Deep learning model is a kind of neural networks that allows multiple hidden layers. There are various deep learning architectures such as convolutional neural networks, deep belief networks and recurrent neural networks. Those have been applied to fields like computer vision, automatic speech recognition, natural language processing, audio recognition and bioinformatics where they have been shown to produce state-of-the-art results on various tasks. Among those architectures, convolutional neural networks and recurrent neural networks are classified as the supervised learning model. And in recent years, those supervised learning models have gained more popularity than unsupervised learning models such as deep belief networks, because supervised learning models have shown fashionable applications in such fields mentioned above. Deep learning models can be trained with backpropagation algorithm. Backpropagation is an abbreviation for "backward propagation of errors" and a common method of training artificial neural networks used in conjunction with an optimization method such as gradient descent. The method calculates the gradient of an error function with respect to all the weights in the network. The gradient is fed to the optimization method which in turn uses it to update the weights, in an attempt to minimize the error function. Convolutional neural networks use a special architecture which is particularly well-adapted to classify images. Using this architecture makes convolutional networks fast to train. This, in turn, helps us train deep, muti-layer networks, which are very good at classifying images. These days, deep convolutional networks are used in most neural networks for image recognition. Convolutional neural networks use three basic ideas: local receptive fields, shared weights, and pooling. By local receptive fields, we mean that each neuron in the first(or any) hidden layer will be connected to a small region of the input(or previous layer's) neurons. Shared weights mean that we're going to use the same weights and bias for each of the local receptive field. This means that all the neurons in the hidden layer detect exactly the same feature, just at different locations in the input image. In addition to the convolutional layers just described, convolutional neural networks also contain pooling layers. Pooling layers are usually used immediately after convolutional layers. What the pooling layers do is to simplify the information in the output from the convolutional layer. Recent convolutional network architectures have 10 to 20 hidden layers and billions of connections between units. Training deep learning networks has taken weeks several years ago, but thanks to progress in GPU and algorithm enhancement, training time has reduced to several hours. Neural networks with time-varying behavior are known as recurrent neural networks or RNNs. A recurrent neural network is a class of artificial neural network where connections between units form a directed cycle. This creates an internal state of the network which allows it to exhibit dynamic temporal behavior. Unlike feedforward neural networks, RNNs can use their internal memory to process arbitrary sequences of inputs. Early RNN models turned out to be very difficult to train, harder even than deep feedforward networks. The reason is the unstable gradient problem such as vanishing gradient and exploding gradient. The gradient can get smaller and smaller as it is propagated back through layers. This makes learning in early layers extremely slow. The problem actually gets worse in RNNs, since gradients aren't just propagated backward through layers, they're propagated backward through time. If the network runs for a long time, that can make the gradient extremely unstable and hard to learn from. It has been possible to incorporate an idea known as long short-term memory units (LSTMs) into RNNs. LSTMs make it much easier to get good results when training RNNs, and many recent papers make use of LSTMs or related ideas.
Fluid muds commonly occur in estuarine environments, but their ancient examples have rarely been studied in terms of depositional characteristics and processes. Cores of estuarine channel deposits of the Early Cretaceous McMurray Formation, Alberta, Canada show various mudstone layers that possess depositional characteristics of high clay-concentration flows. These mudstone layers are examined in detail through microscopic observation of thin sections and classified into three microfacies (<1 to 25 mm thick) on the basis of sedimentary texture and structures. Structureless mudstone (Microfacies 1) consists mainly of clay particles and contains randomly dispersed coarser grains (coarse silt to fine sand). This microfacies is interpreted as being deposited by cohesive mud flows, i.e., fluid muds, which possessed sufficient strength to support suspended coarser grains (quasi-laminar plug flow). Silt-streaked mudstone (Microfacies 2) mainly comprises mudstone with dispersed coarse grains and includes very thin, discontinuous silt streaks of coarse-silt to very-fine-sand grains. The texture similar to Microfacies 1 indicates that Microfacies 2 was also deposited by cohesive fluid muds. The silt streaks are, however, suggestive of the presence of intermittent weak turbulence under the plug (upper transitional plug flow). Heterolithic laminated mudstone (Microfacies 3) is characterized by alternation of relatively thick silt laminae and much thinner clay laminae. It is either parallel-laminated or low-angle cross-laminated, occasionally showing low-amplitude ripple forms. The heterolithic laminae are interpreted as the results of shear sorting in the basal turbulent zone under a cohesive plug. They may represent low-amplitude bed-waves formed under lower transitional plug flows. These three microfacies reflect a range of flow phases of fluid muds, which change with flow velocities and suspended mud concentrations. The results of this study provide important knowledge to recognize fluid-mud deposits in ancient sequences and to better understand depositional processes of mudstones.
