Pectin Nanoporous Structures Prepared via Salt-Induced Phase Separation and Ambient Azeotropic Evaporation Processes.

Polysaccharide nanoporous structures are suitable for various applications, ranging from biomedical scaffolds to adsorption materials, owing to their biocompatibility and large surface areas. Pectin, in particular, can create 3D nanoporous structures in aqueous solutions by binding with calcium cations and creating nanopores by phase separation; this process involves forming hydrogen bonds between alcohols and pectin chains in water and alcohol mixtures and the resulting penetration of alcohols into calcium-bound pectin gels. However, owing to the dehydration and condensation of polysaccharide chains during drying, it has proven to be challenging to maintain the 3D nanoporous structure without using a freeze-drying process or supercritical fluid. Herein, we report a facile method for creating polysaccharide-based xerogels, involving the co-evaporation of water with a nonsolvent (e.g., a low-molecular-weight hydrophobic alcohol such as isopropyl or n-propyl alcohol) at ambient conditions. Experiments and coarse-grained molecular dynamics simulations confirmed that salt-induced phase separation and hydrogen bonding between hydrophobic alcohols and pectin chains were the dominant processes in mixtures of pectin, water, and hydrophobic alcohols. Furthermore, the azeotropic evaporation of water and alcohol mixed in approximately 1:1 molar ratios was maintained during the natural drying process under ambient conditions, preventing the hydration and aggregation of the hydrophilic pectin chains. These results introduce a simple and convenient process to produce 3D polysaccharide xerogels under ambient conditions.

Exploring early life social and executive function development in infants and risk for autism: a prospective cohort study protocol of NICU graduates and infants at risk for cerebral palsy.

BACKGROUND: Delays in early social and executive function are predictive of later developmental delays and eventual neurodevelopmental diagnoses. There is limited research examining such markers in the first year of life. High-risk infant groups commonly present with a range of neurodevelopmental challenges, including social and executive function delays, and show higher rates of autism diagnoses later in life. For example, it has been estimated that up to 30% of infants diagnosed with cerebral palsy (CP) will go on to be diagnosed with autism later in life. METHODS: This article presents a protocol of a prospective longitudinal study. The primary aim of this study is to identify early life markers of delay in social and executive function in high-risk infants at the earliest point in time, and to explore how these markers may relate to the increased risk for social and executive delay, and risk of autism, later in life. High-risk infants will include Neonatal Intensive Care Unit (NICU) graduates, who are most commonly admitted for premature birth and/or cardiovascular problems. In addition, we will include infants with, or at risk for, CP. This prospective study will recruit 100 high-risk infants at the age of 3-12 months old and will track social and executive function across the first 2 years of their life, when infants are 3-7, 8-12, 18 and 24 months old. A multi-modal approach will be adopted by tracking the early development of social and executive function using behavioural, neurobiological, and caregiver-reported everyday functioning markers. Data will be analysed to assess the relationship between the early markers, measured from as early as 3-7 months of age, and the social and executive function as well as the autism outcomes measured at 24 months. DISCUSSION: This study has the potential to promote the earliest detection and intervention opportunities for social and executive function difficulties as well as risk for autism in NICU graduates and/or infants with, or at risk for, CP. The findings of this study will also expand our understanding of the early emergence of autism across a wider range of at-risk groups.

Deep learning model for differentiating nasal cavity masses based on nasal endoscopy images.

BACKGROUND: Nasal polyps and inverted papillomas often look similar. Clinically, it is difficult to distinguish the masses by endoscopic examination. Therefore, in this study, we aimed to develop a deep learning algorithm for computer-aided diagnosis of nasal endoscopic images, which may provide a more accurate clinical diagnosis before pathologic confirmation of the nasal masses. METHODS: By performing deep learning of nasal endoscope images, we evaluated our computer-aided diagnosis system's assessment ability for nasal polyps and inverted papilloma and the feasibility of their clinical application. We used curriculum learning pre-trained with patches of nasal endoscopic images and full-sized images. The proposed model's performance for classifying nasal polyps, inverted papilloma, and normal tissue was analyzed using five-fold cross-validation. RESULTS: The normal scores for our best-performing network were 0.9520 for recall, 0.7900 for precision, 0.8648 for F1-score, 0.97 for the area under the curve, and 0.8273 for accuracy. For nasal polyps, the best performance was 0.8162, 0.8496, 0.8409, 0.89, and 0.8273, respectively, for recall, precision, F1-score, area under the curve, and accuracy. Finally, for inverted papilloma, the best performance was obtained for recall, precision, F1-score, area under the curve, and accuracy values of 0.5172, 0.8125, 0.6122, 0.83, and 0.8273, respectively. CONCLUSION: Although there were some misclassifications, the results of gradient-weighted class activation mapping were generally consistent with the areas under the curve determined by otolaryngologists. These results suggest that the convolutional neural network is highly reliable in resolving lesion locations in nasal endoscopic images.

