DeepPI: Alignment-Free Analysis of Flexible Length Proteins Based on Deep Learning and Image Generator.

With the rapid development of NGS technology, the number of protein sequences has increased exponentially. Computational methods have been introduced in protein functional studies because the analysis of large numbers of proteins through biological experiments is costly and time-consuming. In recent years, new approaches based on deep learning have been proposed to overcome the limitations of conventional methods. Although deep learning-based methods effectively utilize features of protein function, they are limited to sequences of fixed-length and consider information from adjacent amino acids. Therefore, new protein analysis tools that extract functional features from proteins of flexible length and train models are required. We introduce DeepPI, a deep learning-based tool for analyzing proteins in large-scale database. The proposed model that utilizes Global Average Pooling is applied to proteins of flexible length and leads to reduced information loss compared to existing algorithms that use fixed sizes. The image generator converts a one-dimensional sequence into a distinct two-dimensional structure, which can extract common parts of various shapes. Finally, filtering techniques automatically detect representative data from the entire database and ensure coverage of large protein databases. We demonstrate that DeepPI has been successfully applied to large databases such as the Pfam-A database. Comparative experiments on four types of image generators illustrated the impact of structure on feature extraction. The filtering performance was verified by varying the parameter values and proved to be applicable to large databases. Compared to existing methods, DeepPI outperforms in family classification accuracy for protein function inference.

Higher adherence to a Mediterranean-type diet is associated with reduced psychosocial stress levels in baby boomers: a cross-sectional study.

BACKGROUND/OBJECTIVES: This study investigated the relationship between adherence to the Mediterranean diet among Korean baby boomers and their levels of psychosocial stress. SUBJECTS/METHODS: The study included 1,656 adults (889 men and 797 women) born between 1955 and 1963 who participated in the 2005-2006 survey of the community-based Korean Genome and Epidemiology Study (KoGES). The Mediterranean-type diet score (MTDS) was calculated from the semi-quantitative food frequency questionnaire (SQFFQ) data. The psychosocial stress levels were calculated using the psychosocial well-being index-short form (PWI-SF). Logistic regression analyses were performed to analyze the association between the MTDS (tertiles) and the prevalence of high psychosocial stress by gender. RESULTS: The ranges of the MTDS tertile groups were T1 (20-33 points), T2 (34-37 points), and T3 (38-39 points) for men, T1 (20-33 points), T2 (34-37 points), and T3 (38-48 points) for women. In both men and women, the consumption of whole grains, potatoes, fruits, vegetables, legumes, and fish increased with higher MTDS, while the consumption of red meat and dairy products decreased (P for trend < 0.05). As MTDS score increased the intake of energy, fiber, vitamins, and minerals (P for trend < 0.05). Men in the highest MTDS tertile had a 41% lower odds ratio (OR) of high psychosocial stress compared with those in the lowest tertile (OR, 0.59; 95% confidence interval [CI], 0.38-0.91). Similarly, women in the highest tertile of the MTDS had a 39% lower OR of high psychosocial stress compared with those in the lowest tertile (OR, 0.61; 95% CI, 0.40-0.95). CONCLUSION: Promoting adherence to the Mediterranean diet among baby boomers may have a positive impact on reducing their levels of psychosocial stress.

Age-dependent loss of Crls1 causes myopathy and skeletal muscle regeneration failure.

Skeletal muscle aging results in the gradual suppression of myogenesis, leading to muscle mass loss. However, the specific role of cardiolipin in myogenesis has not been determined. This study investigated the crucial role of mitochondrial cardiolipin and cardiolipin synthase 1 (Crls1) in age-related muscle deterioration and myogenesis. Our findings demonstrated that cardiolipin and Crls1 are downregulated in aged skeletal muscle. Moreover, the knockdown of Crls1 in myoblasts reduced mitochondrial mass, activity, and OXPHOS complex IV expression and disrupted the structure of the mitochondrial cristae. AAV9-shCrls1-mediated downregulation of Crls1 impaired muscle regeneration in a mouse model of cardiotoxin (CTX)-induced muscle damage, whereas AAV9-mCrls1-mediated Crls1 overexpression improved regeneration. Overall, our results highlight that the age-dependent decrease in CRLS1 expression contributes to muscle loss by diminishing mitochondrial quality in skeletal muscle myoblasts. Hence, modulating CRLS1 expression is a promising therapeutic strategy for mitigating muscle deterioration associated with aging, suggesting potential avenues for developing interventions to improve overall muscle health and quality of life in elderly individuals.

