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Abstract Background The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. Results We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. Conclusions CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .

Measurement(s) Metabolite Technology Type(s) 1H nuclear magnetic resonance spectroscopy Factor Type(s) Age • Breeds • Sex • ER status • HER2 status • Histological grade • Neutral status Sample Characteristic - Organism Canis lupus familiaris

Comparison of spontaneous canine cancers and human cancers may illuminate future therapeutic avenues. Here, genomic analyses of these tumors highlights a convergence on PI3K-Akt oncogenic pathways.

Li-doped CuSCN films of various compositions were applied as hole-transporting material (HTM) for mesoscopic perovskite solar cells (PSCs). Those films of ~60 nm thickness, spin-coated on the perovskite layer, exhibit significantly higher crystallinity and hole mobility compared with the pristine CuSCN films. Among them, 0.33% Li-doped CuSCN (Li0.33:CuSCN) shows the best performance as the HTM of mesoscopic PSC. Furthermore, by depositing a slight amount of PCPDTBT over the Li0.33:CuSCN layer, the VOC was increased to 1.075 V, resulting in an average PCE of 20.24% and 20.65% for the champion device. These PCE and VOC values are comparable to those of PSC using spiro-OMETAD (PCE: 20.61%, VOC: 1.089 V). Such a remarkable increase can be attributed to the penetration of the PCPDTBT polymer into the grain boundaries of the Li0.33:CuSCN film, and to the interface with the perovskite layer, leading to the removal of defects on the perovskite surface by paving the non-contacting parts, as well as to the tight interconnection of the Li0.33:CuSCN grains. The PSC device with Li0.33:CuSCN showed a high long-term stability similar to that with bare CuSCN, and the introduction of PCPDTBT onto the perovskite/Li0.33:CuSCN further improved device stability, exhibiting 94% of the initial PCE after 100 days.

Short DNA oligonucleotides (~4 mer) have been used to index samples from different sources, such as in multiplex sequencing. Presently, longer oligonucleotides (8-12 mer) are being used as molecular barcodes with which to distinguish among raw DNA molecules in many high-tech sequence analyses, including low-frequent mutation detection, quantitative transcriptome analysis, and single-cell sequencing. Despite some advantages of using molecular barcodes with random sequences, such an approach, however, makes it impossible to know the exact sequences used in an experiment and can lead to inaccurate interpretation due to misclustering of barcodes arising from the occurrence of unexpected mutations in the barcodes. The present study introduces a tool developed for selecting an optimal barcode subset during molecular barcoding. The program considers five barcode factors: GC content, homopolymers, simple sequence repeats with repeated units of dinucleotides, Hamming distance, and complementarity between barcodes. To evaluate a selected barcode set, penalty scores for the factors are defined based on their distributions observed in random barcodes. The algorithm employed in the program comprises two steps: i) random generation of an initial set and ii) optimal barcode selection via iterative replacement. Users can execute the program by inputting barcode length and the number of barcodes to be generated. Furthermore, the program accepts a user's own values for other parameters, including penalty scores, for advanced use, allowing it to be applied in various conditions. In many test runs to obtain 100000 barcodes with lengths of 12 nucleotides, the program showed fast performance, efficient enough to generate optimal barcode sequences with merely the use of a desktop PC. We also showed that VFOS has comparable performance, flexibility in program running, consideration of simple sequence repeats, and fast computation time in comparison with other two tools (DNABarcodes and FreeBarcodes). Owing to the versatility and fast performance of the program, we expect that many researchers will opt to apply it for selecting optimal barcode sets during their experiments, including next-generation sequencing.

Abstract Background Aberrant mutations in KRAS play a critical role in tumor initiation and progression, and are a negative prognosis factor in lung adenocarcinoma (LUAD). Results Using genomic analysis for K-Ras isoforms (K-Ras4A and K-Ras4B) and large-scale multi-omics data, we inspected the overall survival (OS) and disease-free survival (DFS) of LUAD patients based on the abundance of transcript variants by analyzing RNA expression and somatic mutation data from The Cancer Genome Atlas (n = 516). The expression of the minor transcript K-Ras4A and its proportion were positively correlated with the presence of KRAS mutations in LUAD. We found that both K-Ras4A abundance measures (expression and proportion) have a strong association with poor OS (p = 0.0149 and p = 3.18E-3, respectively) and DFS (p = 3.03E-4 and p = 0.0237, respectively), but only in patients harboring KRAS mutations. A Cox regression analysis showed significant results in groups with low expression (hazard ratio (HR) = 2.533, 95% confidence interval (CI) = 1.380−4.651, p = 2.72E-3) and low proportion (HR = 2.549, 95% CI = 1.387−4.684, p = 2.58E-3) of K-Ras4A. Conclusions Based on the above results, we report the possible use of abundance measures for K-Ras4A for predicting the survival of LUAD patients with KRAS mutations.

