Predicting cleavability of peptide sequences by HIV protease via correlation-angle approach

In designing HIV protease inhibitors as potential drugs for AIDS therapy, knowledge about what peptide sequences in polyproteins are cleavable by HIV proteases is very useful. In this article, based on the formulation that any octapeptide can be uniquely expressed as a 160-dimensional vector and the principle that the similarity of any two such vectors is associated with their correlation angle, a new method is proposed to predict the cleavability of a peptide sequence by HIV-1 and HIV-2 proteases. The average predicted accuracy the new method for the 105 peptide sequences whose cleavability by HIV-1 protease is known is 96/105=9.14%, which is about 8% higher than that by the existing method for the same set of data. A considerably high rate of correct prediction was also obtained when the new method was used to predict the HIV-2 protease-cleaved sites in some proteins.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45081/1/10930_2005_Article_BF01028191.pd

How to find simple and accurate rules for viral protease cleavage specificities

<p>Abstract</p> <p>Background</p> <p>Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New methods are being developed that produce large amounts of cleavage information for individual proteases and some have been applied to extract cleavage rules from data. However, the hitherto proposed methods for extracting rules have been neither easy to understand nor very accurate. To be practically useful, cleavage rules should be accurate, compact, and expressed in an easily understandable way.</p> <p>Results</p> <p>A new method is presented for producing cleavage rules for viral proteases with seemingly complex cleavage profiles. The method is based on orthogonal search-based rule extraction (OSRE) combined with spectral clustering. It is demonstrated on substrate data sets for human immunodeficiency virus type 1 (HIV-1) protease and hepatitis C (HCV) NS3/4A protease, showing excellent prediction performance for both HIV-1 cleavage and HCV NS3/4A cleavage, agreeing with observed HCV genotype differences. New cleavage rules (consensus sequences) are suggested for HIV-1 and HCV NS3/4A cleavages. The practical usability of the method is also demonstrated by using it to predict the location of an internal cleavage site in the HCV NS3 protease and to correct the location of a previously reported internal cleavage site in the HCV NS3 protease. The method is fast to converge and yields accurate rules, on par with previous results for HIV-1 protease and better than previous state-of-the-art for HCV NS3/4A protease. Moreover, the rules are fewer and simpler than previously obtained with rule extraction methods.</p> <p>Conclusion</p> <p>A rule extraction methodology by searching for multivariate low-order predicates yields results that significantly outperform existing rule bases on out-of-sample data, but are more transparent to expert users. The approach yields rules that are easy to use and useful for interpreting experimental data.</p

Design and development of a complex narrative intervention delivered by text messages to reduce binge drinking among socially disadvantaged men

Background: Socially disadvantaged men are at high risk of suffering from alcohol-related harm. Disadvantaged groups are less likely to engage with health promotion. There is a need for interventions that reach large numbers at low cost and which promote high levels of engagement with the behaviour change process. The aim of this study was to design a theoretically and empirically based text message intervention to reduce binge drinking by socially disadvantaged men. Results: Following MRC guidance, the intervention was developed in four stages. Stage 1 developed a detailed behaviour change strategy based on existing literature and theory from several areas. These included the psychological theory that would underpin the intervention, alcohol brief interventions, text message interventions, effective behaviour change techniques, narratives in behaviour change interventions and communication theory. In addition, formative research was carried out. A logic model was developed to depict the pathways between intervention inputs, processes and outcomes for behaviour change. Stage 2 created a narrative which illustrated and modelled key steps in the strategy. Stage 3 rendered the intervention into a series of text messages and ensured that appropriate behavioural change techniques were incorporated. Stage 4 revised the messages to ensure comprehensive coverage of the behaviour change strategy and coherence of the narrative. It also piloted the intervention and made final revisions to it. Conclusions: The structured, systematic approach to design created a narrative intervention which had a strong theoretical and empirical basis. The use of a narrative helped make the intervention realistic and allowed key behaviour change techniques to be modelled by characters. The narrative was intended to promote engagement with the intervention. The intervention was rendered into a series of short text messages, and subsequent piloting showed they were acceptable in the target group. Delivery of an intervention by text message offers a low-cost, low-demand method that can reach large numbers of people. This approach provides a framework for the design of behaviour change interventions which could be used for interventions to tackle other health behaviours

Crizotinib in patients with tumors harboring ALK or ROS1 rearrangements in the NCI-MATCH trial.

