• Journal of Food Hygiene and Safety
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• v.24 no.4
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• pp.307-311
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• 2009

The objectives of this study were to compare the biochemical profiles with biogroups for the identification of Cronobacter spp. (formally known as Enterobacter sakazakii) isolates using biochemical identification kits. A total of 38 Cronobacter spp. contained 5 clinical, 31 food, and 2 environmental isolates were used. All isolates were identified as Cronobacter spp. with the Vitek II system and ID 32E kit. The API 20E kit identified all isolates as Cronobacter spp. but the percentage identification was 51.1% for 16 of 38 isolates. These strains were contained to Biogroup 2, 9, 10, and 11. The utilization of inositol is a factor determining the percentage identification of Cronobacter spp. with the API 20E kit.

• Journal of Biosystems Engineering
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• v.42 no.3
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• pp.163-169
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• 2017

Purpose: This study was performed to evaluate the feasibility of using an infrared thermography technique for phenotype analysis of pepper seedlings exposed to a low-temperature environment. Methods: We employed an active thermography technique to evaluate the thermal response of pepper seedlings exposed to low-temperature stress. The temperatures of pepper leaves grown in low-temperature conditions ($5^{\circ}C$, relative humidity [RH] 50%) for four periods (6, 12, 24, and 48 h) were measured in the experimental setting ($23^{\circ}C$, RH 70%) as soon as pepper seedling samples were taken out from the low-temperature environment. We also assessed the visible images of pepper seedling samples that were exposed to low-temperature stress to estimate appearance changes. Results: The greatest appearance change was observed for the low-temperature stressed pepper seedlings that were exposed for 12 h, and the temperature from these pepper seedling leaves was the highest among all samples. In addition, the thermal image of low-temperature stressed pepper seedlings for 6 h exhibited the lowest temperature. Conclusions: We demonstrated that the leaf withering owing to the water deficiency that occurred under low-temperature conditions could induce an increase in temperature in plant leaves using the infrared thermography technique. These results suggested that the time-resolved and averaged thermal signals or temperatures of plants could be significantly associated with the physiological or biochemical characteristics of plants exposed to low-temperature stress.

• Journal of Biosystems Engineering
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• v.42 no.4
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• pp.330-338
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• 2017

Purpose: The smartphone is actively being used in many research fields, primarily in medical and diagnostic applications. However, there are cases in which smartphone-based systems have been developed for agriculture, environment, and food applications. The purpose of this review is to summarize the research cases using smartphone cameras in agriculture, environment, and food. Methods: This review introduces seventeen research cases which used smartphone cameras in agriculture, food, water, and soil applications. These were classified as systems involving "smartphone-camera-alone" and "smartphone camera with optical accessories". Results: Detecting food-borne pathogens, analyzing the quality of foods, monitoring water quality and safety, gathering information regarding plant growth or damage, identifying weeds, and measuring soil loss after rain were presented for the smartphone-camera-alone system. Measuring food and water quality and safety, phenotyping seeds, and soil classifications were presented for the smartphone camera with optical accessories. Conclusions: Smartphone cameras were applied in various areas for several purposes. The use of smartphone cameras has advantages regarding high-resolution imaging, manual or auto exposure and focus control, ease of use, portability, image storage, and most importantly, programmability. The studies discussed were achieved by sensitivity improvements of CCDs (charge-coupled devices) and CMOS (complementary metal-oxide-semiconductor) on smartphone cameras and improved computing power of the smartphone, respectively. A smartphone camera-based system can be used with ease, low cost, in near-real-time, and on-site. This review article presents the applications and potential of the smartphone and the smartphone camera used for various purposes in agriculture, environment, and food.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1150-1159
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• 2018

Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

• Annals of Laboratory Medicine
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• v.38 no.6
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• pp.585-590
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• 2018