SHRIMP zircon U-Pb ages and major element and Sr-Nd isotopic compositions were determined for drill cores (374-3390 m in depth) recovered from three boreholes in the Pohonag basin, southeastern Korea. Shallow-seated volcanic rocks and underlain plutonic rocks were geochemically classified as rhyolite and gabbro-granite, respectively. They showed high-K calc-alkaline trends on the $K_2O-SiO_2$ and AFM diagrams. Zircons from volcanic rocks of borehole PB-1 yielded concordia ages of $66.84{\pm}0.66Ma$ (n=12, MSWD=0.02) and $66.52{\pm}0.55Ma$ (n=12, MSWD=0.46). Zircons from volcanic rocks of borehole PB-2 gave a concordia age of $71.34{\pm}0.85Ma$ (n=11, MSWD=0.79) and a weighted mean $^{206}Pb/^{238}U$ ages of $49.40{\pm}0.37Ma$ (n=11, MSWD=1.9). On the other hand, zircons from plutonic rocks of borehole PB-3 yielded weighted mean $^{206}Pb/^{238}U$ ages of $262.4{\pm}3.6Ma$ (n=21, MSWD=4.5), $252.4{\pm}3.6Ma$ (n=8, MSWD=1.9) and $261.8{\pm}1.5Ma$ (n=31, MSWD=1.3). Detrital zircons from the sedimentary strata overlain the volcanic rocks showed a wide age span from Neoproterozoic to Cenozoic, with the youngest population corresponding to $21.89{\pm}1.1Ma$ (n=15, MSWD=0.04) and $21.68{\pm}1.2Ma$ (n=10, MSWD=19). These dating results indicate that the basement of the Pohang basin is composed of Late Permian plutonic rocks and overlain Late Cretaceous to Eocene volcanic sequences. Miocene sediments were deposited in the uppermost part of the basin, possibly associated with the opening of the East Sea. The Sr-Nd isotopic compositions of the Permian plutonic rocks were comparable with those reported from Permian-Triassic granitoids in the Yeongdeok area, northern Gyeongsang basin. They may have been recycled into parts of the Cretaceous-Paleogene magmatic rocks within the Gyeongsang basin.
With a broad objective for the development of microbial based fertilizers, a total of 373 strains were isolated from rhizoplane and rhizosphere of pepper, tomato, lettuce, pasture, and grass. The efficacy of the isolates to augument overall plant growth was evaluated. After screening for their plant growth promotion and antagonistic properties in vitro efficient strains were further selected. The most efficient strains was characterized by 16S rRNA gene sequences and biochemical techniques and was designated as Bacillus subtilis S37-2. The strains facilitated plant growth and inhibited the plant phathogenic fungi such as Fusarium oxysporum (KACC 40037, Rhizoctonia solani (KACC 40140), and Sclerotinia sclerotiorum (KACC 40457). Pot based bioassay using lettuce as test plant was conducted by inoculating suspension ($10^5$ to $10^8cells\;mL^{-1}$) of B. subtilis S37-2 to the rhizosphere of lettuce cultivated in soil pots. Compared with non-inoculated pots, marked increase in leaf (42.3%) and root mass (48.7%) was observed in the inoculation group where the 50ml of cell mixture ($8.7{\times}10^8cells\;ml^{-1}$) was applied to the rhizosphere of letuce either once or twice. Antagonistic effects of B. subtilis S37-2 strain on S. sclerotiorum (KACC 40457) were tested. All the tested lettuce plants perished after 9 days in treatment containing only S. sclerotiorum, but only 17% of lettuce was perished in the inoculation plot. B. subtilis grew well in the TSB culture medium. The isolates grew better in yeast extracts than peptone and tryptone as nitrogen source. The growth rate was 2~4 times greater at $37^{\circ}C$ as compared with $30^{\circ}C$ incubation temperature. B. subitlis S37-2 produced $0.1{\mu}g\;ml^{-1}$ of IAA (indole 3-acetic acid) in the TSB medium containing L-tryptophan($20mg\;L^{-1}$) in 24 hours.
