Local Change Point Detection and Signal Cleaning using EEMD with applications to Acoustic Shockwaves

The Ensemble Empirical Mode Decomposition (EEMD) has become a preferred technique to decompose nonlinear and non-stationary signals due to its ability to create time-varying basis functions. However, current EEMD signal cleaning techniques are unable to deal with situations where a signal only occurs for a portion of the entire recording length. By combining change point detection and statistical hypothesis testing, we demonstrate how to clean a signal to emphasize unique local changes within each basis function. This not only allows us to observe which frequency bands are undergoing a change, but also leads to improved recovery of the underlying information. Using this technique, we demonstrate improved signal cleaning performance for acoustic shockwave signal detection. The technique is implemented in R via the LCDSC package

Clustering of Primordial Black Holes from QCD Axion Bubbles

We study the clustering of primordial black holes (PBHs) and axion miniclusters produced in the model proposed to explain the LIGO/Virgo events or the seeds of the supermassive black holes (SMBHs) in arXiv:2006.13137. It is found that this model predicts large isocurvature perturbations due to the clustering of PBHs and axion miniclusters, from which we obtain stringent constraints on the model parameters. Specifically, for the axion decay constant $f_a=10^{16}~\mathrm{GeV}$, which potentially accounts for the seeds of the SMBHs, the PBH fraction in dark matter should be $f_\mathrm{PBH}\lesssim7\times 10^{-10}$. Assuming that the mass of PBHs increases by more than a factor of $\mathcal{O}(10)$ due to accretion, this is consistent with the observed abundance of SMBHs. On the other hand, for $f_a=10^{17}~\mathrm{GeV}$ required to produce PBHs of masses detected in the LIGO/Virgo, the PBH fraction should be $f_\mathrm{PBH}\lesssim6\times 10^{-8}$, which may be too small to explain the LIGO/Virgo events, although there is a significant uncertainty in calculating the merger rate in the presence of clustering.Comment: 18 pages, 11 figure

Selective Translation of the Measles Virus Nucleocapsid mRNA by La Protein

Measles, caused by measles virus (MeV) infection, is the leading cause of death in children because of secondary infections attributable to MeV-induced immune suppression. Recently, we have shown that wild-type MeVs induce the suppression of protein synthesis in host cells (referred to as “shutoff”) and that viral mRNAs are preferentially translated under shutoff conditions in infected cells. To determine the mechanism behind the preferential translation of viral mRNA, we focused on the 5′ untranslated region (UTR) of nucleocapsid (N) mRNA. The La/SSB autoantigen (La) was found to specifically bind to an N-5′UTR probe. Recombinant La enhanced the translation of luciferase mRNA containing the N-5′UTR (N-fLuc), and RNA interference of La suppressed N-fLuc translation. Furthermore, recombinant MeV lacking the La-binding motif in the N-5′UTR displayed delayed viral protein synthesis and growth kinetics at an early phase of infection. These results suggest that La induced predominant translation of N mRNA via binding to its 5′UTR under shutoff conditions. This is the first report on a cellular factor that specifically regulates paramyxovirus mRNA translation

Development of a high-throughput field phenotyping rover optimized for size-limited breeding fields as open-source hardware

Phenotyping is a critical process in plant breeding, especially when there is an increasing demand for streamlining a selection process in a breeding program. Since manual phenotyping has limited efficiency, highthroughput phenotyping methods are recently popularized owing to progress in sensor and image processing technologies. However, in a size-limited breeding field, which is common in Japan and other Asian countries, it is challenging to introduce large machinery in the field or fly unmanned aerial vehicles over the field. In this study, we developed a ground-based high-throughput field phenotyping rover that could be easily introduced to a field regardless of the scale and location of the field even without special facilities. We also made the field rover open-source hardware, making its system available to public for easy modification, so that anyone can build one for their own use at a low cost. The trial run of the field rover revealed that it allowed the collection of detailed remote-sensing images of plants and quantitative analyses based on the images. The results suggest that the field rover developed in this study could allow efficient phenotyping of plants especially in a small breeding field

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon

タイヌビエのゲノムを高精度解読 --除草剤に抵抗性を持つ水田の雑草タイヌビエの高精度ゲノム解読に成功--. 京都大学プレスリリース. 2023-11-07.Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32, 337, and 30, 889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production

Host range and receptor utilization of canine distemper virus analyzed by recombinant viruses: Involvement of heparin-like molecule in CDV infection

AbstractWe constructed recombinant viruses expressing enhanced green fluorescent protein (EGFP) or firefly luciferase from cDNA clones of the canine distemper virus (CDV) (a Japanese field isolate, Yanaka strain). Using these viruses, we examined susceptibilities of different cell lines to CDV infection. The results revealed that the recombinant CDVs can infect a broad range of cell lines. Infectivity inhibition assay using a monoclonal antibody specific to the human SLAM molecule indicated that the infection of B95a cells with these recombinant CDVs is mainly mediated by SLAM but the infection of 293 cell lines with CDV is not, implying the presence of one or more alternative receptors for CDV in non-lymphoid tissue. Infection of 293 cells with the recombinant CDV was inhibited by soluble heparin, and the recombinant virus bound to immobilized heparin. Both F and H proteins of CDV could bind to immobilized heparin. These results suggest that heparin-like molecules are involved in CDV infection

Cord Blood Transplantation from Unrelated Donors for Children with Acute Lymphoblastic Leukemia in Japan: The Impact of Methotrexate on Clinical Outcomes