Bioengineered amyloid peptide for rapid screening of inhibitors against main protease of SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evoked a worldwide pandemic. As the emergence of variants has hampered the neutralization capacity of currently available vaccines, developing effective antiviral therapeutics against SARS-CoV-2 and its variants becomes a significant challenge. The main protease (Mpro) of SARS-CoV-2 has received increased attention as an attractive pharmaceutical target because of its pivotal role in viral replication and proliferation. Here, we generated a de novo Mpro-inhibitor screening platform to evaluate the efficacies of Mpro inhibitors based on Mpro cleavage site-embedded amyloid peptide (MCAP)-coated gold nanoparticles (MCAP-AuNPs). We fabricated MCAPs comprising an amyloid-forming sequence and Mpro-cleavage sequence, mimicking in vivo viral replication process mediated by Mpro. By measuring the proteolytic activity of Mpro and the inhibitory efficacies of various drugs, we confirmed that the MCAP-AuNP-based platform was suitable for rapid screening potential of Mpro inhibitors. These results demonstrated that our MCAP-AuNP-based platform has great potential for discovering Mpro inhibitors and may accelerate the development of therapeutics against COVID-19.

Physical activity self-efficacy online intervention for adults with obesity: protocol for a feasibility study.

BACKGROUND: Even without weight loss, adults with obesity can greatly benefit from regular physical activity. The Physical Activity Self-efficacy (PAS) intervention is an online behavioral intervention newly developed to promote physical activity in adults with obesity by providing capability-enhancing learning opportunities. The objective of this manuscript is to describe the protocol for a feasibility study designed to investigate the feasibility and acceptability of implementing the PAS online intervention for adults with obesity recruited from a local weight management center in the United States of America (USA). METHODS: The study design is a prospective, double-blind, parallel-group individual randomized pilot trial. Thirty participants will be randomly assigned to the PAS group or usual care group to achieve a 1:1 group assignment. Recruitment of participants is scheduled to begin on 1 March 2024 at a local weight management center within a private healthcare system in the USA. There are six eligibility criteria for participation in this study (e.g., a body mass index ≥ 25.00 kg/m2). Eligibility verification and data collection will be conducted online. Three waves of data collection will take up to 14 weeks depending on participants' progress in the study. The primary feasibility outcomes in the study will be: (a) participation rate, (b) engagement behavior, and (c) a preliminary effect size estimate for the effect of the PAS intervention on physical activity. Instruments designed to measure demographic information, anthropometric characteristics, self-efficacy, and acceptability will be included in the survey battery. A research-grade accelerometer will be used to measure free-living physical activity objectively. Data will be analyzed using descriptive statistics and inferential statistical models under an intention-to-treat approach. DISCUSSION: Results are intended to inform the preparation of a future definitive randomized controlled trial. TRIAL REGISTRATION: ClinicalTrials.gov, NCT05935111, registered 7 July 2023.

Importance, performance frequency, and predicted future importance of dietitians' jobs by practicing dietitians in Korea: a survey study.

PURPOSE: This study aimed to explore the perceptions held by practicing dietitians of the importance of their tasks performed in current work environments, the frequency at which those tasks are performed, and predictions about the importance of those tasks in future work environments. METHODS: This was a cross-sectional survey study. An online survey was administered to 350 practicing dietitians. They were asked to assess the importance, performance frequency, and predicted changes in the importance of 27 tasks using a 5-point scale. Descriptive statistics were calculated, and the means of the variables were compared across categorized work environments using analysis of variance. RESULTS: The importance scores of all surveyed tasks were higher than 3.0, except for the marketing management task. Self-development, nutrition education/counseling, menu planning, food safety management, and documentation/data management were all rated higher than 4.0. The highest performance frequency score was related to documentation/data management. The importance scores of all duties, except for professional development, differed significantly by workplace. As for predictions about the future importance of the tasks surveyed, dietitians responded that the importance of all 27 tasks would either remain at current levels or increase in the future. CONCLUSION: Twenty-seven tasks were confirmed to represent dietitians' job functions in various workplaces. These tasks can be used to improve the test specifications of the Korean Dietitian Licensing Examination and the curriculum of dietetic education programs.

Rapid deep learning-assisted predictive diagnostics for point-of-care testing.

Prominent techniques such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), and rapid kits are currently being explored to both enhance sensitivity and reduce assay time for diagnostic tests. Existing commercial molecular methods typically take several hours, while immunoassays can range from several hours to tens of minutes. Rapid diagnostics are crucial in Point-of-Care Testing (POCT). We propose an approach that integrates a time-series deep learning architecture and AI-based verification, for the enhanced result analysis of lateral flow assays. This approach is applicable to both infectious diseases and non-infectious biomarkers. In blind tests using clinical samples, our method achieved diagnostic times as short as 2 minutes, exceeding the accuracy of human analysis at 15 minutes. Furthermore, our technique significantly reduces assay time to just 1-2 minutes in the POCT setting. This advancement has the potential to greatly enhance POCT diagnostics, enabling both healthcare professionals and non-experts to make rapid, accurate decisions.

