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Pre-harvest sprouting (PHS) poses a significant global challenge to cereal production, impacting both yield and quality. In this study, we employed genome-wide association studies (GWAS) on diverse rice accessions to identify novel PHS-associated haplotypes. An assessment of 127 cultivated accessions for panicle germination (PHS) and detached grain germination (germination rate of detached grains at the 14th day (D14)) revealed considerable phenotypic variation among rice ecotypes. GWAS analysis identified 91 significant signals at –log10(P-value)>5, including 15 SNPs for PHS and 76 SNPs for D14. A subsequent linkage disequilibrium (LD) block-based GWAS analysis detected 227 significant SNPs for both traits, consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes. Further haplotype analysis identified 32 haplotypes, with 10 specific to cultivated accessions, 19 specific to the wild type, and three shared between them. A phenotypic assessment of major haplotypes revealed significant differences between resistant (Hap1 and Hap2) and susceptible haplotypes (Hap5, Hap27, and Hap28), distinguished by a G/A SNP within a novel gene, Os04g0545200. The identified haplotypes offer promising prospects for haplotype-based breeding aimed at enhancing PHS resistance in rice.

Abstract 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.

As genomic selection emerges as a promising breeding method for both plants and animals, numerous methods have been introduced and applied to various real and simulated data sets. Research suggests that no single method is universally better than others; rather, performance is highly dependent on the characteristics of the data and the nature of the prediction task. This implies that each method has its strengths and weaknesses. In this study, we exploit this notion and propose a different approach. Rather than comparing multiple methods to determine the best one for a particular study, we advocate combining multiple methods to achieve better performance than each method in isolation. In pursuit of this goal, we introduce and develop a computational method of the stacked generalization within ensemble methods. In this method, the meta-model merges predictions from multiple base models to achieve improved performance. We applied this method to plant and animal data and compared its performance with currently available methods using standard performance metrics. We found that the proposed method yielded a lower or comparable mean squared error in predicting phenotypes compared to the current methods. In addition, the proposed method showed greater resistance to overfitting compared to the current methods. Further analysis included statistical hypothesis testing, which showed that the proposed method outperformed or matched the current methods. In summary, the proposed stacked generalization integrates currently available methods to achieve stable and better performance. In this context, our study provides general recommendations for effective practices in genomic selection.

Abstract 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.

Abstract In the domains of wearable electronics, robotics, and the Internet of Things, there is a demand for devices with low power consumption and the capability of multiplex sensing, memory, and learning. Triboelectric nanogenerators (TENGs) offer remarkable versatility in this regard, particularly when integrated with synaptic transistors that mimic biological synapses. However, conventional TENGs, generating only two spikes per cycle, have limitations when used in synaptic devices requiring repetitive high‐frequency gating signals to perform various synaptic plasticity functions. Herein, a multi‐layered micropatterned TENG (M‐TENG) consisting of a polydimethylsiloxane (PDMS) film and a composite film that includes 1H,1H,2H,2H‐perfluorooctyltrichlorosilane/BaTiO3/PDMS are proposed. The M‐TENG generates multiple spikes from a single touch by utilizing separate triboelectric charges at the multiple friction layers, along with a contact/separation delay achieved by distinct spacers between layers. This configuration allows the maximum triboelectric output charge of M‐TENG to reach up to 7.52 nC, compared to 3.69 nC for a single‐layered TENG. Furthermore, by integrating M‐TENGs with an organic electrochemical transistor, the spike number multiplication property of M‐TENGs is leveraged to demonstrate an artificial synaptic device with low energy consumption. As a proof‐of‐concept application, a robotic hand is operated through continuous memory training under repeated stimulations, successfully emulating long‐term plasticity.

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.

Abstract Pulmonary lymphangitic carcinomatosis (PLC) is associated with a poor prognosis in patients with non-small cell lung cancer (NSCLC). We sought to determine prognostic value of pretherapeutic fluorine-18-fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT) in NSCLC with radiologically diagnosed PLC. We retrospectively reviewed 50 NSCLC patients with radiologically diagnosed PLC. Among eight clinical variables and five imaging parameters, metabolic PLC burden, which represents the overall tumor burden of PLC, and cPLC, which represents the location and extent of PLC in a three-grade system, were used. In multivariate analyses for progression-free survival, metabolic PLC burden (P = 0.0181), cPLC (P = 0.0401), and clinical stage (P = 0.0284) were identified as independent prognostic factors. High metabolic PLC burden had a worse prognosis, and the prognosis of cPLC3 was significantly worse than that of cPLC1 or cPLC2. In univariate analyses for overall survival, only age (P = 0.0073) was identified a prognostic factor. In conclusion, FDG PET/CT parameters were identified as independent prognostic factors in NSCLC with radiologically diagnosed PLC. Furthermore, a combination of anatomical and metabolic information about PLC obtained using FDG PET/CT provides insight into the overall tumor burden of PLC and is useful in predicting prognosis.

