TIGA-CUB-manualised psychoanalytic child psychotherapy versus treatment as usual for children aged 5-11 with treatment-resistant conduct disorders and their primary carers: results from a randomised controlled feasibility trial.

BACKGROUND: Parenting programmes are recommended for conduct disorders in 5-11 year olds, but ineffective for 25-33%. A feasibility trial was needed to determine whether a confirmatory trial of second-line, manualised short-term psychoanalytic child psychotherapy (mPCP) versus treatment as usual (TaU) is practicable. METHOD: This was a two-arm, pragmatic, parallel-group, multi-centre, individually-randomised controlled feasibility trial with blinded outcome assessment. Child-primary carer dyads were recruited from National Health Service Child and Adolescent Mental Health Services and mPCP delivered by routine child psychotherapists. RESULTS: Thirty-two dyads (50% of eligible, 95% CI 37 to 63%) were recruited, with 16 randomised to each arm. Eleven (69%) completed ≥50% of 12 week mPCP and 13 (81%) . Follow-up was obtained for 24 (75%) at 4 months and 14/16 (88%) at 8 months. Teacher follow-up was 16 (50%) ≥1 session. Manual adherence was good. Baseline candidate primary outcomes were 37.4 (SD 11.4) and 18.1 (SD 15.7) on the Child Behaviour Checklist/Teacher Report Form externalising scale and 102.8 (SD 28.4) and 58.8 (SD 38.9) on the total score. Health economics data collection was feasible and the trial acceptable to participants. CONCLUSION: Recruitment, teacher follow-up and the manual need some refinement. A confirmatory trial is feasible, subject to funding of research child psychotherapists.

Does extensive genotyping and nasal potential difference testing clarify the diagnosis of cystic fibrosis among patients with single-organ manifestations of cystic fibrosis?

BACKGROUND: The phenotypic spectrum of cystic fibrosis (CF) has expanded to include patients affected by single-organ diseases. Extensive genotyping and nasal potential difference (NPD) testing have been proposed to assist in the diagnosis of CF when sweat testing is inconclusive. However, the diagnostic yield of extensive genotyping and NPD and the concordance between NPD and the sweat test have not been carefully evaluated. METHODS: We evaluated the diagnostic outcomes of genotyping (with 122 mutations included as disease causing), sweat testing and NPD in a prospectively ascertained cohort of undiagnosed patients who presented with chronic sino-pulmonary disease (RESP), chronic/recurrent pancreatitis (PANC) or obstructive azoospermia (AZOOSP). RESULTS: 202 patients (68 RESP, 42 PANC and 92 AZOOSP) were evaluated; 17.3%, 22.8% and 59.9% had abnormal, borderline and normal sweat chloride results, respectively. Only 17 (8.4%) patients were diagnosable as having CF by genotyping. Compared to sweat testing, NPD identified more patients as having CF (33.2%) with fewer borderline results (18.8%). The level of agreement according to kappa statistics (and the observed percentage of agreement) between sweat chloride and NPD in RESP, PANC and AZOOSP subjects was 'moderate' (65% observed agreement), 'poor' (33% observed agreement) and 'fair' (28% observed agreement), respectively. The degree of agreement only improved marginally when subjects with borderline sweat chloride results were excluded from the analysis. CONCLUSIONS: The diagnosis of CF or its exclusion is not always straightforward and may remain elusive even with comprehensive evaluation, particularly among individuals who present at an older age with single-organ manifestations suggestive of CF.

The University of Minnesota Pathway Prediction System: multi-level prediction and visualization.

The University of Minnesota Pathway Prediction System (UM-PPS, http://umbbd.msi.umn.edu/predict/) is a rule-based system that predicts microbial catabolism of organic compounds. Currently, its knowledge base contains 250 biotransformation rules and five types of metabolic logic entities. The original UM-PPS predicted up to two prediction levels at a time. Users had to choose a predicted product to continue the prediction. This approach provided a limited view of prediction results and heavily relied on manual intervention. The new UM-PPS produces a multi-level prediction within an acceptable time frame, and allows users to view prediction alternatives much more easily as a directed acyclic graph.

