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Genome-wide association studies have enabled the identification of important genetic factors in many trait studies. However, only a fraction of the heritability can be explained by known genetic factors, even in the most common diseases. Genetic loci combinations, or epistatic contributions expressed by combinations of single nucleotide polymorphisms (SNPs), have been argued to be one of the critical factors explaining some of the missing heritability, especially in oligogenic/polygenic diseases. Rheumatoid arthritis (RA) is a complex disease with more than 100 reported SNP associations, as well as various HLA haplotypes and amino acids; however, many associations between RA and inter-chromosomal SNP combinations are unknown. To discover novel associations of epistatic interactions with high odds ratios in RA, we applied the LAMPLINK method, a systematic enumerative procedure for identifying high-order SNP combinations, to a Japanese RA cohort (discovery cohort; 4024 patients with RA and 7731 controls). We validated the identified associations in a different Japanese cohort (validation cohort; 810 RA patients and 6303 controls). In this study, we identified 90 significant genetic associations in the discovery cohort. Among these, 74 (82.2%) associations were replicated in the validation cohort, and eight combinations were inter-chromosomal, all of which comprised rs7765379 or rs35265698 located in the HLA region. These two SNPs exhibited strong correlations with valine at amino acid position 11 in HLA-DRB1 (HLA-DRB1-11-Val). Finally, we discovered that rs9624 showed an association with RA through an epistatic interaction with HLA-DRB1-11-Val. Overall, LAMPLINK showed high reliability for identifying epistatic genetic contributions hidden in complex traits., (© 2024. The Author(s), under exclusive licence to The Japan Society of Human Genetics.)

Realizing efficient long-distance intramolecular charge transport based on a hopping mechanism is a key challenge in molecular electronics. In hopping transport, a smaller reorganization energy (λ) and energy difference between hopping sites (Δ E hs ) should lead to a smaller activation energy and faster charge transfer. However, the development of π-extended molecules that meet these requirements is challenging. In this study, we successfully synthesized several nanometer-scale π-extended molecules composed of a fused π-conjugated unit as a hopping site for reducing λ. Conformational twists between fused units effectively localize π-conjugation in each unit, contributing to reducing Δ E hs . The expected electronic structures of the oligomers were confirmed using spectroscopic and electrochemical measurements. Single-molecule conductance measurements exhibited higher conductance and lower activation energy than those of nonfused oligothiophenes. First-principles calculations indicated that smaller λ and Δ E hs values explain the high conductance. These results highlight the efficiency of the proposed molecular design for effective intramolecular hopping transport.

This study introduces a novel microfluidic polymer chip system that employs an embedded anionic surfactant (AS) ion-selective fluorescence optode (AS fluorescence optode) as a detector for measuring AS. The AS fluorescent optode comprises a lactone form of rhodamine B (L-RB) embedded in 2-nitrophenyl octyl ether plasticized poly (vinyl chloride) membrane. The AS fluorescence optode demonstrated a linear correlation between fluorescence intensity peak heights and AS concentrations within the range of less than 20 µM under optimal flow conditions. The limit of detection for AS was approximately 0.06 µM. The microfluidic system was utilized to measure AS levels in environmental samples, such as river water and tap water., (© 2024. The Author(s), under exclusive licence to The Japan Society for Analytical Chemistry.)

The production of textile products is increasing annually, and most of them are disposed of after use without recycling. One of the reasons for the low recycling percentage of discarded textile products is the difficulty of recycling as a single material as these products are produced from a combination of two or more materials. Therefore, a technology to separate materials is necessary to improve the recycling percentage of textile products and to build a sustainable recycling industry. The aim of this study was to separate the most common combination of materials, such as cotton/polyester, in an environmentally friendly technique using hydrothermal treatment with only water. Herein, the optimal treatment conditions for blended fabrics in a high-pressure reactor were studied. Moreover, cotton could be separated by treating the fabrics at 220 to 230 °C for 10 min while maintaining the shape of the fabrics. Additionally, polyester showed a melting point, confirming that polyester could be separated without decomposition into monomers, unlike common chemical recycling. The strength of the separated cotton and the molecular weight of the polyester were evaluated, and a kinetic analysis of the changes due to the treatment was conducted. The activation energy obtained from the Arrhenius plot was 111.8 kJ/mol for PET, which was smaller than 142.6 kJ/mol for cotton. This indicates that the decrease in the molecular weight of PET is more likely to occur than the change in the strength of cotton, suggesting the possibility of separating the materials from the kinetic analysis., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

HLA allele information is essential for a variety of medical applications, such as genomic studies of multifactorial diseases, including immune system and inflammation-related disorders, and donor selection in organ transplantation and regenerative medicine. To obtain this information, an accurate HLA typing method that is applicable for any allele registered in HLA allele databases is needed. Here we describe a method-called HLA-HD-for determining alleles from a current HLA database using next-generation sequencing (NGS) results., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

A 67 years old male had underwent left upper division segmentectomy. On the sixth day after surgery, he had developed unconsciousness, aphasia and unilateral spatial neglect. Brain MRI revealed a cerebral infarction, and percutaneous cerebral thrombectomy was performed. Enhanced computed tomography revealed thrombus formation in the remnant superior pulmonary vein (SPV), left renal infarction and right acute limb ischemia. After starting anticoagulant therapy with apixaban the thrombus reduced and neurological symptoms improved. A thrombus in the SPV may cause serious whole body organ infarction in the same way as a left atrial thrombus. It was suggested that left upper division segmentectomy was associated with the risk of remnant pulmonary vein thrombosis.