An, Song-Ji;Kwon, Jin-Kyung;Yang, Hee-Bum;Choi, Hye-Jeong;Jeong, Hee-Jin;Kim, Yong-Jae;Choi, Gyung-Ja;Kang, Byoung-Cheorl
Korean Journal of Breeding Science
/
v.42
no.4
/
pp.397-406
/
2010
Field screening method has been commonly used for purity test of $F_1$ hybrid seeds in melon and oriental melon. However, as this method takes a lot of time and cost, molecular marker-based purity test is necessary. To develop molecular markers for purity test, thirty pairs of SNP (single nucleotide polymorphism) primers were obtained from melon EST sequences, and 10 polymorphic markers showing HRM (high resolution melting) polymorphisms between parents of two melon cultivars and one oriental melon cultivar were selected. Blind tests were performed to validate usefulness of the selected markers for purity test. Blind test results showed that HRM genotypes were matched with the expected identity of individual sample, $F_1$ hybrid, male or female parents. Three HRM-based SNP markers were converted to CAPS markers for general use which is favor to breeders. We expect that SNP markers developed in this study will be useful for purity test of $F_1$ hybrid seeds in melon and oriental melon.
Ulleung Island is the top of an intraplate alkalic volcano rising 3200 m from sea floor in the East Sea (or Sea of Japan). The emergent 984.6 m consist of eruptive products of basaltic, trachytic and phonolitic magmas, which are divided into Dodong Basaltic Rocks, and Ulleung, Seonginbong and Nari groups. The Maljandeung Tuff in the Nari Group consists of thick pyroclastic sequences which are subdivided into 4 members (N-5, U-4, 3, 2), generating from explosive eruptions during past 18.8~5.6 ka B.P. From chemical data, the Member N-5, phonolitic in composition, is considerably enriched in incompatible elements and REE patterns with significant negative Eu anomalies. The members 4, 3 and 2 are phonolitic to tephriphonolitic in composition, and their REE patterns do not have significant Eu anomalies. In variation trend diagrams, many elements show abrupt compositional gaps between members, and gradual upward-mafic variations from phonolite to tephriphonolite within each member. It suggests a downward-mafic zonation that were evolved into phonolitic zone in the lower part to tephriphonolitic zone in upper part of magma chamber. It is supposed that the chemical stratification generated from multiple mechanisms of thermal gravidiffusion, crystal fractionation, and gradual melting and sequential emplacement. The stratified magmas were explosively erupted to generate a small caldera during short period (11 ka B.P.). Especially both members (U-3, 2) were accumulated by gradually erupting from the upper phonoltic zone to the lower tephriphonoltic zone of the stratified chamber in 8.4 ka B.P. and 5.6 ka B.P. time, respectively.
We purified an antimicrobial peptide from the acidified hemocyte extract of Mytilus coruscus by $C_{18}$ reversed-phase high-performance liquid chromatography (RP-HPLC). The peptide was 4041.866 Da based on matrix-assisted laser desorption ionization time-of-flight mass spectrophotometer (MALDI-TOF/MS) and the 25 amino acids of the N-terminus sequence were identified. Comparison of this sequence of the purified peptide with the N-terminus sequences of other antimicrobial peptides revealed 100% identity with the mytilin B precursor of Mytilus coruscus. We also identified a 312 bp open-reading frame (ORF) encoding 103 amino acids based on the obtained amino acid residues. The nucleotide sequence of this ORF and the amino acid sequence also revealed 100% identity with the mytilin B precursor of Mytilus coruscus. We synthesized two antimicrobial peptides with an alanine residue in the C-terminus, and designated them mytilin B1 and B2. These two antimicrobial peptides showed antimicrobial activity against gram-positive bacteria, including Bacillus cereus and Streptococcus parauberis (minimal effective concentration, MECs $41.6-89.7{\mu}g/ml$), gram-negative bacteria, including Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Providencia stuartii, Pseudomonas aeruginosa, and Vibrio ichthyoenteri (MECs $7.4-39.5{\mu}g/ml$), and the fungus Candida albicans (MECs $26.0-31.8{\mu}g/ml$). This antimicrobial activity was stable under heat and salt conditions. Furthermore, the peptides did not exhibit significant hemolytic activity or cytotoxic effects. These results suggest that mytilin B could be applied as alternative antibiotic agent, and they add to the understanding of the innate immunity of hard-shelled mussels.
