SUnSeT: spectral unmixing of hyperspectral images for phenotyping soybean seed traits.

KEY MESSAGE: Hyperspectral features enable accurate classification of soybean seeds using linear discriminant analysis and GWAS for novel seed trait genes. Evaluating crop seed traits such as size, shape, and color is crucial for assessing seed quality and improving agricultural productivity. The introduction of the SUnSet toolbox, which employs hyperspectral sensor-derived image analysis, addresses this necessity. In a validation test involving 420 seed accessions from the Korean Soybean Core Collections, the pixel purity index algorithm identified seed- specific hyperspectral endmembers to facilitate segmentation. Various metrics extracted from ventral and lateral side images facilitated the categorization of seeds into three size groups and four shape groups. Additionally, quantitative RGB triplets representing seven seed coat colors, averaged reflectance spectra, and pigment indices were acquired. Machine learning models, trained on a dataset comprising 420 accession seeds and 199 predictors encompassing seed size, shape, and reflectance spectra, achieved accuracy rates of 95.8% for linear discriminant analysis model. Furthermore, a genome-wide association study utilizing hyperspectral features uncovered associations between seed traits and genes governing seed pigmentation and shapes. This comprehensive approach underscores the effectiveness of SUnSet in advancing precision agriculture through meticulous seed trait analysis.

Clinical features of COVID-19 among patients with end-stage renal disease on hemodialysis in the context of high vaccination coverage during the omicron surge period: a retrospective cohort study.

BACKGROUND: We determined the clinical presentation and outcomes of the Omicron variant of severe acute respiratory syndrome coronavirus 2 infection in hemodialysis patients and identified the risk factors for severe coronavirus disease (COVID-19) and mortality in the context of high vaccination coverage. METHODS: This was a retrospective cohort study involving hemodialysis patients who were vaccinated against COVID-19 during March-September 2022, when the Omicron variant was predominant, and the COVID-19 vaccination rate was high. The proportion of people with severe COVID-19 or mortality was evaluated using univariate logistic regression. RESULTS: Eighty-three (78.3%) patients had asymptomatic/mild symptoms, 10 (9.4%) had moderate symptoms, and 13 (12.3%) had severe symptoms. Six (5.7%) patients required intensive care admission, two (1.9%) required mechanical ventilation, and one (0.9%) was kept on high-flow nasal cannula. Of the five (4.7%) mortality cases, one was directly attributed to COVID-19 and four to pre-existing comorbidities. Risk factors for both severe COVID-19 and mortality were advanced age; number of comorbidities; cardiovascular diseases; increased levels of aspartate transaminase, lactate dehydrogenase, blood urea nitrogen/creatinine ratio, brain natriuretic peptide, and red cell distribution; and decreased levels of hematocrit and albumin. Moreover, the number of COVID-19 vaccinations wasa protective factor against both severe disease and mortality. CONCLUSIONS: Clinical features of hemodialysis patients during the Omicron surge with high COVID-19 vaccination coverage were significant for low mortality. The risk features for severe COVID-19 or mortality were similar to those in the pre-Omicron period in the context of low vaccination coverage.

Comparison for immunophysiological responses of Jeju and Thoroughbred horses after exercise.

OBJECTIVE: The study was conducted to investigate variations in the immunophysiological responses to exercise-induced stress in Jeju and Thoroughbred horses. METHODS: Blood samples were collected from the jugular veins of adult Jeju (n = 5) and Thoroughbred (n = 5) horses before and after 30 min of exercise. The hematological, biochemical, and immunological profiles of the blood samples were analyzed. Blood smears were stained and observed under a microscope. The concentration of cell-free (cf) DNA in the plasma was determined using real time polymerase chain reaction (PCR). Peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells were separated using Polymorphprep, and the expression of various stress-related and chemokine receptor genes was measured using reverse transcriptase (RT) and real-time PCR. RESULTS: After exercise, Jeju and Thoroughbred horses displayed stress responses with significantly increased rectal temperatures, cortisol levels, and muscle catabolism-associated metabolites. Red blood cell indices were significantly higher in Thoroughbred horses than in Jeju horses after exercise. In addition, exercise-induced stress triggered the formation of neutrophil extracellular traps (NETs) and reduced platelet counts in Jeju horses but not in Thoroughbred horses. Heat shock protein 72 and heat shock protein family A (Hsp70) member 6 expression is rapidly modulated in response to exercise-induced stress in the PBMCs of Jeju horses. The expression of CXC chemokine receptor 4 in PBMCs was higher in Thoroughbred horses than in Jeju horses after exercise. CONCLUSION: In summary, the different immunophysiological responses of Jeju and Thoroughbred horses explain the differences in the physiological and anatomical properties of the two breeds. The physiology of Thoroughbred horses makes them suitable for racing as they are less sensitive to exercise-induced stress compared to that of Jeju horses. This study provides a basis for investigating the link between exercise-induced stresses and the physiological alteration of horses. Hence, our findings show that some of assessed parameters could be used to determine the endurance performance of horses.