Assay for Transposase-Accessible Chromatin using high-throughput sequencing (ATAC-seq) is the popular technique using next-generation sequencing to measure chromatin accessibility and identify open chromatin regions. While read alignment shape information of next-generation sequencing data with intensity information has been used in various bioinformatics methods, few studies have focused on pure shape information alone. In this study, we investigated what types of ATAC-seq read alignment shapes are observed for the promoter region and whether the pure shape information was related or unrelated to other gene features. We introduced a novel concept and pipeline for handling the pure shape information of NGS data as probability distributions and quantifying their dissimilarities by information theory. Based on this concept, we demonstrate that the pure shape information of ATAC-seq data is correlated with chromatin openness and some gene characteristics. On the other hand, it is suggested that the pure information of ATAC-seq read alignment shape is unlikely to contain additional information to explain differences in RNA expression. Our study suggests that viewing the read alignment shape of NGS data as probability distributions enables us to capture the characteristics of the genome-wide landscape of such data in a non-parametric manner., (© 2023 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.)

Gene sets are functional units for living cells. Previously, limited studies investigated the complex relations among gene sets, but documents about their altering patterns across biological conditions still need to be prepared. In this study, we adopted and modified a classical k-nearest neighbor-based association function to detect inter-gene-set similarities. Based on this method, we built multiplex networks of gene sets for the first time; these networks contain layers of gene sets corresponding to different populations of cells. The context-based multiplex networks can capture meaningful biological variation and have considerable differences from knowledge-based networks of gene sets built on Jaccard similarity, as demonstrated in this study. Furthermore, at the scale of individual gene sets, the structural coefficients of gene sets (multiplex PageRank centrality, clustering coefficient, and participation coefficient) disclose the diversity of gene sets from the perspective of structural properties and make it easier to identify unique gene sets. In gene set enrichment analysis (GSEA), each gene set is treated independently, and its contextual and relational attributes are ignored. The structural coefficients of gene sets can supplement GSEA with information about the overall picture of gene sets, promoting the constructive reorganization of the enriched terms and helping researchers better prioritize and select gene sets., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Author(s).)

Natural killer (NK) cells are innate immune cells critical for protective immune responses against infection and cancer. Although NK cells differentiate in the bone marrow (BM) in an interleukin-15 (IL-15)-dependent manner, the cellular source of IL-15 remains elusive. Using NK cell reporter mice, we show that NK cells are localized in the BM in scattered and clustered manners. NK cell clusters overlap with monocyte and dendritic cell accumulations, whereas scattered NK cells require CXCR4 signaling. Using cell-specific IL-15-deficient mice, we show that hematopoietic cells, but not stromal cells, support NK cell development in the BM through IL-15. In particular, IL-15 produced by monocytes and dendritic cells appears to contribute to NK cell development. These results demonstrate that hematopoietic cells are the IL-15 niche for NK cell development in the BM and that BM NK cells are present in scattered and clustered compartments by different mechanisms, suggesting their distinct functions in the immune response., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Group 2 innate lymphoid cells (ILC2s) are critical for the immune response against parasite infection and tissue homeostasis and involved in the pathogenesis of allergy and inflammatory diseases. Although multiple molecules positively regulating ILC2 development and activation have been extensively investigated, the factors limiting their population size and response remain poorly studied. Here, we found that CD45, a membrane-bound tyrosine phosphatase essential for T cell development, negatively regulated ILC2s in a cell-intrinsic manner. ILC2s in CD45-deficient mice exhibited enhanced proliferation and maturation in the bone marrow and hyperactivated phenotypes in the lung with high glycolytic capacity. Furthermore, CD45 signaling suppressed the type 2 inflammatory response by lung ILC2s and alleviated airway inflammation and pulmonary fibrosis. Finally, the interaction with galectin-9 influenced CD45 signaling in ILC2s. These results demonstrate that CD45 is a cell-intrinsic negative regulator of ILC2s and prevents lung inflammation and fibrosis via ILC2s.

Natriuretic peptides exert not only blood-lowering but also kidney-protective effects through guanylyl cyclase-A (GC-A), a natriuretic peptide receptor. Signaling through GC-A has been shown to protect podocytes from aldosterone-induced glomerular injury, and a p38 mitogen-activated protein kinase (MAPK) inhibitor reduced glomerular injury in aldosterone-infused podocyte-specific GC-A knockout mice. To explore the role of p38 MAPK in podocytes, we constructed podocyte-specific p38 MAPK and GC-A double knockout mice (pod-double knockout mice). Unexpectedly, aldosterone-infused and high salt-fed (B-ALDO)-treated pod-double knockout mice resulted in elevated serum creatinine, massive albuminuria, macrophage infiltration, foot process effacement, nephrin and podocin reduction, and additionally, intra-capillary fibrin thrombi, indicating endothelial injury. Microarray analysis showed increased plasminogen activator inhibitor-1 (PAI-1) in glomeruli of B-ALDO-treated pod-double knockout mice. In B-ALDO-treated pod-double knockout mice, PAI-1 increased in podocytes, and treatment with PAI-1 neutralizing antibody ameliorated intra-capillary thrombus formation. In vitro, deletion of p38 MAPK by the CRISPR/Cas9 system and knockdown of GC-A in human cultured podocytes upregulated PAI-1 and transforming growth factor- β1 (TGF-β1). When p38 MAPK knockout podocytes, transfected with a small interfering RNA to suppress GC-A, were co-cultured with glomerular endothelial cells in a transwell system, the expression of TGF-β1 was increased in glomerular endothelial cells. PAI-1 inhibition ameliorated both podocyte and endothelial injury in the transwell system signifying elevated PAI-1 in podocytes is a factor disrupting normal podocyte-endothelial crosstalk. Thus, our results indicate that genetic dual deletion of p38 MAPK and GC-A in podocytes accelerates both podocyte and endothelial injuries, suggesting these two molecules play indispensable roles in podocyte function., (Copyright © 2023 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.)

