Search

Summary Functional interpretation of biological entities such as differentially expressed genes is one of the fundamental analyses in bioinformatics. The task can be addressed by using biological pathway databases with enrichment analysis (EA). However, textual description of biological entities in public databases is less explored and integrated in existing tools and it has a potential to reveal new mechanisms. Here, we present a new R package biotextgraph for graphical summarization of omics' textual description data which enables assessment of functional similarities of the lists of biological entities. We illustrate application examples of annotating gene identifiers in addition to EA. The results suggest that the visualization based on words and inspection of biological entities with text can reveal a set of biologically meaningful terms that could not be obtained by using biological pathway databases alone. The results suggest the usefulness of the package in the routine analysis of omics-related data. The package also offers a web-based application for convenient querying. Availability and implementation The package, documentation, and web server are available at: https://github.com/noriakis/biotextgraph. [ABSTRACT FROM AUTHOR]

Summary The Kyoto Encyclopedia of Genes and Genomes (KEGG) database serves as a valuable systems biology resource and is widely utilized in diverse research fields. However, existing software does not allow flexible visualization and network analyses of the vast and complex KEGG data. We developed ggkegg , an R package that integrates KEGG information with ggplot2 and ggraph. ggkegg enables enhanced visualization and network analyses of KEGG data. We demonstrate the utility of the package by providing examples of its application in single-cell, bulk transcriptome, and microbiome analyses. ggkegg may empower researchers to analyze complex biological networks and present their results effectively. Availability and implementation The package and user documentation are available at: https://github.com/noriakis/ggkegg. [ABSTRACT FROM AUTHOR]

BK polyomavirus-associated nephropathy occurs in kidney transplant recipients under immunosuppressive treatment. BK polyomavirus is implicated in cancer development and invasion, and case reports of renal cell carcinoma and urothelial carcinoma possibly associated with BK polyomavirus has been reported. Further, it has been suggested that the immune responses of KT-related diseases could play a role in the pathogenesis and progression of renal cell carcinoma. Thus, we thought to examine the relationship between BK polyomavirus-associated nephropathy and renal cell carcinoma in terms of gene expression. To identify the common and specific immune responses involved in kidney transplantation-related diseases with a specific focus on BK polyomavirus-associated nephropathy, we performed consensus weighted gene co-expression network analysis on gene profile datasets of renal biopsy samples from different institutions. After the identification of gene modules and validation of the obtained network by immunohistochemistry of the marker across kidney transplantation-related diseases, the relationship between prognosis of renal cell carcinoma and modules was assessed. We included the data from 248 patients and identified the 14 gene clusters across the datasets. We revealed that one cluster related to the translation regulating process and DNA damage response was specifically upregulated in BK polyomavirus-associated nephropathy. There was a significant association between the expression value of hub genes of the identified cluster including those related to cGAS-STING pathway and DNA damage response, and the prognosis of renal cell carcinoma. The study suggested the potential link between kidney transplantation-related diseases, especially specific transcriptomic signature of BK polyomavirus associated nephropathy and renal cell carcinoma. [ABSTRACT FROM AUTHOR]

Background The relationship between chronic kidney disease (CKD) and the gut microbiome, which interact through chronic inflammation, uraemic toxin production and immune response regulation, has gained interest in the development of CKD therapies. However, reports using shotgun metagenomic analysis of the gut microbiome are scarce, especially for early CKD. Here we characterized gut microbiome differences between non-CKD participants and ones with early CKD using metagenomic sequencing. Methods In total, 74 non-CKD participants and 37 participants with early CKD were included based on propensity score matching, controlling for various factors including dietary intake. Stool samples were collected from participants and subjected to shotgun sequencing. Bacterial and pathway abundances were profiled at the species level with MetaPhlAn2 and HUMAnN2, respectively, and overall microbiome differences were determined using Bray–Curtis dissimilarities. Diabetic and non-diabetic populations were analysed separately. Results For diabetic and non-diabetic participants, the mean estimated glomerular filtration rates of the CKD group were 53.71 [standard deviation (SD) 3.87] and 53.72 (SD 4.44), whereas those of the non-CKD group were 72.63 (SD 7.72) and 76.10 (SD 9.84), respectively. Alpha and beta diversities were not significantly different between groups. Based on taxonomic analysis, butyrate-producing species Roseburia inulinivorans , Ruminococcus torques and Ruminococcus lactaris were more abundant in the non-CKD group, whereas Bacteroides caccae and Bacteroides coprocora were more abundant in the non-diabetic CKD group. Conclusions Although gut microbiome changes in individuals with early CKD were subtle, the results suggest that changes related to producing short-chain fatty acids can already be observed in early CKD. [ABSTRACT FROM AUTHOR]

Background: The oral microbiome, which consists of various habitats, has been shown to be influenced by smoking. However, differences in the tongue microbiomes of current and former smokers, as well as their resultant functional consequences, have rarely been investigated in East Asian populations. Methods: We used 16S rRNA amplicon sequencing of tongue-coating samples obtained from East Asian subjects who were current, former, or never smokers to identify differences in their tongue microbiomes and related metagenomic functions. Two sets of participants from 2016 to 2017 (n = 657 and n = 187, respectively) were analyzed separately. Results: We found significant differences between the overall microbiome compositions of current versus never smokers (p = 0.0015), but not between former versus never smokers (p = 0.43) based on the weighted UniFrac distance. Twenty-nine of 43 investigated genera showed significantly different expression levels in current versus never smokers. Neisseria and Capnocytophaga were less abundant, and Streptococcus and Megasphaera were more abundant in current smokers. Moreover, the abundances of metagenomic pathways, including those related to nitrate reduction and the tricarboxylic acid cycle, were significantly different between current and never smokers. Conclusions: The tongue microbiomes and related metagenomic pathways of current smokers differ from those of never smokers among East Asians. [ABSTRACT FROM AUTHOR]