Abstract In the present study, a dual-functional smart film combining the effects of wavelength conversion and amplification of the converted wave by the localized surface plasmon resonance has been investigated for a perovskite solar cell. This dual-functional film, composed of Au nanoparticles coated on the surface of Y2O3:Eu3+ phosphor (Au@Y2O3:Eu3+) nanoparticle monolayer, enhances the solar energy conversion efficiency to electrical energy and long-term stability of photovoltaic cells. Coupling between the Y2O3:Eu3+ phosphor monolayer and ultraviolet solar light induces the latter to be converted into visible light with a quantum yield above 80%. Concurrently, the Au nanoparticle monolayer on the phosphor nanoparticle monolayer amplifies the converted visible light by up to 170%. This synergy leads to an increased solar light energy conversion efficiency of perovskite solar cells. Simultaneously, the dual-function film suppresses the photodegradation of perovskite by UV light, resulting in long-term stability. Introducing the hybrid smart Au@Y2O3:Eu3+ film in perovskite solar cells increases their overall solar-to-electrical energy conversion efficiency to 16.1% and enhances long-term stability, as compared to the value of 15.2% for standard perovskite solar cells. The synergism between the wavelength conversion effect of the phosphor nanoparticle monolayer and the wave amplification by the localized surface plasmon resonance of the Au nanoparticle monolayer in a perovskite solar cell is comparatively investigated, providing a viable strategy of broadening the solar spectrum utilization.

Abstract In four dimensions, ’t Hooft symbols offer a compact and powerful framework for describing the self-dual structures fundamental to instanton physics. Extending this to six dimensions, the six-dimensional ’t Hooft symbols can be constructed using the isomorphism between the Lorentz group Spin(6) and the unitary group SU(4). We demonstrate that the six-dimensional self-dual structures governed by the Hermitian Yang-Mills equations can be elegantly organized using these generalized ’t Hooft symbols. We also present a systematic method for constructing Hermitian Yang-Mills instantons from spin connections on six-dimensional manifolds using the generalized ’t Hooft symbols. We provide a thorough analysis of the topological invariants such as instanton and Euler numbers.

Volumetric muscle loss (VML) frequently results from traumatic incidents and can lead to severe functional disabilities. Hydrogels have been widely employed for VML tissue regeneration, which are unfortunately ineffective because of the lack of intimate contact with injured tissue for structural and mechanical support. Adhesive hydrogels allow for strong tissue connections for wound closure. Nevertheless, conventional adhesive hydrogels exhibit poor tissue adhesion in moist, bleeding wounds due to the hydration layer at the tissue–hydrogel interfaces, resulting in insufficient performance. In this study, we developed a novel, biocompatible, wet tissue adhesive powder hydrogel consisting of dextran-aldehyde (dex-ald) and gelatin for the regeneration of VML. This powder absorbs the interfacial tissue fluid and buffer solution on the tissue, spontaneously forms a hydrogel, and strongly adheres to the tissue via various molecular interactions, including the Schiff base reaction. In particular, the powder composition with a 1:4 ratio of dex-ald to gelatin exhibited optimal characteristics with an appropriate gelation time (258 s), strong tissue adhesion (14.5 kPa), and stability. Dex-ald/gelatin powder hydrogels presented strong adhesion to various organs and excellent hemostasis compared to other wet hydrogels and fibrin glue. A mouse VML injury model revealed that the dex-ald/gelatin powder hydrogel significantly improved muscle regeneration, reduced fibrosis, enhanced vascularization, and decreased inflammation. Consequently, our wet-adhesive powder hydrogel can serve as an effective platform for repairing various tissues, including the heart, muscle, and nerve tissues.

RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification.

