Predicting conserved protein motifs with Sub-HMMs

BackgroundProfile HMMs (hidden Markov models) provide effective methods for modeling the conserved regions of protein families. A limitation of the resulting domain models is the difficulty to pinpoint their much shorter functional sub-features, such as catalytically relevant sequence motifs in enzymes or ligand binding signatures of receptor proteins.ResultsTo identify these conserved motifs efficiently, we propose a method for extracting the most information-rich regions in protein families from their profile HMMs. The method was used here to predict a comprehensive set of sub-HMMs from the Pfam domain database. Cross-validations with the PROSITE and CSA databases confirmed the efficiency of the method in predicting most of the known functionally relevant motifs and residues. At the same time, 46,768 novel conserved regions could be predicted. The data set also allowed us to link at least 461 Pfam domains of known and unknown function by their common sub-HMMs. Finally, the sub-HMM method showed very promising results as an alternative search method for identifying proteins that share only short sequence similarities.ConclusionsSub-HMMs extend the application spectrum of profile HMMs to motif discovery. Their most interesting utility is the identification of the functionally relevant residues in proteins of known and unknown function. Additionally, sub-HMMs can be used for highly localized sequence similarity searches that focus on shorter conserved features rather than entire domains or global similarities. The motif data generated by this study is a valuable knowledge resource for characterizing protein functions in the future

The Reintegration of Veterans

This study explores the attitudes and beliefs of Boise State University students regarding veterans’ reintegration issues. Two hundred eight students in an introductory psychology course participated in an online survey. We found that 88% of respondents know a veteran but 37% don’t know what services are available to them to assist with reintegration issues such as family, mental health and addictions problems. The information gathered assisted us in designing a brochure to serve as a single source of information on reintegration assistance for veterans and their families

Needs assessment: risk, desistance and engagement.

This report recognises the importance of effective and robust assessment for planning and service delivery

Early testing and formative evaluation of the Enablers of Change assessment and sentence planning tool for adults with convictions

The Enablers of Change assessment and sentence planning tool has been designed to assess the risks, needs, strengths and protective factors of adults with convictions. Developed by Interserve, a Community Rehabilitation Company (CRC) provider in England, the tool is an innovation. The first of its kind in the United Kingdom (UK) to operationalise the risk needs and responsivity model with the ‘good lives’ model and desistance principles for the general adult population of low to medium risk of harm individuals managed by CRCs. This paper reports the development, early testing and formative evaluation of the tool and recommendations for it’s onward development. Given that such integration is regarded by many as the ‘holy grail’ of probation practice, this article is of international significance and will make an original contribution to the limited evidence base on operationalising desistance in the management of adults with convictions in the UK and other jurisdictions

Enabling change: developing an assessment tool for adult offenders in England which operationalises risk needs responsivity and desistance principles

This article examines the extent to which the risk needs responsivity (RNR) model and desistance principles have been integrated and operationalised in the development of the Enablers of Change assessment and sentence planning tool developed by a Community Rehabilitation Company provider in England. We consider the constructs which underpin the tool, identifying points of departure and similarity between RNR principles (Bonta and Andrews, 2007), the 'good lives' model (Ward and Maruna, 2007) and desistance principles (McNeil and Weaver, 2010) and their integration. We examine how these constructs have been operationalised in the tool which aims to assess needs, strengths, protective factors and contribute to risk assessment. Given the tool's innovation, this article is of international significance and will make an original contribution to the evidence base on operationalising desistance in the management of people with convictions in England and Wales and other jurisdictions

A photographic essay on landslides across southeastern New South Wales triggered by the rainfall events of 2022

Eastern Australia has experienced a significant magnitude rainfall event of extended duration in the first 7 months of 2022. Across the east coast of New South Wales (NSW) a series of troughs and East Coast Lows occurred during a La Nina weather cycle bringing above average rainfall to the region. As this first half of 2022 La Nina event was drawing to a close the Indian Ocean Dipole entered a negative phase which coincided with another intense East Coast Low in early July 2022 impacting the Illawarra region of NSW. These events caused widespread flooding and significant landslide damage to road and rail infrastructure across the state networks and local government infrastructure across NSW. During this extended wet period in the first 7 months of 2022 more than 200 landslides have been recorded across the Illawarra, Southern Highlands and Blue Mountains regions of NSW whilst many more have occurred across the north coast region. This paper presents a brief and albeit preliminary summary of the rainfall and provides a series of photographs with very brief descriptions of some of these landslide events within southeastern NSW. The intent of the paper is to provide early guidance to AGS members of the nature and form of landslides that have occurred across the Illawarra region. This paper does not discuss the dual fatality resulting from the Wentworth Falls area rockfall of the 5th April

Radiologic Measurements in the Assessment of Patellar Instability: A Systematic Review and Meta-analysis.