Background: Acute kidney injury (AKI) is a critical complication of immune checkpoint inhibitor therapy. Since the etiology of AKI in patients undergoing cancer therapy varies, clarifying underlying causes in individual cases is critical for optimal cancer treatment. Although it is essential to individually analyze immune checkpoint inhibitor-treated patients for underlying pathologies for each AKI episode, these analyses have not been realized. Herein, we aimed to individually clarify the underlying causes of AKI in immune checkpoint inhibitor-treated patients using a new clustering approach with Shapley Additive exPlanations (SHAP). Methods: We developed a gradient-boosting decision tree-based machine learning model continuously predicting AKI within 7 days, using the medical records of 616 immune checkpoint inhibitor-treated patients. The temporal changes in individual predictive reasoning in AKI prediction models represented the key features contributing to each AKI prediction and clustered AKI patients based on the features with high predictive contribution quantified in time series by SHAP. We searched for common clinical backgrounds of AKI patients in each cluster, compared with annotation by three nephrologists. Results: One hundred and twelve patients (18.2%) had at least one AKI episode. They were clustered per the key feature, and their SHAP value patterns, and the nephrologists assessed the clusters' clinical relevance. Receiver operating characteristic analysis revealed that the area under the curve was 0.880. Patients with AKI were categorized into four clusters with significant prognostic differences (p = 0.010). The leading causes of AKI for each cluster, such as hypovolemia, drug-related, and cancer cachexia, were all clinically interpretable, which conventional approaches cannot obtain. Conclusion: Our results suggest that the clustering method of individual predictive reasoning in machine learning models can be applied to infer clinically critical factors for developing each episode of AKI among patients with multiple AKI risk factors, such as immune checkpoint inhibitor-treated patients. [ABSTRACT FROM AUTHOR]

Open in new tab Download slide OBJECTIVES Thoracic endovascular aortic repair (TEVAR) for aortic arch aneurysms is challenging because of anatomical restrictions and the presence of cervical branches. Revascularization of the cervical branch is required when conventional commercial stent grafts are used. TEVAR using fenestrated stent grafts (FSG) often does not require additional procedures to revascularize cervical branches. This study aimed to evaluate the features and initial and midterm outcomes of TEVAR using fenestrated stent grafts. METHODS From April 2007 to December 2016, 101 consecutive patients underwent TEVAR using fenestrated stent grafts for distal aortic arch aneurysms at a single centre. Technical success, complications, freedom from aneurysm-related death, secondary intervention and aneurysm progression were retrospectively investigated. RESULTS All the patients underwent TEVAR using fenestrated stent grafts. The 30-day mortality rate was zero. Cerebral infarction, access route problems and spinal cord injury occurred in 4, 3 and 2 patients, respectively. Each type of endoleak was observed in 38 of the 101 patients during the course of the study; 20/38 patients had minor type 1 endoleaks at the time of discharge. The endoleak disappeared in 2 patients and showed no significant change in 8 patients; however, the aneurysm expanded over time in 10 patients. Additional treatment was performed in 8 of the 10 patients with type 1 endoleaks and dilatation of the aneurysm. The rate of freedom from aneurysm-related death during the observation period was 98%. CONCLUSIONS TEVAR with FSG is a simple procedure, with few complications. Additional treatment has been observed to reduce aneurysm-related deaths, even in patients with endoleaks and enlarged aneurysms. Based on this study, the outcomes of endovascular repair of aortic arch aneurysms using a fenestrated stent graft seem acceptable. [ABSTRACT FROM AUTHOR]

Abstract Everolimus is an inhibitor of mammalian target of rapamycin (mTOR) and reduces the risk of cytomegalovirus (CMV) infection in transplant recipients. Everolimus inhibits mTOR complex 1, which regulates factors involved in several crucial cellular functions and is required for CMV replication. However, it is not clear how everolimus regulates CMV replication and prevents and alleviates CMV infection. Effects of everolimus on CMV infection, spread, and DNA synthesis and release from infected cells were assessed by plaque formation, infectious centre assay, real-time PCR of infected cells, and culture supernatant in CMV-infected cultures with and without everolimus. Everolimus enhanced plaque formation by 3.6 times, but the size of the plaques was reduced to 36.4% of untreated cultures in the absence of a pretreatment period. Everolimus reduced viral adsorption but enhanced the replication efficiency of inoculated virus, resulting in an increase in plaque number in the early phase of infection. Preinfection treatment of cells with everolimus efficiently exhibited its antiviral efficacy, and everolimus delayed and suppressed viral DNA synthesis and release from infected cells. Everolimus had suppressed the spread of infection and reduced the number of total infected cells to 40% of untreated cells on day 9, indicating reduction of the size of CMV lesions to one-sixth in 2–3 replication cycles. Preinfection treatment of the cells with everolimus augmented its suppressive effect on CMV infection and replication. Everolimus reduced the total number of infected cells and limited the CMV lesions, and this reduction in the spread of CMV infection would alleviate CMV infection in transplant recipients. Highlights • Everolimus is an inhibitor of mammalian target of rapamycin (mTOR). • Everolimus reduces the risk of cytomegalovirus infection in transplant recipients. • Everolimus suppressed viral adsorption and delayed and suppressed DNA synthesis and release. • Everolimus suppressed the spread of infection and reduced the number of infected cells to 40% of untreated cells on day 9. • Reduction in the spread of CMV infection would alleviate CMV infection in transplant recipients. [ABSTRACT FROM AUTHOR]

