PS-GO parametric protein search engine.

With the explosive growth of protein-related data, we are confronted with a critical scientific inquiry: How can we effectively retrieve, compare, and profoundly comprehend these protein structures to maximize the utilization of such data resources? PS-GO, a parametric protein search engine, has been specifically designed and developed to maximize the utilization of the rapidly growing volume of protein-related data. This innovative tool addresses the critical need for effective retrieval, comparison, and deep understanding of protein structures. By integrating computational biology, bioinformatics, and data science, PS-GO is capable of managing large-scale data and accurately predicting and comparing protein structures and functions. The engine is built upon the concept of parametric protein design, a computer-aided method that adjusts and optimizes protein structures and sequences to achieve desired biological functions and structural stability. PS-GO utilizes key parameters such as amino acid sequence, side chain angle, and solvent accessibility, which have a significant influence on protein structure and function. Additionally, PS-GO leverages computable parameters, derived computationally, which are crucial for understanding and predicting protein behavior. The development of PS-GO underscores the potential of parametric protein design in a variety of applications, including enhancing enzyme activity, improving antibody affinity, and designing novel functional proteins. This advancement not only provides a robust theoretical foundation for the field of protein engineering and biotechnology but also offers practical guidelines for future progress in this domain.

Real-Time Classification of Anxiety in Virtual Reality Therapy Using Biosensors and a Convolutional Neural Network.

Virtual Reality Exposure Therapy is a method of cognitive behavioural therapy that aids in the treatment of anxiety disorders by making therapy practical and cost-efficient. It also allows for the seamless tailoring of the therapy by using objective, continuous feedback. This feedback can be obtained using biosensors to collect physiological information such as heart rate, electrodermal activity and frontal brain activity. As part of developing our objective feedback framework, we developed a Virtual Reality adaptation of the well-established emotional Stroop Colour-Word Task. We used this adaptation to differentiate three distinct levels of anxiety: no anxiety, mild anxiety and severe anxiety. We tested our environment on twenty-nine participants between the ages of eighteen and sixty-five. After analysing and validating this environment, we used it to create a dataset for further machine-learning classification of the assigned anxiety levels. To apply this information in real-time, all of our information was processed within Virtual Reality. Our Convolutional Neural Network was able to differentiate the anxiety levels with a 75% accuracy using leave-one-out cross-validation. This shows that our system can accurately differentiate between different anxiety levels.

PROFASA-a web-based protein fragment and structure analysis workstation.

Introduction: In the field of bioinformatics and computational biology, protein structure modelling and analysis is a crucial aspect. However, most existing tools require a high degree of technical expertise and lack a user-friendly interface. To address this problem, we developed a protein workstation called PROFASA. Methods: PROFASA is an innovative protein workstation that combines state-of-the-art protein structure visualisation techniques with cutting-edge tools and algorithms for protein analysis. Our goal is to provide users with a comprehensive platform for all protein sequence and structure analyses. PROFASA is designed with the idea of simplifying complex protein analysis workflows into one-click operations, while providing powerful customisation options to meet the needs of professional users. Results: PROFASA provides a one-stop solution that enables users to perform protein structure evaluation, parametric analysis and protein visualisation. Users can use I-TASSER or AlphaFold2 to construct protein models with one click, generate new protein sequences, models, and calculate protein parameters. In addition, PROFASA offers features such as real-time collaboration, note sharing, and shared projects, making it an ideal tool for researchers and teaching professionals. Discussion: PROFASA's innovation lies in its user-friendly interface and one-stop solution. It not only lowers the barrier to entry for protein computation, analysis and visualisation tools, but also opens up new possibilities for protein research and education. We expect PROFASA to advance the study of protein design and engineering and open up new research areas.

Anxiety classification in virtual reality using biosensors: A mini scoping review.

