Auditory evoked response to an oddball paradigm in children wearing cochlear implants.

Objective: Although children with cochlear implants (CI) achieve remarkable success with their device, considerable variability remains in individual outcomes. Here, we explored whether auditory evoked potentials recorded during an oddball paradigm could provide useful markers of auditory processing in this pediatric population.

Methods: High-density electroencephalography (EEG) was recorded in 75 children listening to standard and odd noise stimuli: 25 had normal hearing (NH) and 50 wore a CI, divided between high language (HL) and low language (LL) abilities.

Analysis of BRCA1 variants in double-strand break repair by homologous recombination and single-strand annealing.

Missense substitutions of uncertain clinical significance in the BRCA1 gene are a vexing problem in genetic counseling for women who have a family history of breast cancer. In this study, we evaluated the functions of 29 missense substitutions of BRCA1 in two DNA repair pathways. Repair of double-strand breaks by homology-directed recombination (HDR) had been previously analyzed for 16 of these BRCA1 variants, and 13 more variants were analyzed in this study.

Use of a high resolution melting assay to analyze HIV diversity in HIV-infected Ugandan children.

Background: We used a novel high resolution melting (HRM) diversity assay to analyze HIV diversity in Ugandan children (age 0.6-12.4 years) who were enrolled in an observational study of antiretroviral treatment (ART).

Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection.

Background: Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM) diversity assay to compare HIV diversity in adults with different stages of HIV infection.

Association of HIV diversity and survival in HIV-infected Ugandan infants.

Background: The level of viral diversity in an HIV-infected individual can change during the course of HIV infection, reflecting mutagenesis during viral replication and selection of viral variants by immune and other selective pressures. Differences in the level of viral diversity in HIV-infected infants may reflect differences in viral dynamics, immune responses, or other factors that may also influence HIV disease progression. We used a novel high resolution melting (HRM) assay to measure HIV diversity in Ugandan infants and examined the relationship between diversity and survival through 5 years of age.

Analysis of HIV diversity using a high-resolution melting assay.

HIV viruses are usually genetically homogeneous shortly after infection, and become more heterogeneous over time. We developed a high-resolution melting (HRM) assay to analyze HIV diversity without sequencing. Plasma samples from the HIVNET 012 trial were obtained from nine Ugandan mother-infant pairs.

Analysis of drug resistance in children receiving antiretroviral therapy for treatment of HIV-1 infection in Uganda.

We analyzed drug resistance in HIV-infected Ugandan children who received antiretroviral therapy in a prospective, observational study (2004-2006); some children had prior single-dose nevirapine (sdNVP) exposure. Children received stavudine (d4T), lamivudine (3TC), and nevirapine (NVP); treatment was continued if they were clinically and immunologically stable. Samples with >1,000 copies/ml HIV RNA were analyzed by using the ViroSeq HIV Genotyping System (ViroSeq).

Analysis of nevirapine resistance mutations in cloned HIV type 1 variants from HIV-infected Ugandan infants using a single-step amplification-sequencing method (AmpliSeq).

We analyzed the genetic linkage of nevirapine (NVP) resistance mutations and the genetic complexity of HIV-1 variants in Ugandan infants who were HIV infected despite single dose (SD) prophylaxis. Plasma samples were obtained from six HIV-infected infants who had two or more NVP resistance mutations detected by population sequencing (ViroSeq). ViroSeq PCR products were cloned and transformed, and a single-step amplification-sequencing reaction (AmpliSeq) was used to analyze NVP resistance mutations in cloned HIV-1 variants directly from bacterial colonies.

Comparison of LigAmp and an ASPCR assay for detection and quantification of K103N-containing HIV variants.

We compared the ability of the LigAmp assay and an ASPCR assay to detect and quantify K103N-containing HIV variants in samples from 63 women who received single-dose nevirapine in a clinical trial. Samples were first analyzed with the ViroSeq HIV Genotyping system, and ViroSeq PCR products were used as templates for the LigAmp and ASPCR assays. A cutoff of 0.

Population genetic structure of earthworms (Lumbricus rubellus) in soils contaminated by heavy metals.

The genetic structure of earthworm (Lumbricus rubellus) populations from plots (N = 3) contaminated by sewage sludge (containing Cd, Cu, Pb, Zn) and reference plots (N = 3) was compared. Earthworms (N = 30-40 per plot) were collected during May 2000 and electrophoretic analyses were used to assess genetic variation at three polymorphic loci (GPI, LAP, PGM). Allele and genotype frequencies for GPI and PGM differed significantly between sludge and reference populations.