Improving the Three-Dimensional Printability of Potato Starch Loaded onto Food Ink.

This study focuses on improving the 3D printability of pea protein with the help of food inks designed for jet-type 3D printers. Initially, the food ink base was formulated using nanocellulose-alginate with a gradient of native potato starch and its 3D printability was evaluated. The 3D-printed structures using only candidates for the food ink base formulated with or without potato starch exhibited dimensional accuracy exceeding 95% on both the X and Y axes. However, the accuracy of stacking on the Z-axis was significantly affected by the ink composition. Food ink with 1% potato starch closely matched the CAD design, with an accuracy of approximately 99% on the Z-axis. Potato starch enhanced the stacking of 3D-printed structures by improving the electrostatic repulsion, viscoelasticity, and thixotropic behavior of the food ink base. The 3D printability of pea protein was evaluated using the selected food ink base, showing a 46% improvement in dimensional accuracy on the Z-axis compared to the control group printed with a food ink base lacking potato starch. These findings suggest that starch can serve as an additive support for high-resolution 3D jet-type printing of food ink material.

Trichosanthis Semen Exerts Neuroprotective Effects in Alzheimer's Disease Models by Inhibiting Amyloid-ß Accumulation and Regulating the Akt and ERK Signaling Pathways.

Background: Alzheimer's disease (AD), the most common form of dementia, is characterized by memory loss and the abnormal accumulation of senile plaques composed of amyloid-ß (Aß) protein. Trichosanthis Semen (TS) is a traditional herbal medicine used to treat phlegm-related conditions. While TS is recognized for various bioactivities, including anti-neuroinflammatory effects, its ability to attenuate AD remains unknown. Objective: To evaluate the effects of TS extract (TSE) on neuronal damage, Aß accumulation, and neuroinflammation in AD models. Methods: Thioflavin T and western blot assays were used to assess effects on Aß aggregation in vitro. TS was treated to PC12 cells with Aß to assess the neuroprotective effects. Memory functions and histological brain features were investigated in TSE-treated 5×FAD transgenic mice and mice with intracerebroventricularly injected Aß. Results: TSE disrupted Aß aggregation and increased the viability of cells and phosphorylation of both protein kinase B (Akt) and extracellular signal-regulated kinase (ERK) in vitro. TSE treatment also suppressed the accumulation of Aß plaques in the brain of 5×FAD mice, protected neuronal cells in both the subiculum and medial septum, and upregulated Akt/ERK phosphorylation in the hippocampus. Moreover, TSE ameliorated the memory decline and glial overactivation observed in 5×FAD mice. As assessing whether TS affect Aß-induced neurotoxicity in the Aß-injected mice, the effects of TS on memory improvement and neuroinflammatory inhibition were confirmed. Conclusions: TSE disrupted Aß aggregation, protected neurons against Aß-induced toxicity, and suppressed neuroinflammation, suggesting that it can suppress the development of AD.

Cross-cultural adaptation of the Korean Synkinesis Assessment Questionnaire: A validation study.

Objective: The Synkinesis Assessment Questionnaire (SAQ) is a reliable tool to assess synkinesis symptoms; however, it is yet to be validated in Korea. Thus, this study aimed to translate and validate the Korean SAQ. Methods: This validation study was set in a clinic in Seoul, Korea, that provides general integrative medicine services. A total of 100 participants with facial palsy were enrolled. Participants completed the SAQ, House-Brackmann grade (HB grade), Sunnybrook Facial Grading System (SB), and Facial Disability Index (FDI). The forward-backward translation method was followed. Of the 100 participants, 31 underwent a second assessment for test-retest reliability. Internal consistency and test-retest reliability were evaluated using Cronbach's alpha coefficient. The construct validity of the Korean version of the SAQ was tested using Spearman's rank correlation coefficient. Results: The internal consistency score for the SAQ was 0.789, and the test-retest reliability score was 0.787. According to Spearman's rank correlation coefficient, the SAQ correlations to the synkinesis subdomain of SB score, total SB score, HB grade, and physical function domain in the FDI score were 0.366 (p < .001), -0.386 (p < .001), 0.315 (p = .001), and -0.269 (p = .007), respectively. All values were statistically significant. Conclusions: The Korean SAQ is a valid and reliable tool used to evaluate synkinesis in patients with facial palsy. Level of Evidence: Level 3.

Advancing diagnostic efficacy using a computer vision-assisted lateral flow assay for influenza and SARS-CoV-2 detection.