Supervised classification of handwritten digits via physical reservoir computing (PRC) using electrochemistry with a three-electrode electrochemical setup was demonstrated. Short-term memory required for the PRC was realized for 3 bit pulse patterns by adjusting the formation/reduction ratio of gold oxides, showing a wide potential of electrochemistry as resources of PR devices., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

We report a magnetic response of Au/1,6-hexanedithiol/Au single-molecule junctions at room temperature using a mechanically controllable break junction method. The electrical resistance of the junction was found to increase up to 5.5% under a magnetic field. This phenomenon could originate from the unpaired charge at the Au/S interface.

Objectives: We conducted an analysis of first-time tolvaptan users (≥80 years old) to determine the factors associated with the prognosis of elderly patients with heart failure., Methods: We retrospectively analyzed 66 consecutive patients with worsening heart failure (aged ≥80 years) who were admitted to Fujita Health University Bantane Hospital from 2011 to 2016 and treated with tolvaptan. Differences between the in-hospital death and survival groups were evaluated. Multivariate logistic regression analysis was also performed to identify the risk factors for mortality., Results: Sixty-six patients were included, and 26 patients died during the index hospitalization. The patients who died had a significantly higher prevalence of ischemic heart disease; a higher heart rate; higher levels of plasma C-reactive protein, blood urea nitrogen (BUN), and creatinine; a lower serum albumin level; and a lower estimated glomerular filtration rate than surviving patients. The proportion of patients requiring early initiation of tolvaptan treatment (within 3 days of admission) was significantly higher in surviving patients. On the basis of multivariate logistic regression analysis, although a high heart rate and high BUN levels were independent factors for in-hospital prognosis, they were not significantly associated with the early use of tolvaptan (≤3 days vs. ≥4 days; odds ratio=0.39; 95% confidence interval=0.07-2.21; p=0.29)., Conclusions: This study revealed that a higher heart rate and higher BUN levels were independent factors for in-hospital prognosis in elderly patients who received tolvaptan and that early tolvaptan use may not always be effective in elderly patients., Competing Interests: Hideo Izawa has received grant support through his institution from Bayer Yakuhin, Ltd., Daiichi Sankyo Co., Ltd., Sumitomo Dainippon Pharma, Kowa Company, Ltd., Ono Pharma, Otsuka, Takeda Pharmaceutical Company, and FUJIFILM Toyama Chemical Co., Ltd. and honoraria for lectures from Otsuka Pharmaceutical Co., Ltd., Novartis AG, and Daiichi Sankyo Co., Ltd.

Recently the phase-field crystal method has attracted considerable attention because it can simulate the atomic behavior of a system on a diffusive timescale. In this study an atomistic simulation model is proposed, which is an extension of the cluster-activation method (CAM) from discrete to continuous space. This approach, called the continuous CAM, can simulate various physical phenomena of atomistic systems on diffusive timescales and employs well-defined atomistic properties, such as interatomic interaction energies, as the main input parameters. The versatility of the continuous CAM was investigated by performing simulations of crystal growth in an undercooled melt, homogeneous nucleation during solidification, and formation of grain boundaries in pure metal.

Background: Aging affects the incidence of diseases such as cancer and dementia, so the development of biomarkers for aging is an important research topic in medical science. While such biomarkers have been mainly identified based on the assumption of a linear relationship between phenotypic parameters, including molecular markers, and chronological age, numerous nonlinear changes between markers and aging have been identified. However, the overall landscape of the patterns in nonlinear changes that exist in aging is unknown., Result: We propose a novel computational method, Data-driven Identification and Classification of Nonlinear Aging Patterns (DICNAP), that is based on functional data analysis to identify biomarkers for aging and potential patterns of change during aging in a data-driven manner. We applied the proposed method to large-scale, public DNA methylation data to explore the potential patterns of age-related changes in methylation intensity. The results showed that not only linear, but also nonlinear changes in DNA methylation patterns exist. A monotonous demethylation pattern during aging, with its rate decreasing at around age 60, was identified as the candidate stable nonlinear pattern. We also analyzed the age-related changes in methylation variability. The results showed that the variability of methylation intensity tends to increase with age at age-associated sites. The representative variability pattern is a monotonically increasing pattern that accelerates after middle age., Conclusion: DICNAP was able to identify the potential patterns of the changes in the landscape of DNA methylation during aging. It contributes to an improvement in our theoretical understanding of the aging process., (© 2023. The Author(s).)

In the field of genomic medical research, the amount of large-scale information continues to increase due to advances in measurement technologies, such as high-performance sequencing and spatial omics, as well as the progress made in genomic cohort studies involving more than one million individuals. Therefore, researchers require more computational resources to analyze this information. Here, we introduce a hybrid cloud system consisting of an on-premise supercomputer, science cloud, and public cloud at the Kyoto University Center for Genomic Medicine in Japan as a solution. This system can flexibly handle various heterogeneous computational resource-demanding bioinformatics tools while scaling the computational capacity. In the hybrid cloud system, we demonstrate the way to properly perform joint genotyping of whole-genome sequencing data for a large population of 11,238, which can be a bottleneck in sequencing data analysis. This system can be one of the reference implementations when dealing with large amounts of genomic medical data in research centers and organizations., (© 2023. The Author(s).)

