DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.

MOTIVATION: Predicting protein structures with high accuracy is a critical challenge for the broad community of life sciences and industry. Despite progress made by deep neural networks like AlphaFold2, there is a need for further improvements in the quality of detailed structures, such as side-chains, along with protein backbone structures. RESULTS: Building upon the successes of AlphaFold2, the modifications we made include changing the losses of side-chain torsion angles and frame aligned point error, adding loss functions for side chain confidence and secondary structure prediction, and replacing template feature generation with a new alignment method based on conditional random fields. We also performed re-optimization by conformational space annealing using a molecular mechanics energy function which integrates the potential energies obtained from distogram and side-chain prediction. In the CASP15 blind test for single protein and domain modeling (109 domains), DeepFold ranked fourth among 132 groups with improvements in the details of the structure in terms of backbone, side-chain, and Molprobity. In terms of protein backbone accuracy, DeepFold achieved a median GDT-TS score of 88.64 compared with 85.88 of AlphaFold2. For TBM-easy/hard targets, DeepFold ranked at the top based on Z-scores for GDT-TS. This shows its practical value to the structural biology community, which demands highly accurate structures. In addition, a thorough analysis of 55 domains from 39 targets with publicly available structures indicates that DeepFold shows superior side-chain accuracy and Molprobity scores among the top-performing groups. AVAILABILITY AND IMPLEMENTATION: DeepFold tools are open-source software available at https://github.com/newtonjoo/deepfold.

Redox-Responsive Gold Nanoparticles Coated with Hyaluronic Acid and Folic Acid for Application in Targeting Anticancer Therapy.

Methotrexate (MTX) has poor water solubility and low bioavailability, and cancer cells can become resistant to it, which limits its safe delivery to tumor sites and reduces its clinical efficacy. Herein, we developed novel redox-responsive hybrid nanoparticles (NPs) from hyaluronic acid (HA) and 3-mercaptopropionic acid (MPA)-coated gold NPs (gold@MPA NPs), which were further conjugated with folic acid (FA). The design of FA-HA-ss-gold NPs aimed at enhancing cellular uptake specifically in cancer cells using an active FA/HA dual targeting strategy for enhanced tumor eradication. MTX was successfully encapsulated into FA-HA-ss-gold NPs, with drug encapsulation efficiency (EE) as high as >98.7%. The physicochemical properties of the NPs were investigated in terms of size, surface charges, wavelength reflectance, and chemical bonds. MTX was released in a sustained manner in glutathione (GSH). The cellular uptake experiments showed effective uptake of FA-HA-ss-gold over HA-ss-gold NPs in the deep tumor. Moreover, the release studies provided strong evidence that FA-HA-ss-gold NPs serve as GSH-responsive carriers. In vitro, anti-tumor activity tests showed that FA-HA-ss-gold/MTX NPs exhibited significantly higher cytotoxic activity against both human cervical cancer (HeLa) cells and breast cancer (BT-20) cells compared to gold only and HA-ss-gold/MTX NPs while being safe for human embryonic kidney (HEK-293) cells. Therefore, this present study suggests that FA-HA-ss-gold NPs are promising active targeting hybrid nanocarriers that are stable, controllable, biocompatible, biodegradable, and with enhanced cancer cell targetability for the safe delivery of hydrophobic anticancer drugs.

Collagen Peptide in a Combinatorial Treatment with Lactobacillus rhamnosus Inhibits the Cariogenic Properties of Streptococcus mutans: An In Vitro Study.