Mutations in SBDS are associated with Shwachman-Diamond syndrome.

Shwachman-Diamond syndrome (SDS; OMIM 260400) is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, hematological dysfunction and skeletal abnormalities. Here, we report identification of disease-associated mutations in an uncharacterized gene, SBDS, in the interval of 1.9 cM at 7q11 previously shown to be associated with the disease. We report that SBDS has a 1.6-kb transcript and encodes a predicted protein of 250 amino acids. A pseudogene copy (SBDSP) with 97% nucleotide sequence identity resides in a locally duplicated genomic segment of 305 kb. We found recurring mutations resulting from gene conversion in 89% of unrelated individuals with SDS (141 of 158), with 60% (95 of 158) carrying two converted alleles. Converted segments consistently included at least one of two pseudogene-like sequence changes that result in protein truncation. SDBS is a member of a highly conserved protein family of unknown function with putative orthologs in diverse species including archaea and eukaryotes. Archaeal orthologs are located within highly conserved operons that include homologs of RNA-processing genes, suggesting that SDS may be caused by a deficiency in an aspect of RNA metabolism that is essential for development of the exocrine pancreas, hematopoiesis and chrondrogenesis.

Comparing the American and European diagnostic guidelines for cystic fibrosis: same disease, different language?

BACKGROUND: The American and European cystic fibrosis (CF) guidelines recommend different diagnostic criteria. This study assessed diagnostic concordance between these recommendations. METHODS: Subjects with single organ manifestations suggestive of CF (chronic sinopulmonary disease (RESP), chronic/recurrent pancreatitis (PANC) or obstructive azoospermia (AZOOSP)) were prospectively evaluated by sweat test, nasal potential difference and genotyping. Concordance in diagnostic outcomes between the two algorithms was measured using observed agreement and κ statistics. RESULTS: A total of 208 subjects were evaluated. Observed agreement was 84.8% and level of agreement was excellent (κ=0.87) between the American and European recommendations. The RESP phenotype was associated with the highest degree of concordance (observed agreement ≥90%, κ=0.92) compared with the PANC (observed agreement 86%, κ=0.65) and AZOOSP (observed agreement 80%, κ=0.87) phenotypes. Incorporation of nasal potential difference into the American algorithm failed to improve the overall degree of concordance (good agreement level; κ=0.75); the level of agreement was unchanged in RESP and PANC subjects, but reduced in AZOOSP subjects (from excellent to good). Extensive genotyping had limited clinical utility in the diagnosis of CF in both algorithms. CONCLUSIONS: Despite inconsistencies between the American and European diagnostic recommendations, concordance in diagnostic outcomes among subjects presenting with single organ manifestations of CF was good to excellent. These diagnostic guidelines provide guidance and promote rigorous evaluation for the diagnosis of CF but neither guideline should be regarded as dogma.

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access.

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.msi.umn.edu/) began in 1995 and now contains information on almost 1200 compounds, over 800 enzymes, almost 1300 reactions and almost 500 microorganism entries. Besides these data, it includes a Biochemical Periodic Table (UM-BPT) and a rule-based Pathway Prediction System (UM-PPS) (http://umbbd.msi.umn.edu/predict/) that predicts plausible pathways for microbial degradation of organic compounds. Currently, the UM-PPS contains 260 biotransformation rules derived from reactions found in the UM-BBD and scientific literature. Public access to UM-BBD data is increasing. UM-BBD compound data are now contributed to PubChem and ChemSpider, the public chemical databases. A new mirror website of the UM-BBD, UM-BPT and UM-PPS is being developed at ETH Zürich to improve speed and reliability of online access from anywhere in the world.

Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach.