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.

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, −log10p-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.

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.

Abstract The purpose of this retrospective study was to investigate the role in staging and prognostic value of pretherapeutic fluorine-18-fluorodeoxyglucose (F-18 FDG) positron emission tomography (PET)/computed tomography (CT) in patients with gastric mucosa-associated lymphoid tissue (MALT) lymphoma without high-grade transformation (HT). We retrospectively reviewed 115 consecutive patients with histopathologically confirmed gastric MALT lymphoma without HT who underwent pretherapeutic F-18 FDG PET/CT. Kaplan–Meier and Cox proportional-hazards regression analyses were used to identify independent prognostic factors for disease free survival (DFS) among 13 clinical parameters and three PET parameters. In two of 115 patients (1.7%), the clinical stage appeared higher according to F-18 FDG PET/CT. In univariate analysis, Helicobacter pylori (HP) infection (P = 0.023), treatment modality (P

Abstract Multifunctional electronic skins have attracted considerable attention for soft electronics including humanoid robots, wearable devices, and health monitoring systems. Simultaneous detection of multiple stimuli in a single self‐powered device is desired to simplify artificial somatosensory systems. Here, inspired by the structure and function of human skin, an ultrasensitive self‐powered multimodal sensor is demonstrated based on an interlocked ferroelectric copolymer microstructure. The triboelectric and pyroelectric effects of ferroelectric microstructures enable the simultaneous detection of mechanical and thermal stimuli in a spacer‐free single device, overcoming the drawbacks of conventional devices, including complex fabrication, structural complexity, and high‐power consumption. Furthermore, the interlocked microstructure induces electric field localization during ferroelectric polarization, leading to enhanced output performance. The multimodal tactile sensor provides ultrasensitive pressure and temperature detection capability (2.2 V kPa−1, 0.27 nA °C−1) over a broad range (0.1–98 kPa, −20 °C < ΔT

Objective To evaluate the cases of osteoporotic compression fracture with kyphotic deformity treated with modified pedicle subtraction osteotomy and analyze the usefulness of this osteotomy. Methods Twenty patients (nine men, 11 women; mean age, 66.4 years; mean follow‐up duration, 39.6 months) who underwent modified pedicle subtraction osteotomy at our hospital between November 2003 and July 2012 with a minimum follow‐up period of 2 years were included. All cases were injuries induced by a fall incurred while standing or lifting heavy objects without high‐energy trauma. The mean bone mineral density‐dual energy x‐ray absorptiometry (BMD‐DEXA) was 0.673 g/cm2 (0.571–0.740 g/cm2), which was ‐2SD below normal, indicating severe osteoporosis. The indications for surgery included gait disturbance due to severe pain with pseudarthrosis, increased kyphotic angle, and progressive neurological symptoms. We evaluated Japanese Orthopaedic Association scores, Oswestry Disability Index scores, bone union, change in kyphotic angle, estimated blood loss, complications, and the patient's overall clinical satisfaction. Results The collapsed vertebrae were thoracic (T9, 11, 12) in 13 cases and lumbar (L1) in seven cases. The mean pre‐ and post‐operative kyphotic angles were 26.2 ± 9.9 degrees and 8.3 ± 8.1 degrees, showing an 18.3‐degree correction. Plain radiography at the last follow‐up showed a mean angle of 17.9 ± 12.6 degrees, indicating a 9.5‐degree correction loss. The overall correction was 8.2 degrees. Bony union was achieved at the last follow‐up in all cases. Clinical outcomes showed improvement in mean Japanese Orthopaedic Association score from 13.2 to 21.7 and mean Oswestry Disability Index score from 40.3 to 13.6. Overall clinical patient satisfaction showed 12 excellent results, five moderate results, and three poor results. Mean operation time was 4.2 h (range, 4–6 h). The overall mean estimated blood loss (EBL) was 1098 mL (range, 750–1370 mL). The mean hospital stay was 3.6 weeks (range, 2–6 weeks). There was one case of cauda equina syndrome at 2 days postoperatively, and two cases of screw loosening. There were no cases of distal junctional kyphosis, but there were two cases of proximal junctional kyphosis. Conclusions Despite limited correction of kyphotic angle, our modified pedicle subtraction osteotomy technique resulted in satisfactory outcomes in our patients, who had persistent severe back pain, increased kyphotic angle with pseudarthrosis, and progressive neurologic deficits. Nevertheless, this procedure requires careful follow‐up and strict surgical indications because of the risk of neurological damage and technical problems.

