Data Resource Profile: The Cancer Public Library Database in South Korea.

This paper provides a comprehensive overview of the Cancer Public Library Database (CPLD), established under the Korean Clinical Data Utilization for Research Excellence project (K-CURE). The CPLD links data from four major population-based public sources: the Korea National Cancer Incidence Database in the Korea Central Cancer Registry, cause-of-death data in Statistics Korea, the National Health Information Database in the National Health Insurance Service, and the National Health Insurance Research Database in the Health Insurance Review & Assessment Service. These databases are linked using an encrypted resident registration number. The CPLD, established in 2022 and updated annually, comprises 1,983,499 men and women newly diagnosed with cancer between 2012 and 2019. It contains data on cancer registration and death, demographics, medical claims, general health checkups, and national cancer screening. The most common cancers among men in the CPLD were stomach (16.1%), lung (14.0%), colorectal (13.3%), prostate (9.6%), and liver (9.3%) cancers. The most common cancers among women were thyroid (20.4%), breast (16.6%), colorectal (9.0%), stomach (7.8%), and lung (6.2%) cancers. Among them, 571,285 died between 2012 and 2020 owing to cancer (89.2%) or other causes (10.8%). Upon approval, the CPLD is accessible to researchers through the K-CURE portal. The CPLD is a unique resource for diverse cancer research to investigate medical use before a cancer diagnosis, during initial diagnosis and treatment, and long-term follow-up. This offers expanded insight into healthcare delivery across the cancer continuum, from screening to end-of-life care.

Social Inequities in the Survival of Liver Cancer: A Nationwide Cohort Study in Korea, 2007-2017.

BACKGROUND: To analyze the effects of socioeconomic status (type of insurance and income level) and cancer stage on the survival of patients with liver cancer in Korea. METHODS: A retrospective cohort study was constructed using data from the Healthcare Big Data Platform project in Korea between January 1, 2007, and December 31, 2017. A total of 143,511 patients in Korea diagnosed with liver cancer (International Classification of Diseases, 10th Revision [ICD-10] codes C22, C220, and C221) were followed for an average of 11 years. Of these, 110,443 died. The patient's insurance type and income level were used as indicators of socioeconomic status. Unadjusted and adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated using a Cox proportional hazards regression model to analyze the relationship between the effects of sex, age, and cancer stage at first diagnosis (Surveillance, Epidemiology, and the End Results; SEER), type of insurance, and income level on the survival of patients with liver cancer. The interactive effects of the type of insurance, income level, and cancer stage on liver cancer death were also analyzed. RESULTS: The lowest income group (medical aid) showed a higher risk for mortality (HR (95% CI); 1.37 (1.27-1.47) for all patients, 1.44 (1.32-1.57) for men, and 1.16 (1.01-1.34) for women) compared to the highest income group (1-6) among liver cancer (ICD-10 code C22) patients. The risk of liver cancer death was also higher in the lowest income group with a distant cancer stage (SEER = 7) diagnosis than for any other group. CONCLUSION: Liver cancer patients with lower socioeconomic status and more severe cancer stages were at greater risk of death. Reducing social inequalities is needed to improve mortality rates among patients in lower social class groups who present with advanced cancer.

Complete genome sequence of Lactococcus taiwanensis strain K_LL004, encoding hydrolytic enzymes of plant polysaccharides isolated from grasshopper (Oxya chinensis sinuosa).

The Lactococcus taiwanensis strain K_LL004 was isolated from the gut of a grasshopper (Oxya chinensis sinuosa) collected from local farm in Korea. L. taiwanensis strain K_LL004 is the functional probiotic candidate with an ability to hydrolyse plant polysaccharides. The complete genome of the L. taiwanensis strain K_LL004 contains one circular chromosome (1,995,099 bp) with a guanine + cytosine (GC) content of 38.8%. Moreover, 1,929 Protein-coding sequence, 19 rRNA genes, and 62 tRNA genes were identified based on results of annotation. L. taiwanensis strain K_LL004 has a gene, which encodes hydrolytic enzymes such as beta-glucosidase and beta-xylosidase, that hydrolyzes plant polysaccharides.

CD19/CD22 bispecific chimeric antigen receptor­NK­92 cells are developed and evaluated.