Dental caries is caused by the formation of cariogenic biofilm, leading to localized areas of enamel demineralization. Streptococcus mutans, a cariogenic pathogen, has long been considered as a microbial etiology of dental caries. We hypothesized that an antagonistic approach using a prebiotic collagen peptide in combination with probiotic Lactobacillus rhamnosus would modulate the virulence of this cariogenic biofilm. In vitro S. mutans biofilms were formed on saliva-coated hydroxyapatite discs, and the inhibitory effect of a combination of L. rhamnosus and collagen peptide on S. mutans biofilms were evaluated using microbiological, biochemical, confocal imaging, and transcriptomic analyses. The combination of L. rhamnosus with collagen peptide altered acid production by S. mutans, significantly increasing culture pH at an early stage of biofilm formation. Moreover, the 3D architecture of the S. mutans biofilm was greatly compromised when it was in the presence of L. rhamnosus with collagen peptide, resulting in a significant reduction in exopolysaccharide with unstructured and mixed bacterial organization. The presence of L. rhamnosus with collagen peptide modulated the virulence potential of S. mutans via down-regulation of eno, ldh, and atpD corresponding to acid production and proton transportation, whereas aguD associated with alkali production was up-regulated. Gly-Pro-Hyp, a common tripeptide unit of collagen, consistently modulated the cariogenic potential of S. mutans by inhibiting acid production, similar to the bioactivity of a collagen peptide. It also enhanced the relative abundance of commensal streptococci (S. oralis) in a mixed-species biofilm by inhibiting S. mutans colonization and dome-like microcolony formation. This work demonstrates that food-derived synbiotics may offer a useful means of disrupting cariogenic communities and maintaining microbial homeostasis.

Aspects of Psychiatric Comorbidities in Breast Cancer Patients in Tertiary Hospitals Due to COVID-19 Outbreak in South Korea: A Single Center Longitudinal Cohort Study.

Background and Objectives: This study aimed to analyze the prevalence of mental disorders in patients with breast cancer at Ajou University Hospital. In addition, the patterns and prevalence of mental disorders according to the occurrence of coronavirus disease (COVID-19) were analyzed. Materials and Methods: From 1 January 2008 to 30 June 2021, psychiatric disorders were identified in 5174 female patients diagnosed with breast cancer at Ajou University Hospital. Based on the time when COVID-19 occurred, the pattern of onset of mental disorders in patients with breast cancer was analyzed. In addition, the prevalence of mental disorders according to the time of breast cancer diagnosis and age was evaluated. Results: A year before the diagnosis of breast cancer, 371 patients were diagnosed with a mental disorder. Of these, 201 patients were diagnosed with stress and adjustment disorders, and 97 patients had anxiety disorders. The overall frequency of psychiatric disorders after breast cancer diagnosis peaked two months later. Among psychiatric disorders reported before the COVID-19 pandemic, the proportion of stress/adaptation disorders was 52%, and among psychiatric disorders reported after the pandemic, it was significantly higher at 94.7%. Anxiety was found to be high in the elderly group aged ≥ 60 years, and the prevalence of stress and adjustment disorders tended to increase in the non-elderly group. Conclusions: Breast cancer patients showed different patterns of psychiatric disorders according to age, time of breast cancer diagnosis, and the occurrence of COVID-19. Owing to the COVID-19 pandemic, delays in treatment and anxiety about infection have increased the rate of stress and adjustment disorders in cancer patients. Mental health management during the pandemic and after cancer diagnosis can improve the quality of life of patients with cancer.

Characterization of Marine Organism Extracellular Matrix-Anchored Extracellular Vesicles and Their Biological Effect on the Alleviation of Pro-Inflammatory Cytokines.

Representative marine materials such as biopolymers and bioceramics contain bioactive properties and are applied in regenerative medicine and tissue engineering. The marine organism-derived extracellular matrix (ECM), which consists of structural and functional molecules, has been studied as a biomaterial. It has been used to reconstruct tissues and improve biological functions. However, research on marine-derived extracellular vesicles (EVs) among marine functional materials is limited. Recent studies on marine-derived EVs were limited to eco-system studies using bacteria-released EVs. We aimed to expand the range of representative marine organisms such as fish, crustaceans, and echinoderms; establish the extraction process; and study the bioactivity capability of marine EVs. Results confirmed that marine organism ECM-anchored EVs (mEVs) have a similar morphology and cargos to those of EVs in land animals. To investigate physiological effects, lipopolysaccharide (LPS)-infected macrophages were treated with EVs derived from sea cucumber, fish, and shrimp. A comparison of the expression levels of inflammatory cytokine genes revealed that all types of mEVs alleviated pro-inflammatory cytokines, although to different degrees. Among them, the sea cucumber-derived EVs showed the strongest suppression ability. This study showed that research on EVs derived from various types of marine animals can lead to the development of high value-added therapeutics from discarded marine wastes.