Abstract 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.

The 21st century is a high-tech information era in which our lives are closely linked by computer networks. Hence, how to effectively supervise networks and reduce the frequency of network security incidents has now become a research hotspot in cyberspace. Specifically, researchers have shown an increased interest in predicting the network traffic before any untoward incident happens. Optimization and decomposition technologies are the core components of network traffic prediction model which plays an important role in network management. This article discusses past network traffic prediction research and critically examines the optimization and decomposition technologies used in the model, lists the model parameter structure based on the research methodology, the data set used, the evaluation criteria and so on. By comparison, digging out the Particle Swarm Optimization (PSO) algorithm and the Variational Mode Decomposition (VMD) decomposition technique will effectively solve the network traffic model predictive difficulties that have proven to be crucial to improving predictive accuracy and convergence speed strategy.The comprehensive review reveals that PSO and VMD are the most suitable optimization algorithm and decomposition technology for network traffic prediction modeling.

The Internet of Things (IoT) is shaping the current and next generation of the Internet. The vision of IoT is to embed communication capabilities with a highly distributed, ubiquitous and dense heterogeneous devices network. This vision includes the adaptation of secure mobile networks, anytime, anywhere, by anyone or anything with new intelligent applications and services. Many efforts have been made to review the literature related to the IoT for the benefit of IoT development. However, many issues need to be addressed to overtake the full potential of the IoT. Therefore, this paper aims to classify and standardize IoT research areas by considering review papers that were published between 2010 and 2019. This paper analyzes a total of 95 related reviews, which were manually selected from databases based on 6 chosen areas. This paper presents the trends and classification of IoT reviews based on 6 research areas, namely, application, architecture, communication, challenges, technology, and security. IoT communication research has been dominating the trends with 21% of total reviews and more than 100% research growth in the last 10 years. Hence, this paper can provide useful insights into specific emerging areas of IoT to assist future research.

PurposeThe 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 methodsWe 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.ResultsAll 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.ConclusionMET 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.

Abstract 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.

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 FST 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.

Abstract 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.

Abstract 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 (SUVmax), 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 SUVmax 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. SUVmax 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

Abstract 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.

Salinity is one of the major constraints causing soil problems and is considered a limitation to increased rice production in rice-growing countries. This genome-wide association study (GWAS) experiment was conducted to understand the genetic basis of salt tolerance at the seedling stage in Korean rice. After 10 days of salt stress treatment, salt tolerance was evaluated with a standard evaluation system using a visual salt injury score. With 191 Korean landrace accessions and their genotypes, including 266,040 single-nucleotide polymorphisms (SNPs), using a KNU Axiom Oryza 580K Genotyping Array, GWAS was conducted to detect three QTLs with significant SNPs with a −log10(P) threshold of ≥3.66. The QTL of qSIS2, showed −log10(P) = 3.80 and the lead SNP explained 7.87% of total phenotypic variation. The QTL of qSIS4, showed −log10(P) = 4.05 and the lead SNP explained 10.53% of total phenotypic variation. The QTL of qSIS8 showed −log10(P) = 3.78 and the lead SNP explained 7.83% of total phenotypic variation. Among the annotated genes located in these three QTL regions, five genes were selected as candidates (Os04g0481600, Os04g0485300, Os04g0493000, Os04g0493300, and Os08g0390200) for salt tolerance in rice seedlings based on the gene expression database and their previously known functions.

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.

Development of adjacent segment pathology leading to secondary operation is a matter of concern after anterior cervical discectomy and fusion (ACDF). Some studies have reported anatomic difference between races, but no epidemiological data on prevalence of clinical adjacent segment pathology (cASP) among races or continents has been published. The purpose of this study was to compare the prevalence of cASP that underwent surgery after monosegmental ACDF among continents by meta-analysis. MEDLINE, EMBASE, and Cochrane Library with manual searching in key journals, reference lists, and the National Technical Information Service were searched from inception to December 2018. Twenty studies with a total of 2009 patients were included in the meta-analysis. We extracted the publication details, sample size, and prevalence of cASP that underwent surgery. A total of 15 papers from North America, three from Europe, and two from Asia met the inclusion criteria. A total number of 2009 patients underwent monosegmental ACDF, and 113 patients (5.62%) among them had cASP that underwent surgery. The rate of cASP that underwent surgery was 4.99% in the North America, 3.65% in the Europe, 6.34% in the Asia, and there were no statistically significant differences (p = 0.63). The current study using the method of meta-analysis revealed that there were no significant differences in the rate of cASP that underwent surgery after ACDF among the continents.

Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear association between BADH1 and salt stress, we observed the responses of eight phenotypic characteristics (germination percentage (GP), germination energy (GE), germination index (GI), mean germination time (MGT), germination rate (GR), shoot length (SL), root length (RL), and total dry weight (TDW)) to salt stress during the germination stage of 475 rice accessions to investigate their association with BADH1 haplotypes. We found a total of 116 SNPs and 77 InDels in the whole BADH1 gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (p < 0.05) associated with salt stress, including the five SNPs that have been previously reported to be associated with salt tolerance. We observed three predominant haplotypes associated with salt tolerance, Hap_2, Hap_18, and Hap_23, which were Indica specific, indicating a comparatively high number of rice accessions among the associated haplotypes. Eight plant parameters (phenotypes) also showed clear responses to salt stress, and except for MGT (mean germination time), all were positively correlated with each other. Different signatures of domestication for BADH1 were detected in cultivated rice by identifying the highest and lowest Tajima’s D values of two major cultivated ecotypes (Temperate Japonica and Indica). Our findings on these significant associations and BADH1 evolution to plant traits can be useful for future research development related to its gene expression.

Two of the most promising candidate solutions for realizing the next-generation all-IP mobile networks are Mobile IPv6 (MIPv6), which is the host-based and global mobility supporting protocol, and Proxy MIPv6 (PMIPv6), which is the network-based and localized mobility supporting protocol. However, the unprecedented growth of mobile Internet traffic has resulted in the development of distributed mobility management (DMM) architecture by the Internet engineering task force DMM working group. The extension of the basic MIPv6 and PMIPv6 to support their distributed and scalable deployment in the future is one of the major goals of the DMM working group. We propose an all-IP-based mobility management architecture that leverages the concept of Named Data Networking (NDN), which is a distributed content management and addressing architecture. In the proposed solution, mobility support services are distributed among multiple anchor points at the edge of the network, thereby enabling a flat architecture that exploits name-based routing in NDN. Our approach overcomes some of the major limitations of centralized IP mobility management solutions, by extending existing routing protocol and mobility management architecture, to distribute the mobility management function of anchor points in the IP network and optimize the transmission path of mobile traffic.

Internet Engineering Task Force (IETF) has proposed an extension based on Mobile IPv6 (MIPv6), named as network mobility basic support protocol (NEMO-BSP), to support NEMO in IPv6 networks. However, NEMO-BSP inherits all the drawbacks of MIPv6, such as inefficient routing path, high handover latency, and packet encapsulation overhead. To address these drawbacks of NEMO-BSP, this paper proposes an NEMO supporting scheme based on a novel Locator/ID Separation (LIDS) architecture, namely LIDS-NEMO. In LIDS-NEMO, Multiple Virtual Mapping (MVM) scheme is proposed to differentiate the intra-NEMO and inter-NEMO mobility. Besides, packets are transmitted through the most optimized route in LIDS-NEMO. The simulation results show that LIDS-NEMO reduces the signaling cost significantly when compared with NEMO-BSP and it will be a promising scheme to provide NEMO support in the LIDS context.

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.

To observe the possibility of producing haploid plants of Chrysanthemum, anthers of three Korean cultivars ‘Yes Morning’, ‘Hi-Maya’, and pot cultivar ‘Peace Pink’ were cultured. Callus induction among cultivars differed little, but equally good results were obtained with the basal MS medium supplemented with 1 mg/L of 2,4-D, 2 mg/L of BA, 250 mg/L of casein hydrolysate, 45 g/L of sucrose; solidified by 2.75 g/L gelrite. A pretreatment of anthers in media at 4 °C for 48h enhanced the callus induction. Calli were allowed to differentiate on basal MS medium supplemented with 2 mg/L of BA, 0.1 mg/L of NAA, 30 g/L of sucrose; solidified by 2.75 g/L gelrite. Shoot formation from calli in that media slightly differed among cultivars. Multiple shoots elongated from calli were shifted to basal MS medium supplemented with 0.1 mg/L of NAA, 30 g/L of sucrose; solidified by 3 g/L gelrite for rooting. The plantlets with sufficient roots thus obtained were acclimatized and transferred to the soil. Fifty regenerated plantlets from each cultivar were randomly selected for ploidy observation by chromosome counting and haploid plantlet was detected for the garden cultivar ‘Yes morning’.