Anti-CD19 chimeric antigen receptor (CAR)-T cells have improved the outcomes of patients with B cell leukemia and lymphoma. However, their applications and positive outcomes remain limited. CAR-T cells are currently restricted to autologous blood as their source and their use can lead to downregulation of CD19 expression along with complications such as graft-versus-host disease and cytokine release syndrome. The present study aimed to develop anti-CD19/CD22 bispecific CAR structures using an anti-CD22 monoclonal antibody clone from chickens and analyze them in natural killer (NK)-92 cells, a human NK cell line, in vitro and in vivo. Anti-CD19/CD22 CAR-NK-92 cell cytotoxicity was assessed by the survival of target cells and counted using flow cytometry. Anti-CD22/CD19 and loop-structured anti-CD19/CD22 bi-specific CAR-NK-92 cells showed improved efficacy against OCI-Ly7 cells, a human B cell lymphoma cell line, compared with other CAR structures. These results demonstrate the potential of anti-CD19/CD22 bispecific CAR-NK cells and suggested that optimizing CAR structures in NK cells can improve the efficacy of CAR therapy.

Analysis of antibiotic resistance genes in pig feces during the weaning transition using whole metagenome shotgun sequencing.

Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.

Ultrasound findings of subpial hemorrhage in neonates.

PURPOSE: Subpial hemorrhage (SPH) is a subtype of intracranial hemorrhage characterized by damage to the adjacent brain parenchyma. The aim of this study was to describe the sonographic features of SPH in neonates. METHODS: The cranial ultrasound (US) findings of neonates with SPH confirmed by brain magnetic resonance imaging (MRI) were analyzed retrospectively. Initial and follow-up US and MRI scans were reviewed by two pediatric radiologists who were blinded to both clinical history and outcomes. The US features were compared with the MRI findings. RESULTS: Sixteen patients were included (median gestational age, 38 weeks; range, 26 to 40 weeks; 69% term). SPH was detected most often in the temporal lobe (63%), and multiple SPHs were found in seven of 16 neonates, based on MRI. Acute SPH with an underlying venous infarct (UVI) was detected on US in 15 of 16 patients: small or large fan-shaped hyperechoic lesions (n=7 and 4, respectively) and gyriform hyperechoic lesions (n=4). The sonographic yin-yang sign was observed in three of the four large fan-shaped SPH cases. The accompanying findings on US were intraventricular hemorrhage (four out of six MRI-confirmed cases), and concurrent periventricular venous infarcts (five out of nine MRI-confirmed cases). In five patients, subpial cysts were observed on follow-up US or MRI (n=4 and n=4, respectively). CONCLUSION: Acute SPH with UVI can appear as a peripheral fan-shaped or gyriform hyperechoic lesion on cranial US. SPH can be detected and suspected based on the US features of SPH with the accompanying findings.

Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing.

The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.

Biodegradable, Water-Resistant, Anti-Fizzing, Polyester Nanocellulose Composite Paper Straws.

Among plastic items, single-use straws are particularly detrimental to marine ecosystems because such straws, including those made of poly(lactic acid) (PLA), are sharp and extremely slowly degradable in the ocean. While paper straws are promising alternatives, they exhibit hydration-induced swelling even when coated with a non-degradable plastic coating and promote effervescence (fizzing) in soft drinks owing to their surface heterogeneities. In this study, upgraded paper straw is coated with poly(butylene succinate) cellulose nanocrystal (PBS/CNC) composites. CNC increases adhesion to paper owing to their similar chemical structures, optimizes crystalline PBS spherulites through effective nucleation, and reinforces the matrix through its anisotropic and rigid features. The straws are not only anti-fizzing when used with soft drinks owing to their homogeneous and seamless surface coatings, but also highly water-resistant and tough owing to their watertight surfaces. All degradable components effectively decompose under aerobic composting and in the marine environment. This technology contributes to United Nations Sustainable Development Goal 14 (Life Below Water).

Gut microbial shifts by synbiotic combination of Pediococcus acidilactici and lactulose in weaned piglets challenged with Shiga toxin-producing Escherichia coli.

