Using Protein Language Models for Protein Interaction Hot Spot Prediction With Limited Data

BACKGROUND: Protein language models, inspired by the success of large language models in deciphering human language, have emerged as powerful tools for unraveling the intricate code of life inscribed within protein sequences. They have gained significant attention for their promising applications across various areas, including the sequence-based prediction of secondary and tertiary protein structure, the discovery of new functional protein sequences/folds, and the assessment of mutational impact on protein fitness. However, their utility in learning to predict protein residue properties based on scant datasets, such as protein-protein interaction (PPI)-hotspots whose mutations significantly impair PPIs, remained unclear. Here, we explore the feasibility of using protein language-learned representations as features for machine learning to predict PPI-hotspots using a dataset containing 414 experimentally confirmed PPI-hotspots and 504 PPI-nonhot spots. RESULTS: Our findings showcase the capacity of unsupervised learning with protein language models in capturing critical functional attributes of protein residues derived from the evolutionary information encoded within amino acid sequences. We show that methods relying on protein language models can compete with methods employing sequence and structure-based features to predict PPI-hotspots from the free protein structure. We observed an optimal number of features for model precision, suggesting a balance between information and overfitting. CONCLUSIONS: This study underscores the potential of transformer-based protein language models to extract critical knowledge from sparse datasets, exemplified here by the challenging realm of predicting PPI-hotspots. These models offer a cost-effective and time-efficient alternative to traditional experimental methods for predicting certain residue properties. However, the challenge of explaining why specific features are important for determining certain residue properties remains

Consumers’ Perceptions of Nurses Using Recovery-focused Care to Reduce Aggression in All Acute Mental Health Including Forensic Mental Health Services

Recovery-focused care is now the preferred model of care that health professionals can utilize to support people with a mental illness to achieve their personal and clinical recovery. However, there remains a lack of practice guidelines and educational opportunities to support nurses to use recovery-focused care with consumers who may become aggressive. Objective: This paper reports the findings of research conducted with consumers to obtain their perception of how nurses can use recovery-focused care to reduce aggression in all acute mental health including forensic mental health services. Research Design and Methods: Thirty-one people diagnosed with a mental illness participated in this study. The constructivist grounded theory method guided data collection, coding, and analysis to generate categories that described the consumer perspective. Results: Five categories emerged, and these were: 1) see the person as an individual with a unique lived experience, 2) dialogue to explore the reason for the behaviour, 3) use positive communication to encourage self-management, 4) promote personal comfort to de-escalate the risk for aggression, and 5) travel alongside the person to co-produce strategies for reducing aggression. Conclusion: The findings may be tested in future research to translate recovery principles into acute mental health settings. They can also be incorporated into nursing education and professional development training to increase understanding of consumer perspective of recovery-focused care in all acute mental health including forensic mental health services

Effects of Music Therapy and Piano Lesson on Academic Achievement, Classroom Behaviors, and Self-Esteem of At- Risk Students: A Pilot Study

There is a need for research that explores the effects of music lesson on intellectual, behavioral, and emotional functioning of at-risk students who attend regular public school. Some students might benefit more from a direct approach utilizing therapeutic goals and interventions in music therapy while others may be more profoundly impacted by an indirect approach such as piano instruction. It is worthwhile to compare the effects of music lessons and music therapy incorporating music instruction on non-musical behaviors of at-risk students. The purpose of this study is to compare the effects of piano instruction and music therapy incorporating piano instruction on academic achievement, classroom behaviors, and self-esteem in at-risk students. Participants were 32 at-risk elementary school students (2nd, 3 rd, and 4th graders). They were randomly assigned to one of 10 weeks of 30 minute, one-to-one training conditions: music therapy incorporated piano instruction (n=11), piano instruction (n=11), and no-training (n=10). Participants’ language and math scores, Teacher’s Ratings of Classroom Behaviors (TRCB), and Coopersmith Self-Esteem Inventory were measured. There was no statistically significant difference between the training conditions. The present study investigated the effect of two different forms of music instruction; music therapy and piano instruction for at-risk students. With the breadth of variables to be considered and the conclusions drawn by some studies that music may indeed have a significant impact on this particular population, further research is warranted

Defining the chromatin signature of inducible genes in T cells

BACKGROUND Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the chromatin characteristics of genes that respond to T cell activation. RESULTS To facilitate comparison of genes with similar basal expression levels, we used expression-profiling data to bin genes according to their basal expression levels. We found that inducible genes in the lower basal expression bins, especially rapidly induced primary response genes, were more likely than their non-responsive counterparts to display the histone modifications of active genes, have RNA polymerase II (Pol II) at their promoters and show evidence of ongoing basal elongation. There was little or no evidence for the presence of active chromatin marks in the absence of promoter Pol II on these inducible genes. In addition, we identified a subgroup of genes with active promoter chromatin marks and promoter Pol II but no evidence of elongation. Following T cell activation, we find little evidence for a major shift in the active chromatin signature around inducible gene promoters but many genes recruit more Pol II and show increased evidence of elongation. CONCLUSIONS These results suggest that the majority of inducible genes are primed for activation by having an active chromatin signature and promoter Pol II with or without ongoing elongation

Iron and zinc nutrition among premenopausal women

Premenopausal women are at increased risk of iron deficiency and this thesis indicated Australian women may also be at risk of zinc deficiency. There is a strong need to assess zinc status in the Australian population. Unlike other food sources of iron and zinc, meat consumption positively influenced iron and zinc status

Community of Ownership of Learning

New model of teaching and learning was introduced in our school to meet the needs of our students who seek greater autonomy connectivity as well as opportunities for socio-experiential learning The Connected Learning Pedagogy CLP was designed to mine the learning potential of the new social and digital media domain to create a community of ownership of learning promoting collaboration and connectedness among students lecturers and parents To support the implementation of CLP laboratories were equipped with computers and tablet PCs Through them students were connected to various social and digital media such as Facebook Moodle YouTube and iDe Lite ITE video portal to conduct their required research and learning The tablet PCs provided lecturers with the added advantage of mobility during lessons allowing them to facilitate the learning process with ease Students were engaged in many exciting ways through Apps in the tablet PCs In addition parents were connected to students learning through PRISM ITE Parents Real-time Information System on Mobile With the mobile apps PRISM parents are connected to realtime data on their child s learnin

Current Continuing Professional Education Practice among Malaysian Nurses

Nurses need to participate in CPE to update their knowledge and increase their competencies. This research was carried out to explore their current practice and the future general needs for CPE. This cross-sectional descriptive study involved registered nurses from government hospitals and health clinics from Peninsular Malaysia. Multistage cluster sampling was used to recruit 1000 nurses from four states of Malaysia. Self-explanatory questionnaires were used to collect the data, which were analyzed using SPSS version 16. Seven hundred and ninety-two nurses participated in this survey. Only 80% (562) of the nurses had engaged in CPE activities during the past 12 months. All attendance for the various activities was below 50%. Workshops were the most popular CPE activity (345, 43.6%) and tertiary education was the most unpopular activity (10, 1.3%). The respondents did perceive the importance of future CPE activities for career development. Mandatory continuing professional education (MCPE) is a key measure to ensure that nurses upgrade their knowledge and skills; however, it is recommended that policy makers and nurse leaders in the continuing professional development unit of health service facilities plan CPE activities to meet registered nurses' (RNs) needs and not simply organizational requirements