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.

Evaluation of the genetic diversity among populations is an essential prerequisite for the preservation of endangered species. Thousands of new accessions are introduced into germplasm institutes each year, thereby necessitating assessment of their molecular diversity before elimination of the redundant genotypes. Of the protocols that facilitate the assessment of molecular diversity, SSRPs (simple sequence repeat polymorphisms) or microsatellite variation is the preferred system since it detects a large number of DNA polymorphisms with relatively simple technical complexity. The paucity of information on DNA sequences has limited their widespread utilization in the assessment of genetic diversity of minor or neglected crop species. However, recent advancements in DNA sequencing and PCR technologies in conjunction with sophisticated computer software have facilitated the development of SSRP markers in minor crops. This review examines the development and molecular nature of SSR markers, and their utilization in many aspects of plant genetics and ecology.

In Wireless Sensor Networks (WSNs), transmission errors occur frequently due to node failure, battery discharge, contention or interference by objects. Although Directed Diffusion has been considered as a prominent data-centric routing algorithm, it has some weaknesses due to unexpected network errors. In order to address these problems, we proposed a radio-aware routing algorithm to improve the reliability of Directed Diffusion in lossy WSNs. The proposed algorithm is aware of the network status based on the radio information from MAC and PHY layers using a cross-layer design. The cross-layer design can be used to get detailed information about current status of wireless network such as a link quality or transmission errors of communication links. The radio information indicating variant network conditions and link quality was used to determine an alternative route that provides reliable data transmission under lossy WSNs. According to the simulation result, the radio-aware reliable routing algorithm showed better performance in both grid and random topologies with various error rates. The proposed solution suggested the possibility of providing a reliable transmission method for QoS requests in lossy WSNs based on the radio-awareness. The energy and mobility issues will be addressed in the future work.

In recent years, a few protocol bridge research projects have been announced to enable a seamless integration of Wireless Sensor Networks (WSNs) with the TCP/IP network. These studies have ensured the transparent end-to-end communication between two network sides in the node-centric manner. Researchers expect this integration will trigger the development of various application domains. However, prior research projects have not fully explored some essential features for WSNs, especially the reusability of sensing data and the data-centric communication. To resolve these issues, we suggested a new protocol bridge system named TinyONet. In TinyONet, virtual sensors play roles as virtual counterparts of physical sensors and they dynamically group to make a functional entity, Slice. Instead of direct interaction with individual physical sensors, each sensor application uses its own WSN service provided by Slices. If a new kind of service is required in TinyONet, the corresponding function can be dynamically added at runtime. Beside the data-centric communication, it also supports the node-centric communication and the synchronous access. In order to show the effectiveness of the system, we implemented TinyONet on an embedded Linux machine and evaluated it with several experimental scenarios.

BADH1 and BADH2 are two homologous genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcribed region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP (T/A) in exon 4 is highly correlated with salt tolerance index (STI) (P

Olfactory sensory function declines with age; though, the underlying molecular changes that occur in the olfactory bulb (OB) are relatively unknown. An important cellular signaling molecule involved in the processing, modulation, and formation of olfactory memories is nitric oxide (NO). However, excess NO can result in the production of peroxynitrite to cause oxidative and nitrosative stress. In this study, we assessed whether changes in the expression of 3-nitrotyrosine (3-NT), a neurochemical marker of peroxynitrite and thus oxidative damage, exists in the OB of young, adult, middle-aged, and aged mice. Our results demonstrate that OB 3-NT levels increase with age in normal C57BL/6 mice. Moreover, in aged mice, 3-NT immunoreactivity was found in some blood vessels and microglia throughout the OB. Notably, large and strongly immunoreactive puncta were found in mitral and tufted cells, and these were identified as lipofuscin granules. Additionally, we found many small-labeled puncta within the glomeruli of the glomerular layer and in the external plexiform layer, and these were localized to mitochondria and discrete segments of mitral and tufted dendritic plasma membranes. These results suggest that mitral and tufted cells are potential cellular targets of nitration, along with microglia and blood vessels, in the OB during aging.