MOTIVATION: Current methods for the prediction of biodegradation products and pathways of organic environmental pollutants either do not take into account domain knowledge or do not provide probability estimates. In this article, we propose a hybrid knowledge- and machine learning-based approach to overcome these limitations in the context of the University of Minnesota Pathway Prediction System (UM-PPS). The proposed solution performs relative reasoning in a machine learning framework, and obtains one probability estimate for each biotransformation rule of the system. As the application of a rule then depends on a threshold for the probability estimate, the trade-off between recall (sensitivity) and precision (selectivity) can be addressed and leveraged in practice. RESULTS: Results from leave-one-out cross-validation show that a recall and precision of approximately 0.8 can be achieved for a subset of 13 transformation rules. Therefore, it is possible to optimize precision without compromising recall. We are currently integrating the results into an experimental version of the UM-PPS server. AVAILABILITY: The program is freely available on the web at http://wwwkramer.in.tum.de/research/applications/biodegradation/data. CONTACT: kramer@in.tum.de.

The behavioral phenotype of school-age children with shwachman diamond syndrome indicates neurocognitive dysfunction with loss of Shwachman-Bodian-Diamond syndrome gene function.

OBJECTIVE: To investigate the cognitive, behavioral and adaptive functioning of children with Shwachman-Diamond syndrome (SDS). STUDY DESIGN: Thirty-two children with SDS (6-17 years) were evaluated by use of standardized neuropsychological tests. Results were compared with normative data, unaffected siblings (n = 13), and age-and sex-matched children with cystic fibrosis (CF; n = 20). RESULTS: Although intragroup variability in performance was evident, children with SDS displayed weaker overall intellectual reasoning, higher-order language skills, perceptual reasoning, visual-motor processing speed, visual motor- integration, visual executive problem-solving, attention, and aspects of academic achievement, as well as lower functional level of independence relative to the general population. Significant issues with behavior were also identified, including prior formal diagnoses and social problems. Lower abilities were found relative to sibling and CF control subjects and were not associated with secondary complications of SDS, age, or sex. CONCLUSION: Neurocognitive deficits in subjects with SDS are largely independent of family environment and having a chronic illness and are likely the consequences of Shwachman-Bodian-Diamond syndrome gene dysfunction. There is a need for a broad-based approach to the assessment of cognitive function and appropriate remediation of individuals with SDS.

Evidence of a generalized defect of acinar cell function in Shwachman-Diamond syndrome.

BACKGROUND: : Because the acinar cells of the exocrine pancreas in patients with Shwachman-Diamond syndrome (SDS) are severely depleted, we hypothesized that a similar deficiency may be present in acinar cells of the parotid gland. PATIENTS AND METHODS: : We determined serum pancreatic isoamylase and parotid amylase activities in 16 patients with SDS, 13 healthy controls, and 13 disease controls (cystic fibrosis or fibrosing pancreatitis). Parotid amylase and electrolyte concentrations were measured in stimulated parotid gland secretions. Starch digestion was assessed by breath hydrogen testing in patients with SDS (with and without enzyme supplements) and healthy controls. RESULTS: : Serum pancreatic and parotid isoamylase values were lower in the patients with SDS than in the healthy controls (P < 0.0001 and P = 0.0002, respectively). Serum pancreatic isoamylase, but not parotid isoamylase, was significantly lower in the disease controls than in the healthy controls (P < 0.0001 and P = 0.17, respectively). Secreted parotid gland amylase concentration (units per milligram of protein) in patients with SDS was lower than that in the healthy controls (P = 0.04), whereas the disease controls were comparable to the healthy subjects (P = 0.09). Secreted parotid chloride concentration was inversely correlated with amylase concentration in the patients with SDS (P = 0.01), but no correlation was seen in the healthy controls or disease controls. When patients with SDS ingested starch without enzyme supplementation, their breath hydrogen excretion was significantly higher than that in the healthy controls (P = 0.009). Following starch ingestion with enzymes, breath hydrogen in the patients with SDS was lower (P < 0.05) than with no enzyme treatment, and no different from controls (P = 0.37). CONCLUSIONS: : Mutations in the SBDS gene cause a generalized functional abnormality of exocrine acinar cells.

The University of Minnesota pathway prediction system: predicting metabolic logic.