CXCL5 secreted from macrophages during cold exposure mediates white adipose tissue browning.

Adipose tissue affects metabolic-related diseases because it consists of various cell types involved in fat metabolism and adipokine release. CXC ligand 5 (CXCL5) is a member of the CXC chemokine family and is highly expressed by macrophages in white adipose tissue (WAT). In this study, we generated and investigated the function of CXCL5 in knockout (KO) mice using CRISPR/Cas9. The male KO mice did not show significant phenotype differences in normal conditions. However, proteomic analysis revealed that many proteins involved in fatty acid beta-oxidation and mitochondrial localization were enriched in the inguinal WAT (iWAT) of Cxcl5 KO mice. Cxcl5 KO mice also showed decreased protein and transcript expression of genes associated with thermogenesis, including uncoupling protein 1 (UCP1), a well-known thermogenic gene, and increased expression of genes associated with inflammation. The increase in UCP1 expression in cold conditions was significantly retarded in Cxcl5 KO mice. Finally, we found that CXCL5 treatment increased the expression of transcription factors that mediate Ucp1 expression and Ucp1 itself. Collectively, our data show that Ucp1 expression is induced in adipocytes by CXCL5, which is secreted upon ß-adrenergic stimulation by cold stimulation in M1 macrophages. Our data indicate that CXCL5 plays a crucial role in regulating energy metabolism, particularly upon cold exposure. These results strongly suggest that targeting CXCL5 could be a potential therapeutic strategy for people suffering from disorders affecting energy metabolism.

Proteomic analysis of aqueous humor in canine primary angle-closure glaucoma in American Cocker Spaniel dogs.

OBJECTIVE: To analyze proteomic profiles of the aqueous humor (AH) of canines with primary angle-closure glaucoma (PACG) and identify associated protein alterations. ANIMALS STUDIED: Six American Cocker Spaniels with PACG and six American Cocker Spaniels without ocular diseases. METHODS: Aqueous humor samples were collected from six American Cocker Spaniels with PACG at Seoul National University, VMTH, and six healthy Cocker Spaniels without ocular disease at Irion Animal Hospital. For the PACG group, AH samples were obtained by anterior chamber paracentesis prior to glaucoma treatment. For the AH control group, AH samples were collected from patients anesthetized for other reasons. Total AH protein concentration was determined by the bicinchoninic acid (BCA) assay. AH protein samples were quantified by liquid chromatography-mass spectrometry (LC-MS/MS). Raw MS spectra were processed using MaxQuant software 30, and the Gene Ontology (GO) enrichment analysis was performed using ClueGO. RESULTS: The AH protein concentration in the PACG group (10.49 ± 17.98 µg/µl) was significantly higher than that of the control group (0.45 ± 0.11 µg/µl; p < .05). A total of 758 proteins were identified in the AH. Several proteins both significantly increased (n = 69) and decreased (n = 252) in the PACG group compared to those in the control group. GO enrichment analysis showed that the "response to wounding," "negative regulation of endopeptidase activity," and "cell growth" pathways were the most enriched terms in the PACG group compared to the control group. The top 5 proteins that were significantly increased in the AH of the PACG group were secreted phosphoprotein 1 (SPP1), peptidoglycan recognition proteins 2 (PGLYRP2), tyrosine 3-monooxygenase (YWHAE), maltase-glucoamylase (MGAM), and vimentin (VIM). CONCLUSIONS: Gene Ontology enrichment analysis using the proteomic data showed that proteins and pathways related to inflammation were significantly upregulated in the various stage of PACG. Proteomic analysis of the AH from the PACG may provide valuable insights into PACG pathogenesis.

Korean Grammatical Error Correction Based on Transformer with Copying Mechanisms and Grammatical Noise Implantation Methods.