Cord blood transplantation (CBT) from an unrelated donor is recognized as one of the major treatment modalities in allogeneic stem cell transplantation (SCT) for children with hematologic malignancies. We analyzed the clinical outcomes of CBT for children with acute lymphoblastic leukemia (ALL) in Japan and identified the risk factors for the transplant outcomes. From 1997 to 2006, 332 children with ALL underwent CBT from unrelated donors, 270 of which had no prior transplant. Their disease statuses at transplant were first complete remission (CR) (n = 120), second CR (n = 71), and more advanced stages (n = 75). As preconditioning for SCT, total body irradiation (TBI) was given to 194 patients and, for the prophylaxis of graft-versus-host disease (GVHD), methotrexate (MTX) was given to 159 patients. The cumulative incidents of neutrophil and platelet recovery (>20 K) were 88.5% and 78.4%, respectively. The incidents of grade II-IV, III-IV acute GVHD (aGVHD), and chronic GVHD (cGVHD) were 45.6%, 20.4%, and 19.2%, respectively, and treatment-related mortality was 22.6%. The 5-year event-free survival (EFS) and overall survival (OS) at CR1, CR2, and advanced status were 47.4%, 45.5%, 15.0%, and 63.7%, 59.7%, and 20.7%, respectively. Multivariate analysis revealed that MTX with calcineurin inhibitor (CNI) was associated with decreased incidence of grade II-IV GVHD (CNI alone: hazard ratio [HR] = 1.74, 95% confidence interval [CI] = 1.06-2.83, P = .027; CNI + prednisolone (PSL), HR = 1.61, 95% CI = 1.03-2.50, P = .036), III-IV aGVHD (CNI alone: HR = 3.02, 95% CI = 1.55-5.91, P = 0.001; CNI + PSL, HR = 1.89, 95% CI = 0.93-3.83, P = .078), or cGVHD (CNI alone: HR = 1.78, 95% CI = 0.83-3.82, P = .143; CNI + PSL, HR = 2.44, 95% CI = 1.24-4.82, P = .01), compared with CNI alone or CNI + PSL. At an advanced stage of disease, GVHD prophylaxis with MTX + CNI is associated with improved OS compared with CNI alone (CNI alone: HR = 3.20, 95% CI = 1.43-7.15, P = .005; CNI + PSL, HR = 1.47, CI = 0.67-3.20, P = .332). Our retrospective study showed that CBT for children with ALL is feasible and GVHD prophylaxis with MTX + CNI is associated with significant favorable outcomes in prevention of aGVHD and cGVHD as well as survival advantage in advanced cases

The DsbA-L gene is associated with respiratory function of the elderly via its adiponectin multimeric or antioxidant properties

Oxidative stress and inflammation play a key role in the age-related decline in the respiratory function. Adipokine in relation to the metabolic and inflammatory systems is attracting growing interest in the field of respiratory dysfunction. The present clinical and experimental studies investigated the role of the disulfide bond-forming oxidoreductase A-like protein (DsbA-L) gene, which has antioxidant and adiponectin multimeric (i.e. activation) properties, on the respiratory function of the elderly. We performed a retrospective longitudinal genotype-phenotype relationship analysis of 318 Japanese relatively elderly participants (mean age ± standard deviation: 67.0 ± 5.8 years) during a health screening program and an in vitro DsbA-L knock-down evaluation using 16HBE14o-cells, a commonly evaluated human airway epithelial cell line. The DsbA-L rs1917760 polymorphism was associated with a reduction in the ratio of forced expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) and %FEV1 and with the elevation of the prevalence of FEV1/FVC < 70%. We also confirmed that the polymorphism was associated with a decreased respiratory function in relation to a decrease in the ratio of high-molecular-weight adiponectin/total adiponectin (as a marker of adiponectin multimerization) and an increase in the oxidized human serum albumin (as an oxidative stress marker). Furthermore, we clarified that DsbA-L knock-down induced oxidative stress and up-regulated the mucus production in human airway epithelial cells. These findings suggest that the DsbA-L gene may play a role in protecting the respiratory function of the elderly, possibly via increased systemic adiponectin functions secreted from adipocytes or through systemic and/or local pulmonary antioxidant properties

White Paper from Workshop on Large-scale Parallel Numerical Computing Technology (LSPANC 2020): HPC and Computer Arithmetic toward Minimal-Precision Computing

In numerical computations, precision of floating-point computations is a key factor to determine the performance (speed and energy-efficiency) as well as the reliability (accuracy and reproducibility). However, precision generally plays a contrary role for both. Therefore, the ultimate concept for maximizing both at the same time is the minimal-precision computing through precision-tuning, which adjusts the optimal precision for each operation and data. Several studies have been already conducted for it so far (e.g. Precimoniuos and Verrou), but the scope of those studies is limited to the precision-tuning alone. Hence, we aim to propose a broader concept of the minimal-precision computing system with precision-tuning, involving both hardware and software stack. In 2019, we have started the Minimal-Precision Computing project to propose a more broad concept of the minimal-precision computing system with precision-tuning, involving both hardware and software stack. Specifically, our system combines (1) a precision-tuning method based on Discrete Stochastic Arithmetic (DSA), (2) arbitrary-precision arithmetic libraries, (3) fast and accurate numerical libraries, and (4) Field-Programmable Gate Array (FPGA) with High-Level Synthesis (HLS). In this white paper, we aim to provide an overview of various technologies related to minimal- and mixed-precision, to outline the future direction of the project, as well as to discuss current challenges together with our project members and guest speakers at the LSPANC 2020 workshop; https://www.r-ccs.riken.jp/labs/lpnctrt/lspanc2020jan/