The University of Minnesota pathway prediction system (UM-PPS, http://umbbd.msi.umn.edu/predict/) recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions, and predicts transformations of these groups based on biotransformation rules. Rules are based on the University of Minnesota biocatalysis/biodegradation database (http://umbbd.msi.umn.edu/) and the scientific literature. As rules were added to the UM-PPS, more of them were triggered at each prediction step. The resulting combinatorial explosion is being addressed in four ways. Biodegradation experts give each rule an aerobic likelihood value of Very Likely, Likely, Neutral, Unlikely or Very Unlikely. Users now can choose whether they view all, or only the more aerobically likely, predicted transformations. Relative reasoning, allowing triggering of some rules to inhibit triggering of others, was implemented. Rules were initially assigned to individual chemical reactions. In selected cases, these have been replaced by super rules, which include two or more contiguous reactions that form a small pathway of their own. Rules are continually modified to improve the prediction accuracy; increasing rule stringency can improve predictions and reduce extraneous choices. The UM-PPS is freely available to all without registration. Its value to the scientific community, for academic, industrial and government use, is good and will only increase.

Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection.

Meta-predictors make predictions by organizing and processing the predictions produced by several other predictors in a defined problem domain. A proficient meta-predictor not only offers better predicting performance than the individual predictors from which it is constructed, but it also relieves experimentally researchers from making difficult judgments when faced with conflicting results made by multiple prediction programs. As increasing numbers of predicting programs are being developed in a large number of fields of life sciences, there is an urgent need for effective meta-prediction strategies to be investigated. We compiled four unbiased phosphorylation site datasets, each for one of the four major serine/threonine (S/T) protein kinase families-CDK, CK2, PKA and PKC. Using these datasets, we examined several meta-predicting strategies with 15 phosphorylation site predictors from six predicting programs: GPS, KinasePhos, NetPhosK, PPSP, PredPhospho and Scansite. Meta-predictors constructed with a generalized weighted voting meta-predicting strategy with parameters determined by restricted grid search possess the best performance, exceeding that of all individual predictors in predicting phosphorylation sites of all four kinase families. Our results demonstrate a useful decision-making tool for analysing the predictions of the various S/T phosphorylation site predictors. An implementation of these meta-predictors is available on the web at: http://MetaPred.umn.edu/MetaPredPS/.

Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction.

MOTIVATION: The University of Minnesota Pathway Prediction System (UM-PPS) is a rule-based expert system to predict plausible biodegradation pathways for organic compounds. However, iterative application of these rules to generate biodegradation pathways leads to combinatorial explosion. We use data from known biotransformation pathways to rationally determine biotransformation priorities (relative reasoning rules) to limit this explosion. RESULTS: A total of 112 relative reasoning rules were identified and implemented. In one prediction step, i.e. as per one generation predicted, the use of relative reasoning decreases the predicted biotransformations by over 25% for 50 compounds used to generate the rules and by about 15% for an external validation set of 47 xenobiotics, including pesticides, biocides and pharmaceuticals. The percentage of correctly predicted, experimentally known products remains at 75% when relative reasoning is used. The set of relative reasoning rules identified, therefore, effectively reduces the number of predicted transformation products without compromising the quality of the predictions. AVAILABILITY: The UM-PPS server is freely available on the web to all users at the time of submission of this manuscript and will be available following publication at http://umbbd.msi.umn.edu/predict/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Meta-prediction of protein subcellular localization with reduced voting.

Meta-prediction seeks to harness the combined strengths of multiple predicting programs with the hope of achieving predicting performance surpassing that of all existing predictors in a defined problem domain. We investigated meta-prediction for the four-compartment eukaryotic subcellular localization problem. We compiled an unbiased subcellular localization dataset of 1693 nuclear, cytoplasmic, mitochondrial and extracellular animal proteins from Swiss-Prot 50.2. Using this dataset, we assessed the predicting performance of 12 predictors from eight independent subcellular localization predicting programs: ELSPred, LOCtree, PLOC, Proteome Analyst, PSORT, PSORT II, SubLoc and WoLF PSORT. Gorodkin correlation coefficient (GCC) was one of the performance measures. Proteome Analyst is the best individual subcellular localization predictor tested in this four-compartment prediction problem, with GCC = 0.811. A reduced voting strategy eliminating six of the 12 predictors yields a meta-predictor (RAW-RAG-6) with GCC = 0.856, substantially better than all tested individual subcellular localization predictors (P = 8.2 x 10(-6), Fisher's Z-transformation test). The improvement in performance persists when the meta-predictor is tested with data not used in its development. This and similar voting strategies, when properly applied, are expected to produce meta-predictors with outstanding performance in other life sciences problem domains.