Lateral flow assays (LFAs) have emerged as indispensable tools for point-of-care testing during the pandemic era. However, the interpretation of results through unassisted visual inspection by untrained individuals poses inherent limitations. In our study, we propose a novel approach that combines computer vision (CV) and lightweight machine learning (ML) to overcome these limitations and significantly enhance the performance of LFAs. By incorporating CV-assisted analysis into the LFA assay, we achieved a remarkable three-fold improvement in analytical sensitivity for detecting Influenza A and for SARS-CoV-2 detection. The obtained R2 values reached approximately 0.95, respectively, demonstrating the effectiveness of our approach. Moreover, the integration of CV techniques with LFAs resulted in a substantial amplification of the colorimetric signal specifically for COVID-19 positive patient samples. Our proposed approach, which incorporates a simple machine learning algorithm, provides substantial enhancements in assay sensitivity, improving diagnostic efficacy and accessibility of point-of-care testing without requiring significant additional resources. Moreover, the simplicity of the machine learning algorithm enables its standalone use on a mobile phone, further enhancing its practicality for point-of-care testing.

Investigation of theoretical maximum water yield and efficiency-optimized temperature for cyclopentane hydrate-based desalination.

Hydrate-based desalination (HBD) shows promise as a freshwater production technology for saline water. Liquid-phase hydrate formers, with their ability to facilitate hydrate formation at atmospheric pressure, have gained attention for their high energy efficiency in HBD. This study explored cyclopentane (CP) HBD by experimentally measuring the thermodynamic properties of CP hydrate in saline solutions and developing a theoretical framework to estimate the water yield of CP HBD under various operating conditions. The measured dissociation enthalpy of CP hydrate was found to be 12 % and 22 % lower compared to those of propane and R134a hydrates, respectively. The equilibrium dissociation temperatures of CP hydrate at different NaCl concentrations under atmospheric pressure were experimentally measured and then predicted using the Hu-Lee-Sum correlation. The theoretically achievable maximum salinity and water yield for CP HBD were calculated in the temperature range of 268-280 K and the initial salinity range of 0-8 wt.%. Additionally, the concept of HBD heat efficiency, representing the maximum amount of pure water producible per unit of heat, was introduced to identify an optimal operating condition for the HBD process. Efficiency-maximized temperatures, where the HBD heat efficiency reached its peaks, were determined for various initial salinities in the process, for example, 273.4 K for NaCl 3.5 wt.% solution. This novel approach provides invaluable guidance for determining the most energy-efficient operating conditions in the HBD process and establishes a solid foundation for further advancements in this field.

Tumor-Promoting Role of GNA14 in Colon Cancer Development.

Recent studies have shown that mutations in members of the G-protein α family contribute to the onset and progression of cancer. However, the role of GNA14 in CRC remains unknown. In this study, we examined the effect of GNA14 on CRC through genetic approaches in vitro and in vivo. We found that GNA14 knockdown by small interfering RNA (siRNA) inhibited the proliferation of CRC cells SW403 and HT29. Gna14 knockout mice developed normally without obvious abnormalities. However, the number of polyps in the small intestine was significantly reduced in Gna14 knockout mice compared to control mice after mating with ApcMin mice, a representative CRC mouse model. In particular, deletion of the Gna14 inhibited polyp growth, especially in the distal end of the small intestine. Histological examination showed that Gna14 knockout mice suppressed malignant tumor progression due to decreased proliferation and increased apoptosis in polyps compared to controls. In addition, GNA14 knockdown in CRC cells resulted in downregulation of ERK phosphorylation and ß-catenin and ß-catenin phosphorylation at S675. Similarly, ERK phosphorylation and phospho-ß-catenin phosphorylation at S675 were decreased in polyps of Gna14 knockout mice. Collectively, these analyses show that GNA14 may accelerate CRC cell proliferation and malignant tumor progression through ERK and ß-catenin pathways.

Lifetime-configurable soft robots via photodegradable silicone elastomer composites.

Developing soft robots that can control their own life cycle and degrade on-demand while maintaining hyperelasticity is a notable research challenge. On-demand degradable soft robots, which conserve their original functionality during operation and rapidly degrade under specific external stimulation, present the opportunity to self-direct the disappearance of temporary robots. This study proposes soft robots and materials that exhibit excellent mechanical stretchability and can degrade under ultraviolet light by mixing a fluoride-generating diphenyliodonium hexafluorophosphate with a silicone resin. Spectroscopic analysis revealed the mechanism of Si─O─Si backbone cleavage using fluoride ion (F-) and thermal analysis indicated accelerated decomposition at elevated temperatures. In addition, we demonstrated a robotics application by fabricating electronics integrated gaiting robot and a fully closed-loop trigger disintegration robot for autonomous, application-oriented functionalities. This study provides a simple yet novel strategy for designing life cycle mimicking soft robotics that can be applied to reduce soft robotics waste, explore hazardous areas, and ensure hardware security with on-demand destructive material platforms.