Idiopathic pulmonary fibrosis (IPF) is a progressive disease characterized by severe lung fibrosis and a poor prognosis. Although the biomolecules related to IPF have been extensively studied, molecular mechanisms of the pathogenesis and their association with serum biomarkers and clinical findings have not been fully elucidated. We constructed a Bayesian network using multimodal data consisting of a proteome dataset from serum extracellular vesicles, laboratory examinations, and clinical findings from 206 patients with IPF and 36 controls. Differential protein expression analysis was also performed by edgeR and incorporated into the constructed network. We have successfully visualized the relationship between biomolecules and clinical findings with this approach. The IPF-specific network included modules associated with TGF-β signaling (TGFB1 and LRC32), fibrosis-related (A2MG and PZP), myofibroblast and inflammation (LRP1 and ITIH4), complement-related (SAA1 and SAA2), as well as serum markers, and clinical symptoms (KL-6, SP-D and fine crackles). Notably, it identified SAA2 associated with lymphocyte counts and PSPB connected with the serum markers KL-6 and SP-D, along with fine crackles as clinical manifestations. These results contribute to the elucidation of the pathogenesis of IPF and potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Summary When investigating gene expression profiles, determining important directed edges between genes can provide valuable insights in addition to identifying differentially expressed genes. In the subsequent functional enrichment analysis (EA), understanding how enriched pathways or genes in the pathway interact with one another can help infer the gene regulatory network (GRN), important for studying the underlying molecular mechanisms. However, packages for easy inference of the GRN based on EA are scarce. Here, we developed an R package, CBNplot , which infers the Bayesian network (BN) from gene expression data, explicitly utilizing EA results obtained from curated biological pathway databases. The core features include convenient wrapping for structure learning, visualization of the BN from EA results, comparison with reference networks, and reflection of gene-related information on the plot. As an example, we demonstrate the analysis of bladder cancer-related datasets using CBNplot , including probabilistic reasoning, which is a unique aspect of BN analysis. We display the transformability of results obtained from one dataset to another, the validity of the analysis as assessed using established knowledge and literature, and the possibility of facilitating knowledge discovery from gene expression datasets. Availability and implementation The library, documentation and web server are available at https://github.com/noriakis/CBNplot. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

BK polyomavirus-associated nephropathy is one of serious complications in transplant recipients. Everolimus–a mammalian target of rapamycin inhibitor–has been shown to reduce the incidence of BK polyomavirus infection in transplant recipients. In this study, the effects of everolimus were examined on viral replication and the spread of infection in BK polyomavirus-infected cultures. BK polyomavirus replicated in renal and pulmonary cells, contrary to that in hepatocytes, and spread as diffusely scattered patterns of infected cells, unlike plaque formation through the cell-to-cell mode. BK polyomavirus is stable to heat up to 65 °C with a particle per infectivity ratio of 5000, and the replication cycle was for approximately 34 h. Everolimus administration remarkably reduced the viral replication to 20% in cells treated with 0.1–10 ng/mL, the concentration at which everolimus reached the serum of transplant recipients. In addition, it reduced the amount of viral capsid protein 1 at 5 ng/mL without reducing the ratio of viral capsid protein 1 versus β-actin, and it also retained the pattern of viral capsid protein 1 localization in the nuclei. Everolimus suppressed the number of infected cells to 32.8% during a 14-day treatment, indicating the reduction of BK polyomavirus-infected cell mass to 18.8% of untreated cultures by modifying cellular functions. The reduction in the total number of BK polyomavirus infected cells by everolimus indicates that everolimus alleviates BK polyomavirus infection, including nephropathy in transplant recipients. • The fundamental characteristics of BK polyomavirus (BKPyV) are elucidated. • The replication cycle of BKPyV was approximately 34 h with a particle per infectivity ratio of 5000. • BKPyV spread as diffusely scattered patterns, unlike plaque formation through the cell-to-cell mode. • Everolimus at 0.1–10 ng/mL significantly reduced viral replication to 20% in one replication cycle. • Everolimus suppressed the number of BKPyV-infected cells to 32.8%, one-fifth in three-dimension during a 14-day treatment. [ABSTRACT FROM AUTHOR]

Favipiravir, a broad-spectrum RNA-dependent RNA polymerase inhibitor, inhibits the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at significantly lower concentrations than the plasma trough levels achieved by the dosage adopted for influenza treatment and exhibits efficacy against coronavirus disease 2019 (COVID-19) pneumonia. Although high doses of favipiravir are required due to the molecule being a purine analog, its conversion into the active form in infected cells with active viral RNA synthesis enhances the antiviral specificity and selectivity as a chain terminator with lethal mutagenesis. Another characteristic feature is the lack of generation of favipiravir-resistant virus. COVID-19 pneumonia is caused by strong cell-mediated immunity against virus-infected cells, and the inflammatory response induced by adaptive immunity continues to peak for 3 to 5 days despite antiviral treatment. This has also been observed in herpes zoster (HZ) and cytomegalovirus (CMV) pneumonia. Inflammation due to an immune response may mask the effectiveness of favipiravir against COVID-19 pneumonia. Favipiravir significantly shortened the recovery time in patients with mild COVID-19 pneumonia by 3 days with the start of treatment by the 5th day of symptom onset. Since both CMV and COVID-19 pneumonia are caused by adaptive immunity and prevention of cytomegalovirus pneumonia is the standard treatment due to difficulties in treating refractory CMV pneumonia, COVID-19 pneumonia should be prevented with early treatment as well. In the present study, we have comprehensively reviewed the optimal antiviral therapy for COVID-19 based on clinical trials of favipiravir for the treatment of COVID-19 pneumonia and the concurrently established therapies for other viral infections, particularly HZ and CMV pneumonia. Optimally, antivirals should be administered immediately after COVID-19 diagnosis, similar to that after influenza diagnosis, to prevent COVID-19 pneumonia and complications resulting from microangiopathy. [ABSTRACT FROM AUTHOR]

