Complete genome sequence of Citrobacter braakii ASE1 generated by PacBio sequencing.

We report the complete genome sequence of Citrobacter braakii ASE1 generated by the PacBio Sequel II platform. This bacterium was isolated from the soil of a lettuce farm in Salinas, CA, USA, in 2020. The genome consists of a single circular chromosome of 5,021,820 bp with a 52.2% GC content.

INSANet: INtra-INter Spectral Attention Network for Effective Feature Fusion of Multispectral Pedestrian Detection.

Pedestrian detection is a critical task for safety-critical systems, but detecting pedestrians is challenging in low-light and adverse weather conditions. Thermal images can be used to improve robustness by providing complementary information to RGB images. Previous studies have shown that multi-modal feature fusion using convolution operation can be effective, but such methods rely solely on local feature correlations, which can degrade the performance capabilities. To address this issue, we propose an attention-based novel fusion network, referred to as INSANet (INtra-INter Spectral Attention Network), that captures global intra- and inter-information. It consists of intra- and inter-spectral attention blocks that allow the model to learn mutual spectral relationships. Additionally, we identified an imbalance in the multispectral dataset caused by several factors and designed an augmentation strategy that mitigates concentrated distributions and enables the model to learn the diverse locations of pedestrians. Extensive experiments demonstrate the effectiveness of the proposed methods, which achieve state-of-the-art performance on the KAIST dataset and LLVIP dataset. Finally, we conduct a regional performance evaluation to demonstrate the effectiveness of our proposed network in various regions.

Identification of Terpene Compositions in the Leaves and Inflorescences of Hybrid Cannabis Species Using Headspace-Gas Chromatography/Mass Spectrometry.

Although cannabidiol and tetrahydrocannabinol in Cannabis species exert their pharmacological effects via the endocannabinoid system, it is believed that other phytochemicals, particularly terpenes, can modulate therapeutic outcomes through the entourage effect. Therefore, to gain a better understanding of the pharmacological effects of Cannabis, obtaining information on phytochemical compositions, including mono-, di-, and sesqui-terpenes in Cannabis species is essential. Applying a sophisticated analytical method is indispensable. In this study, headspace-gas chromatography/mass spectrometry (HS-GC/MS) was employed to identify major terpenes in the leaves and inflorescences of hybrid Cannabis species. The incubation time and temperature conditions for HS-GC/MS were optimized. This method was successfully applied to the leaves (n = 9) and inflorescences (n = 7) of hybrid Cannabis species. A total of 26 terpenes in Cannabis species were detected, and six major components, such as α-pinene (9.8-2270 µg/g), ß-pinene (2.6-930 µg/g), myrcene (0.7-17,400 µg/g), limonene (1.3-300 µg/g), ß-caryophyllene (60-3300 µg/g), and α-humulene (40-870 µg/g), were quantified. Each sample showed different terpene compositions, but six major terpenes among all the terpenes detected were consistently found in both the leaves and inflorescences of hybrid Cannabis species. In this study, the six major terpenes' potential in hybrid Cannabis species was evaluated as biomarkers to distinguish hybrid Cannabis species samples. This study contributes to a better understanding of the entourage effect of Cannabis-based botanical drugs.

Effective Interaction between Homo- and Heteropolymer Block of Poly(n-butyl acrylate)-b-poly(methyl methacrylate-r-styrene) Diblock Copolymers.

We investigated the segregation behavior of a molten diblock copolymer, poly(n-butyl acrylate)-b-poly(methyl methacrylate-r-styrene) (PBA-b-P(MMA-r-S)), wherein styrene (S) is incorporated as a comonomer in the second block to modulate the effective interaction between homopolymer and a random copolymer block. The temperature dependence of the effective interaction parameter χeff between n-butyl acrylate (BA) and the average monomer of the MMA-r-S random block was evaluated from small-angle X-ray scattering (SAXS) analysis using the random phase approximation (RPA) approach. The calculated χeff, as a function of the styrene fraction in the random copolymer block, shows a good agreement with the mean-field binary interaction model. This consistency indicates that the effective interaction between component BA and the average monomer of the random copolymer block is smaller than the interactions between pure components (χBA,MMA,χBA,S). The present study suggests that the introduction of a random copolymer block to a block copolymer can effectively reduce the degree of incompatibility of the block copolymer system without altering the constituent species, which may serve as a viable methodology in designing novel thermoplastic elastomers based on triblock or multiblock copolymers.