Various conjugative plasmids were obtained by exogenous plasmid capture, biparental mating, and/or triparental mating methods from different environmental samples in Japan. Based on phylogenetic analyses of their whole-nucleotide sequences, new IncP/P-1 plasmids that could be classified into novel subgroups were obtained. Mini-replicons of the plasmids were constructed, and each of them was incompatible with at least one of the IncP/P-1 plasmids, although they showed diverse iteron sequences in their oriV regions. There were two large clades of IncP/P-1 plasmids, clade I and II. Plasmids in clade I and II included antibiotic resistance genes. Notably, nucleotide compositions of newly found plasmids exhibited different tendencies compared with those of the previously well-studied IncP/P-1 plasmids. Indeed, the host range of plasmids of clade II was different from that of clade I. Although few PromA plasmids have been reported, the number of plasmids belonging to PromAβ, and -γ subgroups detected in this study was close to that of IncP/P-1 plasmids. The host ranges of PromAγ and PromAδ plasmids were broad and transferred to different and distinct classes of Proteobacteria . Interestingly, PromA plasmids and many IncP/P-1 plasmids do not carry any accessory genes. These findings indicate the presence of "hitherto-unnoticed" conjugative plasmids, including IncP/P-1 or PromA derivative ones in nature. These plasmids would have important roles in the exchange of various genes, including antibiotic resistance genes, among different bacteria in nature. IMPORTANCE Plasmids are known to spread among different bacteria. However, which plasmids spread among environmental samples and in which environments they are present is still poorly understood. This study showed that unidentified conjugative plasmids were present in various environments. Different novel IncP/P-1 plasmids were found, whose host ranges were different from those of known plasmids, showing wide diversity of IncP/P-1 plasmids. PromA plasmids, exhibiting a broad host range, were diversified into several subgroups and widely distributed in varied environments. These findings are important for understanding how bacteria naturally exchange their genes, including antibiotic resistance genes, a growing threat to human health worldwide.

Purpose: To identify susceptibility genes for macular neovascularization (MNV) development in central serous chorioretinopathy (CSC)., Design: Genome-wide survival analysis using a longitudinal cohort study., Participants: We included 402 and 137 patients with CSC but without MNV at their first visit from the Kyoto CSC Cohort and Kobe CSC dataset, respectively. All patients underwent detailed ophthalmic examinations, including multimodal imaging, such as fundus autofluorescence, spectral-domain OCT, and fluorescein angiography/indocyanine green angiography or OCT angiography., Methods: We conducted a genome-wide survival analysis using the Kyoto CSC Cohort. We applied the Cox proportional hazard model to adjust for age, sex, and the first principal component. Single nucleotide polymorphisms (SNPs) with P values < 1.0 × 10 -5 were carried forward to the replication in the Kobe CSC dataset. Moreover, we evaluated the contribution of previously reported age-related macular degeneration (AMD) susceptibility loci. We used FUMA and ToppFun for the functional enrichment analysis., Main Outcome Measures: The association between SNPs and MNV development in patients with CSC., Results: Rs370974631 near ARMS2 displayed a genome-wide significant association in the meta-analysis of discovery and replication result (hazard ratio [HR] meta , 3.63; P meta  = 5.76 × 10 -9 ). Among previously reported AMD susceptibility loci, we additionally identified CFH rs800292 (HR, 0.39, P = 2.55 × 10 -4 ), COL4A3 rs4276018 (HR, 0.26, P = 1.56 × 10 -3 ), and B3GALTL rs9564692 (HR, 0.56, P = 8.30 × 10 -3 ) as susceptibility loci for MNV development in CSC. The functional enrichment analysis revealed significant enrichment of 8 pathways (GO:0051561, GO:0036444, GO:0008282, GO:1990246, GO:0015272, GO:0030955, GO:0031420, and GO:0005242) related to ion transport., Conclusions: ARMS2, CFH, COL4A3, and B3GALTL were identified as susceptibility genes for MNV development in CSC. These 4 genes are known as susceptibility genes for AMD, whereas COL4A3 and B3GALTL were previously reported to be polypoidal choroidal vasculopathy (PCV)-specific susceptibility genes. Our findings revealed the shared genetic susceptibility between PCV and MNV secondary to CSC., (Copyright © 2022 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.)

Contrast-associated acute kidney injury (CA-AKI) is a complication of percutaneous coronary intervention (PCI). Because proteinuria is a sentinel marker of renal dysfunction, we assessed its role in predicting CA-AKI in patients undergoing PCI. A total of 1,254 patients undergoing PCI were randomly assigned to a derivation (n = 840) and validation (n = 414) dataset. We identified the independent predictors of CA-AKI where CA-AKI was defined by the new criteria issued in 2020, by a multivariate logistic regression in the derivation dataset. We created a risk score from the remaining predictors. The discrimination and calibration of the risk score in the validation dataset were assessed by the area under the receiver-operating characteristic curves (AUC) and Hosmer-Lemeshow test, respectively. A total of 64 (5.1%) patients developed CA-AKI. The 3 variables of the risk score were emergency procedures, serum creatinine, and proteinuria, which were assigned 1 point each based on the correlation coefficient. The risk score demonstrated a good discriminative power (AUC 0.789, 95% CI 0.766-0.912) and significant calibration. It was strongly associated with the onset of CA-AKI (Cochran-Armitage test, p < 0.0001). Our risk score that included proteinuria was simple to obtain and calculate, and may be useful in assessing the CA-AKI risk before PCI., (© 2022. The Author(s).)