Effects of mushroom extract on textural properties and muscle protein degradation of bovine longissimus dorsi muscle.

We investigated the effects of Sarcodon aspratus, Agaricus bisporus, and Lentinula edodes aqueous extracts on the tenderization of bovine longissimus dorsi muscle. Meat quality and muscle protein degradation were examined as well. Beef chunks were marinated in distilled water (control), 5% S. aspratus (SA), 5% A. bisporus (AB), or 5% L. edodes (LE) extracts. SA was shown to have a higher enzymatic activity (p < 0.001) and water-holding capacity than LE (p < 0.01). SA and AB extracts exhibited lower shear force values compared with the control (p < 0.05). SA, AB, and LE showed superior muscle proteolytic effects compared with the control. SA demonstrated the ability to degrade myosin heavy chains and actin, which was not observed after AB and LE extract treatments. This suggests that SA extract may affect tenderization. Taken together, our results show that aqueous extract of S. aspratus affects the tenderness of the bovine longissimus dorsi muscle.

Cylindrical posts of Ag/SiO2/Au multi-segment layer patterns for highly efficient surface enhanced Raman scattering.

We fabricated a regular array of Ag/SiO2/Au multi-segment cylindrical nanopatterns to create a highly efficient surface enhanced Raman scattering (SERS) active substrate using an advanced soft-nanoimprint lithographic technique. The SERS spectra results for Rhodamine 6G (R6G) molecules on the Ag/SiO2/Au multi-segment nanopatterns show that the highly ordered patterns and interlayer thickness are responsible for enhancing the sensitivity and reproducibility, respectively, The multi-segment nanopattern with a silica interlayer generates significant SERS enhancement (~EF = 1.2 x 106) as compared to that of the bimetallic (Ag/Au) nanopatterns without a dielectric gap (~EF = 1.0 x 104). Further precise control of the interlayer distances between the two metals plays an essential role in enhancing SERS performance for detecting low concentrations of analytes such as fluorescent (Rhodamine 6G) and DNA molecules. Therefore, the highly ordered multi-segment patterns provide great sensitivity and reproducibility of SERS based detection, resulting in a high performance of the SERS substrate.

Comparative metabolomic analysis in horses and functional analysis of branched chain (alpha) keto acid dehydrogenase complex in equine myoblasts under exercise stress.

The integration of metabolomics and transcriptomics may elucidate the correlation between the genotypic and phenotypic patterns in organisms. In equine physiology, various metabolite levels vary during exercise, which may be correlated with a modified gene expression pattern of related genes. Integrated metabolomic and transcriptomic studies in horses have not been conducted to date. The objective of this study was to detect the effect of moderate exercise on the metabolomic and transcriptomic levels in horses. In this study, using nuclear magnetic resonance (NMR) spectroscopy, we analyzed the concentrations of metabolites in muscle and plasma; we also determined the gene expression patterns of branched chain (alpha) keto acid dehydrogenase kinase complex (BCKDK), which encodes the key regulatory enzymes in branched-chain amino acid (BCAA) catabolism, in two breeds of horses, Thoroughbred and Jeju, at different time intervals. The concentrations of metabolites in muscle and plasma were measured by 1H NMR (nuclear magnetic resonance) spectroscopy, and the relative metabolite levels before and after exercise in the two samples were compared. Subsequently, multivariate data analysis based on the metabolic profiles was performed using orthogonal partial least square discriminant analysis (OPLS-DA), and variable important plots and t-test were used for basic statistical analysis. The stress-induced expression patterns of BCKDK genes in horse muscle-derived cells were examined using quantitative reverse transcription polymerase chain reaction (qPCR) to gain insight into the role of transcript in response to exercise stress. In this study, we found higher concentrations of aspartate, leucine, isoleucine, and lysine in the skeletal muscle of Jeju horses than in Thoroughbred horses. In plasma, compared with Jeju horses, Thoroughbred horses had higher levels of alanine and methionine before exercise; whereas post-exercise, lysine levels were increased. Gene expression analysis revealed a decreased expression level of BCKDK in the post-exercise period in Thoroughbred horses.