The NCI-MATCH was designed to characterize the efficacy of targeted therapies in histology-agnostic driver mutation-positive malignancies. Sub-protocols F and G were developed to evaluate the role of crizotinib in rare tumors that harbored either ALK or ROS1 rearrangements. Patients with malignancies that progressed following at least one prior systemic therapy were accrued to the NCI-MATCH for molecular profiling, and those with actionable ALK or ROS1 rearrangements were offered participation in sub-protocols F or G, respectively. There were five patients who enrolled on Arm F (ALK) and four patients on Arm G (ROS1). Few grade 3 or 4 toxicities were noted, including liver test abnormalities, and acute kidney injury. For sub-protocol F (ALK), the response rate was 50% (90% CI 9.8-90.2%) with one complete response among the 4 eligible patients. The median PFS was 3.8 months, and median OS was 4.3 months. For sub-protocol G (ROS1) the response rate was 25% (90% CI 1.3-75.1%). The median PFS was 4.3 months, and median OS 6.2 months. Data from 3 commercial vendors showed that the prevalence of ALK and ROS1 rearrangements in histologies other than non-small cell lung cancer and lymphoma was rare (0.1% and 0.4% respectively). We observed responses to crizotinib which met the primary endpoint for ALK fusions, albeit in a small number of patients. Despite the limited accrual, some of the patients with these oncogenic fusions can respond to crizotinib which may have a therapeutic role in this setting

UNITY : a low-field magnetic resonance neuroimaging initiative to characterize neurodevelopment in low and middle-income settings

DATA AVAILABILITY : Data collected as part of the UNITY network will be made available to researchers from the academic communities at varying levels of granularity depending on site-specific IRB approvals. For some sites, full access to individual raw and processed data will be provided, whilst for others, owing to national policies (e.g., those located in India) may only be able to provide de-identified composite values (e.g., regional volumes, mean relaxometry measures, etc.). The Bill & Melinda Gates Foundation is committed to open access and broad data availability as permitted.Measures of physical growth, such as weight and height have long been the predominant outcomes for monitoring child health and evaluating interventional outcomes in public health studies, including those that may impact neurodevelopment. While physical growth generally reflects overall health and nutritional status, it lacks sensitivity and specificity to brain growth and developing cognitive skills and abilities. Psychometric tools, e.g., the Bayley Scales of Infant and Toddler Development, may afford more direct assessment of cognitive development but they require language translation, cultural adaptation, and population norming. Further, they are not always reliable predictors of future outcomes when assessed within the first 12–18 months of a child’s life. Neuroimaging may provide more objective, sensitive, and predictive measures of neurodevelopment but tools such as magnetic resonance (MR) imaging are not readily available in many low and middle-income countries (LMICs). MRI systems that operate at lower magnetic fields (< 100mT) may offer increased accessibility, but their use for global health studies remains nascent. The UNITY project is envisaged as a global partnership to advance neuroimaging in global health studies. Here we describe the UNITY project, its goals, methods, operating procedures, and expected outcomes in characterizing neurodevelopment in sub-Saharan Africa and South Asia.The Bill & Melinda Gates Foundation, the NIHR Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, and through a Wellcome Trust Investigator Award and a Wellcome Trust Strategic Award.https://www.elsevier.com/locate/dcnhj2024Biochemistry, Genetics and Microbiology (BGM)ImmunologyPaediatrics and Child HealthRadiologySDG-03:Good heatlh and well-beingSDG-17:Partnerships for the goal

IMMUNOLOGICAL AND BIOCHEMICAL-STUDIES ON THE RELATIONSHIP BETWEEN 2 ACTIN-BINDING PROTEINS, PHOSPHOFRUCTOKINASE AND GELSOLIN

BUSS F, Hinssen H, JOCKUSCH BM. IMMUNOLOGICAL AND BIOCHEMICAL-STUDIES ON THE RELATIONSHIP BETWEEN 2 ACTIN-BINDING PROTEINS, PHOSPHOFRUCTOKINASE AND GELSOLIN. EUROPEAN JOURNAL OF BIOCHEMISTRY. 1988;175(2):251-257