Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure.

Background: The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and significant computational challenges. As the cost of next-generation sequencing (NGS) has decreased, the amount of genomic data has surged globally. However, the cost and complexity of the computational resources required continue to be substantial barriers to leveraging big data.

Absorption Distribution Metabolism Excretion and Toxicity Property Prediction Utilizing a Pre-Trained Natural Language Processing Model and Its Applications in Early-Stage Drug Development.

Machine learning techniques are extensively employed in drug discovery, with a significant focus on developing QSAR models that interpret the structural information of potential drugs. In this study, the pre-trained natural language processing (NLP) model, ChemBERTa, was utilized in the drug discovery process. We proposed and evaluated four core model architectures as follows: deep neural network (DNN), encoder, concatenation (concat), and pipe.

A genome-wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach.

Chicken plumage colouration is an important trait related to productivity in poultry industry. Therefore, the genetic basis for pigmentation in chicken plumage is an area of great interest. However, the colour trait is generally regarded as a qualitative trait and representing colour variations is difficult.

Single nucleotide polymorphism marker combinations for classifying Yeonsan Ogye chicken using a machine learning approach.

Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken () breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks.

Use of a graph neural network to the weighted gene co-expression network analysis of Korean native cattle.

In the general framework of the weighted gene co-expression network analysis (WGCNA), a hierarchical clustering algorithm is commonly used to module definition. However, hierarchical clustering depends strongly on the topological overlap measure. In other words, this algorithm may assign two genes with low topological overlap to different modules even though their expression patterns are similar.

MSENet: Marbling score estimation network for automated assessment of Korean beef.

A novel beef marbling score estimation algorithm is proposed in this work. We develop a marbling score estimation network (MSENet), which simultaneously performs marbling score estimation and eye muscle area segmentation. The proposed MSENet includes a segmentation module, a bridge block, and a marbling scoring module.

Automated Classification of Normal Control and Early-Stage Dementia Based on Activities of Daily Living (ADL) Data Acquired from Smart Home Environment.

With the global trend toward an aging population, the increasing number of dementia patients and elderly living alone has emerged as a serious social issue in South Korea. The assessment of activities of daily living (ADL) is essential for diagnosing dementia. However, since the assessment is based on the ADL questionnaire, it relies on subjective judgment and lacks objectivity.

The structural and magnetic properties of BaFeO nanoparticles: effect of residual sodium ions.

We studied the structural and magnetic properties of BaFeO (BaM) nanoparticles synthesized by a co-precipitation route based on a modified citrate process. The lattice contraction of co-precipitated BaM nanoparticles is detected after prolonged sintering at 900 °C. In addition, investigation with X-ray photoelectron spectroscopy (XPS) provides evidence of a highly enhanced population of oxygen vacancies.

Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs.

A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array.

Enhanced Crystallinity and Luminescence Characteristics of Hexagonal Boron Nitride Doped with Cerium Ions According to Tempering Temperatures.

Hexagonal boron nitride was synthesized by pyrolysis using boric acid and melamine. At this time, to impart luminescence, rare earth cerium ions were added to synthesize hexagonal boron nitride nanophosphor particles exhibiting deep blue emission. To investigate the changes in crystallinity and luminescence according to the re-heating temperature, samples which had been subjected to pyrolysis at 900 °C were subjected to re-heating from 1100 °C to 1400 °C.

Hybrid Nanoparticle Layers Toward Enhanced Luminescence of Phosphor Plates for White LEDs.

MgF porous nanoparticle-silica hybrid coating layers were utilized to enhance luminescence efficiency of phosphor plates for white light-emitting diodes (wLEDs). Silica and chemically synthesized porous MgF nanoparticles were sequentially deposited by spin coating on the phosphor plate with phosphor-in-glass (PiG) configuration. Microscopic investigation the hybrid film suggested intermixing of silica and porous MgF nanoparticles.

High-Energy, Short-Duration Bursts of Coherent Terahertz Radiation from an Embedded Plasma Dipole.

