms. The prospective validation of this score based on six criteria (risk factors and simple clinical signs) was done in 1994-5. The sensitivity (76.7%), compared with results from other studies, was acceptable for diagnosing cervical infection (Neisseria gonorrhoeae and/or Chlamydia trachomatis) but the specificity was low (50.6%). In addition, the diagnostic values for diagnosing vaginal infection (Trichomonas vaginalis and/or Candida albicans) were poor. We then proposed to evaluate an alternative flowchart for the screening of cervical and vaginal infections. METHODS: In this study, 646 pregnant women were enrolled. Each woman was interviewed and examined by a physician and then was subjected to reference laboratory examinations. An algorithm in two steps, combining a risk assessment score at the beginning of a hierarchical process, followed by a second step more specifically applied to a limited number of women, was developed and evaluated. RESULTS: The prevalence rate was 11.3% for cervical infection and 39.5% for vaginal infection. The first step of the algorithm, applied to all pregnant women, is based on four criteria (age, marital status, dyspareunia, coloured vaginal discharge). It allows classification of the women into three classes: high, low, and intermediate risk of cervical infection. Only the patients with intermediate risk were submitted to further investigations including speculum and microscopic examination, and subsequently chlamydial antigen detection. This flowchart was 83.6% and 81.2% sensitive and 63.4% and 62.7% specific for predicting cervical infection and vaginal infection, respectively. CONCLUSION: Similar strategies using simple rapid tests for chlamydial and gonococcal infection would certainly constitute a good diagnostic tool. This theoretical model needs to be evaluated prospectively, not only to confirm their diagnostic value but also to evaluate their feasibility, reliability and acceptability, as well as their cost effectiveness.

Algorithms↗
PubMed1998

Prospective evaluation of a flow chart using a risk assessment for the diagnosis of STDs in primary healthcare centres in Libreville, Gabon.

BACKGROUND: The serious impact of STDs on women and children in particular, and the linkage between STDs and HIV infection are a profound concern to public health worldwide. One of the main strategies against STDs is based on early diagnosis and treatment. However, this approach is limited by the lack of appropriate laboratory facilities. A syndromic approach has been recommended by the WHO but needs to be evaluated under field conditions. A preliminary cross sectional study on STD prevalence and risk factors in Libreville showed that 13.5% of pregnant women had gonococcal and/or chlamydial infection which justifies systematic screening of STDs. Based on the results of this study, different flow charts with or without a risk factor assessment (score) were designed. The flow chart with the best performances for diagnosing chlamydial or gonococcal cervical infection and routinely acceptable, was a score algorithm, based on two risk factors (age and marital status) and four simple clinical signs (pelvic or lumbar pain, vaginal discharge and its characteristics). Sensitivity and specificity were 76.9% and 40.4% respectively. Thus, the objective of this study was to evaluate this strategy under field conditions. METHODS: A prospective study among pregnant women attending antenatal clinics was done. The score was applied to each woman by a midwife and a physician, and specimens were collected for the reference laboratory tests. Validation of the algorithm was done by comparing the performances with the gold standard laboratory diagnosis. RESULTS: 646 pregnant women were enrolled. The prevalence of cervical infection was 11.3. The sensitivity and specificity of this algorithm recorded by the midwives were 73.3% and 54.8%, respectively and by the physician 76.7% and 50.6%. The proportion of women correctly classified by the midwives and by the physician was not significantly different. CONCLUSION: The score applied was well accepted by healthcare workers and patients, and was routinely practised. Results obtained by the midwives and by the physician were similar. Thus, the use of flow charts which adds a risk assessment to the syndromic approach for diagnosing cervical infections is feasible. However, the performances of such flow charts need to be improved before being used routinely.

Adult↗
PubMed1996

The effects of two types of exposure on attitudes toward aspects of juvenile delinquency.

Four violent juvenile offenders from a local correctional facility spoke to a class of U.S. undergraduates studying abnormal psychology. Two weeks later, the students attended a tour sponsored by the correctional facility that had provided the speakers. The results of a semantic differential scale administered both before and after the talk and tour indicated that the students attitudes became significantly more positive for the 3 dimensions assessed by the scale: juvenile delinquent, state correctional facility for juvenile delinquents, and treatment staff for juvenile delinquents. The talk and the tour appeared to be equally effective in bringing about positive changes in the students attitudes.

Adolescent↗
PubMed1996

Epidemiological and molecular characteristics of HIV infection in Gabon, 1986-1994.

