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1.  Longitudinal family effects on substance use among an at-risk adolescent sample 
Addictive behaviors  2014;41:185-191.
Adult and peer factors may influence whether adolescents use alcohol and other drugs (AOD). This longitudinal study examined the direct effects of adult monitoring, perceived adult AOD use, and cultural values on adolescent AOD use.
Participants were 193 at-risk adolescents referred to a California diversion program called Teen Court for a first-time AOD offense. We assessed youth reports of past 30 day AOD use (any alcohol use, heavy drinking, marijuana use), demographics, changes in parental monitoring and family values (from baseline to follow-up 180 days later), as well as family structure and perceived adult substance use at follow-up.
Adolescents who reported that a significant adult in their life used marijuana were more likely to have increased days of drinking, heavy drinking, and marijuana use at follow-up. Higher levels of familism (importance the teen places on their family’s needs over their own needs) and being in a nuclear family served as protective factors for future alcohol use. Additionally, poor family management was associated with increased alcohol use and heavy drinking.
Findings highlight how family management and perceptions of adult marijuana use influence subsequent adolescent AOD use, and how an increase in familism over time is associated with a decrease in adolescent drinking. Tailoring interventions, by including the teen’s family and/or providing support to adults who use AOD may be crucial for improving interventions for adolescent AOD use.
PMCID: PMC4314308  PMID: 25452064
Parental Monitoring; Adolescents; Substance Use
2.  Treatment of comorbid alcohol use disorders and depression with cognitive-behavioural therapy and motivational interviewing: a meta-analysis 
Addiction (Abingdon, England)  2014;109(3):394-406.
Background and Aims
To review published studies on the effectiveness of combining cognitive-behavioural therapy (CBT) and motivational interviewing (MI) to treat comorbid clinical and subclinical alcohol use disorder (AUD) and major depression (MDD) and estimate the effect of this compared with usual care.
We conducted systematic literature searches in PubMed, PsycINFO and Embase up to June 2013 and identified additional studies through cross-references in included studies and systematic reviews. Twelve studies comprising 1721 patients met our inclusion criteria. The studies had sufficient statistical power to detect small effect sizes.
CBT/MI proved effective for treating subclinical and clinical AUD and MDD compared with controls, with small overall effect sizes at post-treatment [g = 0.17, confidence interval (CI) = 0.07–0.28, P < 0.001 for decrease of alcohol consumption and g = 0.27, CI: 0.13–0.41, P < 0.001 for decrease of symptoms of depression, respectively]. Subgroup analyses revealed no significant differences for both AUD and MDD. However, digital interventions showed a higher effect size for depression than face-to-face interventions (g = 0.73 and g = 0.23, respectively, P = 0.030).
Combined cognitive-behavioural therapy and motivational interviewing for clinical or subclinical depressive and alcohol use disorders has a small but clinically significant effect in treatment outcomes compared with treatment as usual.
PMCID: PMC4227588  PMID: 24304463
Alcohol use disorders; cognitive-behavioural therapy; comorbidity; major depression; meta-analysis; motivational interviewing; randomized controlled trials; treatment effect
3.  Examining the sustainment of the Adolescent-Community Reinforcement Approach in community addiction treatment settings: protocol for a longitudinal mixed method study 
Although evidence-based treatments are considered the gold standard for clinical practice, it is widely recognized that evidence-based treatment implementation in real world practice settings has been limited. To address this gap, the federal government provided three years of funding, training and technical assistance to 84 community-based treatment programs to deliver an evidence-based treatment called the Adolescent-Community Reinforcement Approach (A-CRA). Little is known about whether such efforts lead to long-term A-CRA sustainment after the initial funding ends.
We will use a longitudinal mixed method data analytic approach to characterize sustainment over time and to examine the factors associated with the extent to which A-CRA is sustained. We will use implementation data collected during the funding period (e.g., organizational functioning, staff certification rates and penetration) and supplement it with additional data collected during the proposed project period regarding implementation quality and the hypothesized predictors of sustainment (i.e., inner and outer contextual variables) collected over three waves from 2013 to 2015 representing program sustainment up to five years post-initial funding.