BACKGROUND: Anxiety prediction can be used for enhancing Virtual Reality applications. We aimed to assess the evidence on whether anxiety can be accurately classified in Virtual Reality. METHODS: We conducted a scoping review using Scopus, Web of Science, IEEE Xplore, and ACM Digital Library as data sources. Our search included studies from 2010 to 2022. Our inclusion criteria were peer-reviewed studies which take place in a Virtual Reality environment and assess the user's anxiety using machine learning classification models and biosensors. RESULTS: 1749 records were identified and out of these, 11 (n = 237) studies were selected. Studies had varying numbers of outputs, from two outputs to eleven. Accuracy of anxiety classification for two-output models ranged from 75% to 96.4%; accuracy for three-output models ranged from 67.5% to 96.3%; accuracy for four-output models ranged from 38.8% to 86.3%. The most commonly used measures were electrodermal activity and heart rate. CONCLUSION: Results show that it is possible to create high-accuracy models to determine anxiety in real time. However, it should be noted that there is a lack of standardisation when it comes to defining ground truth for anxiety, making these results difficult to interpret. Additionally, many of these studies included small samples consisting of mostly students, which may bias the results. Future studies should be very careful in defining anxiety and aim for a more inclusive and larger sample. It is also important to research the application of the classification by conducting longitudinal studies.

An Overview of Alphafold's Breakthrough.

This paper presents a short summary of the protein folding problem, what it is and why it is significant. Introduces the CASP competition and how accuracy is measured. Looks at different approaches for solving the problem followed by a review of the current breakthroughs in the field introduced by AlphaFold 1 and AlphaFold 2.

Determining the need for a breast cancer awareness educational intervention for women with mild/moderate levels of intellectual disability: A qualitative descriptive study.

OBJECTIVE: Following a review of the existing body of literature, this study aimed to explore the need for a breast cancer awareness intervention specifically targeted at women with mild/moderate levels of intellectual disability (ID) and provide perspectives on the preferred processes and content underpinning an intervention. METHODS: A qualitative, descriptive design using semi-structured, individual (n = 5) and focus group (n = 5) interviews were used to engage with a non-probability, purposive sample of key stakeholders (n = 25) including women with mild/moderate levels of ID, caregivers and healthcare professionals. Data were analysed using qualitative content analysis. RESULTS: Findings highlighted that an educational intervention should focus on breast awareness as opposed to breast cancer awareness. Additionally, findings identified that a combined breast awareness and healthy living intervention could be effective. However, the intervention needs to have a multimodal, hands-on, person-centred approach to learning which is underpinned by theory. Furthermore, integrating the caregivers and healthcare professionals into the intervention is recommended. CONCLUSION: Findings from this study provide a foundation for developing and implementing a theoretically underpinned, multimodal, breast awareness and healthy living educational intervention for women with mild/moderate levels of ID.

Pepblock Builder VR - An Open-Source Tool for Gaming-Based Bio-Edutainment in Interactive Protein Design.

Proteins mediate and perform various fundamental functions of life. This versatility of protein function is an attribute of its 3D structure. In recent years, our understanding of protein 3D structure has been complemented with advances in computational and mathematical tools for protein modelling and protein design. 3D molecular visualisation is an essential part in every protein design and protein modelling workflow. Over the years, stand-alone and web-based molecular visualisation tools have been used to emulate three-dimensional view on computers. The advent of virtual reality provided the scope for immersive control of molecular visualisation. While these technologies have significantly improved our insights into protein modelling, designing new proteins with a defined function remains a complicated process. Current tools to design proteins lack user-interactivity and demand high computational skills. In this work, we present the Pepblock Builder VR, a gaming-based molecular visualisation tool for bio-edutainment and understanding protein design. Simulating the concepts of protein design and incorporating gaming principles into molecular visualisation promotes effective game-based learning. Unlike traditional sequence-based protein design and fragment-based stitching, the Pepblock Builder VR provides a building block style environment for complex structure building. This provides users a unique visual structure building experience. Furthermore, the inclusion of virtual reality to the Pepblock Builder VR brings immersive learning and provides users with "being there" experience in protein visualisation. The Pepblock Builder VR works both as a stand-alone and VR-based application, and with a gamified user interface, the Pepblock Builder VR aims to expand the horizons of scientific data generation to the masses.

Defining breast cancer awareness and identifying barriers to breast cancer awareness for women with an intellectual disability: A review of the literature.

INTRODUCTION: Incidence rates for developing breast cancer are similar for women regardless of intellectual ability. However, women with an intellectual disability present with advanced breast cancers, which often have a poor prognosis. METHOD: A structured narrative review of the literature was performed to explore the concepts of breast awareness and breast cancer awareness and subsequently, identify barriers to breast cancer awareness encountered by women with an intellectual disability. RESULTS: A total of 22 studies involving people with varying levels of intellectual disability informed this review. The barriers to breast cancer awareness encountered by women with an intellectual disability include: lack of their understanding, the role of the carer and literacy issues. CONCLUSION: Identifying the barriers to breast cancer awareness for women with an intellectual disability will help to facilitate breast cancer awareness which has the potential to result in better long-term outcomes through an early diagnosis of breast cancer.