New top-down approach for fabricating high-aspect-ratio complex nanostructures with 10 nm scale features.

We describe a new patterning technique, named "secondary sputtering lithography" that enables fabrication of ultrahigh-resolution (ca. 10 nm) and high aspect ratio (ca. 15) patterns of three-dimensional various shapes. In this methodology, target materials are etched and deposited onto the side surface of a prepatterned polymer by using low Ar ion bombarding energies, based on the angular distribution of target particles by ion-beam bombardment. After removal of the prepatterned polymer, high aspect ratios and high-resolution patterns of target materials are created.

Effect of methylsulfonylmethane on oxidative stress and CYP3A93 expression in fetal horse liver cells.

OBJECTIVE: Stress-induced cytotoxicity caused by xenobiotics and endogenous metabolites induces the production of reactive oxygen species and often results in damage to cellular components such as DNA, proteins, and lipids. The cytochrome P450 (CYP) family of enzymes are most abundant in hepatocytes, where they play key roles in regulating cellular stress responses. We aimed to determine the effects of the antioxidant compound, methylsulfonylmethane (MSM), on oxidative stress response, and study the cytochrome P450 family 3 subfamily A (CYP3A) gene expression in fetal horse hepatocytes. METHODS: The expression of hepatocyte markers and CYP3A family genes (CYP3A89, CYP3A93, CYP3A94, CYP3A95, CYP3A96, and CYP3A97) were assessed in different organ tissues of the horse and fetal horse liver-derived cells (FHLCs) using quantitative reverse transcription polymerase chain reaction. To elucidate the antioxidant effects of MSM on FHLCs, cell viability, levels of oxidative markers, and gene expression of CYP3A were investigated in H2O2-induced oxidative stress in the presence and absence of MSM. RESULTS: FHLCs exhibited features of liver cells and simultaneously maintained the typical genetic characteristics of normal liver tissue; however, the expression profiles of some liver markers and CYP3A genes, except that of CYP3A93, were different. The expression of CYP3A93 specifically increased after the addition of H2O2 to the culture medium. MSM treatment reduced oxidative stress as well as the expression of CYP3A93 and heme oxygenase 1, an oxidative marker in FHLCs. CONCLUSION: MSM could reduce oxidative stress and hepatotoxicity in FHLCs by altering CYP3A93 expression and related signaling pathways.

Crack-Assisted Charge Injection into Solvent-Free Liquid Organic Semiconductors via Local Electric Field Enhancement.

Non-volatile liquid organic semiconducting materials have received much attention as emerging functional materials for organic electronic and optoelectronic devices due to their remarkable advantages. However, charge injection and transport processes are significantly impeded at interfaces between electrodes and liquid organic semiconductors, resulting in overall lower performance compared to conventional solid-state electronic devices. Here we successfully demonstrate efficient charge injection into solvent-free liquid organic semiconductors via cracked metal structures with a large number of edges leading to local electric field enhancement. For this work, thin metal films on deformable polymer substrates were mechanically stretched to generate cracks on the metal surfaces in a controlled manner, and charge injection properties into a typical non-volatile liquid organic semiconducting material, (9-2-ethylhexyl)carbazole (EHCz), were investigated in low bias region (i.e., ohmic current region). It was found that the cracked structures significantly increased the current density at a fixed external bias voltage via the local electric field enhancement, which was strongly supported by field intensity calculation using COMSOL Multiphysics software. We anticipate that these results will significantly contribute to the development and further refinement of various organic electronic and optoelectronic devices based on non-volatile liquid organic semiconducting materials.

The Role of Layer-Controlled Graphene for Tunable Microwave Heating and Its Applications to the Synthesis of Inorganic Thin Films.

In this paper, we present the first method for precisely controlling the heat generated by microwave heating by tuning the number of graphene layers grown by chemical vapor deposition. The conductivity of the graphene increases linearly with the number of graphene layers, indicating that Joule heating plays a primary role in the temperature control of the graphene layer. In this method, we successfully synthesize TiO2 and MoS2 thin films, which do not interact well with microwaves, on a layer-controlled graphene substrate for a very short time (3 min) through microwave heating.