Gaining a better understanding of the factors that influence the evidence-based treatment sustainment may lead to more effective dissemination strategies and ultimately improve the quality of care being delivered in community-based addiction treatment settings.
PMCID: PMC4243817  PMID: 25116509
Sustainment; Evidence-based treatments; Adolescent substance use treatment; Mixed methods; Longitudinal data analyses
4.  InterProScan 5: genome-scale protein function classification 
Bioinformatics  2014;30(9):1236-1240.
Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code.
Availability and implementation: InterProScan is distributed via FTP at and the source code is available from
Contact: or or
PMCID: PMC3998142  PMID: 24451626
5.  Continuous quality improvement (CQI) in addiction treatment settings: design and intervention protocol of a group randomized pilot study 
Few studies have designed and tested the use of continuous quality improvement approaches in community based substance use treatment settings. Little is known about the feasibility, costs, efficacy, and sustainment of such approaches in these settings.
A group-randomized trial using a modified stepped wedge design is being used. In the first phase of the study, eight programs, stratified by modality (residential, outpatient) are being randomly assigned to the intervention or control condition. In the second phase, the initially assigned control programs are receiving the intervention to gain additional information about feasibility while sustainment is being studied among the programs initially assigned to the intervention.
By using this design in a pilot study, we help inform the field about the feasibility, costs, efficacy and sustainment of the intervention. Determining information at the pilot stage about costs and sustainment provides value for designing future studies and implementation strategies with the goal to reduce the time between intervention development and translation to real world practice settings.
PMCID: PMC3906762  PMID: 24467770
Continuous quality improvement; Group randomized controlled pilot trial; Stepped wedge design; Costs; Sustainment; Feasibility
6.  The moderating effects of group cognitive behavioral therapy for depression among substance users 
This study examined the prospective longitudinal relationship between changes in depressive symptoms on alcohol and/or drug (i.e., substance) use among addiction treatment participants and whether group cognitive behavioral therapy for depression (GCBT-D) moderated the relationship. Using a quasi-experimental intent-to-treat design, 299 residential addiction treatment clients with depressive symptoms (Beck Depression Inventory-II (BDI-II) >17) were assigned to either usual care (n = 159) or usual care plus a 16-session GCBT-D intervention (n = 140). Two follow-up interviews were conducted, one three months after the baseline interview corresponding to the end of the intervention, and three months later. Parallel process growth modeling was used to examine changes in depressive symptoms and the associated changes in abstinence and negative consequences from substance use over time. Treatment group was included as a moderator of the association. Participants in the GCBT-D condition showed a greater increase in abstinence and greater decreases in depressive symptoms and negative consequences over time. There were significant interaction effects such that the associations between depressive symptoms, negative consequences, and abstinence changes were larger in the usual care condition compared to the GCBT-D condition. The results suggest that the intervention may be effective by attenuating the association between depressive symptoms and substance use outcomes. These findings contribute to the emerging literature on the prospective longitudinal associations between depressive symptoms and substance use changes by being the first to examine it among a sample receiving GCBT-D in an addiction treatment setting.
PMCID: PMC3416919  PMID: 22564202
co-occurring disorders; depression; substance use; cognitive behavioral therapy; treatment moderation
7.  A Randomized Controlled Trial of a Group Motivational Interviewing Intervention for Adolescents with a First Time Alcohol or Drug Offense 
Journal of substance abuse treatment  2013;45(5):10.1016/j.jsat.2013.06.005.
Group Motivational Interviewing (MI) interventions that target youth at-risk for alcohol and other drug (AOD) use may prevent future negative consequences. Youth in a teen court setting (n=193; 67% male, 45% Hispanic; mean age 16.6 (SD = 1.05) were randomized to receive either a group MI intervention, Free Talk, or usual care (UC). We examined client acceptance, intervention feasibility and conducted a preliminary outcome evaluation. Free Talk teens reported higher quality and satisfaction ratings, and MI integrity scores were higher for Free Talk groups. AOD use and delinquency decreased for both groups at three months, and 12-month recidivism rates were lower but not significantly different for the Free Talk group compared to UC. Results contribute to emerging literature on MI in a group setting. A longer term follow-up is warranted.