Reactive oxygen species-mediated endoplasmic reticulum stress response induces apoptosis of Mycobacterium avium-infected macrophages by activating regulated IRE1-dependent decay pathway.

Mycobacterium avium, a slow-growing nontuberculous mycobacterium, causes fever, diarrhoea, loss of appetite, and weight loss in immunocompromised people. We have proposed that endoplasmic reticulum (ER) stress-mediated apoptosis plays a critical role in removing intracellular mycobacteria. In the present study, we investigated the role of the regulated IRE1-dependent decay (RIDD) pathway in macrophages during M. avium infection based on its role in the regulation of gene expression. The inositol-requiring enzyme 1 (IRE1)/apoptosis signal-regulating kinase 1 (ASK1)/c-Jun N-terminal kinase (JNK) signalling pathway was activated in macrophages after infection with M. avium. The expression of RIDD-associated genes, such as Bloc1s1 and St3gal5, was decreased in M. avium-infected macrophages. Interestingly, M. avium-induced apoptosis was significantly suppressed by pretreatment with irestatin (inhibitor of IRE1α) and 4µ8c (RIDD blocker). Macrophages pretreated with N-acetyl cysteine (NAC) showed decreased levels of reactive oxygen species (ROS), IRE1α, and apoptosis after M. avium infection. The expression of Bloc1s1 and St3gal5 was increased in NAC-pretreated macrophages following infection with M. avium. Growth of M. avium was significantly increased in irestatin-, 4µ8c-, and NAC-treated macrophages compared with the control. The data indicate that the ROS-mediated ER stress response induces apoptosis of M. avium-infected macrophages by activating IRE1α-RIDD. Thus, activation of IRE1α suppresses the intracellular survival of M. avium in macrophages.

TNF-α-mediated ER stress causes elimination of Mycobacterium fortuitum reservoirs by macrophage apoptosis.

Mycobacterium fortuitum (MF), a rapidly growing nontuberculosis mycobacterium, is recognized as an important human pathogen. We investigated whether the endoplasmic reticulum (ER) stress response is associated with the apoptosis of MF-infected macrophages. The expression of ER molecular chaperones was significantly induced by MF infection. We found that MF-induced reactive oxygen species (ROS) generation plays a critical role in the induction of ER stress-mediated apoptosis. Excess TNF-α in the ER led to ER stress-mediated apoptosis during MF infection. The intracellular survival of MF was significantly increased by TNF-α knockdown compared with the control. This is the first report of MF-induced TNF-α as a cause of ER stress in macrophages. Furthermore, we found that TLR2-mediated ER stress response contributed to the elimination of intracellular MF in vivo. These results suggest that TNF-α-mediated ER stress during MF infection contributes to the suppression of intracellular survival of MF in macrophages. Our findings provide new insight into the importance of ER stress in mycobacterial infection.-Oh, S.-M., Lim, Y.-J., Choi, J.-A., Lee, J., Cho, S.-N., Go, D., Kim, S.-H., Song, C.-H. TNF-α-mediated ER stress causes elimination of Mycobacterium fortuitum reservoirs by macrophage apoptosis.

Rapid determination of ß-lactam antimicrobial resistance in bacteria by a liquid chromatography-mass spectrometry-based method.