Chemical transformation of cannabidiol into psychotropic cannabinoids under acidic reaction conditions: Identification of transformed products by GC-MS.

Recently, cannabidiol (CBD), one of the major components of the Cannabis species, has been a focus in the cannabis industry due to its various pharmacological effects. Interestingly, CBD can be converted into several psychoactive cannabinoids, such as 9-tetrahydrocannabinol (Δ9-THC) and its structural isomers, under acidic reaction conditions. In this study, chemical transformation of CBD in ethanol solution was conducted with variation in pH at 2.0, 3.5, and 5.0 by addition of 0.1 M hydrochloric acid (HCl). These resulting solutions were derivatized with trimethylsilyl (TMS) reagent and analyzed using GC/MS-scan mode. Time profiles of CBD degradation and transformation of products were examined according to variations in pH and temperature. Several transformed products produced after the acidic reaction of CBD were identified by matching retention times and mass spectra to authentic standards. Regarding the identification of products without authentic standards, the EI-mass spectra of such cannabinoid-OTMS derivatives were interpreted according to structural class, suggesting mass fragmentation pathways. From the GC/MS data, Δ9-THC, CBC, and ethoxy-hexahydrocannabinol (HHC) analogs were shown to be major components, and THC isomers (Δ8- and Δ10-THCs) and 9-hydroxy-HHC were observed as minor components. Using time profile data, the acidity of the reaction solution was an important factor in degradation of CBD. Degradation of CBD and formation of THC rarely occurred at pH 5.0, even at 70 °C with a long process time of 24 h. In contrast, degradation of CBD occurred readily at pH 3.5 and 30 °C over a short process time and was further accelerated by lowering pH, increasing temperature, and lengthening the process time. Based on profile data and identified transformed products, formation pathways from the degradation of CBD under acidic reaction conditions are suggested. Among the transformed products, seven components are known to have psychoactive effects. Thus, industrial CBD manufacturing processes in food and cosmetic products should be carefully controlled. These results will provide important guidelines on the control of manufacturing processes, storage, fermentation processes, and new regulation in industrial applications of CBD.

Testing the bipolar assumption of Singer-Loomis Type Deployment Inventory for Korean adults using classification and multidimensional scaling.

In this study, we explored whether the Korean version of Singer Loomis Type Deployment Inventory II (K-SLTDI) captures the opposing tendencies of Jung's theory of psychological type. The types are Extroverted Sensing, Extroverted Intuition, Extroverted Feeling, Extroverted Thinking, Introverted Sensing, Introverted Intuition, Introverted Feeling, and Introverted Thinking. A nationwide online survey was conducted in South Korea. We performed multidimensional scaling and classification analyses based on 521 Korean adult profiles with eight psychological types to test the bipolarity assumption. The results showed that the Procrustes-rotated four-dimensional space successfully represented four types of opposing tendencies. Moreover, the bipolarity assumption in the four dimensions of Jungian typology was tested and compared between lower and higher psychological distress populations via cluster analysis. Lastly, we explored patterns of responses in lower and higher psychological distress populations using intersubject correlation. Both similarity analyses and classification results consistently support the theoretical considerations on the conceptualization of Jung's type in independent order that the types could be derived without bipolar assumption as Singer and Loomis expected in their Type Development Inventory. Limitations in our study include the sample being randomly selected internet users during the COVID-19 pandemic, despite excellence in the use of the internet in the general Korean population.