PMCID: PMC3826597  PMID: 23891459
8.  EBI metagenomics—a new resource for the analysis and archiving of metagenomic data 
Nucleic Acids Research  2013;42(Database issue):D600-D606.
Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource ( that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.
PMCID: PMC3965009  PMID: 24165880
9.  The effectiveness of community-based delivery of an evidence-based treatment for adolescent substance use 
This study evaluates the effectiveness of Motivational Enhancement Therapy/Cognitive Behavioral Therapy-5 (MET/CBT-5) when delivered in community practice settings relative to standard community-based adolescent treatment. A quasi-experimental strategy was used to adjust for pre-treatment differences between the MET/CBT-5 sample (n = 2293) and those who received standard care (n = 458). Results suggest that youth who received MET/CBT-5 fared better than comparable youth in the control group on five out of six 12-month outcomes. A low follow-up rate (54%) in the MET/CBT-5 sample raised concerns about nonresponse bias in the treatment effect estimates. Sensitivity analyses suggest that while modest differences in outcomes between the MET/CBT-5 nonrespondents and respondents would yield no significant differences between the two groups on two of the six outcomes, very large differences in outcomes between responders and nonresponders would be required for youth receiving MET/CBT-5 to have fared better had they received standard outpatient care.
PMCID: PMC3319520  PMID: 22209657
adolescent outpatient treatment; marijuana; outcomes; evidence supported treatments; quality assurance
10.  Treating depression and substance use: A randomized controlled trial 
Few integrated substance use and depression treatments have been developed for delivery in outpatient substance abuse treatment settings. To meet the call for more ‘transportable’ interventions, we conducted a pilot study to test a group cognitive behavioral therapy (CBT) for depression and substance use that was designed for delivery by outpatient substance abuse treatment counselors. Seventy-three outpatient clients were randomized to usual care enhanced with group CBT or usual care alone, and assessed at three time points (baseline, three and six months post-baseline). Our results demonstrated that the treatment was acceptable and feasible for delivery by substance abuse treatment staff, despite challenges with recruiting clients. Both depressive symptoms and substance use were reduced by the intervention, but were not significantly different from the control group. These results suggest that further research is warranted to enhance the effectiveness of treatment for co-occurring disorders in these settings.
PMCID: PMC3345298  PMID: 22301087
addiction; co-occurring disorders; cognitive behavioral therapy; depression; group therapy
11.  Do client attributes moderate the effectiveness of a group cognitive behavioral therapy for depression in addiction treatment? 
The study goal was to determine whether client attributes were associated with outcomes from group cognitive behavioral therapy for depression (GCBT-D) as delivered in community-based addiction treatment settings. Data from 299 depressed residential clients assigned to receive either usual care (N=159) or usual care plus GCBT-D (N=140) were examined. Potential moderators included gender, race/ethnicity, education, referral status, and problem substance use. Study outcomes at six months post-baseline included changes in depressive symptoms, mental health functioning, negative consequences from substance use and percentage of days abstinent. Initial examination indicated that non-Hispanic Whites had significantly better outcomes than other racial/ethnic groups on two of the four outcomes. After correcting for multiple testing, none of the examined client attributes moderated the treatment effect. GCBT-D appears effective, however the magnitude and consistency of treatment effects indicate that it may be less helpful among members of racial/ethnic minority groups and is worthy of future study.
PMCID: PMC3729474  PMID: 22828976
12.  Intervening with practitioners to improve the quality of prevention: One year findings from a randomized trial of Assets-Getting To Outcomes 
The journal of primary prevention  2013;34(3):173-191.