Conventional antimicrobial susceptibility tests (ASTs) are very time consuming and insufficiently precise to promptly select a proper antimicrobial treatment. This difficulty disrupts the management of infections and exacerbates the development of antimicrobial resistance. Generally, antimicrobial resistance involves the chemical modification of an antimicrobial compound to an inactive form by an enzyme released by bacteria. This modification causes a structural change and is followed by a characteristic mass shift of the antimicrobials. Using this mechanism, we developed a new liquid chromatography-mass spectrometry method to rapidly determine the degree of resistance of Salmonella enterica subspecies enterica serovar Typhimurium (Salmonella Typhimurium), Escherichia coli, and Staphylococcus aureus to amoxicillin, ampicillin, and penicillin G, respectively. This method was successfully applied to 20 bacterial isolates from Korean slaughterhouses and farms. There were 18-Da mass shifts in resistant strains compared with susceptible strains of Salmonella Typhimurium, E. coli, and S. aureus, and the intensities of the hydrolyzed penicillin mass spectra were much higher in resistant strains than those in susceptible strains, which together indicate the reliability of this method. A comparison of the mass spectrometry-derived results with that from conventional ASTs revealed an identical classification of the tested bacteria according to sensitivity and resistance. Notably, this assay method requires only 2 h for determining the susceptibility status of a strain. This newly developed method is able to determine the extent of antimicrobial resistance qualitatively and quantitatively within a very short time and could be used to replace conventional AST methods. Graphical abstract Rapid determination of ß-lactam antimicrobial resistance in bacteria by LC-MS/MS.

Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN.

Improvement and year-to-year stabilization of biomass yields are primary objectives for the development of a low-input switchgrass feedstock production system using microbial endophytes. An earlier investigation of the effect of Burkholderia phytofirmans strain PsJN on switchgrass germplasm demonstrated differential responses between genotypes. PsJN inoculation of cv. Alamo (lowland ecotype) increased the plant root system, shoot length, and biomass yields, whereas it had no beneficial effect on cv. Cave-in-Rock (upland ecotype). To understand the gene networks governing plant growth promotion responses triggered by PsJN, the gene expression profiles were analysed in these two hosts, following seedling inoculation. The Affymetrix platform switchgrass expressed sequence tag (EST) microarray chip representing 122 972 probe sets, developed by the DOE BioEnergy Science Center, was employed to assess transcript abundance at 0.5, 2, 4, and 8 DAI (days after PsJN inoculation). Approximately 20 000 switchgrass probe sets showed significant responses in either cultivar. Switchgrass identifiers were used to map 19 421 genes in MapMan software. There were apparent differences in gene expression profiling between responsive and non-responsive cultivars after PsJN inoculation. Overall, there were 14 984 and 9691 genes affected by PsJN inoculation in Alamo and Cave-in-Rock, respectively. Of these, 394 are annotated as pathogenesis-related genes. In the responsive cv. Alamo, 68 pathogenesis-related genes were affected, compared with only 10 in the non-responsive cv. Cave-in-Rock. At the very early stage at 0.5 DAI, both cultivars exhibited similar recognition and defence responses, such as genes in signalling and proteolysis, after which the defence reaction in the responsive cv. Alamo became weaker while it was sustained in non-responsive cv. Cave-in-Rock.

Establishment and Characterization of Immortalized Human Dermal Papilla Cells Expressing Human Papillomavirus 16 E6/E7.

Primary human dermal papilla cells (HDPCs) are often preferred in studies on hair growth and regeneration. However, primary HDPCs are limited by their reduced proliferative capacity, decreased hair induction potential, and extended doubling times at higher passages. To overcome these limitations, pTARGET vectors containing human papillomavirus16 (HPV16) E6/E7 oncogenes were transfected into HDPCs and selected using G-148 to generate immortalized cells here. HPV16 E6/E7 oncogenes were efficiently transfected into primary HDPCs. Immortalized HDPC showed higher proliferative activity than primary HDPC, confirming an increased proliferation rate. Expression of p53 and pRb proteins was downregulated by E6 and E7, respectively. E6/E7 expressing HDPC cells revealed that cyclin-dependent kinase (CDK) inhibitor p21 expression was decreased, while cell cycle-related genes and proteins (CDK2 and cyclin E) and E2F family genes were upregulated. Immortalized HDPCs maintained their responsiveness to Wnt/ß-catenin pathway and hair follicle formation capability, as indicated by their aggregative properties and stemness. E6/E7 immortalized HDPCs may facilitate in vitro hair growth and regeneration studies.