Near field communications technology and the potential to reduce medication errors through multidisciplinary application.

BACKGROUND: Patient safety requires optimal management of medications. Electronic systems are encouraged to reduce medication errors. Near field communications (NFC) is an emerging technology that may be used to develop novel medication management systems. METHODS: An NFC-based system was designed to facilitate prescribing, administration and review of medications commonly used on surgical wards. Final year medical, nursing, and pharmacy students were recruited to test the electronic system in a cross-over observational setting on a simulated ward. Medication errors were compared against errors recorded using a paper-based system. RESULTS: A significant difference in the commission of medication errors was seen when NFC and paper-based medication systems were compared. Paper use resulted in a mean of 4.09 errors per prescribing round while NFC prescribing resulted in a mean of 0.22 errors per simulated prescribing round (P=0.000). Likewise, medication administration errors were reduced from a mean of 2.30 per drug round with a Paper system to a mean of 0.80 errors per round using NFC (P<0.015). A mean satisfaction score of 2.30 was reported by users, (rated on seven-point scale with 1 denoting total satisfaction with system use and 7 denoting total dissatisfaction). CONCLUSIONS: An NFC based medication system may be used to effectively reduce medication errors in a simulated ward environment.

Bioluminescent bacterial imaging in vivo.

This video describes the use of whole body bioluminesce imaging (BLI) for the study of bacterial trafficking in live mice, with an emphasis on the use of bacteria in gene and cell therapy for cancer. Bacteria present an attractive class of vector for cancer therapy, possessing a natural ability to grow preferentially within tumors following systemic administration. Bacteria engineered to express the lux gene cassette permit BLI detection of the bacteria and concurrently tumor sites. The location and levels of bacteria within tumors over time can be readily examined, visualized in two or three dimensions. The method is applicable to a wide range of bacterial species and tumor xenograft types. This article describes the protocol for analysis of bioluminescent bacteria within subcutaneous tumor bearing mice. Visualization of commensal bacteria in the Gastrointestinal tract (GIT) by BLI is also described. This powerful, and cheap, real-time imaging strategy represents an ideal method for the study of bacteria in vivo in the context of cancer research, in particular gene therapy, and infectious disease. This video outlines the procedure for studying lux-tagged E. coli in live mice, demonstrating the spatial and temporal readout achievable utilizing BLI with the IVIS system.

Murine bioluminescent hepatic tumour model.

This video describes the establishment of liver metastases in a mouse model that can be subsequently analysed by bioluminescent imaging. Tumour cells are administered specifically to the liver to induce a localised liver tumour, via mobilisation of the spleen and splitting into two, leaving intact the vascular pedicle for each half of the spleen. Lewis lung carcinoma cells that constitutively express the firefly luciferase gene (luc1) are inoculated into one hemi-spleen which is then resected 10 minutes later. The other hemi-spleen is left intact and returned to the abdomen. Liver tumour growth can be monitored by bioluminescence imaging using the IVIS whole body imaging system. Quantitative imaging of tumour growth using IVIS provides precise quantitation of viable tumour cells. Tumour cell death and necrosis due to drug treatment is indicated early by a reduction in the bioluminescent signal. This mouse model allows for investigating the mechanisms underlying metastatic tumour-cell survival and growth and can be used for the evaluation of therapeutics of liver metastasis.

Ex vivo culture of patient tissue & examination of gene delivery.

This video describes the use of patient tissue as an ex vivo model for the study of gene delivery. Fresh patient tissue obtained at the time of surgery is sliced and maintained in culture. The ex vivo model system allows for the physical delivery of genes into intact patient tissue and gene expression is analysed by bioluminescence imaging using the IVIS detection system. The bioluminescent detection system demonstrates rapid and accurate quantification of gene expression within individual slices without the need for tissue sacrifice. This slice tissue culture system may be used in a variety of tissue types including normal and malignant tissue and allows us to study the effects of the heterogeneous nature of intact tissue and the high degree of variability between individual patients. This model system could be used in certain situations as an alternative to animal models and as a complementary preclinical mode prior to entering clinical trial.