Grammatical Error Correction (GEC) is the task of detecting and correcting various grammatical errors in texts. Many previous approaches to the GEC have used various mechanisms including rules, statistics, and their combinations. Recently, the performance of the GEC in English has been drastically enhanced due to the vigorous applications of deep neural networks and pretrained language models. Following the promising results of the English GEC tasks, we apply the Transformer with Copying Mechanism into the Korean GEC task by introducing novel and effective noising methods for constructing Korean GEC datasets. Our comparative experiments showed that the proposed system outperforms two commercial grammar check and other NMT-based models.

Role of growth factors in hematopoietic stem cell niche.

Hematopoietic stem cells (HSCs) produce new blood cells everyday throughout life, which is maintained by the self-renewal and differentiation ability of HSCs. This is not controlled by the HSCs alone, but rather by the complex and exquisite microenvironment surrounding the HSCs, which is called the bone marrow niche and consists of various bone marrow cells, growth factors, and cytokines. It is essential to understand the characteristic role of the stem cell niche and the growth factors in the niche formation. In this review, we describe the role of the bone marrow niche and factors for niche homeostasis, and also summarize the latest research related to stem cell niche.

Platelet Factor 4 as a Novel Exosome Marker in MALDI-MS Analysis of Exosomes from Human Serum.

Exosomes are nanosized vesicles commonly found in biological fluids as a result of a secretion process involving endosomes and multivesicular bodies. The isolation and analysis of exosomes can be useful for noninvasive clinical diagnosis of a variety of human diseases. We investigated the utility of analyzing exosomal proteins, using matrix-assisted laser desorption/ionization combined with Fourier-transform ion cyclotron resonance mass spectrometry (MALDI-FTICR-MS), as a means of determining the presence of exosomes. MALDI-FTICR-MS analyses of exosomes enriched from human serum via centrifugation in a mass range of m/z 1000-20 000 yielded a distinctive protein around m/z 7766. The high mass accuracy and resolution of MALDI-FTICR-MS allowed for reliable comparisons against a protein database, through which the protein was identified as platelet factor 4 (PLF4), whose singly charged protein peak has an elemental composition of C341H577N96O101S4+, with a theoretical most abundant isotopic peak at m/z 7765.194 and a theoretical average peak at m/z 7766. The MALDI-TOF MS analysis of exosomes from the serum of 27 patients with different states of liver diseases provided the most abundant PLF4 peak for each mass spectrum, along with several additional minor peaks. In conclusion, MALDI-MS is suitable as an alternative exosome detection method, serving as a valuable confirmation tool, greatly decreasing the time and workload associated with exosome identification.

Effects of incubation temperature and acetonitrile amount on microwave-assisted tryptic digestion of proteins.

The effects of incubation temperature and acetonitrile (ACN) amount on microwave-assisted tryptic digestion of horse skeletal muscle myoglobin (MYG) and bovine serum albumin (BSA) were investigated. Microwave-assisted tryptic digestion was performed on BSA or MYG solutions containing different amounts (0, 10, and 20%) of ACN for different times (10, 20, 30, 40, and 50 min) at different temperatures (25, 37, and 55 °C). Conventional overnight tryptic digestion was also conducted with gentle mixing at 37 °C for 16 h. Digested samples were analyzed using matrix-assisted laser desorption/ionization mass spectrometry. Similar sequence coverage (SC) values were obtained under most conditions except when the protein sample solutions were digested with 20% ACN at 55 °C, which provided the lowest SC for both MYG and BSA for all investigated digestion times. Considering the missed cleavage (MC) ratios for 50-min microwave-assisted digestion, the highest MC ratio, (i.e., lowest trypsin activity) was observed for the digestion condition of 20% ACN at 55 °C for both proteins, while the lowest MC ratio was observed with 0% ACN at 25 °C for MYG and with 0% ACN at 55 °C for BSA. Conventional overnight tryptic digestion at 37 °C provided more completely cleaved peptides than 50-min microwave-assisted tryptic digestion at the same temperature.

Microwave-Assisted Protein Digestion in a Plate Well for Facile Sampling and Rapid Digestion.