[Impact of Anthropometric Indices of Obesity on the Risk of Incident Hypertension in Adults with Prehypertension: A Secondary Analysis of a Cohort Study].

PURPOSE: This study aimed to investigate the impact of anthropometric indices of obesity (body mass index [BMI], waist circumference, waist hip ratio, and body fat percentage) on the incidence of hypertension in adults with prehypertension. METHODS: A longitudinal study design using secondary data form the Korean Genome and Epidemiology Study was employed. The study included 1,838 adults with prehypertension tracked every two years from 2001 to 2018. Statistical analyses, including frequency assessments, number of cases per 1,000 person-years, log-rank tests, Kaplan-Meier curves, and Cox's proportional hazards regression, were conducted using SPSS version 25. RESULTS: Over the observation period (15,783.6 person-years), 1,136 individuals developed hypertension. The incidence of hypertension was significantly higher in the obesity groups defined by BMI (hazard ratio [HR] = 1.33), waist circumference (HR = 1.34), waist hip ratio (HR = 1.29), and body fat percentage (HR = 1.31) compared to the non-obese group. These findings indicate an increased risk of hypertension associated with obesity as measured by these indices. CONCLUSION: The study underscores the importance of avoiding obesity to prevent hypertension in individuals with prehypertension. Specifically, BMI, waist circumference, waist hip circumference, and body fat percentage were identified as significant risk factors for hypertension. The results suggest the need for individualized weight control interventions, emphasizing the role of health professionals in addressing the heightened hypertension risk in this population.

Phorbal-12-mysristate-13-acetate-induced inflammation is restored by protectin DX through PPARγ in human promonocytic U937 cells.

AIMS: Protectin DX (PDX), a specialized pro-resolving mediator, is an important pharmaceutical compound with potential antioxidant and inflammation-resolving effects. However, the fundamental mechanism by which PDX's ameliorate chronic inflammatory diseases has not yet been elucidated. This study aims to evaluate the anti-inflammatory properties and PPARγ-mediated mechanisms of PDX in phorbal-12-mysristate-13-acetate (PMA)-stimulated human promonocytic U937 cells. MAIN METHODS: We confirmed the effects of PDX on expressions of pro-inflammatory cytokines, mediators, and CD14 using conventional PCR, RT-qPCR, ELISA, and flow cytometry. Using western blotting, immunofluorescence, and reactive oxygen species (ROS) determination, we observed that PDX regulated PMA-induced signaling cascades. Molecular docking analysis and a cellular thermal shift assay were conducted to verify the interaction between PDX and the proliferator-activated receptor-γ (PPARγ) ligand binding domain. Western blotting was then employed to explore the alterations in PPARγ expression levels and validate PDX as a PPARγ full agonist. KEY FINDINGS: PDX attenuated protein and mRNA expression levels of interleukin-6, tumor necrosis factor-α, and cyclooxygenase-2 in PMA-treated U937 cells. PDX acts as a PPARγ agonist, exerting a modulating effect on the ROS/JNK/c-Fos signaling pathways. Furthermore, PDX reduced human monocyte differentiation antigen CD14 expression levels. SIGNIFICANCE: PPARγ exhibits pro-resolving effects to regulate the excessive inflammation. These results suggest that PDX demonstrates the resolution of inflammation, indicating the potential for therapeutic targeting of chronic inflammatory diseases.

Application of Cartilage Extracellular Matrix to Enhance Therapeutic Efficacy of Methotrexate.