The primary objective of this study was to investigate the fundamental phase change characteristics of a nanoemulsion using differential scanning calorimetry (DSC). Tetradecane, which has a slightly higher melting point than water, was utilized as the phase change material for the nanoemulsion. The melting point of the nanoemulsion, the melting peak temperature, and latent heat were examined in detail. Regarding the fundamental phase change characteristics of the nanoemulsion, it was found that its phase change characteristics were strongly affected by the temperature-scanning rate of the DSC. Moreover, it was confirmed that the phase change behavior does not change with repeated solidification and melting. [ABSTRACT FROM AUTHOR]

The body sizes of individuals of the choosing and chosen sexes in a mate choice may affect sequential mating of females. We examined the effects of the body sizes of females and their mates on attributes of female first mating, and the effects of body sizes of females and their previous and potential future mates on female remating in the adzuki bean beetle, Callosobruchus chinensis. Large- and small-sized adults were derived from larvae reared under conditions of low and high density in a bean, respectively. The speed of first mating of large females was not affected by the size of courting males, whereas small females initiated mating more rapidly when courted by small males. The remating probability of large females was not affected by first male size, whereas small females that mated first with smaller males were more likely to remate. These data suggest that pre- and post-copulatory female choices for male size depend on the female's size, and the small females might be more willing to copulate with smaller males but prefer larger males to sire their offspring after copulation. A possible explanation for this preference is that small females may suffer greater harm from copulating with larger males. [ABSTRACT FROM AUTHOR]

Moyamoya disease (MMD) is a rare cerebrovascular disease endemic in East Asia. The p.R4810K mutation in RNF213 gene confers a risk of MMD, but other factors remain largely unknown. We tested the association of gut microbiota with MMD. Fecal samples were collected from 27 patients with MMD, 7 patients with non-moyamoya intracranial large artery disease (ICAD) and 15 control individuals with other disorders, and 16S rRNA were sequenced. Although there was no difference in alpha diversity or beta diversity between patients with MMD and controls, the cladogram showed Streptococcaceae was enriched in patient samples. The relative abundance analysis demonstrated that 23 species were differentially abundant between patients with MMD and controls. Among them, increased abundance of Ruminococcus gnavus > 0.003 and decreased abundance of Roseburia inulinivorans < 0.002 were associated with higher risks of MMD (odds ratio 9.6, P = 0.0024; odds ratio 11.1, P = 0.0051). Also, Ruminococcus gnavus was more abundant and Roseburia inulinivorans was less abundant in patients with ICAD than controls (P = 0.046, P = 0.012). The relative abundance of Ruminococcus gnavus or Roseburia inulinivorans was not different between the p.R4810K mutant and wildtype. Our data demonstrated that gut microbiota was associated with both MMD and ICAD. [ABSTRACT FROM AUTHOR]

Finding damage inside pipes is important for the inspection of complex pipes used in nuclear power plants and chemical plants. A number of studies have investigated the mechanisms of an actuator with an electric cable to provide locomotion through various devices in complex pipes. An in-pipe robot capable of movement in narrow complex pipes has not yet been developed. In the present paper, we propose a globular magnetic actuator group that exhibits a very high thrust force and is capable of free reversible motion in complex pipes. Two actuators of the same size and characteristics are coupled by the magnetic connection method, which generates almost no mechanical loss. The globular magnetic actuator group capable of reversible motion through elongation and contraction of eight shape-memory-alloy (SMA) coils was fabricated. Experimental results indicate that the prototype actuator group is able to climb at a rate of 29 mm/s in a straight pipe while pulling a load mass of 48 g. [ABSTRACT FROM AUTHOR]

This paper proposes a globular magnetic actuator of a new type that exhibits a very high thrusting force and is capable of a reversible motion in a complex pipe. The globular magnetic actuator of the reversible type due to opening and closing of a compound material by using elongation and contraction of four shape-memory-alloy (SMA) coils was fabricated. The globular magnetic actuator moves by difference in frictional force between forward and backward supporting force of the compound material. Experimental result shows that the prototype actuator was able to climb at 18 mm/s in the straight pipe when pulling the load mass of 24 g. In addition, the measurement of an average speed carried out for two patterns of movement in a complex pipe with many curved parts and step parts. The prototype actuator was able to move in the complex pipe over the average speed of 35 mm/s. This actuator has many possible applications, including small pipe inspection and maintenance. [ABSTRACT FROM AUTHOR]

