CDD: a Conserved Domain Database for the functional annotation of proteins

NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

Mindfulness Training Improves Attentional Task Performance in Incarcerated Youth: A Group Randomized Controlled Intervention Trial

We investigated the impact of cognitive behavioral therapy and mindfulness training (CBT/MT) on attentional task performance in incarcerated adolescents. Attention is a cognitive system necessary for managing cognitive demands and regulating emotions. Yet persistent and intensive demands, such as those experienced during high-stress intervals like incarceration and the events leading to incarceration, may deplete attention resulting in cognitive failures, emotional disturbances, and impulsive behavior. We hypothesized that CBT/MT may mitigate these deleterious effects of high stress and protect against degradation in attention over the high-stress interval of incarceration. Using a group randomized controlled trial design, we randomly assigned dormitories of incarcerated youth, ages 16 to 18, to a CBT/MT intervention (youth n = 147) or an active control intervention (youth n = 117). Both arms received approximately 750 minutes of intervention in a small-group setting over a 3-5 week period. Youth in the CBT/MT arm also logged the amount of out-of-session time spent practicing MT exercises. The Attention Network Test was used to index attentional task performance at baseline and 4 months post-baseline. Overall, task performance degraded over time in all participants. The magnitude of performance degradation was significantly less in the CBT/MT vs. control arm. Further, within the CBT/MT arm, performance degraded over time in those with no outside-of-class practice time, but remained stable over time in those who practiced mindfulness exercises outside of the session meetings. Thus, these findings suggest that sufficient CBT/MT practice may protect against functional attentional impairments associated with high-stress intervals. Keywords: adolescent development, incarcerated adolescents, detained adolescents, stress, attention, mindfulness meditation

The Treatment Ambassador Program: A Highly Acceptable and Feasible Community-Based Peer Intervention for South Africans Living with HIV Who Delay or Discontinue Antiretroviral Therapy.

We conducted a novel pilot randomized controlled trial of the Treatment Ambassador Program (TAP), an 8-session, peer-based, behavioral intervention for people with HIV (PWH) in South Africa not on antiretroviral therapy (ART). PWH (43 intervention, 41 controls) completed baseline, 3- and 6-month assessments. TAP was highly feasible (90% completion), with peer counselors demonstrating good intervention fidelity. Post-intervention interviews showed high acceptability of TAP and counselors, who supported autonomy, assisted with clinical navigation, and provided psychosocial support. Intention-to-treat analyses indicated increased ART initiation by 3 months in the intervention vs. control arm (12.2% [5/41] vs. 2.3% [1/43], Fisher exact p-value = 0.105; Cohen\u27s h = 0.41). Among those previously on ART (off for \u3e 6 months), 33.3% initiated ART by 3 months in the intervention vs. 14.3% in the control arm (Cohen\u27s h = 0.45). Results suggest that TAP was highly acceptable and feasible among PWH not on ART

The Effect of Peer-Driven Intervention on Rates of Screening for AIDS Clinical Trials Among African Americans and Hispanics

OBJECTIVES: We examined the efficacy of a peer-driven intervention to increase rates of screening for AIDS clinical trials among African Americans and Hispanics living with HIV/AIDS. METHODS: We used a randomized controlled trial design to examine the efficacy of peer-driven intervention (6 hours of structured sessions and the opportunity to educate 3 peers) compared with a time-matched control intervention. Participants were recruited using respondent-driven sampling (n = 342; 43.9% female; 64.9% African American, 26.6% Hispanic). Most participants (93.3%) completed intervention sessions and 64.9% recruited or educated peers. Baseline and post-baseline interviews (94.4% completed) were computer-assisted. A mixed model was used to examine intervention effects on screening. RESULTS: Screening was much more likely in the peer-driven intervention than in the control arm (adjusted odds ratio [AOR] = 55.0; z = 5.49, P < .001); about half of the participants in the intervention arm (46.0%) were screened compared with 1.6% of controls. The experience of recruiting and educating each peer also increased screening odds among those who were themselves recruited and educated by peers (AOR = 1.4; z = 2.06, P < .05). CONCLUSIONS: Peer-driven intervention was highly efficacious in increasing AIDS clinical trial screening rates among African Americans and Hispanics living with HIV/AIDS