BACKGROUND: Rheumatoid arthritis (RA) is characterized by chronic inflammation and joint damage. Methotrexate (MTX), a commonly used disease-modifying anti-rheumatic drug (DMARD) used in RA treatment. However, the continued use of DMARDs can cause adverse effects and result in limited therapeutic efficacy. Cartilage extracellular matrix (CECM) has anti-inflammatory and anti-vascular effects and promotes stem cell migration, adhesion, and differentiation into cartilage cells. METHODS: CECM was assessed the dsDNA, glycosaminoglycan, collagen contents and FT-IR spectrum of CECM. Furthermore, we determined the effects of CECM and MTX on cytocompatibility in the SW 982 cells and RAW 264.7 cells. The anti-inflammatory effects of CECM and MTX were assessed using macrophage cells. Finally, we examined the in vivo effects of CECM in combination with MTX on anti-inflammation control and cartilage degradation in collagen-induced arthritis model. Anti-inflammation control and cartilage degradation were assessed by measuring the serum levels of RA-related cytokines and histology. RESULTS: CECM in combination with MTX had no effect on SW 982, effectively suppressing only RAW 264.7 activity. Moreover, anti-inflammatory effects were enhanced when low-dose MTX was combined with CECM. In a collagen-induced arthritis model, low-dose MTX combined with CECM remarkably reduced RA-related and pro-inflammatory cytokine levels in the blood. Additionally, low-dose MTX combined with CECM exerted the best cartilage-preservation effects compared to those observed in the other therapy groups. CONCLUSION: Using CECM as an adjuvant in RA treatment can augment the therapeutic effects of MTX, reduce existing drug adverse effects, and promote joint tissue regeneration.

Injectable and Multifunctional Hydrogels Based on Poly(N-acryloyl glycinamide) and Alginate Derivatives for Antitumor Drug Delivery.

Chemotherapy is a conventional treatment that uses drugs to kill cancer cells; however, it may induce side effects and may be incompletely effective, leading to the risk of tumor recurrence. To address this issue, we developed novel injectable thermal/near-infrared (NIR)-responsive hydrogels to control drug release. The injectable hydrogel formulation was composed of biocompatible alginates, poly(N-acryloyl glycinamide) (PNAGA) copolymers with an upper critical solution temperature, and NIR-responsive cross-linkers containing coumarin groups, which were gelated through bioorthogonal inverse electron demand Diels-Alder reactions. The hydrogels exhibited quick gelation times (120-800 s) and high drug loading efficiencies (>90%). The hydrogels demonstrated a higher percentage of drug release at 37 °C than that at 25 °C due to the enhanced swelling behavior of temperature-responsive PNAGA moieties. Upon NIR irradiation, the hydrogels released most of the entrapped doxorubicin (DOX) (97%) owing to the cleavage of NIR-sensitive coumarin ester groups. The hydrogels displayed biocompatibility with normal cells, while induced antitumor activity toward cancer cells. DOX/hydrogels treated with NIR light inhibited tumor growth in nude mice bearing tumors. In addition, the injected hydrogels emitted red fluorescence upon excitation at a green wavelength, so that the drug delivery and hydrogel degradation in vivo could be tracked in the xenograft model.

Deep learning-radiomics integrated noninvasive detection of epidermal growth factor receptor mutations in non-small cell lung cancer patients.

This study focused on a novel strategy that combines deep learning and radiomics to predict epidermal growth factor receptor (EGFR) mutations in patients with non-small cell lung cancer (NSCLC) using computed tomography (CT). A total of 1280 patients with NSCLC who underwent contrast-enhanced CT scans and EGFR mutation testing before treatment were selected for the final study. Regions of interest were segmented from the CT images to extract radiomics features and obtain tumor images. These tumor images were input into a convolutional neural network model to extract 512 image features, which were combined with radiographic features and clinical data to predict the EGFR mutation. The generalization performance of the model was evaluated using external institutional data. The internal and external datasets contained 324 and 130 EGFR mutants, respectively. Sex, height, weight, smoking history, and clinical stage were significantly different between the EGFR-mutant patient groups. The EGFR mutations were predicted by combining the radiomics and clinical features, and an external validation dataset yielded an area under the curve (AUC) value of 0.7038. The model utilized 1280 tumor images, radiomics features, and clinical characteristics as input data and exhibited an AUC of approximately 0.81 and 0.78 during the primary cohort and external validation, respectively. These results indicate the feasibility of integrating radiomics analysis with deep learning for predicting EGFR mutations. CT-image-based genetic testing is a simple EGFR mutation prediction method, which can improve the prognosis of NSCLC patients and help establish personalized treatment strategies.