The Bird Track Site in the Haman Formation in Yongsanri (Natural Monument No. 222) was reported on the named Koreanaornis hamanensis and Jindongornipes kimi sauropod footprint Brontopodus and ichnospecies Ochlichnus formed by Nematoda. This site has outstanding academic value because it is where the second-highest number of bird tracks have been reported in the world. However, only 25% of the site remains after being designated a natural monument in 1969. This is due to artificial damage caused by worldwide fame and quarrying for flat stone used in Korean floor heating systems. The Haman Formation, including this fossil site, has lithofacies showing reddish-grey siltstone and black shale, alternately. The boundary of the two rocks is progressive, and sedimentary structures like ripple marks and sun cracks can clearly be found. This site was divided into seven formations according to sedimentary sequences and structures. The results of a nondestructive deterioration evaluation showed that chemical and biological damage rates were very low for all formations. Also, physical damage displayed low rates with 0.49% on exfoliation, 0.04% on blistering, 0.28% on break-out; however, the joint crack index was high, 6.20. Additionally, efflorescence was observed on outcrops at the backside and the northwestern side. Physical properties measured by an indirect ultrasonic analysis were found to be moderately weathered (MW). Above all, the southeastern side was much fresher, though some areas around the column of protection facility appeared more weathered. Furthermore, five kinds of discontinuity surface can be found at this site, with the bedding plane showing the higher share. There is the possibility of toppling failure occurring at this site but stable on plane and wedge failure by means of stereographic projection. We concluded that the overall level of deterioration and stability were relatively fine. However, continuous monitoring and conservation treatment and management should be performed as situations such as the physicochemical weathering of the fossil layer, and the efflorescence of the mortar adjoining the protection facility's column appear to be challenging to control.
Watermelon (Citrullus lanatus) is an economically important vegetable crop all over the world, which has functional compounds such as lycopene and citrulline. Gummy stem blight caused by Didymella bryoniae is one of the most devastative diseases in watermelon. Single nucleotide polymorphisms (SNPs), which are genetic variations occurring between individuals with respect to a single base, were often used to construct genetic linkage maps and develop molecular markers linked to a variety of horticultural traits and resistance to several diseases. In this study, we developed high-resolution melting (HRM) markers based on SNPs generated from NGS resequencing of two parents in watermelon. Plant materials were C. lanatus '920533' (female and susceptible parent), C. amarus 'PI 189225' (male and resistant parent), and their $F_1$ and $F_2$ progenies. A total of 13.6 Gbp ('920533') and 13.1 Gbp ('PI 189225') of genomic sequences were obtained using NGS analysis. A total of 6.09 million SNPs between '920533' and 'PI 189225' were detected, and 354,860 SNPs were identified as potential HRM primer sets. From these, a total of 330 primer sets for HRM analysis were designed. As a result, a total of 61 HRM markers that have polymorphic melting curves were developed. These HRM markers can be used for the construction of SNP-based linkage maps and for the analysis of quantitative trait loci (QTLs) related to gummy stem blight resistance.
International trade is one of the primary ways that non-native species spread worldwide. Korea and China are geographically close and have a large mutual trade volume. To investigate the population movement of the invasive whitefly(Bemisia tabaci Gennadius) between the two countries, we compared the biotype distribution, insecticidal response, and the TYLCV(tomato yellow leaf curl virus) viruliferous rate of local populations collected in 2019. Based on the mitochondrial DNA COI sequences of B. tabaci, only the Q biotype was found in all populations in Korea, whereas the B biotype (14.3%) and Q biotype (85.7%) were found in China. In the haplotype composition of the B. tabaci Q biotype, only the Q1 group[Q1H1(79.8%) and Q1H2(20.2%)] was observed in China, but the Q1 group [Q1H1(1.7%) and Q1H2(97.5%)] and the Q2 group(only one individual) were found in Korea. The Korean populations showed high mortality(more than 80%) from 15 commercial insecticides, but the Chinese populations showed significantly low mortality from eight insecticides. No TYLCV infections were observed in the Korean populations while the average TYLCV viruliferous rate was 21.4% in the Chinese populations. Taken together, the results suggest that the population structures of B. tabaci in the two countries are different and may have different immigration histories.
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