Abstract: The sequential glycosylation of a soybean isoflavone, daidzein, with cultured suspension cells of Eucalyptus perriniana and cyclodextrin glucanotransferase was studied. Daidzein was converted into two glycosylation products, daidzein 7-O-β-d-glucopyranoside (39%) and daidzein 7-O-[6-O-(β-d-glucopyranosyl)]-β-d-glucopyranoside (β-gentiobioside, 6%), by cultured E. perriniana cells. Further glycosylation of daidzein 7-O-β-glucoside with cyclodextrin glucanotransferase gave daidzein 7-O-[4-O-(α-d-glucopyranosyl)]-β-d-glucopyranoside (β-maltoside, 26%), daidzein 7-O-β-maltotrioside (15%), and daidzein 7-O-β-maltotetraoside (7%). [Copyright &y& Elsevier]

Many contemporary archaeologists would agree that archaeology can be, and should be, practiced in an ethical manner. Following this incentive, current archaeology seeks to formalize the practitioners' understanding of the ethical practice of archaeology, usually by examining the morality of archaeologists' actions in the practice and/or the ethical consequences of archaeology. In this paper, I will discuss a potential consequence of this institutional formalisation of disciplinary ethics, which tends to isolate the archaeologist's ethical intention from the practice of archaeology. [ABSTRACT FROM AUTHOR]

This paper proposes a neural network for moving object recognition based on the visual system. The proposed network has a structure focusing on the parallel hierarchy of visual information processing and can recognize moving objects. The network is composed of a movement detection module, a moving object estimation module, and a moving object recognition module. The movement detection module uses a neural network which is a model of the motion recognition aspect of vision and recognizes motion. The moving object estimation module uses a hierarchical neural network with the backpropagation (BP) algorithm, and infers moving objects based on the features of the motion. The moving object recognition module uses a multiple-structured neural network which is obtained by improvement of the inhibition mechanism and recognizes moving objects on the basis of shape features. The information is transmitted from the movement detection module to the moving object recognition module through the moving object estimation module. With this mechanism, the motion recognition and pattern recognition processes are integrated, and moving objects can be recognized. A computer simulation is performed on the recognition of a walking human, and the effectiveness of the proposed network is demonstrated. © 2004 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 87(9): 46–55, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20115 [ABSTRACT FROM AUTHOR]

• Acute kidney injury (AKI) occurs frequently in the intensive care unit and it is important to identify high-risk patients. • We proposed a system to predict AKI using convolutional neural networks with providing the basis of prediction. • The proposed system could predict AKI in moderate performance, and provided the reasonable interpretation. Acute kidney injury (AKI) occurs frequently in in-hospital patients, especially in the intensive care unit (ICU), due to various etiologies including septic shock. It is clinically important to identify high-risk patients at an early stage and perform the appropriate intervention. We proposed a system to predict AKI using one-dimensional convolutional neural networks (1D-CNN) with the real-time calculation of the probability of developing AKI, along with the visualization of the rationale behind prediction using score-weighted class activation mapping and guided backpropagation. The system was applied to predicting developing AKI based on the KDIGO guideline in time windows of 24 to 48 h using data of 0 to 24 h after admission to ICU. The comparison result of multiple algorithms modeling time series data indicated that the proposed 1D-CNN model achieved higher performance compared to the other models, with the mean area under the receiver operating characteristic curve of 0.742 ± 0.010 for predicting stage 1, and 0.844 ± 0.029 for stage 2 AKI using the input of the vital signs, the demographic information, and serum creatinine values. The visualization results suggested the reasonable interpretation that time points with higher respiratory rate, lower blood pressure, as well as lower SpO2, had higher attention in terms of predicting AKI, and thus important for prediction. We presumed the proposed system's potential usefulness as it could be applied and transferred to almost any ICU setting that stored the time series data corresponding to vital signs. [ABSTRACT FROM AUTHOR]

A three-phase cage rotor induction machine works as an induction generator if it is driven by a prime mover and self-excited by a capacitor connected to its terminal and residual magnetism of the machine. The machine of this type is called a self-excited induction generator and is used mainly as an independent power source isolated from a commercial power network. The reactive output power of the induction generator is limited because the capacitance used for self-excitation is fixed. The article analyzes the experimental facts from theoretical viewpoints taking into account the core saturation characteristics of the machine. The relation between the machine and circuit constants and the control range is clarified.

This article produces a simplified scheme in which the converter on the generator side controls both the reactive and real output powers without using the reactive power controller. The generator proposed in this article can be operated stably not only in steady state, but also in transient state. The induction generator is driven by a dc motor and these output power is converted to dc power, and dc power is converted to ac power of constant frequency through a separately excited inverter. The reactive power required for excitation of induction generator is supplied by the generator converter operating at control angle of advance.

An induction generator has been proposed that works stably over a wide-speed range. The only disadvantage of this generator is that a reactive power has to be supplied from a power source on the inverter side. This article proposes a means to solve the difficulty by connecting a dc chopper to the dc side of the inverter. The chopper works not only as a bypass circuit of dc current but also as a forced commutation circuit of inverter. A scheme is proposed to control the primary flux to keep the total efficiency maximum over wide ranges of generator speed and output power. In this case, the power factor of induction machine at low and output power level is also improved. A disadvantage of the proposed scheme is that the main circuit and the control circuit are a little complicated.