Small-Angle X-ray Scattering Analysis on the Estimation of Interaction Parameter of Poly(n-butyl acrylate)-b-poly(methyl methacrylate).

The temperature dependence of the Flory-Huggins interaction parameter χ for poly(n-butyl acrylate)-b-poly(methyl methacrylate) (PBA-b-PMMA) was quantified from small-angle X-ray scattering (SAXS) analysis using random phase approximation (RPA) theory. It was found from the χ estimation (χ=0.0103+14.76/T) that the enthalpic contribution, χH, a measure for temperature susceptibility of χ, is 1.7-4.5 folds smaller for PBA-b-PMMA than for the conventional styrene-diene-based block copolymers, which have been widely used for thermoplastic elastomers. This finding suggests that these fully acrylic components can be a desirable chemical pair for constituting terpolymers applied for thermally stable and mechanically resilient elastomers.

Consumption of Antioxidant-Rich "Cerrado" Cashew Pseudofruit Affects Hepatic Gene Expression in Obese C57BL/6J High Fat-Fed Mice.

The pseudofruit of A. othonianum Rizzini, "Cerrado" cashew pulp, has been described as rich in flavonoids, phenolic compounds, and vitamin C. The objective of this work was to evaluate the beneficial health effects seen with the addition of "Cerrado" cashew pulp (CP) to an obesogenic high fat diet provided to C57BL/6J male mice. In week 9, the HF-fed group had a significantly higher baseline glucose concentration than the LF- or HF+CP-fed groups. In RNAseq analysis, 4669 of 5520 genes were found to be differentially expressed. Among the genes most upregulated with the ingestion of the CP compared to HF were Ph1da1, SLc6a9, Clec4f, and Ica1 which are related to glucose homeostasis; Mt2 that may be involved steroid biosynthetic process; and Ciart which has a role in the regulation of circadian rhythm. Although "Cerrado" CP intake did not cause changes in the food intake or body weight of fed mice with HF diet, carbohydrate metabolism appeared to be improved based on the observed changes in gene expression.

Robust Three-Dimensional (3D) Expansion of Bovine Intestinal Organoids: An In Vitro Model as a Potential Alternative to an In Vivo System.

Intestinal organoids offer great promise for disease-modelling-based host-pathogen interactions and nutritional research for feed efficiency measurement in livestock and regenerative medicine for therapeutic purposes. However, very limited studies are available on the functional characterisation and three-dimensional (3D) expansion of adult stem cells in livestock species compared to other species. Intestinal crypts derived from intestinal organoids under a 3D culture system from the small intestine in adult bovine were successfully established and characterised for functionality testing, including the cellular potentials and genetic properties based on immunohistochemistry, immunocytochemistry, epithelial barrier permeability assay, QuantSeq 3' mRNA-Seq. data and quantitative reverse transcription-polymerase chain reaction. Intestinal organoids were long-term cultivated over several passages of culture without loss of the recapitulating capacity of crypts, and they had the specific expression of several specific markers involved in intestinal stem cells, intestinal epithelium, and nutrient absorption. In addition, they showed the key functionality with regard to a high permeability for compounds of up to FITC-dextran 4 kDa, while FITC-dextran 40 kDa failed to enter the organoid lumen and revealed that the genetic properties of bovine intestinal organoids were highly similar to those of in vivo. Collectively, these results provide a reliable method for efficient isolation of intestinal crypts from the small intestine and robust 3D expansion of intestinal organoids in adult bovine and demonstrate the in vitro 3D organoids mimics the in vivo tissue topology and functionality. Finally, intestinal organoids are potential alternatives to in vivo systems and will be facilitated as the practical model to replace animal experiments for various purposes in the fields of animal biotechnology.

DIGREM: an integrated web-based platform for detecting effective multi-drug combinations.