Protein digestion is one of the most important processes in proteomic analysis. Here, we report microwave-assisted protein digestion in a plate well, which allows for facile sampling as well as rapid protein digestion based on the combination of highly stable enzyme immobilization and 3D printing technologies. Trypsin (TR) was immobilized on polystyrene-based nanofibers via an enzyme coating (EC) approach. The EC with stabilized TR activity was assembled with the 3D-printed structure in the plate well (EC/3D), which provides two separated compartments for the solution sampling and the TR-catalyzed protein digestion, respectively. EC/3D can effectively prevent the interference of sampling by accommodating EC in the separated compartment from the sampling hole in the middle. EC/3D in the plate well maintained its protein digestion performance under shaking over 160 days. Microwave irradiation enabled the digestion of bovine serum albumin within 10 min, generating the MALDI-TOF MS results of 75.0% sequence coverage and 61 identified peptides. EC/3D maintained its protein digestion performance under microwave irradiation after 30 times of recycled uses. EC/3D in the plate well has demonstrated its potential as a robust and facile tool for the development of an automated protein digestion platform. The combination of stable immobilized enzymes and 3D-printed structures can be potentially utilized not only for the protein digestion, but also for many other enzyme applications, including bioconversion and biosensors.

Inducible HGF-secreting Human Umbilical Cord Blood-derived MSCs Produced via TALEN-mediated Genome Editing Promoted Angiogenesis.

Mesenchymal stem cells (MSCs) promote therapeutic angiogenesis to cure serious vascular disorders. However, their survival period and cytokine-secretory capacity are limited. Although hepatocyte growth factor (HGF) can accelerate the rate of angiogenesis, recombinant HGF is limited because of its very short half-life (<3-5 minutes). Thus, continuous treatment with HGF is required to obtain an effective therapeutic response. To overcome these limitations, we produced genome-edited MSCs that secreted HGF upon drug-specific induction. The inducible HGF expression cassette was integrated into a safe harbor site in an MSC chromosome using the TALEN system, resulting in the production of TetOn-HGF/human umbilical cord blood-derived (hUCB)-MSCs. Functional assessment of the TetOn-HGF/hUCB-MSCs showed that they had enhanced mobility upon the induction of HGF expression. Moreover, long-term exposure by doxycycline (Dox)-treated TetOn-HGF/hUCB-MSCs enhanced the anti-apoptotic responses of genome-edited MSCs subjected to oxidative stress and improved the tube-formation ability. Furthermore, TetOn-HGF/hUCB-MSCs encapsulated by arginine-glycine-aspartic acid (RGD)-alginate microgel induced to express HGF improved in vivo angiogenesis in a mouse hindlimb ischemia model. This study showed that the inducible HGF-expressing hUCB-MSCs are competent to continuously express and secrete HGF in a controlled manner. Thus, the MSCs that express HGF in an inducible manner are a useful therapeutic modality for the treatment of vascular diseases requiring angiogenesis.

Seasonal patterns and bloom dynamics of phytoplankton based on satellite-derived chlorophyll-a in the eastern yellow sea.

Satellite-derived chlorophyll-a concentration (Chl-a) is essential for assessing environmental conditions, yet its application in the optically complex waters of the eastern Yellow Sea (EYS) is challenged. This study refines the Chl-a algorithm for the EYS employing a switching approach based on normalized water-leaving radiance at 555 nm wavelength according to turbidity conditions to investigate phytoplankton bloom patterns in the EYS. The refined Chl-a algorithm (EYS algorithm) outperforms prior algorithms, exhibiting a strong alignment with in situ Chl-a. Employing the EYS algorithm, seasonal and bloom patterns of Chl-a are detailed for the offshore and nearshore EYS areas. Distinct seasonal Chl-a patterns and factors influencing bloom initiation differed between the areas, and the peak Chl-a during the bloom period from 2018 to 2020 was significantly lower than the average year in both areas. Specifically, bimodal and unimodal peak patterns in Chl-a were observed in the offshore and nearshore areas, respectively. By investigating the relationships between environmental factors and bloom parameters, we identified that major controlling factors governing bloom initiation were mixed layer depth (MLD) and suspended particulate matter (SPM) in the offshore and nearshore areas, respectively. Additionally, this study proposed that the recent decrease in the peak Chl-a might be caused by rapid environmental changes such as the warming trend of sea surface temperature (SST) and the limitation of nutrients. For example, external forcing, phytoplankton growth, and nutrient dynamics can change due to increased SST and limitation of nutrients, which can lead to a decrease in Chl-a. This study contributes to understanding phytoplankton dynamics in the EYS, highlighting the importance of region-specific considerations in comprehending Chl-a patterns and bloom dynamics.