Development of alternatives to in-feed antibiotics in the swine industry have been the focused of many pig gut microbiota studies to improve animal health. In this study, we evaluated the effects of probiotic Pediococcus acidilactici (PRO), prebiotic lactulose (PRE), and their synbiotic combination (SYN) on gut microbiota using 16S rRNA gene sequencing in weaned piglets challenged with Shiga-toxin producing Escherichia coli (STEC). Our data showed that prebiotics, probiotics and synbiotics improved the intestinal health in weaned piglets. No significant differences were observed in species richness and species diversity in weaned piglets fed prebiotics, probiotics and their synbiotic combination. However, beta diversity analysis revealed distinct clustering of the microbiota of according to dietary treatment and by oral challenge of STEC. At the phylum level, Firmicutes to Bacteroidetes ratio was lower in the dietary treatment groups than the control group. Oral supplementation of prebiotics, probiotics and synbiotics enriched the abundance of Prevotella and Roseburia. Succinivibrio was elevated in PRO group; however, Phascolarctobacterium was depleted with STEC challenge regardless of dietary treatment. Overall, our data showed that administration of synbiotics in piglets improved intestinal health through gut microbiota modulation. Our data indicated that prebiotics, probiotics and their synbiotic combination could promote intestinal health through gut microbiota modulation in weaned piglets.

Fecal microbiome shifts by different forms of copper supplementations in growing pigs.

Copper is an essential mineral for pigs, thus it is used as a feed additive in the forms of copper sulfate. Therefore, this study aimed at characterizing the fecal microbiota shifts in pigs as fed by different forms of copper supplementation. 40 growing pigs aged 73 ± 1 days with an average weight of 30.22 ± 1.92kg were randomly divided into 5 groups. The control group (CON) fed with basal diet, while treatment groups were fed a basal diet supplemented with 100 ppm/kg of copper sulfate (CuSO4), Cu-glycine complex (CuGly), Cu-amino acid complex (CuAA), and Cu-hydroxy(4methylthio)butanoate chelate complex (CuHMB) for 28 days of trial, respectively. The data presented the comparison between inorganic and organic copper supplementation through gut microbiota in growing pigs. Alpha and Beta diversity anaylsis resulted in copper supplementation did shifted gut microbioal community structure. At the phylum level, Firmicutes and Bacteroidetes were the most abundant phyla at all times regardless of treatment. At the genus level, the relative abundances of Prevotella, Lactobacillus, Megasphaera, and SMB53 of the CuGly and CuHMB groups were significantly higher than those of copper sulfate and basal diet groups. Overall, this study may provide the potential role of organic copper replacing inorganic copper, resulting in increased beneficial bacteria in the pig gut.

The transcription factor ORA59 exhibits dual DNA binding specificity that differentially regulates ethylene- and jasmonic acid-induced genes in plant immunity.

Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens in a synergistic and interdependent manner, while JA and ET also have independent roles in certain processes, e.g. in responses to wounding and flooding, respectively. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, of which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) GDSL LIPASE 1 (GLIP1) depends on ET for gene expression and pathogen resistance. Here, promoter analysis of GLIP1 revealed ERELEE4 as the critical cis-element for ET-responsive GLIP1 expression. In a yeast one-hybrid screening, ORA59 was isolated as a specific transcription factor that binds to the ERELEE4 element, in addition to the well-characterized GCC box. We found that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in gene promoters. Notably, ORA59 exhibited a differential preference for GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. JA and ET induced ORA59 phosphorylation, which was required for both activity and specificity of ORA59. Furthermore, RNA-seq and virus-induced gene silencing analyses led to the identification of ORA59 target genes of distinct functional categories in JA and ET pathways. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.

Rheological Percolation of Cellulose Nanocrystals in Biodegradable Poly(butylene succinate) Nanocomposites: A Novel Approach for Tailoring the Mechanical and Hydrolytic Properties.

Although biodegradable plastics are gradually emerging as an effective solution to alleviate the burgeoning plastic pollution, their performance is currently trivial for commercialization. A proposed two-pronged strategy to overcome this limitation includes (1) preparation of the nanocomposites from biorenewable nano-fillers to preserve their biodegradability and (2) tailoring their properties to meet the diverse demands in various applications. Herein, we report the preparation of biodegradable nanocomposites composed of poly(butylene succinate) (PBS) and cellulose nanocrystals (CNCs) (loading of 0.2-3.0 wt%) and propose a rheological strategy to tailor their performances. Depending on the shear frequencies, the rheological evaluation revealed two percolation thresholds at approximately 0.8 and 1.5 wt%. At high shear frequencies, the disappearance of the first threshold (0.8 wt%) and the sole persistence of the second one (1.5 wt%) indicated the collapse of the immature network of partially interconnected CNCs. The tensile and hydrolytic properties of the nanocomposites were found to undergo drastic changes at the thresholds. The tensile strength increased by 17% (from 33.3 to 39.2 MPa) up to 0.8 wt% CNC loading. However, the reinforcing efficiency of CNC decreases sharply with further incorporation, reaching nearly zero at 1.5 wt%. On the other hand, hydrolytic degradation of the nanocomposites was rapidly accelerated above 1.5 wt% CNC loading. Therefore, a thorough understanding of the rheological properties of nanocomposites is essential for the design and development of materials with tailored properties.