MOTIVATION: Synergistic drug combinations are a promising approach to achieve a desirable therapeutic effect in complex diseases through the multi-target mechanism. However, in vivo screening of all possible multi-drug combinations remains cost-prohibitive. An effective and robust computational model to predict drug synergy in silico will greatly facilitate this process. RESULTS: We developed DIGREM (Drug-Induced Genomic Response models for identification of Effective Multi-drug combinations), an online tool kit that can effectively predict drug synergy. DIGREM integrates DIGRE, IUPUI_CCBB, gene set-based and correlation-based models for users to predict synergistic drug combinations with dose-response information and drug-treated gene expression profiles. AVAILABILITY AND IMPLEMENTATION: http://lce.biohpc.swmed.edu/drugcombination. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A two-stage approach of gene network analysis for high-dimensional heterogeneous data.

Gaussian graphical models have been widely used to construct gene regulatory networks from gene expression data. Most existing methods for Gaussian graphical models are designed to model homogeneous data, assuming a single Gaussian distribution. In practice, however, data may consist of gene expression studies with unknown confounding factors, such as study cohort, microarray platforms, experimental batches, which produce heterogeneous data, and hence lead to false positive edges or low detection power in resulting network, due to those unknown factors. To overcome this problem and improve the performance in constructing gene networks, we propose a two-stage approach to construct a gene network from heterogeneous data. The first stage is to perform a clustering analysis in order to assign samples to a few clusters where the samples in each cluster are approximately homogeneous, and the second stage is to conduct an integrative analysis of networks from each cluster. In particular, we first apply a model-based clustering method using the singular value decomposition for high-dimensional data, and then integrate the networks from each cluster using the integrative $\psi$-learning method. The proposed method is based on an equivalent measure of partial correlation coefficients in Gaussian graphical models, which is computed with a reduced conditional set and thus it is useful for high-dimensional data. We compare the proposed two-stage learning approach with some existing methods in various simulation settings, and demonstrate the robustness of the proposed method. Finally, it is applied to integrate multiple gene expression studies of lung adenocarcinoma to identify potential therapeutic targets and treatment biomarkers.

Integrative Analysis of Gene Networks and Their Application to Lung Adenocarcinoma Studies.

The construction of gene regulatory networks (GRNs) is an essential component of biomedical research to determine disease mechanisms and identify treatment targets. Gaussian graphical models (GGMs) have been widely used for constructing GRNs by inferring conditional dependence among a set of gene expressions. In practice, GRNs obtained by the analysis of a single data set may not be reliable due to sample limitations. Therefore, it is important to integrate multiple data sets from comparable studies to improve the construction of a GRN. In this article, we introduce an equivalent measure of partial correlation coefficients in GGMs and then extend the method to construct a GRN by combining the equivalent measures from different sources. Furthermore, we develop a method for multiple data sets with a natural missing mechanism to accommodate the differences among different platforms in multiple sources of data. Simulation results show that this integrative analysis outperforms the standard methods and can detect hub genes in the true network. The proposed integrative method was applied to 12 lung adenocarcinoma data sets collected from different studies. The constructed network is consistent with the current biological knowledge and reveals new insights about lung adenocarcinoma.

Sparse estimation of gene-gene interactions in prediction models.

Current assessment of gene-gene interactions is typically based on separate parallel analysis, where each interaction term is tested separately, while less attention has been paid on simultaneous estimation of interaction terms in a prediction model. As the number of interaction terms grows fast, sparse estimation is desirable from statistical and interpretability reasons. There is a large literature on sparse estimation, but there is a natural hierarchy between the interaction and its corresponding main effects that requires special considerations. We describe random-effect models that impose sparse estimation of interactions under both strong and weak-hierarchy constraints. We develop an estimation procedure based on the hierarchical-likelihood argument and show that the modelling approach is equivalent to a penalty-based method, with the advantage of the models being more transparent and flexible. We compare the procedure with some standard methods in a simulation study and illustrate its application in an analysis of gene-gene interaction model to predict body-mass index.