Ubiquitin ligase RNF20 coordinates sequential adipose thermogenesis with brown and beige fat-specific substrates.

In mammals, brown adipose tissue (BAT) and inguinal white adipose tissue (iWAT) execute sequential thermogenesis to maintain body temperature during cold stimuli. BAT rapidly generates heat through brown adipocyte activation, and further iWAT gradually stimulates beige fat cell differentiation upon prolonged cold challenges. However, fat depot-specific regulatory mechanisms for thermogenic activation of two fat depots are poorly understood. Here, we demonstrate that E3 ubiquitin ligase RNF20 orchestrates adipose thermogenesis with BAT- and iWAT-specific substrates. Upon cold stimuli, BAT RNF20 is rapidly downregulated, resulting in GABPα protein elevation by controlling protein stability, which stimulates thermogenic gene expression. Accordingly, BAT-specific Rnf20 suppression potentiates BAT thermogenic activity via GABPα upregulation. Moreover, upon prolonged cold stimuli, iWAT RNF20 is gradually upregulated to promote de novo beige adipogenesis. Mechanistically, iWAT RNF20 mediates NCoR1 protein degradation, rather than GABPα, to activate PPARγ. Together, current findings propose fat depot-specific regulatory mechanisms for temporal activation of adipose thermogenesis.

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.

Periodontitis of maxillary teeth screened by community periodontal index is associated with chronic rhinosinusitis defined by EPOS 2020 guideline.

We aimed to evaluate the association between periodontitis in the upper jaw and chronic rhinosinusitis (CRS) using the nationwide Korean National Health and Nutrition Examination Survey (KNHANES) data. In this cross-sectional study, data of KNHANES participants enrolled between 2008 and 2012 were reviewed. Periodontitis of the upper teeth was diagnosed by dentists according to the community periodontal index with standardized methods. CRS was diagnosed by otorhinolaryngologists according to the European Position Paper on Rhinosinusitis and Nasal Polyps 2020 with nasal endoscopy findings. We also evaluated the association between periodontitis and CRS according to smoking and drinking status. Univariate and multivariate logistic regression analyses were performed. Overall, 28,761 participants were eligible for analysis, and 210 were diagnosed with CRS. Periodontitis was associated with CRS diagnosis (odds ratio [OR] = 1.391, 95% confidence interval [CI] = 1.013-1.912). Non-drinkers showed no significant association between periodontitis and CRS (OR = 1.142, 95% CI 0.746-1.749). However, among drinkers, periodontitis was significantly associated with CRS (OR = 1.733, 95% CI 1.091-2.753). The number of smokers with CRS was not statistically sufficient and a logistic regression model based on smoking status could not be generated. Individuals with periodontitis in the upper jaw may need to consult an otorhinolaryngologist for comorbid CRS especially according to drinking status.

Primary Production in the Kara, Laptev, and East Siberian Seas.

Understanding of the primary production of phytoplankton in the Kara Sea (KS), the Laptev Sea (LS), and the East Siberian Sea (ESS) remains limited, despite the recognized importance of phytoplankton in the Arctic Ocean. To address this knowledge gap, we conducted three NABOS (Nansen and Amundsen Basins Observational System) expeditions in 2013, 2015, and 2018 to measure in situ primary production rates using a 13C-15N dual-tracer method and examine their major controlling factors. The main goals in this study were to investigate regional heterogeneity in primary production and derive its contemporary ranges in the KS, LS, and ESS. The daily primary production rates in this study (99 ± 62, 100 ± 77, and 56 ± 35 mg C m-2 d-1 in the KS, LS, and ESS, respectively) are rather different from the values previously reported in each sea mainly because of spatial and regional differences. Among the three seas, a significantly lower primary production rate was observed in the ESS in comparison to those in the KS and LS. This is likely mainly because of regional differences in freshwater content based on the noticeable relationship (Spearman, rs = -0.714, p < 0.05) between the freshwater content and the primary production rates observed in this study. The contemporary ranges of the annual primary production based on this and previous studies are 0.96-2.64, 0.72-50.52, and 1.68-16.68 g C m-2 in the KS, LS, and ESS, respectively. Further intensive field measurements are warranted to enhance our understanding of marine microorganisms and their community-level responses to the currently changing environmental conditions in these poorly studied regions of the Arctic Ocean.