We review magnetic and superconducting properties of UT2Al3 (T = Pd, Ni) and UGe2 together with URu2Si2. For UPd2Al3, we have suggested that the superconducting attractive paring interaction is mediated by magnetic excitons. Knight shift measurements of UNi2Al3 show an odd parity pairing in contrast to an even parity formation in UPd2Al3. The ac magnetic susceptibility measurements of UGe2 indicate that the volume fraction of superconductivity grows with increasing pressure, suggesting inhomogeneous coexistence of superconductivity and ferromagnetism. Recent dc magnetization measurements on UGe2 exhibit a step like hysteresis loop at low temperatures. An analysis of the data suggests that a magnetic domain size is smaller than a superconducting coherence length. Finally, we report the observation of an anomaly appearing in the thermal expansion of URu2Si2 under high pressures, which can be ascribed to the phase transition between a hidden and antiferromagnetic order. [Copyright &y& Elsevier]

Amylase genes reside in a structurally complex locus, and their copy numbers vary greatly, and several studies have reported their association with obesity. The mechanism of this effect was partially explained by changes in the oral and gut microbiome compositions; however, a detailed mechanism has been unclarified. In this study, we showed their association with diabetes in addition to obesity, and further discovered a plausible mechanism of this association based on the function of commensal bacteria. First, we confirmed that the amylase copy number in the population tends to be larger than that reported in other studies and that there is a positive association between obesity and diabetes (p = 1.89E–2 and 8.63E–3). Second, we identified that relative abundance of some genus level microbiome, Capnocytophaga, Dialister, and previously reported bacteria, were significantly associated with amylase copy numbers. Finally, through functional gene-set analysis using shotgun sequencing, we observed that the abundance of genes in the Acarbose pathway in the gut microbiome was significantly decreased with an increase in the amylase copy number (p-value = 5.80E–4). Our findings can partly explain the mechanism underlying obesity and diabetes in populations with high amylase copy numbers. [ABSTRACT FROM AUTHOR]

Quasicrystals are metallic alloys that possess long-range, aperiodic structures with diffraction symmetries forbidden to conventional crystals. Since the discovery of quasicrystals by Schechtman et al. in 1984, there has been considerable progress in resolving their geometric structure. For example, it is well known that the golden ratio of mathematics and art occurs over and over again in their crystal structure. However, the characteristic properties of the electronic states-whether they are extended as in periodic crystals or localized as in amorphous materials-are still unresolved. Here we report the first observation of quantum (T?=?0) critical phenomena of the Au-Al-Yb quasicrystal-the magnetic susceptibility and the electronic specific heat coefficient arising from strongly correlated 4f electrons of the Yb atoms diverge as T?0. Furthermore, we observe that this quantum critical phenomenon is robust against hydrostatic pressure. By contrast, there is no such divergence in a crystalline approximant, a phase whose composition is close to that of the quasicrystal and whose unit cell has atomic decorations (that is, icosahedral clusters of atoms) that look like the quasicrystal. These results clearly indicate that the quantum criticality is associated with the unique electronic state of the quasicrystal, that is, a spatially confined critical state. Finally we discuss the possibility that there is a general law underlying the conventional crystals and the quasicrystals. [ABSTRACT FROM AUTHOR]

LIGA process has been developed in the 2.5-dimensional world. We introduced new technologies of a 3D X-ray lithography and a worm injection molding with an unscrewing de-molding mechanism, and succeeded in the deployment of a 3D LIGA process. Furthermore, we fabricated a spiral microcoil using the 3D-LIGA process and a metallization technique combining flat and smooth electroplating and isotropic chemical etching. The microcoil diameter was 0.5 mm and the length was 1 mm. The width of coil lines was 10µm and the pitch was 20µm. Characteristics of this microcoil as an inductor combine the inductance of 91 nH and the quality factor of 5.8 at the frequency of 1 GHz. © 2008 Wiley Periodicals, Inc. Electr Eng Jpn, 166(1): 43–51, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.20679 [ABSTRACT FROM AUTHOR]

In this paper, a novel version of the dual voltage converter is presented with improved voltage regulation and enabling a wide range of voltage control by using self-turn-off devices (power transistors) instead of diodes. Further, this system operates with unity displacement factor. We have obtained the analytical expressions of this circuit. The results are, however, quite complex. We could calculate values of the voltage and current waveforms by using a computer. The calculated values are essentially in agreement with the experimental values. Experimentally, an ideal load characteristics with null voltage regulation was obtained by the conduction angle control for power transistors. Further, a wide range of voltage from 220 V to 39 V was obtained. A disadvantage for this system is the requirement for snubber circuits with a larger value of capacitor in order to suppress the surge voltages a turn-off periods. [ABSTRACT FROM AUTHOR]

Background: Automated classification of glomerular pathological findings is potentially beneficial in establishing an efficient and objective diagnosis in renal pathology. While previous studies have verified the artificial intelligence (AI) models for the classification of global sclerosis and glomerular cell proliferation, there are several other glomerular pathological findings required for diagnosis, and the comprehensive models for the classification of these major findings have not yet been reported. Whether the cooperation between these AI models and clinicians improves diagnostic performance also remains unknown. Here, we developed AI models to classify glomerular images for major findings required for pathological diagnosis and investigated whether those models could improve the diagnostic performance of nephrologists.Methods: We used a dataset of 283 kidney biopsy cases comprising 15,888 glomerular images that were annotated by a total of 25 nephrologists. AI models to classify seven pathological findings: global sclerosis, segmental sclerosis, endocapillary proliferation, mesangial matrix accumulation, mesangial cell proliferation, crescent, and basement membrane structural changes, were constructed using deep learning by fine-tuning of InceptionV3 convolutional neural network. Subsequently, we compared the agreement to truth labels between majority decision among nephrologists with or without the AI model as a voter.Results: Our model for global sclerosis showed high performance (area under the curve: periodic acid-Schiff, 0.986; periodic acid methenamine silver, 0.983); the models for the other findings also showed performance close to those of nephrologists. By adding the AI model output to majority decision among nephrologists, out of the 14 constructed models, the results of the majority decision showed improvement in sensitivity for 10 models (four of them were statistically significant) and specificity for eight models (five significant).Conclusion: Our study showed a proof-of-concept for the classification of multiple glomerular findings in a comprehensive method of deep learning and suggested its potential effectiveness in improving diagnostic accuracy of clinicians. [ABSTRACT FROM AUTHOR]