There continues to be a gap in prevention outcomes achieved in research trials vs. “real world” practice. This article summarizes interim findings from a randomized trial testing Assets-Getting To Outcomes (AGTO), a two-year intervention to build prevention practitioners’ capacity to implement positive youth development-oriented prevention practices in 12 prevention coalitions in Maine. A survey of coalition members was used to assess change on individual practitioners’ prevention capacity between Baseline and one year later. Structured interviews with 32 program leaders (16 intervention, 16 control) were used to assess changes in prevention practices during the same time period. Change in prevention capacity over time between intervention and control did not differ, however in secondary analyses of only those assigned to the AGTO condition, AGTO users had evidenced greater improvement in their self-efficacy to conduct Assets-based programming and the frequency with which they engaged in AGTO behaviors. Non-users’ self-efficacy of AGTO declined. Interview ratings showed improvement in several key areas of performance among intervention programs. Improvement was associated with the number of technical assistance hours received. These results suggest that, after one year, AGTO is beginning to improve the capacity of community practitioners who make use of it.
PMCID: PMC3703481  PMID: 23605473
technical assistance; implementation support; capacity building
13.  Group Cognitive-Behavioral Therapy for Clients With Major Depression in Residential Substance Abuse Treatment 
The BRIGHT (Building Recovery by Improving Goals, Habits, and Thoughts) study was a community-based effectiveness trial that compared residential substance abuse treatment with residential treatment plus group cognitive-behavioral therapy (CBT) for depression. This brief report focuses on the subgroup of participants with major depression.
The authors used a quasi-experimental design and an intent-to-treat analysis. Out of 299 participants enrolled, 135 had major depression. Primary outcomes were change in depression symptoms, mental health functioning, and days of alcohol use and problematic substance use.
At the three-month follow-up, participants with major depression reported lower depression symptoms and better functioning, compared with participants with major depression who received usual care. At six months, functioning continued to be higher and problem substance use was lower. Conclusions: Group CBT was an effective treatment for major depression for clients in residential substance abuse treatment. These results extend the effectiveness of group CBT for major depression to a new setting, patient population, and type of provider.
PMCID: PMC3680631  PMID: 22638007
14.  Training Addiction Counselors to Implement an Evidence-Based Intervention: Strategies for Increasing Organizational and Provider Acceptance 
Cognitive and behavioral practice  2012;20(2):232-244.
One barrier to widespread public access to empirically supported treatments (ESTs) is the limited availability and high cost of professionals trained to deliver them. Our earlier work from two clinical trials demonstrated that front-line addiction counselors could be trained to deliver a manualized, group-based cognitive behavioral therapy (GCBT) for depression, a prototypic example of an EST, with a high level of adherence and competence. This follow-up article provides specific recommendations for the selection and initial training of counselors, and for the structure and process of their ongoing clinical supervision. Unique challenges in working with counselors unaccustomed to traditional clinical supervision are highlighted. The recommendations are based on comprehensive feedback derived from clinician notes taken throughout the clinical trials, a focus group with counselors conducted one year following implementation, and interviews with key organization executives and administrators.
PMCID: PMC3666576  PMID: 23734072
addiction counselor; training; Cognitive Behavioral Therapy (CBT); depression
15.  The effects of employment among adolescents at-risk for future substance use 
Addictive behaviors  2012;38(3):1616-1619.
This paper explores the association between work intensity, alcohol and/or other drug (AOD) use, and related risk factors and consequences among an at-risk youth sample that has received a first-time AOD offense. This study extends previous research focused primarily on school-based samples.
We examined the association between work intensity, AOD use, AOD-related consequences, and social environment among adolescents referred to a diversion program called Teen Court (N=193). Participants were surveyed prior to the start of the Teen Court program. Mean age was 17 (SD=1.1), 67% of the sample was male; and 45% Hispanic or Latino/a, 45.1% white; 10% other.
Greater work intensity among these youth was related to greater alcohol-related negative consequences and greater contact with co-workers who engaged in risky behaviors, but it was not significantly associated with past month AOD use.
Understanding the relationship between work intensity and AOD use among youth who are at-risk is critical to informing clinicians and public officials about the potential effects of employment in this population. Findings suggest that work intensity may be associated with negative consequences from alcohol use and increased contact with risky co-workers, all of which could contribute to the development of problems in the future.
