Clinical Feasibility of Deep Learning-Based Attenuation Correction Models for Tl-201 Myocardial Perfusion SPECT

PURPOSE

We aimed to develop deep learning (DL)-based attenuation correction models for Tl-201 myocardial perfusion SPECT (MPS) images and evaluate their clinical feasibility.

PATIENTS AND METHODS

We conducted a retrospective study of patients with suspected or known coronary artery disease. We proposed a DL-based image-to-image translation technique to transform non-attenuation-corrected images into CT-based attenuation-corrected (CT AC ) images. The model was trained using a modified U-Net with structural similarity index (SSIM) loss and mean squared error (MSE) loss and compared with other models. Segment-wise analysis using a polar map and visual assessment for the generated attenuation-corrected (GEN AC ) images were also performed to evaluate clinical feasibility.

RESULTS

This study comprised 657 men and 328 women (age, 65 ± 11 years). Among the various models, the modified U-Net achieved the highest performance with an average mean absolute error of 0.003, an SSIM of 0.990, and a peak signal-to-noise ratio of 33.658. The performance of the model was not different between the stress and rest datasets. In the segment-wise analysis, the myocardial perfusion of the inferior wall was significantly higher in GEN AC images than in the non-attenuation-corrected images in both the rest and stress test sets ( P < 0.05). In the visual assessment of patients with diaphragmatic attenuation, scores of 4 (similar to CT AC images) or 5 (indistinguishable from CT AC images) were assigned to most GEN AC images (65/68).

CONCLUSIONS

Our clinically feasible DL-based attenuation correction models can replace the CT-based method in Tl-201 MPS, and it would be useful in case SPECT/CT is unavailable for MPS.

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Sinonasal microbiome and inflammatory profiles in fungal ball and chronic rhinosinusitis

OBJECTIVE

Fungal balls (FB) are the main form of non-invasive fungal rhinosinusitis found in immunocompetent hosts. Bacterial coinfection affects clinical symptoms. We investigated the sinonasal microbiome and inflammatory profiles in FB and chronic rhinosinusitis (CRS) patients.

METHODS

Thirty-three participants were prospectively recruited. Nasal swab samples and sinonasal tissues were collected from controls, and FB and CRS patients. DNA extraction and microbiome analysis using V3-V4 region 16S rRNA sequencing were performed. Inflammatory cytokine levels in the sinonasal tissues, blood eosinophil counts, and serum total IgE were measured.

RESULTS

No significant differences were observed in species richness or evenness measures. The phylogenetic tree demonstrated that the FB samples were different from the controls. The sinus bacteria composition differed among the groups. At the phylum level, Firmicutes in FB were significantly depleted compared with those in CRS, while Proteobacteria were more enriched in FB than that in controls and CRS. At the genus level, in FB, Staphylococcus and Corynebacterium were significantly decreased compared to those in the controls. The prevalence of Haemophilus was the highest in FB. Blood eosinophil counts and IL-5 and periostin levels in the sinonasal tissue of the FB group were significantly lower than those in the CRS group.

CONCLUSIONS

FB patients had different microbiome compositions and fewer type 2 inflammatory profiles than CRS patients did. However, whether these findings cause FB or result from bacterial and/or fungal infection remains unclear. Further studies are needed to reveal how these differences occur and affect the development of FB and clinical symptoms.

Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies

The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.

Harnessing γ-TMT Genetic Variations and Haplotypes for Vitamin E Diversity in the Korean Rice Collection

Gamma-tocopherol methyltransferase (γ-TMT), a key gene in the vitamin E biosynthesis pathway, significantly influences the accumulation of tocochromanols, thereby determining rice nutritional quality. In our study, we analyzed the γ-TMT gene in 475 Korean rice accessions, uncovering 177 genetic variants, including 138 SNPs and 39 InDels. Notably, two functional SNPs, tmt-E2-28,895,665-G/A and tmt-E4-28,896,689-A/G, were identified, causing substitutions from valine to isoleucine and arginine to glycine, respectively, across 93 accessions. A positive Tajima's D value in the indica group suggests a signature of balancing selection. Haplotype analysis revealed 27 haplotypes, with two shared between cultivated and wild accessions, seven specific to cultivated accessions, and 18 unique to wild types. Further, profiling of vitamin E isomers in 240 accessions and their association with haplotypes revealed that Hap_2, distinguished by an SNP in the 3' UTR (tmt-3UTR-28,897,360-T/A) exhibited significantly lower α-tocopherol (AT), α-tocotrienol (AT3), total tocopherol, and total tocotrienol, but higher γ-tocopherol (GT) in the japonica group. Additionally, in the indica group, Hap_2 showed significantly higher AT, AT3, and total tocopherol, along with lower GT and γ-tocotrienol, compared to Hap_19, Hap_20, and Hap_21. Overall, this study highlights the genetic landscape of γ-TMT and provides a valuable genetic resource for haplotype-based breeding programs aimed at enhancing nutritional profiles.

The Feasibility of Fast, Four-Dimensional Computed Tomography-Based O-Ring Linac Plans for Stereotactic Body Radiotherapy in Patients with Poor Performance Status

PURPOSE/OBJECTIVE(S)

As patients with poor performance status cannot endure long treatment times, it can lead to unplanned and prolonged radiation treatment or discontinuation of treatment. Moreover, prolonged radiation treatment appears to negatively affect survival for patients. We aimed to verify the feasibility of fast 4DCT-based O-ring linear accelerator (LINAC) treatment in lung 4D stereotactic body radiotherapy (SBRT).

MATERIALS/METHODS

This study included data of 38 patients who received lung 4D-SBRT. Gating20-70% plans were based on 4DCT data obtained at phase values ranging from 20-70% using a C-arm LINAC. Non-GatingFB plans were retrospectively established based on 4DCT data obtained at phase values of 0-90% using an O-ring LINAC. The prescribed dose of 4,800 cGy was delivered to PTV in four fractions. The conformity index (CI), homogeneity index (HI), and gradient measurement (GM) of the PTV were analyzed to compare dosimetric data between Gating20-70% and Non-GatingFB plans. Organs at risks (OARs) were analyzed in accordance with the RTOG 0915 protocol. Treatment delivery time and total monitor units (MU) were analyzed to compare the efficiency of treatment delivery. Statistical comparisons were performed using the Wilcoxon signed-rank test (p<0.05).