The spread through air spaces (STAS) is recognized as a negative prognostic factor in patients with early-stage lung adenocarcinoma. The present study aimed to develop a machine learning model for the prediction of STAS using peritumoral radiomics features extracted from preoperative CT imaging. A total of 339 patients who underwent lobectomy or limited resection for lung adenocarcinoma were included. The patients were randomly divided (3:2) into training and test cohorts. Two prediction models were created using the training cohort: a conventional model based on the tumor consolidation/tumor (C/T) ratio and a machine learning model based on peritumoral radiomics features. The areas under the curve for the two models in the testing cohort were 0.70 and 0.76, respectively (P = 0.045). The cumulative incidence of recurrence (CIR) was significantly higher in the STAS high-risk group when using the radiomics model than that in the low-risk group (44% vs. 4% at 5 years; P = 0.002) in patients who underwent limited resection in the testing cohort. In contrast, the 5-year CIR was not significantly different among patients who underwent lobectomy (17% vs. 11%; P = 0.469). In conclusion, the machine learning model for STAS prediction based on peritumoral radiomics features performed better than the C/T ratio model., (© 2022. The Author(s).)

The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies.

Comparing multiple single-cell expression datasets such as cytometry and scRNA-seq data between case and control donors provides information to elucidate the mechanisms of disease. We propose a completely data-driven computational biological method for this task. This overcomes the challenges of conventional cellular subset-based comparisons and facilitates further analyses such as machine learning and gene set analysis of single-cell expression datasets., (© 2021. The Author(s).)

Genome-wide association studies have demonstrated that polygenic risks shape Alzheimer's disease (AD). To elucidate the polygenic architecture of AD phenotypes at a cellular level, we established induced pluripotent stem cells from 102 patients with AD, differentiated them into cortical neurons and conducted a genome-wide analysis of the neuronal production of amyloid β (Aβ). Using such a cellular dissection of polygenicity (CDiP) approach, we identified 24 significant genome-wide loci associated with alterations in Aβ production, including some loci not previously associated with AD, and confirmed the influence of some of the corresponding genes on Aβ levels by the use of small interfering RNA. CDiP genotype sets improved the predictions of amyloid positivity in the brains and cerebrospinal fluid of patients in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Secondary analyses of exome sequencing data from the Japanese ADNI and the ADNI cohorts focused on the 24 CDiP-derived loci associated with alterations in Aβ led to the identification of rare AD variants in KCNMA1., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Background: There have been several reports about the prognosis of teeth adjacent to edentulous spaces for implant-supported fixed prostheses (ISFPs) and removable partial dentures (RPDs). However, there are few reports about the prognosis of the other remaining teeth comparing ISFPs with RPDs., Purpose: The aim of this study was to evaluate and compare the prognosis of the remaining teeth for ISFPs and RPDs in terms of survival and complication-free rates., Methods: Subjects were partially edentulous patients with ISFPs or RPDs inserted in 2003-2016. Teeth adjacent to edentulous spaces (A-teeth), teeth not adjacent to edentulous spaces (R-teeth), and teeth opposing edentulous spaces (O-teeth) were investigated. The endpoints were tooth extraction and complications. A multivariate cox regression model was used to estimate the risk factors for survival of the investigated teeth., Results: A total of 233 (ISFP: 89, RPD: 144) patients were included in the statistical analyses. An IFSP prosthesis, when compared to an RPD prosthesis did not significantly decrease the tooth loss rate for A-teeth (hazard ratio [HR]: 0.76; 95% confidence interval [CI]: 0.30-1.92), for R-teeth (HR: 0.54; 95% CI: 0.28-1.05), or for O-teeth (HR: 0.45; 95% CI: 0.10-2.09)., Conclusions: In partially edentulous spaces, the difference between ISFPs and RPDs does not affect the prognosis of teeth adjacent to edentulous spaces, teeth not adjacent to edentulous spaces, and teeth opposing edentulous spaces. Namely, our findings suggest that it depends largely on the tooth type, jaw, endodontic therapy performed, not on the type of prostheses., (© 2022 Wiley Periodicals LLC.)

Genetic epidemiology is a rapidly advancing field due to the recent availability of large amounts of omics data. In recent years, it has become possible to obtain omics information at the single-cell level, so genetic epidemiological models need to be updated to integrate with single-cell expression data. In this perspective paper, we propose a cell population-based framework for genetic epidemiology in the single-cell era. In this framework, genetic diversity influences phenotypic diversity through the diversity of cell population profiles, which are defined as high-dimensional probability distributions of the state spaces of biomolecules of each omics layer. We discuss how biomolecular experimental measurement data can capture the different properties of this distribution. In particular, single-cell data constitute a sample from this population distribution where only some coordinate values are observable. From a data analysis standpoint, we introduce methodology for feature extraction from cell population profiles. Finally, we discuss how this framework can be applied not only to genetic epidemiology but also to systems biology., (© 2021 Wiley Periodicals LLC.)

Among v-raf murine sarcoma viral oncogene homolog B1 inhibitors, vemurafenib causes a higher incidence of nephrotoxicity. Bai et al. reported that vemurafenib-induced nephrotoxicity is not directly caused by viral oncogene homolog B1 inhibition but is partly caused by ferrochelatase inhibition in renal tubular epithelial cells. Because several other protein kinase inhibitors are also known to cause ferrochelatase inhibition, further studies are needed to elucidate the role of ferrochelatase in renal function and injury., (Copyright © 2021 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.)