Abstract Background Mixed reality (MR) is helpful in hand training for patients with stroke, allowing them to fully submerge in a virtual space while interacting with real objects. The recognition of individual finger movements is required for MR rehabilitation. This study aimed to assess the effectiveness of updated MR-board 2, adding finger training for patients with stroke. Methods Twenty-one participants with hemiplegic stroke (10 with left hemiplegia and 11 with right hemiplegia; nine female patients; 56.7 ± 14.2 years of age; and onset of stroke 32.7 ± 34.8 months) participated in this study. MR-board 2 comprised a board plate, a depth camera, plastic-shaped objects, a monitor, a palm-worn camera, and seven gamified training programs. All participants performed 20 self-training sessions involving 30-min training using MR-board 2. The outcome measurements for upper extremity function were the Fugl–Meyer assessment (FMA) upper extremity score, repeated number of finger flexion and extension (Repeat-FE), the thumb opposition test (TOT), Box and Block Test score (BBT), Wolf Motor Function Test score (WMFT), and Stroke Impact Scale (SIS). One-way repeated measures analysis of variance and the post hoc test were applied for the measurements. MR-board 2 recorded the fingers’ active range of motion (AROM) and Dunnett’s test was used for pairwise comparisons. Results Except for the FMA-proximal score (p = 0.617) and TOT (p = 0.005), other FMA scores, BBT score, Repeat-FE, WMFT score, and SIS stroke recovery improved significantly (p

BackgroundThe association between preterm birth and Mycoplasma species such as Mycoplasma hominis and Ureaplasma urealyticum has been extensively investigated. In a clinical setting, conventional diagnostic methods for them involve culture methods for Mycoplasma spp. and Ureaplasma spp., along with PCR tests. However, the clinical utility of these tests remains controversial, highlighting the necessity for more robust and reliable methods for identifying and understanding Mycoplasma infections.ObjectiveThis study aimed to assess the distribution of microbiota in pregnant women with Mycoplasma hominis and Ureaplasma urealyticum infection by the comparison of conventional diagnostic methods with vaginal microbial community analysis.Study DesignThis prospective case–control study involved 228 Korean pregnant women and utilized vaginal microbial community analysis, Ureaplasma/Mycoplasma culture, and 12-multiplex PCR for sexually transmitted diseases. Cross-correlation analysis in SPSS 27 compared the results of two conventional methods with vaginal microbial community analysis. R software generated box plots depicting the relative abundance of microorganisms. Network analysis was conducted using Cytoscape.ResultsPositive Ureaplasma urealyticum culture findings were observed in 60.2% of patients, with 76.4% positive for Ureaplasma parvum PCR and 13.2% positive for Ureaplasma urealyticum PCR. Mycoplasma hominis culture was positive only in two patients, while Mycoplasma hominis PCR was positive in eight women. Vaginal microbial community analysis identified significant differences in relative abundances of Gardnerella species type I and Fannyhessea vaginae between the Ureaplasma urealyticum PCR positive and negative groups. Mycoplasma hominis PCR positive patients exhibited significant differences in 11 bacterial species, including Gardnerella species I and Fannyhessea vaginae.ConclusionThis study suggests that STD-PCR may be more accurate than Ureaplasma/Mycoplasma culture for the diagnosis of Mycoplasma hominis and Ureaplasma urealyticum infection. Also, the presence of Gardnerella species I and Fannyhessea vaginae implies their potential influences on Ureaplasma urealyticum and Mycoplasma hominis infections based on results of vaginal microbial community analysis. Therefore, vaginal microbial community analysis may give the more information of their pathophysiology.

Interventional recanalization is an effective treatment option for postoperative portal vein occlusion. A transhepatic or transsplenic approach is preferred, whereas a percutaneous transmesenteric route enables antegrade cannulation. Here, we present a case of successful percutaneous transmesenteric recanalization in a patient with a postoperative portal vein graft occlusion.