RESULTS

For the PTV, there was no significant difference in the CI or HI between Gating20-70% and Non-GatingFB plans (CI: 1.337±0.137, 1.335±0.174, HI: 0.939±0.015, 0.939±0.016, all at p>0.05). However, there was a significant difference in GM between Gating20-70% and Non-GatingFB plan (1.528±0.206 cm, 1.381±0.222 cm, p<0.001). For OARs, all plans met the criteria for dose constraint. There was a significant difference between Gating20-70% and Non-GatingFB plans except in the spinal cord. In particular, D1000cc and D1500cc values for the ipsilateral lung for Gating20-70% plans were 31.6% and 59.9% lower than those for Non-GatingFB plans (D1000cc: 50.780±132.061 cGy, 34.755±102.480 cGy, p<0.001, D1500cc: 6.641±14.598 cGy, 2.666±7.926 cGy, p<0.001). Treatment delivery time was 92% longer for Gating20-70% plans than for Non-GatingFB plans (5.0±0.4 min, 9.6±3.3 min, p = 0.043). The total MU value for Gating20-70% plans was 9.6% higher than that for Non-GatingFB plans (3665.8±230.7, 4016±236.9, p = 0.039).

CONCLUSION

When compared to OARs both plans were acceptable per RTOG-0915 protocol, but significant differences were between Non-GatingFB and Gating20-70% plans. However, treatment delivery time of Non-GatingFB plans decreased by 47.9% than Gating20-70% plans. We verified the feasibility of fast 4DCT-based O-ring LINAC treatment for patients who cannot endure long treatment times due to poor performance status in lung 4D-SBRT. In further study, we will analyze dosimetric differences and treatment delivery efficiency considering tumor motion according to tumor location.

A Machine Learning Approach Using [18F]FDG PET-Based Radiomics for Prediction of Tumor Grade and Prognosis in Pancreatic Neuroendocrine Tumor

PURPOSE

We sought to develop and validate machine learning (ML) models for predicting tumor grade and prognosis using 2-[18F]fluoro-2-deoxy-D-glucose ([18F]FDG) positron emission tomography (PET)-based radiomics and clinical features in patients with pancreatic neuroendocrine tumors (PNETs).

PROCEDURES

A total of 58 patients with PNETs who underwent pretherapeutic [18F]FDG PET/computed tomography (CT) were retrospectively enrolled. PET-based radiomics extracted from segmented tumor and clinical features were selected to develop prediction models by the least absolute shrinkage and selection operator feature selection method. The predictive performances of ML models using neural network (NN) and random forest algorithms were compared by the areas under the receiver operating characteristic curves (AUROCs) and validated by stratified five-fold cross validation.

RESULTS

We developed two separate ML models for predicting high-grade tumors (Grade 3) and tumors with poor prognosis (disease progression within two years). The integrated models consisting of clinical and radiomic features with NN algorithm showed the best performances than the other models (stand-alone clinical or radiomics models). The performance metrics of the integrated model by NN algorithm were AUROC of 0.864 in the tumor grade prediction model and AUROC of 0.830 in the prognosis prediction model. In addition, AUROC of the integrated clinico-radiomics model with NN was significantly higher than that of tumor maximum standardized uptake model in predicting prognosis (P < 0.001).

CONCLUSIONS

Integration of clinical features and [18F]FDG PET-based radiomics using ML algorithms improved the prediction of high-grade PNET and poor prognosis in a non-invasive manner.

Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice

Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.

Direct comparison of diagnostic and clinical values between Tc-99 m DPD and Tc-99 m PYP scintigraphy in patients with cardiac amyloidosis

BACKGROUND

Technetium-99 m 3,3-diphosphono-1,2-propanodicarboxylic acid (DPD) and technetium-99 m sodium pyrophosphate (PYP) are the two most commonly used radiotracers for cardiac amyloidosis (CA), but no studies have directly compared them. Therefore, in this study, we directly compared the diagnostic and clinical utility of DPD and PYP scintigraphy in patients with CA.

METHODS

Ten patients with CA were enrolled. Eight clinical variables and 12 scintigraphic parameters were used. Clinical variables were age, sex, estimated glomerular filtration rate (eGFR), N-terminal pro brain natriuretic peptide (NT-proBNP), and the results of electromyography (EMG), a sensory test, electrocardiogram, and echocardiography (EchoCG). Four heart retention ratios (heart/whole-body profile, heart/pelvis, heart/skull, and heart/contralateral lung) were calculated from the DPD and PYP scans and two visual scoring systems (Perugini and Dorbala systems) were used. Comparative analyses were performed between radiotracers and between visual scoring systems using clinical variables and scintigraphic parameters.

RESULTS

Twenty DPD parameters and nine PYP parameters had significant associations with age, eGFR, NT-proBNP, EchoCG, and EMG. DPD parameters had more frequent significant associations with clinical variables than PYP parameters. Compared to visual scores in the DPD scan, the proportion of patients with higher visual scores in the PYP scan was relatively greater than those with lower visual scores, and there were more patients with a visual score of 2 or higher in PYP scans than DPD scans.

CONCLUSIONS

DPD scintigraphy may reflect the disease severity of CA better than PYP scintigraphy, whereas PYP scintigraphy may be a more sensitive imaging modality for identifying CA involvement.

Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice

Rice is a globally cultivated crop and is primarily a staple food source for more than half of the world's population. Various single-nucleotide polymorphism (SNP) arrays have been developed and utilized as standard genotyping methods for rice breeding research. Considering the importance of SNP arrays with more inclusive genetic information for GWAS and genomic selection, we integrated SNPs from eight different data resources: resequencing data from the Korean World Rice Collection (KRICE) of 475 accessions, 3,000 rice genome project (3 K-RGP) data, 700 K high-density rice array, Affymetrix 44 K SNP array, QTARO, Reactome, and plastid and GMO information. The collected SNPs were filtered and selected based on the breeder's interest, covering all key traits or research areas to develop an integrated array system representing inclusive genomic polymorphisms. A total of 581,006 high-quality SNPs were synthesized with an average distance of 200 bp between adjacent SNPs, generating a 580 K Axiom Rice Genotyping Chip (580 K _ KNU chip). Further validation of this array on 4,720 genotypes revealed robust and highly efficient genotyping. This has also been demonstrated in genome-wide association studies (GWAS) and genomic selection (GS) of three traits: clum length, heading date, and panicle length. Several SNPs significantly associated with cut-off, -log₁₀ p-value >7.0, were detected in GWAS, and the GS predictabilities for the three traits were more than 0.5, in both rrBLUP and convolutional neural network (CNN) models. The Axiom 580 K Genotyping array will provide a cost-effective genotyping platform and accelerate rice GWAS and GS studies.