OBJECTIVE: To describe trends in the prevalence of HIV-1 infection in different populations in Gabon, and the molecular characteristics of circulating HIV strains. METHODS: Data were collected on HIV prevalence through sentinel surveillance surveys in different populations in Libreville (the capital) and in Franceville. In Libreville, a total of 7082 individuals (hospitalized patients, tuberculosis patients, pregnant women, asymptomatic adults, prisoners) were recruited between 1986 and 1994. In Franceville, we tested 771 pregnant women and 886 healthy asymptomatic adults (1986-1988). Sera were screened for HIV antibodies by enzyme-linked immunosorbent assay (ELISA) and confirmed by Western blot or line immunoassay (LIA). Reactive samples in ELISA were tested for the presence of antibodies to HIV-1 group O viruses by ELISA using V3 peptides from HIV-1 ANT-70 and HIV-1 MVP-5180 followed by confirmation by LIA and a specific Western blot. Seventeen HIV-1 strains were isolated (1988-1993) and a 900 base-pair fragment encoding the env region containing V3, V4, V5 and beginning of gp41 was sequenced and a phylogenetic tree was constructed. RESULTS: HIV prevalence was relatively low and remained stable (0.7-1.6% in pregnant women, 2.1-2.2% in the general population). The prevalence was also stable among prisoners (2.1-2.6%). Among hospitalized and tuberculosis patients prevalence was higher and increased (1.8-12.7% and 1.5-16.2%, respectively). Only three sera had antibodies to HIV-1 group O. The 17 HIV-1 strains represent six different genetic subtypes including type O. CONCLUSION: Our data from 1986 to 1994 show a stable and low HIV prevalence in Gabon, and a high genetic diversity of HIV-1 strains. This, also observed in Cameroon, is in contrast to that found elsewhere in Africa. Differences in rate of spread of HIV infection are probably explained by interplay between numerous factors. The role of different HIV subtypes in the dynamics of the HIV epidemic should be examined further.

Adult↗
PubMed1996

An acute/critical care nurse practitioner program.

To meet the demands for quality care, nursing education and nursing practice must collaborate and integrate services to educate Advanced Practice Nurses (APNs). One teaching hospital's successful APN curriculum is described. Topics addressed include structural reengineering, continuous quality improvement (CQI) and curriculum redesign.

Acute Disease↗
PubMed1996

[Psychometric properties of the French version of the Modified Mini-Mental State (3MS) in elderly patients evaluated in geriatric psychiatry].

OBJECTIVE: This research evaluates the psychometric properties of the French version of the Modified Mini-Mental State (3MS), an instrument for the screening of dementia, in a sample of patients seen in geriatric psychiatry. METHODS: Subjects (N = 94, 63 to 93 years of age) were outpatients of a service in geriatric psychiatry. In addition to the 3MS, a battery of tests evaluating the cognitive functioning and depressive symptomatology was administered. RESULTS: Test-retest reliability coefficient was 0.87 for a subsample of 35 subjects. An exploratory factor analysis revealed 4 factors accounting for 63.2% of the variance. Cut-off scores of 79 to 80 (with years of education > or = 8) and 71 to 72 (with years of education < or = 7) presented the best combination sensitivity/specificity, respectively 0.80 and 0.96. CONCLUSIONS: This study documents the psychometric properties of the French version of the 3MS for use in patients seen in geriatric psychiatry, in suggesting cut-off scores which take into account the level of education. This study underlines the influence of sociodemographic variables on test performance.

Aged↗
PubMed1991

Optimization of in situ hybridization for detection of viral genomes in cultured cells on 96-microwell plates: a cytomegalovirus model.

In situ hybridization (ISH) for identification of infectious replicative cytomegalovirus (CMV) in cell culture microplates (96 microwells) infected by clinical specimens was tested by using a biotin-labeled DNA probe and an avidin-alkaline phosphatase conjugate. A total of 395 specimens were examined by using ISH and a monoclonal antibody (MAb) specific for an early antigen of CMV. Of 47 specimens that gave a positive signal for CMV by ISH, 33 were confirmed virus positive by MAb staining. Of 141 blood samples tested, 4.96% were positive by ISH, and 0.7% were positive by the MAb technique. ISH shows 40% more sensitivity than MAb staining. This technique should be widely applicable for the specific identification of viral isolates (e.g., herpesvirus, myxovirus, paramyxovirus, and enterovirus) in cell culture 96-microwell microplates, thereby making it feasible to screen a larger number of samples than is possible with classical methods using conventional culture tubes, shell vials, or 24-well plates.

Antibodies, Monoclonal↗