Evaluating the Prevalence of Foodborne Pathogens in Livestock Using Metagenomics Approach.

Food safety is the most important global health issue due to foodborne pathogens after consumption of contaminated food. Foodborne bacteria such as Escherichia coli, Salmonella enterica, Staphylococcus aureus, Campylobacter spp., Bacillus cereus, Vibrio spp., Yersinia enterocolitica and Clostridium perfringens are leading causes of the majority of foodborne illnesses and deaths. These foodborne pathogens often come from the livestock feces, thus, we analyzed fecal microbial communities of three different livestock species to investigate the prevalence of foodborne pathogens in livestock feces using metagenomics analysis. Our data showed that alpha diversities of microbial communities were different according to livestock species. The microbial diversity of cattle feces was higher than that of chicken or pig feces. Moreover, microbial communities were significantly different among these three livestock species (cattle, chicken, and pig). At the genus level, Staphylococcus and Clostridium were found in all livestock feces, with chicken feces having higher relative abundances of Staphylococcus and Clostridium than cattle and pig feces. Genera Bacillus, Campylobacter, and Vibrio were detected in cattle feces. Chicken samples contained Bacillus, Listeria, and Salmonella with low relative abundance. Other genera such as Corynebacterium, Streptococcus, Neisseria, Helicobacter, Enterobacter, Klebsiella, and Pseudomonas known to be opportunistic pathogens were also detected in cattle, chicken, and pig feces. Results of this study might be useful for controlling the spread of foodborne pathogens in farm environments known to provide natural sources of these microorganisms.

Oral Vaccination against Lawsoniaintracellularis Changes the Intestinal Microbiome in Weaned Piglets.

Lawsoniaintracellularis, which causes porcine proliferative enteropathy (PPE), is a common swine intestinal pathogen that is prevalent in pig production sites worldwide. In this study, the alteration in the microbiome composition of weaned pigs was investigated in response to vaccination against L. intracellularis, using 16S rRNA gene sequencing. A total of 64 crossbred (Duroc × [Landrace × Yorkshire]) healthy weanling pigs weaned at 4 weeks of age were randomly assigned to four treatment groups (four pigs/pen; four pens/treatment), using a randomized complete block design for the 42-day trial. Pigs in the treatment groups were orally administered with three different doses (1 dose = 2 mL) of vaccine against L. intracellularis (Enterisol® Ileitis, Boehringer Ingelheim Vetmedica GmbH), namely the following: LAW1 (0.5 dose), LAW2 (1 dose), LAW3 (2 dose). A non-vaccinated group served as a negative control (CONT). Alpha diversity analysis revealed that vaccination led to significant changes in species evenness but not species richness of the gut microbiota. Beta diversity analysis revealed that vaccination against L. intracellularis caused a significant shift in the microbial community structure. At the genus level, there was a significant increase in Streptococcus and a significant decrease in Clostridium in the fecal microbiota of vaccinated pigs, regardless of dose.

Biosynthesis of Polyhydroxybutyrate with Cellulose Nanocrystals Using Cupriavidus necator.

Polyhydroxybutyrate (PHB) is a natural polyester synthesized by several microorganisms. Moreover, it has excellent biodegradability and is an eco-friendly material because it converts water and carbon dioxide as final decomposition products. However, the applications of PHB are limited because of its stiffness and brittleness. Because cellulose nanocrystals (CNCs) have excellent intrinsic mechanical properties such as high specific strength and modulus, they may compensate for the insufficient physical properties of PHB by producing their nanocomposites. In this study, natural polyesters were extracted from Cupriavidus necator fermentation with CNCs, which were well-dispersed in nitrogen-limited liquid culture media. Fourier-transform infrared spectroscopy results revealed that the additional O-H peak originating from cellulose at 3500-3200 cm-1 was observed for PHB along with the C=O and -COO bands at 1720 cm-1. This suggests that PHB-CNC nanocomposites could be readily obtained using C. necator fermented in well-dispersed CNC-supplemented culture media.