Genome-Scale Profiling and High-Throughput Analyses Unravel the Genetic Basis of Arsenic Content Variation in Rice

Ionomics, the study of the composition of mineral nutrients and trace elements in organisms that represent the inorganic component of cells and tissues, has been widely studied to explore to unravel the molecular mechanism regulating the elemental composition of plants. However, the genetic factors of rice subspecies in the interaction between arsenic and functional ions have not yet been explained. Here, the correlation between As and eight essential ions in a rice core collection was analyzed, taking into account growing condition and genetic factors. The results demonstrated that the correlation between As and essential ions was affected by genetic factors and growing condition, but it was confirmed that the genetic factor was slightly larger with the heritability for arsenic content at 53%. In particular, the cluster coefficient of japonica (0.428) was larger than that of indica (0.414) in the co-expression network analysis for 23 arsenic genes, and it was confirmed that the distance between genes involved in As induction and detoxification of japonica was far than that of indica. These findings provide evidence that japonica populations could accumulate more As than indica populations. In addition, the cis-eQTLs of AIR2 (arsenic-induced RING finger protein) were isolated through transcriptome-wide association studies, and it was confirmed that AIR2 expression levels of indica were lower than those of japonica. This was consistent with the functional haplotype results for the genome sequence of AIR2, and finally, eight rice varieties with low AIR2 expression and arsenic content were selected. In addition, As-related QTLs were identified on chromosomes 5 and 6 under flooded and intermittently flooded conditions through genome-scale profiling. Taken together, these results might assist in developing markers and breeding plans to reduce toxic element content and breeding high-quality rice varieties in future.

Value of C-11 methionine PET/CT in patients with intracranial germinoma

Purpose

The purpose of this study was to investigate the value of C-11 methionine (MET) positron emission tomography (PET)/computed tomography (CT) in patients with intracranial germinoma (IG).

Material and methods

We conducted a retrospective analysis of 21 consecutive patients with pathologically confirmed IGs and eight patients with intracranial non-germinomas (INGs) located in a similar region. Clinical characteristics, imaging findings, and tumor markers such as α-fetoprotein (AFP) and β-human chorionic gonadotropin (HCG) were used as clinical variables. Maximum standardized uptake value (SUVmax), tumor-to-normal tissue (T/N) ratio, and visual scoring of tumor were used as MET PET parameters.

Results

All IGs were well visualized on MET PET with a three-grade visual scoring system. In addition, SUVmax of IGs was higher than that of INGs (P = 0.005). Pre-treatment (Pre-Tx) T/N ratio was significantly correlated with pre-Tx serum HCG (P = 0.031). Moreover, MET PET parameters showed significant associations with tumor location, sex, KRAS variant, and symptoms.

Conclusion

MET PET/CT could be a useful diagnostic tool in patients suspected of having IGs. In addition, the MET avidity of tumor is a potential surrogate biomarker of HCG, which has been used as a diagnostic marker for IGs. Tumor MET parameters also had significant differences according to tumor locations, sex, symptoms, and KRAS mutation. However, MET avidity of tumors had no significant prognostic value.

Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2

INTRODUCTION

Fragrance is an important economic and quality trait in rice. The trait is controlled by the recessive gene betaine aldehyde dehydrogenase 2 (BADH2) via the production of 2-acetyl-1-pyrroline (2AP).

OBJECTIVES

Variation in BADH2 was evaluated at the population, genetic, transcriptional, and metabolic levels to obtain insights into fragrance regulation in rice.

METHODS

Whole-genome resequencing of the Korean World Rice Collection of 475 rice accessions, including 421 breeding lines and 54 wild accessions, was performed. Transcriptome analyses of a subset of 279 accessions, proteome analyses of 64 accessions, and volatile profiling of 421 breeding lines were also performed.

RESULTS

We identified over 3.1 million high-quality single nucleotide polymorphisms (SNPs) in Korean rice collection. Most SNPs were present in intergenic regions (79%), and 190,148 SNPs (6%) were located in the coding sequence, of which 53% were nonsynonymous. In total, 38 haplotypes were identified in the BADH2 coding region, including four novel haplotypes (one in cultivated and three in wild accessions). Tajima's D values suggested that BADH2 was under balancing selection in japonica rice. Furthermore, we identified 316 expression quantitative trait loci (eQTL), including 185 cis-eQTLs and 131 trans-eQTLs, involved in BADH2 regulation. A protein quantitative trait loci (pQTL) analysis revealed the presence of trans-pQTLs; 13 pQTLs were mapped 1 Mbp from the BADH2 region. Based on variable importance in projection (VIP) scores, 15 volatile compounds, including 2AP, discriminated haplotypes and were potential biomarkers for rice fragrance.

CONCLUSION

We generated a catalog of haplotypes based on a resequencing analysis of a large number of rice accessions. eQTLs and pQTLs associated with BADH2 gene expression and protein accumulation are likely involved in the regulation of 2AP variation in fragrant rice. These data improve our understanding of fragrance and provide valuable information for rice breeding.

Possible association between oral health and sleep duration: A cross-sectional study based on the Korean National Health and Nutrition Examination Surveys from 2010 to 2015

This study was performed to investigate the association between oral health and sleep duration in South Korean subjects using 2010-2015 data from the Korean National Health and Nutrition Examination Survey (KNHANES).Cross-sectional data on 35,599 adults over the age of 19 years who completed KNHANES were analyzed. All participants reported subjective oral health status and their daily average sleep duration using a self-reported questionnaire. Sleep duration and oral health status were divided into 3 categories: ≤5, 6-8, ≥9 h/day and good, fair, poor, respectively.The overall prevalence of poor oral health status was 43.8%. Univariate analysis demonstrated that poor oral health status was significantly associated with age, smoking, alcohol, diabetes, education, income, depression, marital status, and sleep duration. After adjusting for covariates (age, sex, diabetes mellitus, hypertension, obesity, smoking, income, education, marital status), sleep durations of ≤5 hours (OR = 1.42; 95% CI, 1.26-1.60) and ≥9 hours (OR = 1.21; 95% CI, 1.04-1.40) were significantly associated with poor oral health, compared to a sleep duration of 6-8 hours. Short or long sleep duration was more likely to have an impact on the development of poor oral health status in men than in women. A significant relationship between sleep duration and oral health status was found in participants younger than 60 years.This is the first report that both short and long sleep durations are significantly associated with the development of poor oral health status. The effect of short or long sleep duration on poor oral health was more significant in younger subjects and in men.

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1-C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima's D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima's D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.

Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by F _ST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.

Performance Evaluation of a Deep Learning System for Differential Diagnosis of Lung Cancer With Conventional CT and FDG PET/CT Using Transfer Learning and Metadata

PURPOSE

We aimed to evaluate the performance of a deep learning system for differential diagnosis of lung cancer with conventional CT and FDG PET/CT using transfer learning (TL) and metadata.

