Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD <2.0 Å), the DPM-HMM method performs as well or better than the best templates, demonstrating that our automated method recaptures these canonical loops without inclusion of any IgG specific terms or manual intervention. In cases with poor or few good templates (mean RMSD >7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/

Constitutive Activation of PrfA Tilts the Balance of Listeria monocytogenes Fitness Towards Life within the Host versus Environmental Survival

PrfA is a key regulator of Listeria monocytogenes pathogenesis and induces the expression of multiple virulence factors within the infected host. PrfA is post-translationally regulated such that the protein becomes activated upon bacterial entry into the cell cytosol. The signal that triggers PrfA activation remains unknown, however mutations have been identified (prfA* mutations) that lock the protein into a high activity state. In this report we examine the consequences of constitutive PrfA activation on L. monocytogenes fitness both in vitro and in vivo. Whereas prfA* mutants were hyper-virulent during animal infection, the mutants were compromised for fitness in broth culture and under conditions of stress. Broth culture prfA*-associated fitness defects were alleviated when glycerol was provided as the principal carbon source; under these conditions prfA* mutants exhibited a competitive advantage over wild type strains. Glycerol and other three carbon sugars have been reported to serve as primary carbon sources for L. monocytogenes during cytosolic growth, thus prfA* mutants are metabolically-primed for replication within eukaryotic cells. These results indicate the critical need for environment-appropriate regulation of PrfA activity to enable L. monocytogenes to optimize bacterial fitness inside and outside of host cells

Progressive myoclonic ataxia associated with coeliac disease. The myoclonus is of cortical origin, but the pathology is in the cerebellum.

We report four patients with a progressive myoclonic ataxic syndrome and associated coeliac disease. The onset of the neurological syndrome followed the gastrointestinal and other manifestations of coeliac disease while on a gluten-free diet, in the absence of overt features of malabsorption or nutritional deficiency. The condition progressed despite strict adherence to diet. The neurological syndrome was dominated by action and stimulus sensitive myoclonus of cortical origin with mild ataxia and infrequent seizures. Plasmapharesis and immunosuppressive treatment were tried in two patients but were not beneficial. Post-mortem examination of the brain in one case showed selective symmetrical atrophy of the cerebellar hemispheres with Purkinje cell loss and Bergmann astrocytosis, and with preservation of the cerebral hemispheres and brainstem. Coeliac disease should be considered in the differential diagnosis of all patients presenting with a progressive myoclonic ataxic syndrome

The effectiveness of diversion programmes for offenders using Class A drugs: a systematic review and meta-analysis

Background and Aims: Community-based offenders are an under-researched group. We reviewed existing literature for evidence on the effectiveness of community-based diversion programmes for Class A drug-using offenders. Methods: 31 databases, online resources and bibliographies were searched for studies published 1985 to 2012, with an update search March 2016. No geographic restrictions were applied although only English language papers were considered. Included studies involved community-based Criminal Justice System diversion of Class A drug users via voluntary or court-mandated treatment services. Results: 16 studies were initially included from the US (10), UK (4), Canada (1), Australia (1). In a meta-analysis, there was evidence for a small impact of diversion to treatment on drug use reduction (for primary Class A drug use: OR random effects 1.68, CI 1.12-2.53, and use of other drugs: OR random effects 2.60, 1.70-3.98). Class A drug users were less likely to complete treatment (OR random effects 0.90, 0.87-0.94) than users of other drugs. There was uncertainty surrounding results for offending, which were not pooled due to lack of comparability of outcome measures and heterogeneity. Individually, studies pointed to a minor effect of diversion on offending. Findings remained unchanged following an update review (March 2016: US [3], Australia [1]). Conclusions: Treatment accessed via community-based diversion schemes is effective at reducing drug use in Class A drug-using offenders. Evidence of a reduction in offending as a result of diversion schemes for Class A drug users is uncertain. Poor methodological quality and data being largely limited to US methamphetamine users limits the evidence available. Further research is needed to determine whether diversion is effective in settings outside the US and which drug-using offenders may benefit.</p

Clinical relevance of serum antibodies to extracellular N-methyl-d-aspartate receptor epitopes.