The study aimed to identify factors related to bone mineral density (BMD) among older patients with heart failure (HF). A total of 70 consecutive patients with HF aged 65 years or older who were admitted to an acute hospital due to worsening condition were enrolled before discharge. BMD of the femoral neck was evaluated using the DEXA method. Physical function, as well as echocardiographic and laboratory findings including biomarker of HF severity were collected. Bivariate and multiple regression analyses were employed to determine the association between BMD and the clinical variables. Bivariate analysis determined that age, grip strength, walking speed, serum albumin, and N-terminal pro B-type natriuretic peptide (NT-proBNP) were significantly correlated with BMD (P < 0.01), whereas other clinical parameters were not. The multiple regression analysis identified NT-proBNP as an independent related factor for BMD after adjusting with confounding clinical variables. NT-proBNP was independently related to BMD among older patients with HF. Our results suggest the inclusion of bone fracture prevention strategies in disease management programs, especially for older patients with HF., (© 2021. Springer Japan KK, part of Springer Nature.)

Human immune systems are very complex, and the basis for individual differences in immune phenotypes is largely unclear. One reason is that the phenotype of the immune system is so complex that it is very difficult to describe its features and quantify differences between samples. To identify the genetic factors that cause individual differences in whole lymphocyte profiles and their changes after vaccination without having to rely on biological assumptions, we performed a genome-wide association study (GWAS), using cytometry data. Here, we applied computational analysis to the cytometry data of 301 people before receiving an influenza vaccine, and 1, 7, and 90 days after the vaccination to extract the feature statistics of the lymphocyte profiles in a nonparametric and data-driven manner. We analyzed two types of cytometry data: measurements of six markers for B cell classification and seven markers for T cell classification. The coordinate values calculated by this method can be treated as feature statistics of the lymphocyte profile. Next, we examined the genetic basis of individual differences in human immune phenotypes with a GWAS for the feature statistics, and we newly identified seven significant and 36 suggestive single-nucleotide polymorphisms associated with the individual differences in lymphocyte profiles and their change after vaccination. This study provides a new workflow for performing combined analyses of cytometry data and other types of genomics data.

In this paper, the electronic structure and transport properties of a ductile thermoelectric material α-Ag2S are examined using first-principles calculations combined with the Boltzmann transport equation within a constant relaxation-time approximation. The use of the exchange-correlation functional SCAN + rVV10 successfully describes the geometric and electronic structure of α-Ag2S with a direct bandgap value of 0.99 eV, which is consistent with the previous experimental observations. Based on the calculations of the formation energy of typical intrinsic defects, it is found that intrinsic defect formation greatly affects the conductivity of the system where silver vacancy and interstitial silver act as p-type and n-type defects, respectively. Large Seebeck coefficients at room-temperature, of around -760 μV K-1 for n-type and 1400 μV K-1 for p-type, are realized. It is also suggested that the doping of fully filled d-block elements such as Cu and Au not only maintained the Seebeck coefficients at high values but also improved electrical conductivity by more than 1.4 times, leading to the improvement of the power factor by up to 40% compared to the non-doped sample at low carrier concentration.

Correction for 'Intrinsic defect formation and the effect of transition metal doping on transport properties in a ductile thermoelectric material α-Ag 2 S: a first-principles study' by Ho Ngoc Nam et al., Phys. Chem. Chem. Phys., 2021, DOI: .

The total synthesis of berberine and selected analogues. And their evaluation as amyloid β (Aβ) aggregation inhibitors is described. The key step in the synthesis, the assembly of the berberine framework, was accomplished using an intermolecular Heck reaction. Berberine analog 17 incorporating a tertiary amine moiety showed good anti Aβ aggregation activity, water solubility, and almost no toxicity to nerve cells., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2021 Elsevier Masson SAS. All rights reserved.)

The cell's movement and morphological change are two interrelated cellular processes. An integrated analysis is needed to explore the relationship between them. However, it has been challenging to investigate them as a whole. The cell's trajectory can be described by its speed, curvature, and torsion. On the other hand, the three-dimensional (3D) cell shape can be studied by using a shape descriptor such as spherical harmonic (SH) descriptor, which is an extension of a Fourier transform in 3D space. We propose a novel method using parallel-transport (PT) to integrate these shape-movement data by using moving frames as the 3D-shape coordinate system. This moving frame is purely determined by the velocity vector. On this moving frame, the movement change will influence the coordinate system for shape analysis. By analyzing the change of the SH coefficients over time in the moving frame, we can observe the relationship between shape and movement. We illustrate the application of our approach using simulated and real datasets in this paper., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2021. Published by The Company of Biologists Ltd.)

The development of several-nanometer-scale π-conjugated systems for efficient intramolecular hopping charge transport remains a significant challenge. To construct localized electronic structures at the same energy in a molecule, a series of oligothiophenes, with lengths up to 10 nm and periodically twisted structures, was synthesized. Single-molecule conductance measurements of the twisted molecules revealed resistances lower than those of planar oligothiophenes. This study provides a rational molecular design to improve the intramolecular hopping charge transport in materials.

Objectives: There are benefits of exercise-based cardiac rehabilitation (CR) in patients with heart failure (HF), but their underlying molecular mechanisms remain elusive. The effect of CR on the expression profile of circulating microRNAs (miRNAs), which are short noncoding RNAs that regulate posttranscriptional expression of target genes, is unknown. If miRNAs respond to changes following CR for HF, then serum profiling of miRNAs may reveal cardioprotective mechanisms of CR., Methods: This study enrolled three hospitalized patients with progressed systolic HF and three normal volunteer controls. In patients, CR was initiated after improvement of HF, which included 2 weeks of bicycle ergometer and resistance exercises. Genome-wide expression profiling of circulating miRNAs was performed using microarrays for the patients (mean±SD age, 60.0±12.2 years) and controls (58.7±0.58 years). Circulating miRNA expression profiles were compared between patients with HF before and after CR and the controls., Results: Expression levels of two miRNAs were significantly different in patients before CR compared with controls and patients after CR. The expression of hsa-miR-125b-1-3p was significantly downregulated and that of hsa-miR-1290 was significantly upregulated in patients before CR., Conclusions: When performing CR, expression of certain circulating miRNAs in patients with HF is restored to nonpathological levels. The benefits of CR for HF may result from regulation of miRNAs through multiple effects of gene expression.