METHODS

A total of 359 patients with a lung mass or nodule who underwent noncontrast chest CT and FDG PET/CT prior to treatment were enrolled retrospectively. All pulmonary lesions were classified by pathology (257 malignant, 102 benign). Deep learning classification models based on ResNet-18 were developed using the pretrained weights obtained from ImageNet data set. We propose a deep TL model for differential diagnosis of lung cancer using CT imaging data and metadata with SUVmax and lesion size derived from PET/CT. The area under the receiver operating characteristic curve (AUC) of the deep learning model was measured as a performance metric and verified by 5-fold cross-validation.

RESULTS

The performance metrics of the conventional CT model were generally better than those of the CT of PET/CT model. Introducing metadata with SUVmax and lesion size derived from PET/CT into baseline CT models improved the diagnostic performance of the CT of PET/CT model (AUC = 0.837 vs 0.762) and the conventional CT model (AUC = 0.877 vs 0.817).

CONCLUSIONS

Deep TL models with CT imaging data provide good diagnostic performance for lung cancer, and the conventional CT model showed overall better performance than the CT of PET/CT model. Metadata information derived from PET/CT can improve the performance of deep learning systems.

Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers

The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC₁F₁ and BC₂F₁ individuals. Seven BC₂F₁ lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC₂F₂ grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC₂F₂ lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.

Ribosomal protein S3 associates with the TFIIH complex and positively regulates nucleotide excision repair

In mammalian cells, the bulky DNA adducts caused by ultraviolet radiation are mainly repaired via the nucleotide excision repair (NER) pathway; some defects in this pathway lead to a genetic disorder known as xeroderma pigmentosum (XP). Ribosomal protein S3 (rpS3), a constituent of the 40S ribosomal subunit, is a multi-functional protein with various extra-ribosomal functions, including a role in the cellular stress response and DNA repair-related activities. We report that rpS3 associates with transcription factor IIH (TFIIH) via an interaction with the xeroderma pigmentosum complementation group D (XPD) protein and complements its function in the NER pathway. For optimal repair of UV-induced duplex DNA lesions, the strong helicase activity of the TFIIH complex is required for unwinding damaged DNA around the lesion. Here, we show that XP-D cells overexpressing rpS3 showed markedly increased resistance to UV radiation through XPD and rpS3 interaction. Additionally, the knockdown of rpS3 caused reduced NER efficiency in HeLa cells and the overexpression of rpS3 partially restored helicase activity of the TFIIH complex of XP-D cells in vitro. We also present data suggesting that rpS3 is involved in post-excision processing in NER, assisting TFIIH in expediting the repair process by increasing its turnover rate when DNA is damaged. We propose that rpS3 is an accessory protein of the NER pathway and its recruitment to the repair machinery augments repair efficiency upon UV damage by enhancing XPD helicase function and increasing its turnover rate.

Clinical value of dual-phase F-18 sodium fluoride PET/CT for diagnosing bone metastasis in cancer patients with solitary bone lesion

Background

The present study aimed to investigate whether dual-phase F-18 sodium-fluoride (NaF) positron emission tomography/computed tomography (PET/CT) could improve the diagnostic accuracy of detecting bone metastasis in cancer patients with a solitary bone lesion compared to conventional F-18 NaF PET/CT.

Methods

We retrospectively enrolled 113 cancer patients who underwent dual-phase F-18 NaF PET/CT for the differential diagnosis of a solitary bone lesion seen on bone scintigraphy. According to the dual-phase PET/CT protocol, an early-phase scan was acquired immediately after radiotracer injection and a conventional F-18 NaF PET/CT scan was performed. The diagnostic abilities of the visual analysis of conventional and dual-phase PET/CT scans and two quantitative parameters (lesion-to-blood pool uptake ratio on early-phase scan and lesion-to-bone uptake ratio on conventional scan) for detecting bone metastasis were compared. The final diagnosis of bone metastasis was made by histopathological confirmation or follow-up imaging studies.

Results

A metastatic bone lesion was diagnosed in 28 patients (24.8%). The sensitivity, specificity, and accuracy were 100.0%, 70.6%, and 77.9%, respectively, for visual analysis of conventional F-18 NaF PET/CT, 92.9%, 42.4%, 54.9%, respectively, for lesion-to-bone uptake ratio, 96.4%, 88.2%, and 90.3%, respectively, for visual analysis of dual-phase PET/CT, and 92.9%, 81.2%, and 83.2%, respectively, for lesion-to-blood pool uptake ratio. Visual analysis of dual-phase PET/CT was shown to have the highest area under the receiver operating characteristic curve value (0.923; 95% CI, 0.858-0.965) among all parameters.

Conclusions

Dual-phase F-18 NaF PET/CT showed a high diagnostic ability for detecting bone metastasis with improved specificity and accuracy compared to conventional F-18 NaF PET/CT in cancer patients. Dual-phase F-18 NaF PET/CT might help diagnose bone metastasis in patients with malignancies who were shown to have a solitary bone lesion on bone scintigraphy.

Metabolic radiogenomics in lung cancer: associations between FDG PET image features and oncogenic signaling pathway alterations

This study investigated the associations between image features extracted from tumor ¹⁸F-fluorodeoxyglucose (FDG) uptake and genetic alterations in patients with lung cancer. A total of 137 patients (age, 62.7 ± 10.2 years) who underwent FDG positron emission tomography/computed tomography (PET/CT) and targeted deep sequencing analysis for a tumor lesion, comprising 61 adenocarcinoma (ADC), 31 squamous cell carcinoma (SQCC), and 45 small cell lung cancer (SCLC) patients, were enrolled in this study. From the tumor lesions, 86 image features were extracted, and 381 genes were assessed. PET features were associated with genetic mutations: 41 genes with 24 features in ADC; 35 genes with 22 features in SQCC; and 43 genes with 25 features in SCLC (FDR < 0.05). Clusters based on PET features showed an association with alterations in oncogenic signaling pathways: Cell cycle and WNT signaling pathways in ADC (p = 0.023, p = 0.035, respectively); Cell cycle, p53, and WNT in SQCC (p = 0.045, 0.009, and 0.029, respectively); and TGFβ in SCLC (p = 0.030). In addition, SUV_peak and SUV_max were associated with a mutation of the TGFβ signaling pathway in ADC (FDR = 0.001, < 0.001). In this study, PET image features had significant associations with alterations in genes and oncogenic signaling pathways in patients with lung cancer.

Radiogenomics Based on PET Imaging

Radiogenomics or imaging genomics is a novel omics strategy of associating imaging data with genetic information, which has the potential to advance personalized medicine. Imaging features extracted from PET or PET/CT enable assessment of in vivo functional and physiological activity and provide comprehensive tumor information non-invasively. However, PET features are considered secondary to features on conventional imaging, and there has not yet been a review of the radiogenomic approach using PET features. This review article summarizes the current state of PET-based radiogenomic research for cancer, which discusses some of its limitations and directions for future study.