Background: Although testing to detect weak D antigens using the antihuman globulin reagent is not required for D- patients in many countries, it is routinely performed in Korea. However, weak D testing can be omitted in D- patients with a C-E- phenotype as this indicates complete deletion of the RHD gene, except in rare cases. We designed a new algorithm for weak D testing, which consisted of RhCE phenotyping followed by weak D testing in C+ or E+ samples, and compared it with the current algorithm with respect to time and cost-effectiveness. Methods: In this retrospective study, 74,889 test results from January to July 2017 in a tertiary hospital in Korea were analyzed. Agreement between the current and proposed algorithms was evaluated, and total number of tests, time required for testing, and test costs were compared. With both algorithms, RHD genotyping was conducted for samples that were C+ or E+ and negative for weak D testing. Results: The algorithms showed perfect agreement (agreement=100%; ${\kappa}=1.00$). By applying the proposed algorithm, 29.56% (115/389 tests/yr) of tests could be omitted, time required for testing could be reduced by 36% (8,672/24,084 min/yr), and the test cost could be reduced by 16.53% (536.11/3,241.08 USD/yr). Conclusions: Our algorithm omitting weak D testing in D- patients with C-E- phenotype may be a cost-effective testing strategy in Korea.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.12
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• pp.1980-1990
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• 2018

Objective: The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome Methods: Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. Results: Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. Conclusion: The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.290-296
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• 2019

Objective: Pigs share many physiological, anatomical and genomic similarities with humans, which make them suitable models for biomedical researches. Understanding the genetic status of Yucatan miniature pigs (YMPs) and their association with human diseases will help to assess their potential as biomedical model animals. This study was performed to identify non-synonymous single nucleotide polymorphisms (nsSNPs) in selective sweep regions of the genome of YMPs and present the genetic nsSNP distributions that are potentially associated with disease occurrence in humans. Methods: nsSNPs in whole genome resequencing data from 12 YMPs were identified and annotated to predict their possible effects on protein function. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 analyses were used, and gene ontology (GO) network and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Results: The results showed that 8,462 genes, encompassing 72,067 nsSNPs were identified, and 118 nsSNPs in 46 genes were predicted as deleterious. GO network analysis classified 13 genes into 5 GO terms (p<0.05) that were associated with kidney development and metabolic processes. Seven genes encompassing nsSNPs were classified into the term associated with Alzheimer's disease by referencing the genetic association database. The KEGG pathway analysis identified only one significantly enriched pathway (p<0.05), hsa04080: Neuroactive ligand-receptor interaction, among the transcripts. Conclusion: The number of deleterious nsSNPs in YMPs was identified and then these variants-containing genes in YMPs data were adopted as the putative human diseases-related genes. The results revealed that many genes encompassing nsSNPs in YMPs were related to the various human genes which are potentially associated with kidney development and metabolic processes as well as human disease occurrence.

• Journal of Ginseng Research
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• v.48 no.3
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• pp.310-322
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• 2024

Background: Osteosarcopenia is a common condition characterized by the loss of both bone and muscle mass, which can lead to an increased risk of fractures and disability in older adults. The study aimed to elucidate the response of various mouse strains to treatment with Rg3, one of the leading ginsenosides, on musculoskeletal traits and immune function, and their correlation. Methods: Six Collaborative Cross (CC) founder strains induced muscle atrophy and bone loss with dexamethasone (15 mg/kg) treatment for 1 month, and half of the mice for each strain were orally administered Rg3 (20 mg/kg). Different responses were observed depending on genetic background and Rg3 treatment. Results: Rg3 significantly increased grip strength, running performance, and expression of muscle and bone health-related genes in a two-way analysis of variance considering the genetic backgrounds and Rg3 treatment. Significant improvements in grip strength, running performance, bone area, and muscle mass, and the increased gene expression were observed in specific strains of PWK/PhJ. For traits related to muscle, bone, and immune functions, significant correlations between traits were confirmed following Rg3 administration compared with control mice. The phenotyping analysis was compiled into a public web resource called Rg3-OsteoSarco. Conclusion: This highlights the complex interplay between genetic determinants, pathogenesis of muscle atrophy and bone loss, and phytochemical bioactivity and the need to move away from single inbred mouse models to improve their translatability to genetically diverse humans. Rg3-OsteoSarco highlights the use of CC founder strains as a valuable tool in the field of personalized nutrition.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.8
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• pp.3727-3731
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• 2016