Complete magnesiothermic reduction reaction of vertically aligned mesoporous silica channels to form pure silicon nanoparticles.

Owing to its simplicity and low temperature conditions, magnesiothermic reduction of silica is one of the most powerful methods for producing silicon nanostructures. However, incomplete reduction takes place in this process leaving unconverted silica under the silicon layer. This phenomenon limits the use of this method for the rational design of silicon structures. In this effort, a technique that enables complete magnesiothermic reduction of silica to form silicon has been developed. The procedure involves magnesium promoted reduction of vertically oriented mesoporous silica channels on reduced graphene oxides (rGO) sheets. The mesopores play a significant role in effectively enabling magnesium gas to interact with silica through a large number of reaction sites. Utilizing this approach, highly uniform, ca. 10 nm sized silicon nanoparticles are generated without contamination by unreacted silica. The new method for complete magnesiothermic reduction of mesoporous silica approach provides a foundation for the rational design of silicon structures.

Fabrication of sub-20 nm nano-gap structures through the elastomeric nano-stamp assisted secondary sputtering phenomenon.

We describe a highly efficient method for fabricating controllable and reliable sub-20 nm scale nano-gap structures through an elastomeric nano-stamp with an embedded ultra-thin pattern. The stamp consists of ultrahigh resolution (approximately 10 nm) and high aspect ratio (ca. 15) metal nano-structures, which are obtained by secondary sputtering lithography (SSL). The nano-gap structures fabricated in this fashion achieve a high resolution and meet the requirements of minimal cost, high reliability, controllability, reproducibility, and applicability to different materials. Further, we demonstrate that this method enables the fabrication of SERS substrates for detection at the single-molecule level.

High quality reduced graphene oxide through repairing with multi-layered graphene ball nanostructures.

We present a simple and up-scalable method to produce highly repaired graphene oxide with a large surface area, by introducing spherical multi-layered graphene balls with empty interiors. These graphene balls are prepared via chemical vapor deposition (CVD) of Ni particles on the surface of the graphene oxides (GO). Transmission electron microscopy and Raman spectroscopy results reveal that defects in the GO surfaces are well repaired during the CVD process, with the help of nickel nanoparticles attached to the functional groups of the GO surface, further resulting in a high electrical conductivity of 18,620 S/m. In addition, the graphene balls on the GO surface effectively prevent restacking of the GO layers, thus providing a large surface area of 527 m(2)/g. Two electrode supercapacitor cells using this highly conductive graphene material demonstrate ideal electrical double layer capacitive behavior, due to the effective use of the outstanding electric conductivity and the large surface area.

Analyzing solution-phase time-resolved x-ray diffraction data by isolated-solute models.

Extracting transient structural information of a solute from time-resolved x-ray diffraction (TRXD) data is not trivial because the signal from a solution contains not only the solute-only term as in the gas phase, but also solvent-related terms. To obtain structural insights, the diffraction signal in q space is often Fourier sine transformed (FT) into r space, and molecular dynamics (MD) simulation-aided signal decomposition into the solute, cage, and solvent terms has so far been indispensable for a clear-cut assignment of structural features. Here we present a convenient method of comparative structural analysis without involving MD simulations by incorporating only isolated-species models for the solute. FT is applied to both the experimental data and candidate isolated-solute models, and comparison of the correlation factors between the experimental FT and the model FTs can distinguish the best candidate among isolated-solute models for the reaction intermediates. The low q region whose influence by solvent-related terms is relatively high can be further excluded, and this mode of truncated Fourier transform (TFT) improves the correlation factors and facilitates the comparison. TFT analysis has been applied to TRXD data on the photodissociation of C(2)H(4)I(2) in two different solvents (methanol and cyclohexane), HgI(2) in methanol, and I(3) (-) in methanol excited at 267 nm. The results are consistent with previous conclusions for C(2)H(4)I(2) in methanol and HgI(2) in methanol, and the new TRXD data reveal that the C(2)H(4)I transient radical has a bridged structure in cyclohexane and I(3) (-) in methanol decomposes into I+I(2) (-) upon irradiation at 267 nm. This TFT method should greatly simplify the analysis because it bypasses MD simulations.