Low free T3 to free T4 ratio was associated with low muscle mass and impaired physical performance in community-dwelling aged population

In aged population, the association of thyroid hormones on physical performance, especially within their normal range, has yet to be elucidated. In this study, individuals with low serum free T3/free T4 were likely to have low muscle mass and impaired physical performance.

PURPOSE

We aimed to evaluate the associations of muscle mass, strength, and physical performance with thyroid hormone in an aged euthyroid population from a community-based cohort.

METHODS

We examined 918 men aged over 60 years and 1215 postmenopausal women from the Ansung cohort study. Appendicular skeletal muscle mass divided by square of height (ASM/ht²) was used as the muscle mass index. Hand grip strength was measured using a hydraulic dynamometer. Physical performance was assessed using the short physical performance battery (SPPB).

RESULTS

Participants with higher tertiles of free T3 and free T3/free T4 were younger and had higher ASM/ht², stronger hand grip strength, and higher SPPB scores than those in the lower tertiles. In adjusted models, men within higher tertiles of free T3 had higher ASM/ht² compared with those within lower tertiles (p = 0.033), whereas subjects with higher tertiles of free T4 had lower ASM/ht² compared with those within lower tertiles (p = 0.043). Subjects within higher tertiles of free T3/free T4 had higher ASM/ht² (p < 0.001) and better physical performance (p = 0.048) than those within lower tertiles after adjustments. However, free T3, free T4, or free T3/free T4 was not related to hand grip strength after adjustment for covariates.

CONCLUSION

Our results thus indicate that in an aged euthyroid population, low serum free T3/free T4 was a better index for low muscle mass and impaired physical performance than serum free T3 or free T4 alone.

Characterization of a New qLTG3-1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon

BACKGROUND

Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs, qLTG1 and qLTG3, that control LTG, were mapped using the BC₄F₈ population, which is a cross of Korean elite cultivar Hwaseong and O. rufipogon (IRGC 105491). We have characterized and analyzed the interaction between the two QTLs, by crossing TR20 that has O. rufipogon alleles at qLTG1 and qLTG3 in a Hwaseong background, with Hwaseong, to develop an F₂ population.

RESULTS

The F₂ plants with both qLTG1 and qLTG3 alleles from O. rufipogon showed higher LTG scores, than the plants with only qLTG1 or qLTG3. No significant interaction between the qLTG1 and qLTG3 was observed, indicating that they may regulate LTG via different pathways. Based on its location, qLTG3 appears to be allelic with qLTG3-1, a major QTL known to control LTG. To investigate the genetic differences between the two parents, that were controlling LTG, we compared their qLTG3-1 sequences. In the coding region, three sequence variations leading to amino acid changes were identified between the Hwaseong and O. rufipogon. Of these, a non-synonymous substitution at the 62nd amino acid site, had not previously been reported. To understand the cause of the LTG variations between the parents, we genotyped three sequence variations of qLTG3-1, that were identified in 98 Asian cultivated rice accessions (Oryza sativa L.). The 98 accessions were classified into 5 haplotypes, based on three variations and a 71-bp deletion. Mean low-temperature germination rates were compared among the haplotypes, and haplotype 5 (O. rufipogon-type) showed a significantly higher germination rate than haplotype 2 (Nipponbare-type), and haplotype 3 (Italica Livorno-type).

CONCLUSIONS

The O. rufipogon qLTG3-1 allele can be utilized for the improvement of LTG in rice breeding programs. Nearly isogenic lines harboring both qLTG1 and qLTG3-1 alleles from O. rufipogon, showed higher LTG scores than the NILs with qLTG1 or qLTG3-1 alone, and the two QTLs regulate LTG via different pathways. To our knowledge, this is the first report to detect a new qLTG3-1 allele and analyze the interaction of the two LTG QTLs in a nearly isogenic background.

Functional Haplotype and eQTL Analyses of Genes Affecting Cadmium Content in Cultivated Rice

BACKGROUND

Rice is a major food resource for Asian countries including Korea. However, most Asian countries are facing food safety problems due to cropland contamination by heavy metals. Thus, this study was conducted to investigate genetic factors affecting the expression of cadmium (Cd) gene, and to confirm differences in Cd translocation among cultivars because the current molecular understanding of Cd uptake-transport mechanisms remains insufficient. Associations between genotypes and gene expression level of Cd-related genes such as NRAMP, MTP, and HMA gene families in the rice core collection were analyzed at the genomic level.

RESULTS

Os01g0956700, Os05g0128400 and Os11g0485200 showed strong associations between expression level and genotype in the rice core collection, the regulatory factors that associated with these genes in cis and trans were founded. The association between the expression level and genotype of the candidate gene (Os01g0611300: metal tolerance protein) predicted to affect Cd content in rice by a previous genome-wide association study (GWAS) was also analyzed. Furthermore, as a result of the phylogeny and haplotype analyses of the candidate gene, high-Cd tolerance cultivars were selected. The correlations between Cd and other inorganic components (Mg, Mn, Fe, Cu and Zn) in the roots, stems, leaves and unpolished grain of selected rice cultivars were analyzed.

CONCLUSION

Therefore, these results may be useful for understanding the uptake-transport mechanisms of Cd and other inorganic components via molecular genetics and may help rice breeders develop new low-Cd cultivars in the near future.

Genome-Wide Association Study for Squalene Contents and Functional Haplotype Analysis in Rice

Squalene is an isoprenoid compound that acts as the intermediate metabolite in cholesterol synthesis. Squalene is not very susceptible to peroxidation, and it quenches singlet oxygen in the skin, which is caused by UV exposure and other ionizing radiation sources. Squalene is a precursor to phytosterol synthesis, and it has been widely studied for its ability to reduce oxidation, cancer activity, and cholesterol levels. We performed a genome-wide association study for squalene in rice using 1.6 million high-quality SNPs extracted from 295 accessions' resequencing data. The candidate gene locus Os09g0319800-an orthologue of terpene synthase in Arabidopsis-showed up as the most likely candidate gene amongst the identified loci. Nucleotide variations in the promoter were associated with squalene content variations within the japonica group. The results of this study can provide clues for understanding the mechanisms of squalene biosynthesis in rice.

P3617Systolic blood pressure, glycemic control and clinical outcome in diabetic patients with acute myocardial infarction

Background

Recent blood pressure guidelines recommend intensive blood pressure control in diabetic patients with cardiovascular disease.

Purpose

We sought to investigate combined impact of intensive blood glucose lowering and blood pressure control on clinical outcome in diabetic patients with acute myocardial infarction (AMI) has not been fully investigated yet.