PMCID: PMC3558640  PMID: 23254207
16.  Assessing Motivational Interviewing Integrity for Group Interventions with Adolescents 
The group format is commonly used in alcohol and other drug (AOD) adolescent treatment settings, but little research exists on the use of Motivational Interviewing (MI) in groups. Further, little work has assessed the integrity of MI delivered in group settings. This study describes an approach to evaluate MI integrity using data from a group MI intervention for at-risk youth. Using the Motivational Interviewing Treatment Integrity (MITI) scale 3.1, we coded 140 group sessions, led by three different facilitators. Four trained coders assessed the group sessions. Agreement between raters was evaluated using a method based on limits of agreement, and key decisions used to monitor and calculate group MI integrity are discussed. Results indicated that there was adequate agreement between raters; we also found differences on use of MI between the MI-intervention group and a usual care group on MI global ratings and behavioral counts. This study demonstrates that it is possible to determine whether group MI is implemented with integrity in the group setting and that MI in this setting is different from what takes place in usual care.
PMCID: PMC3540190  PMID: 22642853
17.  Establishing and Evaluating the Key Functions of an Interactive Systems Framework Using an Assets-Getting to Outcomes Intervention 
Community practitioners can face difficulty in achieving outcomes demonstrated by prevention science. Building a community practitioner’s prevention capacity—the knowledge and skills needed to conduct critical prevention practices—could improve the quality of prevention and its outcomes. The purpose of this article is to: (1) describe how an intervention called Assets-Getting To Outcomes (AGTO) was used to establish the key functions of the ISF and present early lessons learned from that intervention’s first 6 months and (2) examine whether there is an empirical relationship between practitioner capacity at the individual level and the performance of prevention at the program level—a relationship predicted by the ISF but untested. The article describes an operationalization of the ISF in the context of a five-year randomized controlled efficacy trial that combines two complementary models designed to build capacity: Getting To Outcomes (GTO) and Developmental Assets. The trial compares programs and individual practitioners from six community-based coalitions using AGTO with programs and practitionersfrom six similar coalitions that are not. In this article, we primarily focus on what the ISF calls innovation specific capacity and discuss how the combined AGTO innovation structures and uses feedback about its capacity-building activities, which can serve as a model for implementing the ISF. Focus group discussions used to gather lessons learned from the first 6 months of the AGTO intervention suggest that while the ISF may have been conceptualized as three distinct systems, in practice they are less distinct. Findings from the baseline wave of data collection of individual capacity and program performance suggest that practitioner capacity predicts, in part, performance of prevention programs. Empirically linking practitioner capacity and performance of prevention provides empirical support for both the ISF and AGTO.
PMCID: PMC3399058  PMID: 22446975
Prevention; Implementation; Technical assistance
18.  Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains 
Nucleic Acids Research  2012;41(Database issue):D499-D507.
Genome3D, available at, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).
PMCID: PMC3531217  PMID: 23203986
19.  MyDas, an Extensible Java DAS Server 
PLoS ONE  2012;7(9):e44180.
A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.
We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.
PMCID: PMC3441562  PMID: 23028496
20.  Metagenomic analysis: the challenge of the data bonanza 
Briefings in Bioinformatics  2012;13(6):743-746.
Several thousand metagenomes have already been sequenced, and this number is set to grow rapidly in the forthcoming years as the uptake of high-throughput sequencing technologies continues. Hand-in-hand with this data bonanza comes the computationally overwhelming task of analysis. Herein, we describe some of the bioinformatic approaches currently used by metagenomics researchers to analyze their data, the issues they face and the steps that could be taken to help overcome these challenges.
PMCID: PMC3504930  PMID: 22962339
metagenomics; next-generation sequencing (NGS); high-throughput sequencing (HTS); functional analysis; environmental bioinformatics
21.  Assessing the Sensitivity of Treatment Effect Estimates to Differential Follow-Up Rates: Implications for Translational Research 
We develop a new tool for assessing the sensitivity of findings on treatment effectiveness to differential follow-up rates in the two treatment conditions being compared. The method censors the group with the higher response rate to create a synthetic respondent group that is then compared with the observed cases in the other condition to estimate a treatment effect. Censoring is done under various assumptions about the strength of the relationship between follow-up and outcomes to determine how informative differential dropout can alter inferences relative to estimates from models that assume the data are missing at random. The method provides an intuitive measure for understanding the strength of the association between outcomes and dropout that would be required to alter inferences about treatment effects. Our approach is motivated by translational research in which treatments found to be effective under experimental conditions are tested in standard treatment conditions. In such applications, follow-up rates in the experimental setting are likely to be substantially higher than in the standard setting, especially when observational data are used in the evaluation. We test the method on a case study evaluation of the effectiveness of an evidence-supported adolescent substance abuse treatment program (Motivational Enhancement Therapy/Cognitive Behavioral Therapy-5 [MET/CBT-5]) delivered by community-based treatment providers relative to its performance in a controlled research trial. In this case study, follow-up rates in the community based settings were extremely low (54%) compared to the experimental setting (95%) giving raise to concerns about non-ignorable drop-out.