The Transition from Thin Basement Membranes to Typical Alport Syndrome Morphology in Children.

Some children with thin basement membranes (TBM) turn out to have Alport syndrome (AS). In our population of 58 children initially diagnosed with TBM, three were eventually diagnosed with AS. As a group, these three were first biopsied at a younger age, and had gross rather than microscopic hematuria. Only one had lamellations initially. Seven others had some degree of basement membrane lamellations at initial biopsy, but none of these have developed other features of AS. We concluded that at least 5% of children initially demonstrating TBM go on to manifest the classical electron-microscopic findings of AS during childhood. Episodes of gross hematuria with TBM can be a significant clue of AS. Genetic and/or immunofluorescent studies for type IV collagen, and continued long-term follow-up should be done in all children with TBM.

Korean, Japanese, and Chinese populations featured similar genes encoding drug-metabolizing enzymes and transporters: a DMET Plus microarray assessment.

BACKGROUND: Interethnic differences in genetic polymorphism in genes encoding drug-metabolizing enzymes and transporters are one of the major factors that cause ethnic differences in drug response. This study aimed to investigate genetic polymorphisms in genes involved in drug metabolism, transport, and excretion among Korean, Japanese, and Chinese populations, the three major East Asian ethnic groups. METHODS: The frequencies of 1936 variants representing 225 genes encoding drug-metabolizing enzymes and transporters were determined from 786 healthy participants (448 Korean, 208 Japanese, and 130 Chinese) using the Affymetrix Drug-Metabolizing Enzymes and Transporters Plus microarray. To compare allele or genotype frequencies in the high-dimensional data among the three East Asian ethnic groups, multiple testing, principal component analysis (PCA), and regularized multinomial logit model through least absolute shrinkage and selection operator were used. RESULTS: On microarray analysis, 1071 of 1936 variants (>50% of markers) were found to be monomorphic. In a large number of genetic variants, the fixation index and Pearson's correlation coefficient of minor allele frequencies were less than 0.034 and greater than 0.95, respectively, among the three ethnic groups. PCA identified 47 genetic variants with multiple testing, but was unable to discriminate ethnic groups by the first three components. Multinomial least absolute shrinkage and selection operator analysis identified 269 genetic variants that showed different frequencies among the three ethnic groups. However, none of those variants distinguished between the three ethnic groups during subsequent PCA. CONCLUSION: Korean, Japanese, and Chinese populations are not pharmacogenetically distant from one another, at least with regard to drug disposition, metabolism, and elimination.

Sunlight-induced self-healing of a microcapsule-type protective coating.

Photopolymerization behavior of a methacryloxypropyl-terminated polydimethylsiloxane (MAT-PDMS) healing agent was investigated in the presence of benzoin isobutyl ether (BIE) photoinitiator by Fourier transform infrared (FT-IR) spectroscopy. MAT-PDMS and BIE were microencapsulated with urea-formaldehyde polymer. The surface and shell morphology of the microcapsules was investigated by scanning electron microscopy (SEM). Mean diameter and size distribution of the microcapsules could be controlled by agitation rate. A coating matrix formulation was prepared by sol-gel reaction of tetraethyl orthosilicate (TEOS) in the presence of a polysiloxane and by subsequent addition of an adhesion promoter. The formulation and microcapsules were mixed to give a self-healing coating formulation, which was then sprayed to surface of cellulose-fiber-reinforced-cement (CRC) board or mortar. Contact angle measurements showed that both the polymerized MAT-PDMS and the prepared coating matrix are hydrophobic, and the coating matrix has good wettability with MAT-PDMS. It was confirmed by optical microscopy and SEM that, when the self-healing coating is damaged, the healing agent is released from ruptured microcapsules and fills the damaged region. The self-healing coating was evaluated as protective coating for mortar, and it was demonstrated by water permeability and chloride ion penetration tests that our system has sunlight-induced self-healing capability. Our self-healing coating is the first example of capsule-type photoinduced self-healing system, and offers the advantages of catalyst-free, environmentally friendly, inexpensive, practical healing.