Method

Korean Acute Myocardial Infarction Registry (KAMIR) – National Institute of Health (NIH) database included 12,179 patients (9,046 men; mean age = 63.6±12.6 year-old) who were discharged alive. Among them, 3,430 (28.2%) had a diabetes mellitus (DM). MACCEs were defined as a composition of all cause death, non-fatal MI, repeat revascularizations including repeated percutaneous coronary intervention and coronary bypass grafting, cerebrovascular accident and rehospitalizations at 1 year. This research was supported by a fund by Research of Korea Centers for Disease Control and Prevention.

Result

We determined cut-off value of discharge systolic blood pressure (SBP) to predict 1-year MACCE in DM and non-DM patients. Discharge SBP of less than 130mmHg was associated with a lower MACCE at 1 year compared to SBP level of 130mmHg or greater (10.8% versus 15.4%; log-rank p=0.001) in DM patients, whereas discharge SBP cut-off level was 140mmHg to discriminate 1-year MACCE in non-DM patients (6.4% versus 8.5%, log-rank p=0.045). In DM patients, there were no significant difference in 1-year MACCEs between patients with HbA1c less than 7% versus 7% or greater (12.0% versus 10.7%; log-rank p=0.325). DM patients were categorized into 4 groups; discharge SBP <130mmHg and HbA1c <7% (Group 1); discharge SBP <130mmHg and HbA1c ≥7% (Group 2); discharge SBP ≥130mmHg and HbA1c <7% (Group 3); discharge SBP ≥130mmHg and HbA1c ≥7% (Group 4). Intensive BP control was associated lower 1-year MACCEs in patients with good glycemic control (Group 1 & 3; 10.7% versus 16.7%; log-rank p=0.009). However, in patients with poor glycemic control, intensive BP control did not improve 1-year MACCEs (Group 2 & 4; 10.6% versus 11.1%; log-rank p=0.761).

Conclusion

Strict BP control is more important than glycemic control to improve short-term clinical outcome in DM patients with AMI. However, in patients with poor glycemic control, strict BP control did not improve clinical outcome.

P3583Optimal procedural strategy to improve clinical outcome in primary percutaneous coronary intervention

Background

Current guideline recommends potent antiplatelet agents and transradial intervention. However, it is uncertain whether routine use of IVUS, thrombus aspiration and glycoprotein IIB-IIIA inhibitor is beneficial for improving clinical outcome in patients with ST-segment elevation myocardial infarction (STEMI).

Purpose

The aim of this study was to investigate optimal procedural strategy to improve clinical outcome.

Methods

A total of 6,046 patients who underwent primary percutaneous coronary intervention (PCI) for STEMI were analyzed from the Korean Acute Myocardial Infarction Registry (KAMIR) – National Institute of Health (NIH) database. MACCEs were defined as a composition of all cause death, non-fatal MI, repeat revascularizations including repeated percutaneous coronary intervention and coronary bypass grafting, cerebrovascular accident and rehospitalizations. This research was supported by a fund by Research of Korea Centers for Disease Control and Prevention.

Results

During the primary PCI, potent antiplatelet agents such as prasugrel and ticagrelor were used in 2342 (38.4%). PCI was performed through transradial approach in 1490 (25.2%). Thrombus aspiration and intravascular ultrasound (IVUS) examination was done in 2204 (36.1%) and 1079 (18.1%), respectively. Glycoprotein IIB-IIIA inhibitor was administered in 1295 (21.7%). Among them, potent antiplatelet agents, transradial intervention, IVUS, and thrombus aspiration significantly reduced MACCEs at 1 year. Glycoprotein IIB-IIIA inhibitor was not effective to improved clinical outcome. In Cox-proportional hazards model, potent antiplatelet agents (hazard ratio 0.82, 95% confidence interval 0.67–0.99; p=0.045) and transradial intervention (hazard ratio 0.61, 95% confidence interval 0.47–0.78; p<0.001) was an independent predictor of MACCEs after adjusting for confounding variables. Combined use of potent antiplatelet agents and transradial intervention (hazard ratio 0.54; 95% confidence interval 0.37–0.80; p=0.002) substantially reduced MACCEs at 1 year.

Conclusion

Among evidence based procedures during the primary PCI, combined use of potent antiplatelet agents and transradial intervention was optimal procedural strategy to improve clinical outcome.

Signatures of differential selection in chloroplast genome between japonica and indica

BACKGROUND

The domestication process of Asian rice (Oryza sativa L.) is complicated. It's well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice.

RESULTS

A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (F_ST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima's D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice.

CONCLUSIONS

Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication.

Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice

The history of the domestication of rice is controversial, as it remains unknown whether domestication processes occurred once or multiple times. To date, genetic architecture and phylogenetic studies based on the rice nuclear genome have been extensively studied, but the results are quite different. Here, we found interesting results for different selections in Oryza sativa based on comprehensive studies of the rice mitochondrial (mt) genome. In detail, 412 rice germplasms were collected from around the world for variant architecture studies. A total of 10632 variants were detected in the mt genome, including 7277 SNPs and 3355 InDels. Selection signal (π_w/π_c) indicated that the selection sites in Oryza sativa L. ssp. japonica were different from those of Oryza sativa L. indica rice. The fixation index (F_ST) was higher between indica and japonica than between indica and wild rice. Moreover, haplotype and phylogenetic analyses also revealed indica clusters and japonica clusters that were well separated from wild rice. As mentioned above, our studies indicate that the selection sites of the indica type were different from those of the japonica type. This means that indica and japonica have experienced different domestication processes. We also found that japonica may have experienced a bottleneck event during domestication.

Improved detection of metastatic lymph nodes in oesophageal squamous cell carcinoma by combined interpretation of fluorine-18-fluorodeoxyglucose positron-emission tomography/computed tomography

Background

We sought to evaluate the diagnostic performance of fluorine-18-fluorodeoxyglucose positron-emission tomography/computed tomography (¹⁸F-FDG PET/CT) in the detection of metastatic lymph nodes by combined interpretation of PET/CT images in patients with oesophageal squamous cell carcinoma.

Methods

Two hundred three patients with oesophageal squamous cell carcinoma underwent ¹⁸F-FDG PET/CT before oesophagectomy and lymph node dissection. Maximum standardized uptake value (SUV_max), mean Hounsfield unit (HU), short axis diameter (size), and visual CT attenuation (high, iso-, low) were evaluated on noncontrast CT and PET images following PET/CT scan. In this combined interpretation protocol, the high attenuated lymph nodes were considered benign, even if the SUV_max value was high. The diagnostic accuracy of each method was compared using the postoperative histologic result as a reference standard.