A multimodal imaging instrument has been developed that integrates scanning near‐field optical microscopy with nanofocused synchrotron X‐ray diffraction imaging. The instrument allows for the simultaneous nanoscale characterization of electronic/near‐field optical properties of materials together with their crystallographic structure, facilitating the investigation of local structure–property relationships. The design, implementation and operating procedures of this instrument are reported. The scientific capabilities are demonstrated in a proof‐of‐principle study of the insulator–metal phase transition in samarium sulfide (SmS) single crystals induced by applying mechanical pressure via a scanning tip. The multimodal imaging of an in situ tip‐written region shows that the near‐field optical reflectivity can be correlated with the heterogeneously transformed structure of the near‐surface region of the crystal. [ABSTRACT FROM AUTHOR]

The Ag–In–Ce alloy is an approximant crystal to a Tsai-type quasicrystal and exhibits heavy-fermion (Kondo) physics. This new type of Kondo material exhibits spin-glass ordering below the freezing temperature Tf ∼ 0.3 K at ambient pressure. Here we investigated the effect of hydrostatic pressure on the Ag–In–Ce alloy. Spin-glass features, such as the frequency-dependent cusp near Tf in the ac magnetic susceptibility curve, were observed even under external pressure. In addition, the C/T value (where C is the specific heat) increased with decreasing temperature and exhibited a broad peak above Tf. The Tf increased as the pressure increased up to its highest value in the experiment (approximately 2.6 GPa). [ABSTRACT FROM AUTHOR]

The hexagonal ZrNiAl-type (space group: P 2m) and the tetragonal Mo2FeB2-type (space group: P4/mbm) structures, which are formed in the same Yb-based alloys and exhibit physical properties related to valence-fluctuation, can be regarded as approximants of a hypothetical dodecagonal quasicrystal. Using Pd-Sn-Yb system as an example, a model of quasicrystal structure has been constructed, of which five-dimensional crystal (space group: P12/mmm, a DD = 5.66 Å and c = 3.72 Å) consists of four types of acceptance regions located at the following crystallographic sites; Yb [0 0 0 0 0], Pd[1/3 0 1/3 0 1/2], Pd[1/3 1/3 1/3 1/3 0] and Sn[1/2 00 1/2 1/2]. In the three-dimensional space, the quasicrystal is composed of three types of columns, of which c-projections correspond to a square, an equilateral triangle and a three-fold hexagon. They are fragments of two known crystals, the hexagonal α-YbPdSn and the tetragonal Yb2Pd2Sn structures. The model of the hypothetical quasicrystal may be applicable as a platform to treat in a unified manner the heavy fermion properties in the two types of Yb-based crystals. [ABSTRACT FROM AUTHOR]

CeCu 6− x Au x is known as a heavy fermion compound that exhibits antiferromagnetism for x ≳ 0 . 1 and non-Fermi-liquid (NFL) behavior around the critical concentration x c ≈ 0 . 1 . Although this material has been studied by means of a lot of experiments, the origin of its NFL is still veiled in mystery. In this study, we examine the magnetic properties of CeCu 6− x Au x for various values of x ( 0 ≤ x ≤ 0.8 ), and discuss the possibility that the quantum valence criticality might be responsible for the low-temperature magnetic properties. [ABSTRACT FROM AUTHOR]

We have examined the potential of Lγ4 emission spectroscopy as a new method for valence determination. Sm Lγ4 emission spectra of a mixed valence compound, SmB6, as well as Sm standard references were recorded using a multicrystal, multidetector spectrometer at 298 K. The Lγ4 spectra exhibited a large chemical shift (∼4.5 eV) and substantial profile changes depending on the Sm oxidation state. Splitting of the Sm Lγ4 band was attributed to spin-dependent atomic multiplets, and valence-dependent edge-shifts of the Sm LI XANES spectra strongly suggest that the chemical shift of the Lγ4 emission is mainly due to the screening effects of the Sm LI core. The Lγ4 spectrum of SmB6 was well reproduced by the averaged spectra of SmS and SmF3, indicating a SmB6 valence of 2.65 ± 0.03. The advantages of the Lγ4 method, including simple data treatment and no need for an excitation energy scan, will encourage its use in several areas of materials science. [ABSTRACT FROM AUTHOR]

Non-Fermi-liquid (NFL), a significant deviation from Fermi-liquid theory, usually emerges near an order-disorder phase transition at absolute zero. Recently, a diverging susceptibility toward zero temperature was observed in a quasicrystal (QC). Since an electronic long-range ordering is normally absent in QCs, this anomalous behaviour should be a new type of NFL. Here we study high-resolution partial-fluorescence-yield x-ray absorption spectroscopy on Yb-based intermediate-valence icosahedral QCs and cubic approximant crystals (ACs), some of which are new materials, to unveil the mechanism of the NFL. We find that for both forms of QCs and ACs, there is a critical lattice parameter where Yb-valence and magnetism concomitantly exhibit singularities, suggesting a critical-valence-fluctuation-induced NFL. The present result provides an intriguing structure–property relationship of matter; size of a Tsai-type cluster (that is a common local structure to both forms) tunes the NFL whereas translational symmetry (that is present in ACs but absent in QCs) determines the nature of the NFL against the external/chemical pressure. [ABSTRACT FROM AUTHOR]