Omics studies attempt to extract meaningful messages from large-scale and high-dimensional data sets by treating the data sets as a whole. The concept of treating data sets as a whole is important in every step of the data-handling procedures: the pre-processing step of data records, the step of statistical analyses and machine learning, translation of the outputs into human natural perceptions, and acceptance of the messages with uncertainty. In the pre-processing, the method by which to control the data quality and batch effects are discussed. For the main analyses, the approaches are divided into two types and their basic concepts are discussed. The first type is the evaluation of many items individually, followed by interpretation of individual items in the context of multiple testing and combination. The second type is the extraction of fewer important aspects from the whole data records. The outputs of the main analyses are translated into natural languages with techniques, such as annotation and ontology. The other technique for making the outputs perceptible is visualization. At the end of this review, one of the most important issues in the interpretation of omics data analyses is discussed. Omics studies have a large amount of information in their data sets, and every approach reveals only a very restricted aspect of the whole data sets. The understandable messages from these studies have unavoidable uncertainty.

Background: Anaerobic threshold (AT) during cardiopulmonary exercise testing (CPET) is not always determinable in patients with heart failure (HF). However, little is known about the clinical features of patients with HF who have indeterminable AT. Therefore, the present study aimed to clarify the clinical features of such patients., Methods: A total of 70 patients with HF (58 males; age: 68±12 years) who underwent CPET during hospitalization were divided into two groups: determinable AT ( n =50) and indeterminable AT ( n =20). Physical function, echocardiographic results, and laboratory findings were subsequently determined., Results: Univariate analyses showed that the indeterminable AT group had significantly higher age and left ventricular ejection fraction, and significantly lower body mass index, calf circumference, handgrip strength, walking speed, serum hemoglobin, and serum albumin than the determinable AT group. Multiple logistic regression analysis identified handgrip strength and walking speed as independent predictive factors for indeterminable AT. Receiver-operating characteristic analyses revealed that handgrip strength of 21.2 kg and walking speed of 0.97 m/s were optimal cutoff values for differentiating patients who were likely to experience indeterminable AT., Conclusions: The present study identified handgrip strength and walking speed as powerful predictors for indeterminable AT with HF., Competing Interests: Hideo Izawa has received grant support through his institution from Takeda, Shionogi, Otsuka, Pfizer, Teijin, and Daiichi-Sankyo and honoraria for lectures from Otsuka and Daiichi-Sankyo.

Objectives: MicroRNAs (miRNA) are functional RNAs that have emerged as pivotal gene expression regulators in cardiac disease. Although several cardiomyocyte miRNAs have been reported to play roles in heart failure progression among patients with idiopathic dilated cardiomyopathy (DCM), the role of circulating miRNAs has not yet been well-examined., Methods: After total RNA extraction from the peripheral blood samples of three control participants and six patients with DCM, miRNA profiling was performed using miRNA arrays. Based on the results of this initial screening, real-time polymerase chain reaction (RT-PCR) was used to perform a quantitative analysis of blood samples from a larger number of matched patients (DCM, n =20; controls, n =5). Finally, the correlations between specific miRNA expression levels and hemodynamic parameters were analyzed., Results: A primary screening of 2,565 miRNAs resulted in the identification of nine miRNA candidates. Quantitative RT-PCR results revealed significantly increased miR-489 expression levels in the DCM group. Moreover, there was a significant positive correlation between miR-489 expression level and left ventricular ejection fraction., Conclusions: Our results suggest that circulating miR-489 could be a potential noninvasive diagnostic biomarker for DCM. Additionally, the quantification of circulating miR-489 may have value as a potential prognostic marker for patients with DCM., Competing Interests: Hideo Izawa has received grant support through his institution from Takeda, Shionogi, Dainippon-Sumitomo, Otsuka, Pfizer, and Daiichi-Sankyo, and honoraria for lectures from Otsuka and Daiichi-Sankyo.

Direct hybridization between the π-orbital of a conjugated molecule and metal electrodes is recognized as a new anchoring strategy to enhance the electrical conductance of single-molecule junctions. The anchor is expected to maintain direct hybridization between the conjugated molecule and the metal electrodes, and control the orientation of the molecule against the metal electrodes. However, fulfilling both requirements is difficult because multipodal anchors aiming at a robust contact with the electrodes often break the π-conjugation, thereby resulting in an inefficient carrier transport. Herein, a new tripodal anchor framework-a 7,7-diphenyl-7H-benzo[6,7]indeno[1,2-b]thiophene (PBIT) derivative-is developed. In this framework, π-conjugation is maintained in the molecular junction, and the tripodal structure makes the molecule stand upright on the metal electrode. Molecular conductance is measured by the break junction technique. A vector-based classification and first-principles transport calculations determine the single-molecule conductance of the tripodal-anchoring structure. The conductance of the PBIT-based molecule is higher than that of the tripodal anchor having sp 3 carbon atoms in the carrier transport pathway. These results demonstrate that extending the π-conjugation to the tripodal leg is an effective strategy for enhancing the conductivities of single-molecule junctions., (© 2020 Wiley-VCH GmbH.)