Results

A total of 1099 nodal stations were dissected and 949 nodal stations were proven to demonstrate metastasis. SUV_max and size of the malignant lymph nodes were higher than those of the benign nodes, and visual CT attenuation was significantly different among the two groups (P < 0.001). Using cutoff values of 2.6 for SUV_max and 10.2 mm for size, the combined interpretation of an SUV_max of more than 2.6 with iso- or low CT attenuation [area under the curve (AUC): 0.846, 95% confidence interval (CI): 0.824–0.867] showed significantly better diagnostic performance for detecting malignant lymph nodes than SUV_max only (AUC: 0.791, 95% CI: 0.766–0.815) and size (AUC: 0.693, 95% CI: 0.665–0.720) methods (P < 0.001) in a receiver operating characteristic curve analysis.

Conclusions

The diagnostic accuracy of PET/CT for nodal metastasis in oesophageal squamous cell carcinoma was improved by the combined interpretation of ¹⁸F-FDG uptake and visual CT attenuation pattern.

Ligament-Saving Laminoplasty for Intraspinal Tumor Excision: A Technical Note

BACKGROUND

Various methods such as laminectomy, laminoplasty, and/or laminotomy can be used to remove intraspinal lesions. However, laminoplasty has generally been known to be able to prevent postoperative instability and deformity and avoid local scarring at operative site. We have described a new laminoplasty technique that can preserve the interspinous ligament during thoracolumbar intraspinal surgery.

METHODS

Ten patients undergoing laminoplastic tumor excision were evaluated preoperatively and postoperatively with neurologic examinations, a pain visual analog scale, and the Oswestry Disability Index. Instability and fusion were evaluated with plain radiography and computed tomography. The operative time, complications, and hospital stay were also assessed.

RESULTS

We assessed the data from 10 patients (12 disc levels) with intradural extramedullary tumor who had undergone a ligament-saving laminoplasty procedure. Of the 10 tumors, 6 were schwannoma, 2 were meningioma, 1 was extra-adrenal paraganglioma, and 1 was metastatic adenocarcinoma. Spinal computed tomography was performed 6 months postoperatively. Complete union of the laminoplasty site was achieved for all 10 patients. The flexion-extension view of the plain radiograph was compared with the preoperative images to evaluate the stability of the operated level. No patient had range of motion limitation or instability.

CONCLUSIONS

Ligament-saving laminoplasty can provide an appropriate surgical view and allow for anatomical reconstruction of the spinal posterior element after excision of spinal cord tumors. This procedure might offer an alternative to classic techniques for selected patients to preserve spinal biomechanical function.

Development of Predictive Models in Patients with Epiphora Using Lacrimal Scintigraphy and Machine Learning

PURPOSE

We developed predictive models using different programming languages and different computing platforms for machine learning (ML) and deep learning (DL) that classify clinical diagnoses in patients with epiphora. We evaluated the diagnostic performance of these models.

METHODS

Between January 2016 and September 2017, 250 patients with epiphora who underwent dacryocystography (DCG) and lacrimal scintigraphy (LS) were included in the study. We developed five different predictive models using ML tools, Python-based TensorFlow, R, and Microsoft Azure Machine Learning Studio (MAMLS). A total of 27 clinical characteristics and parameters including variables related to epiphora (VE) and variables related to dacryocystography (VDCG) were used as input data. Apart from this, we developed two predictive convolutional neural network (CNN) models for diagnosing LS images. We conducted this study using supervised learning.

RESULTS

Among 500 eyes of 250 patients, 59 eyes had anatomical obstruction, 338 eyes had functional obstruction, and the remaining 103 eyes were normal. For the data set that excluded VE and VDCG, the test accuracies in Python-based TensorFlow, R, multiclass logistic regression in MAMLS, multiclass neural network in MAMLS, and nuclear medicine physician were 81.70%, 80.60%, 81.70%, 73.10%, and 80.60%, respectively. The test accuracies of CNN models in three-class classification diagnosis and binary classification diagnosis were 72.00% and 77.42%, respectively.

CONCLUSIONS

ML-based predictive models using different programming languages and different computing platforms were useful for classifying clinical diagnoses in patients with epiphora and were similar to a clinician's diagnostic ability.

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

Anion gap and base deficit are predictors of mortality in acute pesticide poisoning

BACKGROUND:

Acute pesticide poisoning has long been a serious problem as a method of suicide worldwide. This poisoning is a highly fatal condition that requires a rapid and precise diagnosis for adequate treatment. However, various studies on mortality predictor factors have been insufficient for whole pesticide treatments. We hypothesized that the initial plasma anion gap (AG) and base deficit (BD) are reliable prognostic factors.

METHODS:

A retrospective study analyzed 561 patients with a diagnosis of acute pesticide poisoning between January 1, 2014 and June 30, 2017. The initial AG and BD values were divided into quartiles according to the number of patients. Survival at 30 days from admission was estimated using the Kaplan-Meier survival analysis. Receiver-operator characteristic (ROC) curves were drawn, and the areas under the curve for AG and BD for mortality were calculated.

RESULTS:

Fifty-eight (10.3%) of 561 patients died within 30 days. The highest AG quartile (>22 mEq/L) was associated with an increased risk of 30-day hospital mortality. Compared to patients with an AG less than 14.7 mEq/L, these patients had a 4.18-fold higher risk of 30-day hospital mortality and the highest BD quartile (>7.9 mEq/L) was associated with an increased risk of 30-day hospital mortality. Compared to patients with a BD less than 1.4 mEq/L, these patients had 2.23-fold higher risk of 30-day hospital mortality. The areas under the ROC for AG and BD curve were 0.699 and 0.744, respectively.

CONCLUSIONS:

Initial high AG and BD values could predict mortality and require precise intensive care.

Subchondral Bone Restoration of Supra-acetabular Brown Tumor Secondary to Parathyroid Carcinoma: A Case Report

The causes of osteolytic lesions found in radiological examinations are not quite certain. Therefore, to determine the appropriate treatment method, various approaches and analyzes are required to find the real cause. Hyperparathyroidism is one of the diseases which forms osteolytic bone lesions so-called brown tumor. A 55-year-old woman who had painful osteolytic bone lesions in both hip joint areas was diagnosed as parathyroid carcinoma after serial work-up. She underwent parathyroidectomy and follow-up imaging showed a decrease in brown tumor size and bone consolidation in the subchondral bone destruction area. Proper evaluation of osteolytic bone lesions helps to avoid unnecessary operative treatments and the first choice for the treatment of osteolytic bone lesions caused by parathyroid carcinoma is parathyroidectomy.