Emission of radiation from electrons undergoing plasma oscillations (POs) at the plasma frequency has attracted interest because of the existence of intriguing and non-trivial coupling mechanism between the electrostatic PO and the emitted electromagnetic wave. While broadband emission from plasma waves in inhomogeneous plasma is well known, the underlying physics of narrowband emission at the plasma frequency observed in experiments and in solar radio-bursts is obscure. Here we show that a spatially-localized plasma dipole oscillation (PDO) can be generated when electrons are trapped in a moving train of potential wells produced by the ponderomotive force of two slightly detuned laser pulses that collide in plasma and give rise to a burst of quasi-monochromatic radiation.

Safflower bud inhibits RANKL-induced osteoclast differentiation and prevents bone loss in ovariectomized mice.

Background: The powder and extract of safflower seeds are known to be effective in the prevention of bone loss in ovariectomized animals. However, the inhibitory effect and molecular mechanisms of safflower bud (SB), the germinated safflower, on bone destruction is unclear.

Purpose: The present study was designed to investigate the inhibitory effect and molecular mechanism of SB on osteoclastic differentiation and on bone loss in ovarietomized (OVX) mice.

Effects of laser polarizations on shock generation and shock ion acceleration in overdense plasmas.

The effects of laser-pulse polarization on the generation of an electrostatic shock in an overdense plasma were investigated using particle-in-cell simulations. We found, from one-dimensional simulations, that total and average energies of reflected ions from a circular polarization- (CP) driven shock front are a few times higher than those from a linear polarization- (LP) driven one for a given pulse energy. Moreover, it was discovered that the pulse transmittance is the single dominant factor for determining the CP-shock formation, while the LP shock is affected by the plasma scale length as well as the transmittance.

Shock ion acceleration by an ultrashort circularly polarized laser pulse via relativistic transparency in an exploded target.

We investigated ion acceleration by an electrostatic shock in an exploded target irradiated by an ultrashort, circularly polarized laser pulse by means of one- and three-dimensional particle-in-cell simulations. We discovered that the laser field penetrating via relativistic transparency (RT) rapidly heated the upstream electron plasma to enable the formation of a high-speed electrostatic shock. Owing to the RT-based rapid heating and the fast compression of the initial density spike by a circularly polarized pulse, a new regime of the shock ion acceleration driven by an ultrashort (20-40 fs), moderately intense (1-1.

Applying dynamic priority scheduling scheme to static systems of pinwheel task model in power-aware scheduling.

Power-aware scheduling reduces CPU energy consumption in hard real-time systems through dynamic voltage scaling (DVS). In this paper, we deal with pinwheel task model which is known as static and predictable task model and could be applied to various embedded or ubiquitous systems. In pinwheel task model, each task's priority is static and its execution sequence could be predetermined.

Amine-based polar solvent treatment for highly efficient inverted polymer solar cells.

The interfacial dipolar polarization in inverted structure polymer solar cells, which arises spontaneously from the absorption of ethanolamine end groups, such as amine and hydroxyl groups on ripple-structure zinc oxide (ZnO-R), lowers the contact barrier for electron transport and extraction and leads to enhanced electron mobility, suppression of bimolecular recombination, reduction of the contact resistance and series resistance, and remarkable enhancement of the power conversion efficiency.

Bulk synthesis of ordered macroporous silica particles for superhydrophobic coatings.

We report the bulk synthesis of ordered macroporous ceramic particles by the emulsion templating process. Large polystyrene (PS) beads and small silica nanoparticles were assembled simultaneously inside an emulsion, which formed composite structured particles during the evaporation of droplets. Then, by burning out PS beads, macroporous ceramic particle films were produced on substrate.

Enhanced luminescence of Cu-In-S nanocrystals by surface modification.

We have synthesized highly luminescent Cu-In-S nanocrystals by heating the mixture of metal carboxylates and alkylthiol under inert atmosphere. We modified the surface of CIS nanocrystals with zinc carboxylate and subsequent injection of alkylthiol. As a result of the surface modification, highly luminescent CIS@ZnS core/shell nanocrystals were synthesized.

Tailoring the morphology of CdSe nanocrystals by incorporation of Pb.

We have investigated the effects of Pb2+ addition on the morphological development of CdSe nanocrystals. We show that the addition of Pb ions in the initial precursor solution changed the morphology of CdSe nanocrystals to branched rods with high aspect ratio. The branched nanocrystals are mainly composed of wurzite phase grown along the [001] direction and the length of rods in each branched nanocrystal can be increased by increasing the amount of Pb2+ addition to accelerate the anisotropic growth of the nanocrystals.