Effect of homopolymer molecular weight on order-order transition in block copolymer and homopolymer blends.

The order-order transition temperature (T(OOT)) in blends of poly(styrene-b-isoprene-b-styrene) (S-I-S) triblock copolymer and polyisoprene (PI) homopolymer was investigated by using synchrotron small-angle X-ray scattering (SAXS). Pure triblock copolymer undergoes an order-order transition (OOT) from hexagonally ordered cylinder (HEX) to body centered cubic (BCC) phases. In order to investigate the effect of the molecular weight of the added homopolymer on T(OOT) of the triblock copolymer, various low-molecular-weight PI homopolymers were studied. The results revealed that T(OOT) was affected by the PI molecular weight. T(OOT) was reduced for blends having low-molecular-weight PI.

Post-infectious irritable bowel syndrome in patients with Shigella infection.

BACKGROUND AND AIMS: Bacterial gastroenteritis has been known as a risk factor of irritable bowel syndrome (IBS). Several risk factors of post-infectious IBS (PI-IBS) have been documented. The aims of this study were to verify the role of bacterial gastroenteritis in the development of IBS and the risk factors for the development of PI-IBS. The clinical course of PI-IBS was also investigated. METHODS: We recruited 143 patients with shigellosis during its outbreak and 113 controls. Both groups were followed up for 12 months. Bowel symptoms were evaluated by use of questionnaires at 3, 6 and 12 months after the initial recruitment. RESULTS: Complete data were obtained from 101 patients (70.6%) and 102 healthy controls (90.3%). At 12 months, 15 patients and six controls had IBS (adjusted OR; 2.9, 95% CI; 1.1-7.9). Of the 15 patients, five had IBS symptoms consistently for 12 months, three did not have IBS symptoms initially and seven had fluctuating bowel symptoms. The duration of diarrhea was an independent risk factor of PI-IBS. CONCLUSIONS: Bacterial gastroenteritis is a risk factor of IBS and the duration of diarrhea as the index of severity of initial illness is an independent risk factor of PI-IBS. The clinical course of PI-IBS is variable over the 1 year of follow-up.

The diagnostic value of endoprobe for small esophageal leiomyomas derived from the muscularis mucosae.

Esophageal leiomyoma derived from the muscularis mucosae (MM) is a rare condition, and the optimal modality for diagnosis and treatment is controversial. Endoscopic ultrasonography can provide an accurate image of esophageal layer structure, providing information on lesion suitability for potential endoscopic therapy. We attempted to investigate the diagnostic value of a transendoscopic balloon-tipped miniature ultrasonic endoprobe for small esophageal leiomyomas derived from MM. We resected 7 small esophageal leiomyomas derived from MM by endoscopic mucosal resection (EMR), all of which were diagnosed by a balloon-tipped endoprobe. The endosonographic and pathologic features of 7 cases of small esophageal leiomyomas derived from MM were compared. The balloon-tipped endoprobe clearly showed all 7 small esophageal leiomyomas derived from MM, even those under 5 mm in size (smallest lesion, 3.0 mm). The endosonographic characteristics of small esophageal leiomyomas derived from MM were a hypoechoic mass with smooth, regular, and a well-defined outer margin and homogenous inner echogram arising from the second hypoechoic layer. Complete resections were possible in all 7 cases by EMR without any complications. Tumor size was 3.0-13.5 mm (mean 7.8 mm) in maximum diameter. In all cases, endosonographic findings by endoprobe were exactly concordant with pathologic finding in determining the tumors depth in the esophageal wall, tissue origin and characteristics, growth pattern, and size. We detail the balloon-tipped endoprobe is a simple, convenient, and very useful in making accurate diagnosis of small esophageal leiomyomas derived from the MM and the appropriate applications of EMR.