Estimating the Prevalence and Identifying the Correlates of Sexting Behaviors Among Cambodian Male Adolescents.

Male youths are more likely to experience peer pressure that encourages them to engage in risky behaviors than female youths, and this pressure can lead to an increased risk of sexting among male youths. This study aimed to investigate the prevalence of and factors associated with sexting among Cambodian male youths. The correlational cross-sectional study design was utilized. This study surveyed 647 Cambodian male youths aged 15 to 24 years. The measurement included sending or receiving messages (sexts) that contain sexually explicit messages, images, or videos, and affecting factors to sexting. Around 32.5% of participants sent sexts, and 38.9% received them. Open relationships, pornographic website use, perception of friends' sexual activity, frequent thoughts about sex, higher sexual sensation-seeking tendencies, positive attitudes toward sex, and sexual experience were associated with increased likelihood of sending and receiving sexts. Based on the findings of this study, by offering suitable education, guidance, and intervention programs, we can effectively mitigate the adverse repercussions of sexting while fostering healthy sexual behaviors among youths.

Gene-specific machine learning for pathogenicity prediction of rare BRCA1 and BRCA2 missense variants.

Machine learning-based pathogenicity prediction helps interpret rare missense variants of BRCA1 and BRCA2, which are associated with hereditary cancers. Recent studies have shown that classifiers trained using variants of a specific gene or a set of genes related to a particular disease perform better than those trained using all variants, due to their higher specificity, despite the smaller training dataset size. In this study, we further investigated the advantages of "gene-specific" machine learning compared to "disease-specific" machine learning. We used 1068 rare (gnomAD minor allele frequency (MAF) < 0.005) missense variants of 28 genes associated with hereditary cancers for our investigation. Popular machine learning classifiers were employed: regularized logistic regression, extreme gradient boosting, random forests, support vector machines, and deep neural networks. As features, we used MAFs from multiple populations, functional prediction and conservation scores, and positions of variants. The disease-specific training dataset included the gene-specific training dataset and was > 7 × larger. However, we observed that gene-specific training variants were sufficient to produce the optimal pathogenicity predictor if a suitable machine learning classifier was employed. Therefore, we recommend gene-specific over disease-specific machine learning as an efficient and effective method for predicting the pathogenicity of rare BRCA1 and BRCA2 missense variants.

Tissue Engineered Mini-Cornea Model for Eye Irritation Test.

BACKGROUND: Eye irritation tests with animals have been conducted for a long time. However, the subjective decision to irritation, the anatomic/physiologic difference between species and humans, and ethical issues are crucial problems. Various research groups have paid attention to alternative testing methods. In these senses, we fabricated in vitro mini-cornea models with immortalized human corneal epithelial cells (iHCECs) and keratocytes (iHCKs) and used them for irritation tests. This study hypothesized that our mini-cornea model could present different viability tendencies according to test chemicals with different irritancy levels. METHODS: Cells used in this study were characterized with cornea-specific markers by immunocytochemistry and western blot. To make a three-dimensional hemisphere construct like cornea stroma, we cultured iHCKs under modified culture conditions verified by matrix formation and total collagen content. iHCECs were seeded on the construct and cultured at an air-liquid interface. The model was treated with 2-phenoxyethanol, triton X-100, sodium lauryl sulfate, and benzalkonium chloride. RESULTS: iHCECs and iHCKs presented their specific cell markers. In modifying the culture condition, the group treating ascorbic acid (200 µg/ml) presented an intact cellular matrix and included the highest collagen content; thus, we used this condition to fabricate the mini-cornea model. The model shows hemisphere shape and homogenous cell distributions in histological analysis. We observed different sensitivity tendencies by types of chemicals, and the model's viability significantly decreased when the chemical concentration increased. CONCLUSION: In this study, we performed and observed irritation tests using a tissue-engineered mini-cornea model and considered to apply as an alternative approach for animal tests.