Cannabis sativa L. is an industrially valuable plant known for its cannabinoids, such as cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC), renowned for its therapeutic and psychoactive properties. Despite its significance, the cannabis industry has encountered difficulties in guaranteeing consistent product quality throughout the drying process. Hyperspectral imaging (HSI), combined with advanced machine learning technology, has been used to predict phytochemicals that presents a promising solution for maintaining cannabis quality control. We examined the dynamic changes in cannabinoid compositions under diverse drying conditions and developed a non-destructive method to appraise the quality of cannabis flowers using HSI and machine learning. Even when the relative weight and water content remained constant throughout the drying process, drying conditions significantly influenced the levels of CBD, THC, and their precursors. These results emphasize the importance of determining the exact drying endpoint. To develop HSI-based models for predicting cannabis quality indicators, including dryness, precursor conversion of CBD and THC, and CBD : THC ratio, we employed various spectral preprocessing methods and machine learning algorithms, including logistic regression (LR), support vector machine (SVM), k-nearest neighbor (KNN), random forest (RF), and Gaussian naïve Bayes (GNB). The LR model demonstrated the highest accuracy at 94.7–99.7% when used in conjunction with spectral pre-processing techniques such as multiplicative scatter correction (MSC) or Savitzky–Golay filter. We propose that the HSI-based model holds the potential to serve as a valuable tool for monitoring cannabinoid composition and determining optimal drying endpoint. This tool offers the means to achieve uniform cannabis quality and optimize the drying process in the industry.

Heterogeneous integration of two-dimensional materials and the conventional semiconductor has opened opportunities for next-generation semiconductor devices and their processing. Heterogeneous integration has been studied for economical manufacturing by substrate recycling and novel functionalities by a combination of incommensurate materials. However, utilizing the integration requires controlling locations of the integrated architectures. Here, we show area-selective deposition (ASD) of germanium on the graphene/MoS2 stack. Ge nucleation precisely occurred on the surfaces of the patterned graphene/MoS2 stack via dipole engineering. In this study, the growth temperature of ASD of Ge was significantly lower than that based on precursor desorption on SiO2. The first-principles calculations revealed that Ge deposited by ASD on the graphene/MoS2 stack was not affected by charge transfer. This work provides a viable way to utilize atomically thin materials for next-generation semiconductor devices, which can be applicable for “Beyond Moore” and “More Moore” approaches.

Abstract It was shown that Yang-Mills instantons on an internal space can trigger the expansion of our four-dimensional universe as well as the dynamical compactification of the internal space. We generalize the instanton-induced inflation and dynamical compactification to general Einstein manifolds with positive curvature and also to the FLRW metric with spatial curvature. We explicitly construct Yang-Mills instantons on all Einstein manifolds under consideration and find that the homogeneous and isotropic universe is allowed only if the internal space is homogeneous. We then consider the FLRW metric with spatial curvature as a solution of the eight-dimensional Einstein-Yang-Mills theory. We find that open universe (k = −1) admits bouncing solutions unlike the other cases (k = 0, +1).

We present a novel background-independent framework for cosmic inflation, starting with a matrix model. In this framework, inflation is portrayed as a dynamic process responsible for the generation of both space and time. This stands in contrast to conventional inflation, which is characterized as a mere (exponential) expansion of an already existing spacetime, driven by the vacuum energy associated with an inflaton field. We observe that the cosmic inflation is triggered by the condensate of Planck energy into a vacuum and responsible for the dynamical emergence of spacetime. The emergent spacetime picture admits a background-independent formulation so that the inflation is described by a conformal Hamiltonian system which requires neither an inflaton field nor an ad hoc inflation potential. This implies that the emergent spacetime may incapacitate all the rationales to introduce the multiverse hypothesis.

Purpose The objective of this study was to assess the feasibility of incorporating virtual reality/augmented reality (VR/AR) programs into practical tests administered as part of the Korean Radiological Technologists Licensing Examination (KRTLE). This evaluation is grounded in a comprehensive survey that targeted enrolled students in departments of radiology across the nation. Methods In total, 682 students from radiology departments across the nation were participants in the survey. An online survey platform was used, and the questionnaire was structured into 5 distinct sections and 27 questions. A frequency analysis for each section of the survey was conducted using IBM SPSS ver. 27.0. Results Direct or indirect exposure to VR/AR content was reported by 67.7% of all respondents. Furthermore, 55.4% of the respondents expressed that VR/AR could be integrated into their classes, which signified a widespread acknowledgment of VR among the students. With regards to the integration of a VR/AR or mixed reality program into the practical tests for purposes of the KRTLE, a substantial amount of the respondents (57.3%) exhibited a positive inclination and recommended its introduction. Conclusion The application of VR/AR programs within practical tests of the KRTLE will be used as an alternative for evaluating clinical examination procedures and validating job skills.