PMCID: PMC3433078  PMID: 22956890
Non-ignorable drop-out; informative censoring; differential follow-up; nonresponse bias; substance abuse; evidence supported treatments
22.  An effectiveness trial of group cognitive behavioral therapy for patients with persistent depressive symptoms in substance abuse treatment 
Archives of general psychiatry  2011;68(6):577-584.
Although depression frequently co-occurs with substance abuse, few individuals entering substance abuse treatment have access to effective depression treatment.
The Building Recovery by Improving Goals, Habits and Thoughts (BRIGHT) study is a community-based effectiveness trial that compared residential substance abuse treatment to residential treatment plus group cognitive behavioral therapy (CBT) for depression delivered by substance abuse treatment counselors. The authors hypothesized that intervention clients would have improved depression and substance use outcomes as compared to clients receiving usual care.
A nonrandomized controlled trial using a quasi-experimental intent-to-treat design in which four sites were assigned to alternate between the intervention and usual care conditions every four months over a two-and-a-half-year period.
Four treatment programs in Los Angeles County
1,262 clients were screened for persistent depressive symptoms (Beck Depression Inventory-II (BDI-II) >17). 299 clients were assigned to receive either usual care (N=159) or usual care plus the intervention (N=140). Follow-up rates at three and six months after the baseline interview were 88.1% and 86.2% for usual care and 85.7% and 85.0% for the intervention group.
Sixteen two-hour group sessions of CBT for depression
Main Outcome Measures
Change in depression symptoms, mental health functioning, and days of alcohol and substance use.
BRIGHT clients reported significantly fewer depressive symptoms (p<0.001 at three and six months) and had improved mental health functioning (p<0.001 at three-months and p<0.01 at six months). At six months, BRIGHT clients reported fewer drinking days (p<0.05) and fewer days of problem substance use (p<0.05) on days available.
Providing group CBT for depression to clients with persistent depressive symptoms receiving residential substance abuse treatment is associated with improved depression and substance use outcomes. These results provide support for a new model of integrated care.
PMCID: PMC3230556  PMID: 21646576
24.  Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation 
InterPro amalgamates predictive protein signatures from a number of well-known partner databases into a single resource. To aid with interpretation of results, InterPro entries are manually annotated with terms from the Gene Ontology (GO). The InterPro2GO mappings are comprised of the cross-references between these two resources and are the largest source of GO annotation predictions for proteins. Here, we describe the protocol by which InterPro curators integrate GO terms into the InterPro database. We discuss the unique challenges involved in integrating specific GO terms with entries that may describe a diverse set of proteins, and we illustrate, with examples, how InterPro hierarchies reflect GO terms of increasing specificity. We describe a revised protocol for GO mapping that enables us to assign GO terms to domains based on the function of the individual domain, rather than the function of the families in which the domain is found. We also discuss how taxonomic constraints are dealt with and those cases where we are unable to add any appropriate GO terms. Expert manual annotation of InterPro entries with GO terms enables users to infer function, process or subcellular information for uncharacterized sequences based on sequence matches to predictive models.
Database URL: The complete InterPro2GO mappings are available at:
PMCID: PMC3270475  PMID: 22301074
25.  InterPro in 2011: new developments in the family and domain prediction database 
Nucleic Acids Research  2011;40(Database issue):D306-D312.
InterPro ( is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.
PMCID: PMC3245097  PMID: 22096229

Results 1-25 (37)