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information.

BACKGROUND: The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies. DESCRIPTION: The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced. CONCLUSION: MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.

The University of Minnesota Biocatalysis/Biodegradation Database: the first decade.

As the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) starts its second decade, it includes information on over 900 compounds, over 600 enzymes, nearly 1000 reactions and about 350 microorganism entries. Its Biochemical Periodic Tables have grown to include biological information for almost all stable, non-noble-gas elements (http://umbbd.ahc.umn.edu/periodic/). Its Pathway Prediction System (PPS) (http://umbbd.ahc.umn.edu/predict/) is now an internationally recognized, open system for predicting microbial catabolism of organic compounds. Graphical display of PPS rules, a stand-alone version of the PPS and guidance for PPS users are being developed. The next decade should see the PPS, and the UM-BBD on which it is based, find increasing use by national and international government agencies, commercial organizations and educational institutions.

Shwachman-Diamond syndrome is associated with low-turnover osteoporosis.

INTRODUCTION: Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterized by exocrine pancreatic insufficiency and bone marrow dysfunction. These result in malabsorption and hematological abnormalities. A skeletal dysplasia is also an integral feature of SDS. The present study assessed prevalence and determinants of osteopenia and osteoporosis in patients with SDS and disease-causing mutations in the SBDS gene. MATERIALS AND METHODS: Eleven patients (8 males) aged from 5 to 37 years (median 16.7 years) with a genetically confirmed diagnosis of SDS were assessed for fracture history, bone mineral content (BMC), lean tissue mass (LTM) and bone mineral density (BMD) (Hologic Discovery A), osteoporotic vertebral changes, and for blood biochemistry and hematological parameters. Iliac crest bone biopsies were obtained from four patients for histology and histomorphometry. RESULTS: The main findings were: (1) markedly reduced BMD Z-scores at the lumbar spine (median -2.1, range -4.4 to -0.8), proximal femur (median -1.3, range -2.2 to -0.7) and, whole body (median -1.0, range -2.8 to +0.6), and reduced Z-scores for height-adjusted BMC/LTM ratio (median -0.9, range -3.6 to +1.1); (2) vertebral compression fractures in three patients; and (3) blood biochemistry suggestive of mild vitamin D and vitamin K deficiency. Bone biopsies in four patients showed significant low-turnover osteoporosis with reduced trabecular bone volume, low numbers of osteoclasts and osteoblasts, and reduced amount of osteoid. CONCLUSIONS: The results suggest that in addition to the skeletal dysplasia, SDS is associated with a more generalized bone disease characterized by low bone mass, low bone turnover and by vertebral fragility fractures. Osteoporosis may result from a primary defect in bone metabolism, and could be related to the bone marrow dysfunction and neutropenia.

Amiloride-insensitive nasal potential difference varies with the menstrual cycle in cystic fibrosis.