Anti-Osteoarthritic Effects of Cartilage-Derived Extracellular Matrix in a Rat Osteoarthritis Model.

BACKGROUND: The extracellular matrix (ECM) has many functions, such as segregating tissues, providing support, and regulating intercellular communication. Cartilage-derived ECM (CECM) can be prepared via consecutive processes of chemical decellularization and enzyme treatment. The purpose of this study was to improve and treat osteoarthritis (OA) using porcine knee articular CECM. METHODS: We assessed the rheological characteristics and pH of CECM solutions. Furthermore, we determined the effects of CECM on cell proliferation and cytotoxicity in the chondrocytes of New Zealand rabbits. The inhibitory effect of CECM on tumor necrosis factor (TNF)-α-induced cellular apoptosis was assessed using New Zealand rabbit chondrocytes and human synoviocytes. Finally, we examined the in vivo effects of CECM on inflammation control and cartilage degradation in an experimental OA-induced rat model. The rat model of OA was established by injecting monosodium iodoacetate into the intra-articular knee joint. The rats were then injected with CECM solution. Inflammation control and cartilage degradation were assessed by measuring the serum levels of proinflammatory cytokines and C-telopeptide of type II collagen and performing a histomorphological analysis. RESULTS: CECM was found to be biocompatible and non-immunogenic, and could improve cell proliferation without inducing a toxic reaction. CECM significantly reduced cellular apoptosis due to TNF-α, significantly improved the survival of cells in inflammatory environments, and exerted anti-inflammatory effects. CONCLUSION: Our findings suggest that CECM is an appropriate injectable material that mediates OA-induced inflammation.

Redox-Responsive Core-Cross-Linked Micelles of Miktoarm Poly(ethylene oxide)-b-poly(furfuryl methacrylate) for Anticancer Drug Delivery.

The physiological instability of nanocarriers, premature drug leakage during blood circulation, and associated severe side effects cause compromised therapeutic efficacy, which have significantly hampered the progress of nanomedicines. The cross-linking of nanocarriers while keeping the effectiveness of their degradation at the targeted site to release the drug has emerged as a potent strategy to overcome these flaws. Herein, we have designed novel (poly(ethylene oxide))2-b-poly(furfuryl methacrylate) ((PEO2K)2-b-PFMAnk) miktoarm amphiphilic block copolymers by coupling alkyne-functionalized PEO (PEO2K-C≡H) and diazide-functionalized poly(furfuryl methacrylate) ((N3)2-PFMAnk) via click chemistry. (PEO2K)2-b-PFMAnk self-assembled to form nanosized micelles (mikUCL) with hydrodynamic radii in the range of 25∼33 nm. The hydrophobic core of mikUCL was cross-linked by a disulfide-containing cross-linker using the Diels-Alder reaction to avoid unwanted leakage and burst release of a payload. As expected, the resulting core-cross-linked (PEO2K)2-b-PFMAnk micelles (mikCCL) exhibited superior stability under a normal physiological environment and were de-cross-linked to rapidly release doxorubicin (DOX) upon exposure to a reduction environment. The micelles were compatible with HEK-293 normal cells, while DOX-loaded micelles (mikUCL/DOX and mikCCL/DOX) induced high antitumor activity in HeLa and HT-29 cells. mikCCL/DOX preferentially accumulated at the tumor site and was more efficacious than free DOX and mikUCL/DOX for tumor inhibition in HT-29 tumor-bearing nude mice.