Molecular mapping of qBK1 WD , a major QTL for bakanae disease resistance in rice

BACKGROUND

Bakanae or foot rot disease is a prominent disease of rice caused by Gibberella fujikuroi. This disease may infect rice plants from the pre-emergence stage to the mature stage. In recent years, raising rice seedlings in seed boxes for mechanical transplanting has increased the incidence of many seedling diseases; only a few rice varieties have been reported to exhibit resistance to bakanae disease. In this study, we attempted to identify quantitative trait loci (QTLs) conferring bakanae disease resistance from the highly resistant japonica variety Wonseadaesoo.

RESULTS

A primary QTL study using the genotypes/phenotypes of the recombinant inbred lines (RILs) indicated that the locus qBK1 WD conferring resistance to bakanae disease from Wonseadaesoo was located in a 1.59 Mb interval delimited on the physical map between chr01_13542347 (13.54 Mb) and chr01_15132528 (15.13 Mb). The log of odds (LOD) score of qBK1 WD was 8.29, accounting for 20.2% of the total phenotypic variation. We further identified a gene pyramiding effect of two QTLs, qBK WD and previously developed qBK1. The mean proportion of healthy plant for 31 F4 RILs that had no resistance genes was 35.3%, which was similar to that of the susceptible check variety Ilpum. The proportion of healthy plants for the lines with only qBK WD or qBK1 was 66.1% and 55.5%, respectively, which was significantly higher than that of the lines without resistance genes and that of Ilpum. The mean proportion of the healthy plant for 15 F4 RILs harboring both qBK WD and qBK1 was 80.2%, which was significantly higher than that of the lines with only qBK WD or qBK1.

CONCLUSION

Introducing qBK WD or pyramiding the QTLs qBK WD and qBK1 could provide effective tools for breeding rice with bakanae disease resistance. To our knowledge, this is the first report on a gene pyramiding effect that provides higher resistance against bakanae disease.

Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage

Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated. Based on the expression patterns, we found that most of these genes showed a different expression level under control and salt stress conditions. In addition, haplotype network and sequence analysis of one 'key' gene, a transcription factor (Os12g0176700) encoding a SWIRM domain-containing protein, in the interaction network was investigated to explore its possible role in the network. Our study revealed candidate salt tolerance-related genes in rice at the seedling stage, and demonstrated the feasibility of using GWAS to identify genetic architecture underlying salt tolerance. The data generated here may provide resources for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage

Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated. Based on the expression patterns, we found that most of these genes showed a different expression level under control and salt stress conditions. In addition, haplotype network and sequence analysis of one 'key' gene, a transcription factor (Os12g0176700) encoding a SWIRM domain-containing protein, in the interaction network was investigated to explore its possible role in the network. Our study revealed candidate salt tolerance-related genes in rice at the seedling stage, and demonstrated the feasibility of using GWAS to identify genetic architecture underlying salt tolerance. The data generated here may provide resources for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Current-induced morphological evolution and reliability of Ag interconnects fabricated by a printing method based on nanoparticles

Ag interconnects fabricated by a printing method were tested under accelerated temperature and current stressing to investigate their electrical reliability and morphological evolution.

Results from the Survey of Antibiotic Resistance (SOAR) 2012-14 in Thailand, India, South Korea and Singapore

OBJECTIVES

To provide susceptibility data for community-acquired respiratory tract isolates of Streptococcus pneumoniae, Streptococcus pyogenes, Haemophilus influenzae and Moraxella catarrhalis collected in 2012-14 from four Asian countries.

METHODS

MICs were determined using Etest(®) for all antibiotics except erythromycin, which was evaluated by disc diffusion. Susceptibility was assessed using CLSI, EUCAST and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints. For macrolide/clindamycin interpretation, breakpoints were adjusted for incubation in CO2 where available.

RESULTS

Susceptibility of S. pneumoniae was generally lower in South Korea than in other countries. Penicillin susceptibility assessed using CLSI oral or EUCAST breakpoints ranged from 21.2% in South Korea to 63.8% in Singapore. In contrast, susceptibility using CLSI intravenous breakpoints was much higher, at 79% in South Korea and ∼95% or higher elsewhere. Macrolide susceptibility was ∼20% in South Korea and ∼50%-60% elsewhere. Among S. pyogenes isolates (India only), erythromycin susceptibility (∼20%) was lowest of the antibiotics tested. In H. influenzae antibiotic susceptibility was high except for ampicillin, where susceptibility ranged from 16.7% in South Korea to 91.1% in India. South Korea also had a high percentage (18.1%) of β-lactamase-negative ampicillin-resistant isolates. Amoxicillin/clavulanic acid susceptibility for each pathogen (PK/PD high dose) was between 93% and 100% in all countries except for H. influenzae in South Korea (62.5%).

CONCLUSIONS

Use of EUCAST versus CLSI breakpoints had profound differences for cefaclor, cefuroxime and ofloxacin, with EUCAST showing lower susceptibility. There was considerable variability in susceptibility among countries in the same region. Thus, continued surveillance is necessary to track future changes in antibiotic resistance.

Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

BACKGROUND

Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic.

RESULTS

A total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice.

CONCLUSIONS

The chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.

Whole-breast US following mammography and breast MRI in newly diagnosed breast cancer patients: can it be more than just a guidance tool for biopsy?

AIM

To evaluate the role of ultrasound (US) following magnetic resonance imaging (MRI) and mammography in patients with newly diagnosed breast cancers by assessing the additional cancer detection rate of US.

MATERIAL AND METHODS

Two hundred and twenty-five women who had undergone 225 MRI examinations followed by US were included. An US-detected additional cancer was defined as a lesion detected using breast US that had not been detected by MRI, and which was shown to be malignant at histopathology. The rate of additional cancer detection, incidence of additional malignancies, positive predictive value (PPV), and false-positive (FP) rate were analysed. Factors associated with an increase in the additional cancer detection rate were analysed.

RESULTS

The additional cancer detection rate was 0% (0/225) for the ipsilateral breast and 0.9% (2/225) for the contralateral breast, and the PPVs were 0% (0/5) and 100% (2/2), respectively. The overall TP:FP ratio was 0.4 (2:5). The additional cancer detection rate was higher for cases with moderate and severe background parenchymal enhancement than cases with minimal and mild background parenchymal enhancement (p=0.003). The additional cancer detection rate for cases with moderate and severe background parenchymal enhancement was 5.7% (2/35) for the contralateral breast (p=0.003).

CONCLUSION

Preoperative breast US following MRI and mammography can help clinicians screen for contralateral cancers with an additional detection rate of 0.9%. Moreover, whole-breast US might be a useful contralateral screening modality in cases with moderate or marked parenchymal enhancement on breast MRI.