OBJECTIVE: There are now a large number of requests for N-methyl-d-aspartate receptor autoantibody (NMDAR-Ab) tests, and it is important to assess the clinical relevance of all results, particularly when they are reported as 'Low Positive'. METHODS: The clinical data of 56 patients found Positive or Low Positive by the Oxford live cell-based assay were reviewed. An autoimmune basis for the condition was assigned as 'Definite', 'Possible' or 'Unlikely'. The number of core features (encephalopathy, psychiatric, cognitive, epileptic, extrapyramidal and inflammatory cerebrospinal fluid (CSF)) was tabulated. RESULTS: Twenty-five (44.6%) patients had a Definite NMDAR-Ab encephalitis (eight ovarian teratomas, one Hodgkin's lymphoma), 18 (32.1%) a Possible NMDAR-Ab encephalitis and 13 (23.2%) an Unlikely autoimmune syndrome. Serum NMDAR-Ab levels were higher in patients with tumours. Positive NMDAR-Abs were found not only in patients with three or more core features and a Definite syndrome, but also in five patients classified as Possible. Conversely, Low Positive NMDAR-Abs were present in 7 Definite cases as well as in 13 Possible cases. Unlikely patients had mainly Low Positive antibodies and fewer core features. CSF NMDAR-Abs, only available in 11 pairs and at varying time points, broadly related to serum levels and were Positive in 3/3 patients with tumours but in only 2/5 Definite patients, and none of the Possible or Unlikely cases. INTERPRETATION: Using live cell-based assays, Positive and Low Positive antibodies can be of clinical significance. The number of core clinical features should help to select those patients in whom an immunotherapy intervention might be considered, irrespective of the antibody level

Clinical relevance of serum antibodies to extracellular N-methyl-d-aspartate receptor epitopes.

OBJECTIVE: There are now a large number of requests for N-methyl-d-aspartate receptor autoantibody (NMDAR-Ab) tests, and it is important to assess the clinical relevance of all results, particularly when they are reported as 'Low Positive'. METHODS: The clinical data of 56 patients found Positive or Low Positive by the Oxford live cell-based assay were reviewed. An autoimmune basis for the condition was assigned as 'Definite', 'Possible' or 'Unlikely'. The number of core features (encephalopathy, psychiatric, cognitive, epileptic, extrapyramidal and inflammatory cerebrospinal fluid (CSF)) was tabulated. RESULTS: Twenty-five (44.6%) patients had a Definite NMDAR-Ab encephalitis (eight ovarian teratomas, one Hodgkin's lymphoma), 18 (32.1%) a Possible NMDAR-Ab encephalitis and 13 (23.2%) an Unlikely autoimmune syndrome. Serum NMDAR-Ab levels were higher in patients with tumours. Positive NMDAR-Abs were found not only in patients with three or more core features and a Definite syndrome, but also in five patients classified as Possible. Conversely, Low Positive NMDAR-Abs were present in 7 Definite cases as well as in 13 Possible cases. Unlikely patients had mainly Low Positive antibodies and fewer core features. CSF NMDAR-Abs, only available in 11 pairs and at varying time points, broadly related to serum levels and were Positive in 3/3 patients with tumours but in only 2/5 Definite patients, and none of the Possible or Unlikely cases. INTERPRETATION: Using live cell-based assays, Positive and Low Positive antibodies can be of clinical significance. The number of core clinical features should help to select those patients in whom an immunotherapy intervention might be considered, irrespective of the antibody level

Transition to adulthood for young people with intellectual disability: the experiences of their families

Whilst the transition from school to adult roles can be challenging for any adolescent, for those with an intellectual disability it can present as a particularly difficult time both for the individual and their family. The process may involve coordinated planning, collaboration and decision-making among school staff, families and community agencies. This mixed-methods study utilised information from two cohorts: young people with Down syndrome in Western Australia (n = 190) and young people with intellectual disability (of any cause) in Queensland, Australia (n = 150). The parent-report questionnaires administered in both states comprised two parts: part 1 collected information about the individual with intellectual disability including information on health, functioning and service needs, and about specific transition related issues; and part 2 collected information about the health and well-being of their family. The majority (87 %) of parents said that they were involved in decision-making about transition planning but less than two-thirds (59.5 %) of young people were involved in this process. The three most helpful strategies indicated by parents that assisted with transition planning related to the provision of more information about financial assistance, the school transition program and the building of informal community-based supports. A number of themes emerged from the qualitative data which included parents’ views and concerns about the capacity of their young adult to adapt and change to life in adulthood, their difficulty navigating services and programs, issues and challenges around their young person building connectedness, strain on family wellbeing and finances and worry about the longer term future