Background: Numerous diagnostic imaging measurements related to patellar instability have been evaluated in the literature; however, little has been done to compare these findings across multiple studies. Purpose: To review the different imaging measurements used to evaluate patellar instability and to assess the prevalence of each measure and its utility in predicting instability. We focused on reliability across imaging modalities and between patients with and without patellar instability. Study Design: Systematic review; Level of evidence, 4. Methods: We performed a systematic review of the literature using the PubMed, SCOPUS, and Cochrane databases. Each database was searched for variations of the terms patellar instability, patellar dislocation, trochlear dysplasia, radiographic measures, computed tomography, and magnetic resonance imaging. Studies were included if they were published after May 1, 2009, and before May 1, 2019. A meta-analysis using a random effects model was performed on several measurements, comparing instability and control groups to generate pooled values. Results: A total of 813 articles were identified, and 96 articles comprising 7912 patients and 106 unique metrics were included in the analysis. The mean patient age was 23.1 years (95% CI, 21.1-24.5), and 41% were male. The tibial tubercle–trochlear groove (TT-TG) distance was the most frequently included metric (59 studies), followed by the Insall-Salvati ratio and Caton-Deschamps index (both 26 studies). The interobserver intraclass correlation coefficients were excellent or good for the TT-TG distance and Insall-Salvati ratio in 100% of studies reporting them; however, for the Caton-Deschamps index and Blackburne-Peel ratio, they were excellent or good in only 43% and 40% of studies. Pooled magnetic resonance imaging values for TT-TG distance (P \u3c .01), Insall-Salvati ratio (P = .01), and femoral sulcus angle (P = .02) were significantly different between the instability and control groups. Values for tibial tubercle–posterior cruciate ligament distance (P = .36) and Caton-Deschamps index (P = .09) were not significantly different between groups. Conclusion: The most commonly reported measurements for evaluating patellar instability assessed patellar tracking and trochlear morphology. The TT-TG distance was the most common measurement and was greater in the patellar instability group as compared with the control group. In addition, the TT-TG, tibial tubercle-posterior cruciate ligament, and patellar tendon-trochlear groove distances were highly reproducible measurements for patellar tracking, and the Insall-Salvati ratio had superior reproducibility for assessing patellar height

An Intact Social Cognitive Process in Schizophrenia: Situational Context Effects on Perception of Facial Affect

Impaired facial affect recognition is the most consistent social cognitive finding in schizophrenia. Although social situations provide powerful constraints on our perception, little is known about how situational context modulates facial affect recognition in schizophrenia

Skeletal adaptations in young male mice after 4 weeks aboard the International Space Station

Gravity has an important role in both the development and maintenance of bone mass. This is most evident in the rapid and intense bone loss observed in both humans and animals exposed to extended periods of microgravity in spaceflight. Here, cohabitating 9-week-old male C57BL/6 mice resided in spaceflight for ~4 weeks. A skeletal survey of these mice was compared to both habitat matched ground controls to determine the effects of microgravity and baseline samples in order to determine the effects of skeletal maturation on the resulting phenotype. We hypothesized that weight-bearing bones would experience an accelerated loss of bone mass compared to non-weight-bearing bones, and that spaceflight would also inhibit skeletal maturation in male mice. As expected, spaceflight had major negative effects on trabecular bone mass of the following weight-bearing bones: femur, tibia, and vertebrae. Interestingly, as opposed to the bone loss traditionally characterized for most weight-bearing skeletal compartments, the effects of spaceflight on the ribs and sternum resembled a failure to accumulate bone mass. Our study further adds to the insight that gravity has site-specific influences on the skeleton