Amenamevir is a helicase-primase inhibitor of herpes simplex virus (HSV) and varicella-zoster virus (VZV) and is used for the treatment of herpes zoster in Japan. The half maximal effective concentrations (EC 50 s) of acyclovir and sorivudine for VZV increased as the time of treatment was delayed from 6 to 18 h after infection, while those of amenamevir and foscarnet were not affected. Susceptibility of infected cells at 0 and 18 h after infection was examined with four anti-herpes drugs, and the fold increases in EC 50 for acyclovir, sorivudine, amenamevir, and foscarnet were 13.1, 6.3, 1.3, and 1.0, respectively. The increase in the EC 50 s for acyclovir in the late phase of infection in VZV and HSV was abolished by hydroxyurea, a ribonucleotide reductase (RR) inhibitor. The common mechanism affecting antiviral activities of acyclovir to HSV and VZV was examined in HSV-infected cells. The amount of HSV DNA in cells treated with amenamevir at 10 x EC 50 was similar at 0 and 12 h but less than that in cells treated with acyclovir at 10 x EC 50. dGTP, produced through viral RR, peaked at 4 h and decreased thereafter as it was consumed by viral DNA synthesis. Because acyclovir and amenamevir inhibited viral DNA synthesis, thus making dGTP unnecessary, dGTP was significantly more abundant in the presence of acyclovir and amenamevir than in untreated, infected cells. Abundant dGTP supplied by RR may compete with acyclovir triphosphate and attenuate its antiviral activity. In contrast, abundant dGTP did not influence the inhibitory action of amenamevir on viral helicase-primase activity. ATP was significantly decreased at 12 h after infection and significantly more abundant in untreated infected cells compared to cells treated with acyclovir and amenamevir. The anti-herpetic activity of amenamevir was not affected by the replication cycle of VZV and HSV, indicating the suitability of amenamevir for the treatment of herpes zoster and suppressive therapy for genital herpes. • dGTP increased at 4h and thereafter decreased in HSV infected cells. • dGTP significantly increased in cells treated with acyclovir and amenamevir. • ATP decreased in HSV infected cells and furthermore in antiviral-treated cells at 12 h after infection. • Antiviral activity of acyclovir was attenuated by viral RR in the late phase of infection. • Antiviral activity of amenamevir was not affected by the replication cycle of VZV. [ABSTRACT FROM AUTHOR]

Abstract: We report that the electronic structure of SmS at ambient pressure has been studied by the optical conductivity measurement and by the band structure calculation. The spectrum has a direct gap structure at 0.4eV but no clear gap structure expected by other experiments appears at 86meV . The temperature dependence of the Drude weight, however, indicates the evidence of an indirect gap with the gap size of 1000K. These results were well explained by a band structure calculation. [Copyright &y& Elsevier]

Abstract: Elastic neutron scattering experiments on the pressure-induced ferromagnetic superconductor have been carried out under pressures P up to 1.6GPa at temperatures T down to 60mK, to study the correlation between superconductivity and ferromagnetism. No change was observed in ferromagnetic Bragg peak intensities nor a line width at through the superconducting transition temperature under and 1.25GPa, suggesting that the ferromagnetism is not affected by the onset of superconductivity under these two pressures. [Copyright &y& Elsevier]

Abstract: We have prepared single crystals of SmS under various conditions, and studied sample dependence on the specific heat and the electrical resistivity. Some samples exhibit a huge anomaly in the temperature dependence of the specific heat at low temperatures. We show that the anomaly can be ascribed to secondary phases and will give rise to a spurious term in the golden phase. [Copyright &y& Elsevier]

We have measured magnetization curves of the pressure-induced ferromagnetic superconductor UGe2 at temperatures down to 0.5 K under various pressures. The ferromagnetic hysteresis loop is smooth down to about 1 K, but on further decreasing temperature, the hysteresis suddenly changes into a staircase-like curve, and the jump occurs at regular interval of magnetic field. We ascribe this novel finding to the macroscopic quantum tunneling effect (MQT). An analysis based on MQT suggests tiny magnetic domain formation whose size is smaller than the superconducting coherence length. [Copyright &y& Elsevier]

We have measured ac magnetic susceptibility of the ferromagnet UGe2 which shows superconductivity in an external pressure range, P1&les;P&les;P2, in the ferromagnetic phase. When P is close to P1 (∼7 kbar in the present study) in the superconducting phase, the ac magnetic susceptibility indicates an imperfect superconducting shielding effect. It increases with pressure and shows nearly the perfect shielding effect around ∼12 kbar. We have also found that a superconducting onset temperature seems to be almost independent of the pressure below ∼12 kbar. [Copyright &y& Elsevier]

Volume expansion measurements of single crystalline UGe2 samples have been made under pressure. The linear coefficient αV(T) at ambient pressure shows a broad hump at around Tx∼25 K and a sharp transition at TC=52 K. We have observed that the anomaly in ΔαV at Tx becomes prominent and increases in magnitude with increasing pressure. [Copyright &y& Elsevier]