RATIONALE: There is no adequate explanation for gender-based differences in rates of mortality and of deterioration in pulmonary function in cystic fibrosis (CF) patients. One potential explanation is that gender hormones (sex steroids) may modulate the severity of CF lung disease, the principal cause of mortality in CF, by altering respiratory transepithelial ion transport. OBJECTIVE: To determine whether respiratory epithelial ion transport varied during the menstrual cycle of CF females. METHODS: The nasal transepithelial electrical potential difference (NPD) was determined as a measure of ion transport across human respiratory epithelium, coincident with measurements of endogenous serum hormone levels in the luteal and follicular phases of the menstrual cycle in CF females aged 16-22 years. RESULTS: The component of the NPD that is insensitive to the Na(+) transport blocker amiloride, but not the amiloride-sensitive component, changed in association with endogenous, menstrual cycle-induced changes in serum levels of progesterone and estrogen (P=0.02, n=7, paired t-test). Measurements using Cl(-) free perfusates suggested that the changes are not a result of Cl(-) conductance. CONCLUSIONS: Our results suggest that in CF respiratory epithelium amiloride-insensitive, but not amiloride-sensitive, ion transport is altered by female gender hormones in vivo. We speculate that amiloride-insensitive ion transport may contribute to the regulation of human airway surface fluid.

AMOD: a morpholino oligonucleotide selection tool.

AMOD is a web-based program that aids in the functional evaluation of nucleotide sequences through sequence characterization and antisense morpholino oligonucleotide (target site) selection. Submitted sequences are analyzed by translation initiation site prediction algorithms and sequence-to-sequence comparisons; results are used to characterize sequence features required for morpholino design. Within a defined subsequence, base composition and homodimerization values are computed for all putative morpholino oligonucleotides. Using these properties, morpholino candidates are selected and compared with genomic and transcriptome databases with the goal to identify target-specific enriched morpholinos. AMOD has been used at the University of Minnesota to design approximately 200 morpholinos for a functional genomics screen in zebrafish. The AMOD web server and a tutorial are freely available to both academic and commercial users at http://www.secretomes.umn.edu/AMOD/.

TIGA-CUB - manualised psychoanalytic child psychotherapy versus treatment as usual for children aged 5-11 years with treatment-resistant conduct disorders and their primary carers: study protocol for a randomised controlled feasibility trial.

BACKGROUND: The National Institute for Health and Care Excellence (NICE) recommends evidence-based parenting programmes as a first-line intervention for conduct disorders (CD) in children aged 5-11 years. As these are not effective in 25-33% of cases, NICE has requested research into second-line interventions. Child and Adolescent Psychotherapists (CAPTs) address highly complex problems where first-line treatments have failed and there have been small-scale studies of Psychoanalytic Child Psychotherapy (PCP) for CD. A feasibility trial is needed to determine whether a confirmatory trial of manualised PCP (mPCP) versus Treatment as Usual (TaU) for CD is practicable or needs refinement. The aim of this paper is to publish the abridged protocol of this feasibility trial. METHODS AND DESIGN: TIGA-CUB (Trial on improving Inter-Generational Attachment for Children Undergoing Behaviour problems) is a two-arm, pragmatic, parallel-group, multicentre, individually randomised (1:1) controlled feasibility trial (target n = 60) with blinded outcome assessment (at 4 and 8 months), which aims to develop an optimum practicable protocol for a confirmatory, pragmatic, randomised controlled trial (RCT) (primary outcome: child's behaviour; secondary outcomes: parental reflective functioning and mental health, child and parent quality of life), comparing mPCP and TaU as second-line treatments for children aged 5-11 years with treatment-resistant CD and inter-generational attachment difficulties, and for their primary carers. Child-primary carer dyads will be recruited following a referral to, or re-referral within, National Health Service (NHS) Child and Adolescent Mental Health Services (CAMHS) after an unsuccessful first-line parenting intervention. PCP will be delivered by qualified CAPTs working in routine NHS clinical practice, using a trial-specific PCP manual (a brief version of established PCP clinical practice). Outcomes are: (1) feasibility of recruitment methods, (2) uptake and follow-up rates, (3) therapeutic delivery, treatment retention and attendance, intervention adherence rates, (4) follow-up data collection, and (5) statistical, health economics, process evaluation, and qualitative outcomes. DISCUSSION: TIGA-CUB will provide important information on the feasibility and potential challenges of undertaking a confirmatory RCT to evaluate the effectiveness and cost-effectiveness of mPCP. TRIAL REGISTRATION: Current Controlled Trials, ID: ISRCTN86725795 . Registered on 31 May 2016.

The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining.

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.