Background: The most common type of ocular lymphoma is non-Hodgkin lymphoma (NHL), categorized into two groups: indolent (slow growing) and aggressive (rapid growing). Differentiating benign reactive lymphoid hyperplasia (RLH) from malignant ocular adnexal lymphoma (OAL) is challenging. Histopathology, immunohistochemistry (IHC) and flow cytometry have been used as diagnostic tools in such cases. Materials and Methods: In this retrospective case series, from 2002 to 2013 at Farabi Eye Center, 110 patients with ocular lymphoproliferative disease were enrolled. Prevalence, anatomical locations, mean age at diagnosis and the final diagnosis of the disease with IHC were assessed. Comparison between previous pathologic diagnoses and results of IHC was made. Immunoglobulin light chains and B-cell and T-cell markers and other immuno-phenotyping markers including CD20, CD3, CD5, CD23, CD10, CYCLIND1 and BCL2 were evaluated to determine the most accurate diagnosis. The lymphomas were categorized based on revised European-American lymphoma (REAL) classification. Results: Mean age ${\pm}$ SD (years) of the patients was $55.6{\pm}19.3$ and 61% were male. Patients with follicular lymphoma, large B-cell lymphoma or chronic lymphocytic leukemia/small cell lymphoma (CLL/SLL) tended to be older. Nine patients with previous diagnoses of low grade B-cell lymphoma were re-evaluated by IHC and the new diagnoses were as follows: extranodal marginal zone lymphoma(EMZL) (n=1), SLL(n=1), mantle cell lymphoma (MCL) (n=3), reactive lymphoid hyperplasia RLH (n=2). Two cases were excluded due to poor blocks. Flow cytometry reports in these seven patients revealed SLL with positive CD5 and CD23, MCLwith positive CD5 and CyclinD1 and negative CD23, EMZL with negative CD5,CD23 and CD10. One RLH patient was negative for Kappa/Lambda and positive for CD3 and CD20 and the other was positive for all of the light chains, CD3 and CD20. Orbit (49.1%), conjunctiva (16.1%) and lacrimal glands (16.1%) were the most common sites of involvement. Conclusions: Accurate pathological classification of lesions is crucial to determine proper therapeutic approaches. This can be achieved through precise histologic and IHC analyses by expert pathologists.

• Tuberculosis and Respiratory Diseases
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• v.81 no.4
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• pp.289-298
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• 2018

Background: Obstructive airway disease patients with increased variability of airflow and incompletely reversible airflow obstruction are often categorized as having asthma-chronic obstructive pulmonary disease (COPD) overlap syndrome (ACOS). ACOS is heterogeneous with two sub-phenotypes: asthma-ACOS and COPD-ACOS. The objective of this study was to determine the difference in risk of exacerbation between the two sub-phenotypes of ACOS. Methods: A total of 223 patients exhibiting incompletely reversible airflow obstruction with increased variability (spirometrically defined ACOS) were enrolled. These patients were divided into asthma-ACOS and COPD-ACOS according to their physician's diagnosis and smoking history of 10 pack-years. Within-group comparisons were made for asthma-ACOS versus COPD-ACOS and light smokers versus heavy smokers. Results: Compared to patients with COPD-ACOS, patients with asthma-ACOS experienced exacerbation more often despite their younger age, history of light smoking, and better lung function. While the light-smoking group showed better lung function, they made unscheduled outpatient clinic visits more frequently. On multivariate analysis, asthma-ACOS and poor inhaler compliance were significantly associated with more than two unscheduled clinic visits during the previous year. Conclusion: Spirometrically defined ACOS includes heterogeneous subgroups with different clinical features. Phenotyping of ACOS by physician's diagnosis could be significant in predicting future risk of exacerbation.