Changes in Diarrhea Score, Nutrient Digestibility, Zinc Utilization, Intestinal Immune Profiles, and Fecal Microbiome in Weaned Piglets by Different Forms of Zinc.

Twenty weaned piglets with initial body weight of 6.83 ± 0.33 kg (21 day of age, LYD) were randomly assigned to four treatments for a two-week feeding trial to determine the effects of different dietary zinc on nutrient digestibility, intestinal health, and microbiome of weaned piglets. The dietary treatments included a negative control (CON), standard ZnO (ZnO, 2500 ppm), zinc chelate with glycine (Chelate-ZnO, 200 ppm), and nanoparticle-sized ZnO (Nano-ZnO, 200 ppm). At 0 to 1 week, the diarrhea score was decreased in the CON group compared with the ZnO, Chelate-ZnO, and Nano-ZnO group. In overall period, the ZnO and Nano-ZnO groups exhibited improved diarrhea scores compared to the CON group. The apparent total tract digestibility of dry matter and gross energy was the lowest in the CON group after one week. Compared to the ZnO group, the chelate-ZnO group exhibited higher proportion of T-bet+ and FoxP3+ T cells and the nano-ZnO group had higher numbers of RORgt+ and GATA3+ T cells in the mesenteric lymph nodes. ZnO group increased IL-6 and IL-8 levels in the colon tissues and these positive effects were observed in both chelate ZnO and nano-ZnO groups with lower level. The 16S rRNA gene analysis showed that the relative abundance of Prevotella was higher in the ZnO-treated groups than in the CON group and that of Succinivibrio was the highest in the nano-ZnO group. The relative abundance of Lactobacillus increased in the ZnO group. In conclusion, low nano-ZnO levels have similar effects on nutrient digestibility, fecal microflora, and intestinal immune profiles in weaning pigs; thus, nano-ZnO could be used as a ZnO alternative for promoting ZnO utilization and intestinal immunity.

Complete genome sequence of Lactococcus lactis strain K_LL005, a xylose-utilizing bacterium isolated from grasshopper (Oxya chinensis sinuosa).

Lactococcus lactis is a fermentative lactic acid bacterium that is used extensively in food fermentations. The L. lactis strain K_LL005 was isolated from the grasshopper (Oxya chinensis sinuosa) gut in Korea. In this study, we reported the complete genome sequence of Lactococcus lactis K_LL005. The final complete genome assembly consist of one circular chromosome (2,375,093 bp) with an overall guanine + cytosine (G + C) content of 35.0%. Annotation results revealed 2,281 protein-coding sequences (CDSs), 19 rRNAs, and 68 tRNA genes. Lactococcus lactis K_LL005 has a gene encoding xylose metabolism such as xylR, xylA, and xylB (xylRAB).

Complete genome sequence of Salmonella enterica strain K_SA184, multidrug resistance bacterium isolated from lamb (Ovis aries).

Salmonella enterica is a representative foodborne pathogen in the world. The S. enterica strain K_SA184 was isolated from the lamb (Ovis aries), which was collected from a local traditional market in South Korea. In this study, the S. enterica strain K_SA184 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The final complete genome of the S. enterica strain K_SA184 consist of one circular chromosome (4,725,087 bp) with 52.3% of guanine + cytosine (G + C) content, 4,363 of coding sequence (CDS), 85 of tRNA, and 22 of rRNA genes. The S. enterica strain K_SA184 genome includes encoding virulence genes, such as Type III secretion systems and multidrug resistance related genes.

Complete genome sequence of Escherichia coli K_EC180, a bacterium producing shiga-like toxin isolated from swine feces.

Escherichia coli normally colonizes the lower intestine of animals and humans, but some serotypes are foodborne pathogens. The Escherichia coli K_EC180 was isolated from swine feces that were collected from a weaner pig. In this genome announcement, E. coli K_EC180 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The complete chromosome of E. coli K_EC180 is composed of one circular chromosome (5,017,281 bp) with 50.4% of guanine + cytosine (G + C) content, 4,935 of coding sequence (CDS), 88 of tRNA, and 22 of rRNA genes. The complete genome of E. coli K_EC180 contains the toxin genes such as shiga-like toxins (stxA and stxB).