Introduction: A method that utilizes nanosecond bipolar cancellation (BPC) near a quadrupole electrodes to suppress a biological response but cancels the distal BPC at the quadrupole center, i.e., cancellation of cancellation (CANCAN), may allow for a remote focused stimulation at the quadrupole center. Objectives: The primary object of this study was to outline the requirement of the CANCAN implementation and select an effective quadrupole configuration. Results: We have studied three quadrupole electrode configurations, a rod quadrupole, a plate quadrupole (Plate-Q), and a resistor quadrupole. The pulse shapes of electric fields include monophasic pulses, cancellation pulses, and additive pulses. The Plate-Q appears the best for CANCAN as it shows the highest percentage of cancellation pulses among all pulse shapes, allowing for the best spatial focus. Conclusion: For the region of interest characterized in the Plate-Q configuration, the maximum magnitude of bipolar field is twice as that of the unipolar field, which allows for the CANCAN demonstration that involves membrane electropermeabilization., Competing Interests: No competing financial interests exist., (Copyright 2020, Mary Ann Liebert, Inc., publishers.)

Characteristics of high frequency (HF) component based on heart rate variability (HRV) in a large general population remain unclear, particularly on the relationship with daily physical activity. We aimed to characterize the distribution of HF component and examine the association with daily physical activity among community residents. We performed spectral analysis of HRV from 10-second ECG recordings among 9135 residents aged 30 to 74 years in Nagahama City, Japan. HF components were log-transformed to consider the distribution. Simple correlations between HF and age were determined. Age-adjusted mean values of HF component were calculated for each questionnaire item related to daily physical activity. Multiple regression analysis was performed to examine the effect of daily physical activity on HF component value. Mean values of logarithmically-transformed HF component (lnHF) were higher in women than in men (p < 0.001). lnHF was inversely associated with age (r = -0.40, -0.49 for men, women, respectively). Adjusted mean lnHF for physically active people was significantly higher than that in inactive people (p < 0.001). HF components from 10-second ECG recordings were moderately and negatively correlated with age in both sexes, and positively correlated with daily physical activity in the general adult population. Maintaining the level of daily physical activity, especially to exercise regularly could keep the parasympathetic function high.

A dielectric biconical antenna (DiBiCA) for radiating subnanosecond pulses to treat subcutaneous tissue was designed, constructed, and tested. It is composed of a conical wave launcher and truncated conical emitter. In between, there is a short cylinder that provides a space for a ring terminating resistor. The material of the antenna has a dielectric constant of 28, so its size is small (length: 7 cm and aperture diameter: 2.2 cm). It was housed in an oil container to withstand high voltages and avoid surface flashover. The radiated electric field, measured in water, increased as the input voltage increased up to 30 kV but leveled off for higher voltages up to 50 kV, presumably because of losses in the antenna dielectric. The maximum field was 1.5 kV/cm for a depth of 5 mm and 1.0 kV/cm for a depth of 20 mm. Although the dielectric loss mechanism remains to be investigated, the antenna can be useful for noninvasive delivery of subnanosecond pulses to induce biological responses on subcutaneous targets. The DiBiCA radiated pulses were shown to change the viabilities of dendritic cells and macrophages for 10-min exposure. Bioelectromagnetics. 2020;41:413-424. © 2020 Bioelectromagnetics Society., (© 2020 Bioelectromagnetics Society.)

Keratoconus is a common ocular disorder that causes progressive corneal thinning and is the leading indication for corneal transplantation. Central corneal thickness (CCT) is a highly heritable characteristic that is associated with keratoconus. In this two-stage genome-wide association study (GWAS) of CCT, we identified a locus for CCT, namely STON2 rs2371597 (P = 2.32 × 10 -13 ), and confirmed a significant association between STON2 rs2371597 and keratoconus development (P = 0.041). Additionally, strong STON2 expression was observed in mouse corneal epithelial basal cells. We also identified SMAD3 rs12913547 as a susceptibility locus for keratoconus development using predictive analysis with IBM's Watson question answering computer system (P = 0.001). Further GWAS analyses combined with Watson could effectively reveal detailed pathways underlying keratoconus development.

Background: A model that can predict treatment response for a patient with specific baseline characteristics would help decision-making in personalized medicine. The aim of the study is to develop such a model in the treatment of rheumatoid arthritis (RA) patients who receive certolizumab (CTZ) plus methotrexate (MTX) therapy, using individual participant data meta-analysis (IPD-MA)., Methods: We will search Cochrane CENTRAL, PubMed, and Scopus as well as clinical trial registries, drug regulatory agency reports, and the pharmaceutical company websites from their inception onwards to obtain randomized controlled trials (RCTs) investigating CTZ plus MTX compared with MTX alone in treating RA. We will request the individual-level data of these trials from an independent platform (http://vivli.org). The primary outcome is efficacy defined as achieving either remission (based on ACR-EULAR Boolean or index-based remission definition) or low disease activity (based on either of the validated composite disease activity measures). The secondary outcomes include ACR50 (50% improvement based on ACR core set variables) and adverse events. We will use a two-stage approach to develop the prediction model. First, we will construct a risk model for the outcomes via logistic regression to estimate the baseline risk scores. We will include baseline demographic, clinical, and biochemical features as covariates for this model. Next, we will develop a meta-regression model for treatment effects, in which the stage 1 risk score will be used both as a prognostic factor and as an effect modifier. We will calculate the probability of having the outcome for a new patient based on the model, which will allow estimation of the absolute and relative treatment effect. We will use R for our analyses, except for the second stage which will be performed in a Bayesian setting using R2Jags., Discussion: This is a study protocol for developing a model to predict treatment response for RA patients receiving CTZ plus MTX in comparison with MTX alone, using a two-stage approach based on IPD-MA. The study will use a new modeling approach, which aims at retaining the statistical power. The model may help clinicians individualize treatment for particular patients., Systematic Review Registration: PROSPERO registration number pending (ID#157595).