Doshisha University

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

This paper introduces a new open source platform for end-to-end speech processing named ESPnet. ESPnet mainly focuses on end-to-end automatic speech recognition (ASR), and adopts widely-used dynamic neural network toolkits, Chainer and PyTorch, as a main deep learning engine. ESPnet also follows the Kaldi ASR toolkit style for data processing, feature extraction/format, and recipes to provide a complete setup for speech recognition and other speech processing experiments. This paper explains a major architecture of this software platform, several important functionalities, which differentiate ESPnet from other open source ASR toolkits, and experimental results with major ASR benchmarks.

We conducted preregistered replications of 28 classic and contemporary published findings, with protocols that were peer reviewed in advance, to examine variation in effect magnitudes across samples and settings. Each protocol was administered to approximately half of 125 samples that comprised 15,305 participants from 36 countries and territories. Using the conventional criterion of statistical significance ( p < .05), we found that 15 (54%) of the replications provided evidence of a statistically significant effect in the same direction as the original finding. With a strict significance criterion ( p < .0001), 14 (50%) of the replications still provided such evidence, a reflection of the extremely high-powered design. Seven (25%) of the replications yielded effect sizes larger than the original ones, and 21 (75%) yielded effect sizes smaller than the original ones. The median comparable Cohen’s ds were 0.60 for the original findings and 0.15 for the replications. The effect sizes were small (< 0.20) in 16 of the replications (57%), and 9 effects (32%) were in the direction opposite the direction of the original effect. Across settings, the Q statistic indicated significant heterogeneity in 11 (39%) of the replication effects, and most of those were among the findings with the largest overall effect sizes; only 1 effect that was near zero in the aggregate showed significant heterogeneity according to this measure. Only 1 effect had a tau value greater than .20, an indication of moderate heterogeneity. Eight others had tau values near or slightly above .10, an indication of slight heterogeneity. Moderation tests indicated that very little heterogeneity was attributable to the order in which the tasks were performed or whether the tasks were administered in lab versus online. Exploratory comparisons revealed little heterogeneity between Western, educated, industrialized, rich, and democratic (WEIRD) cultures and less WEIRD cultures (i.e., cultures with relatively high and low WEIRDness scores, respectively). Cumulatively, variability in the observed effect sizes was attributable more to the effect being studied than to the sample or setting in which it was studied.

Abstract When a species colonizes an area that it has not previously inhabited, it is called an "invasion", and it can result in the extinction of endemic species. The increase in numbers of humans travelling the world presents opportunities for invasions by organisms and the spread of diseases such as rabies and smallpox. Using the large amount of data from studies in pest control and epidemiology, it is possible to construct mathematical models that can predict which species will become invaders, which habitats are susceptible to invasion, and the biological impact. This book presents a clear and accessible introduction to the modeling of biological invasions. It demonstrates the latest theories and models, and includes data and examples from various case studies showing how these models can be applied to problems from deadly human diseases to the spread of weeds. The present book is based on an earlier one published in Japan (in Japanese) by one of the authors (N.S.), entitled Mathematical modeling for biological invasions (University of Tokyo Press, 1992); this English edition, however, results from the collaboration between two authors. The original Japanese edition is aimed primarily at university undergraduate and graduate students, and its purpose is to introduce to them some of the pioneering works in biological invasion as well as some mathematical models developed by the authors. Necessarily, discussions on many relevant theories, field data, and their references were curtailed in favor of conciseness. For this English edition, we have included more field data, updated some theoretical results according to the latest findings, and rewritten much of the text with a wider audience, including field researchers and scholars, in mind.

Extant research on high-performance work systems (HPWSs) has primarily examined the effects of HPWSs on establishment or firm-level performance from a management perspective in manufacturing settings. The current study extends this literature by differentiating management and employee perspectives of HPWSs and examining how the two perspectives relate to employee individual performance in the service context. Data collected in three phases from multiple sources involving 292 managers, 830 employees, and 1,772 customers of 91 bank branches revealed significant differences between management and employee perspectives of HPWSs. There were also significant differences in employee perspectives of HPWSs among employees of different employment statuses and among employees of the same status. Further, employee perspective of HPWSs was positively related to individual general service performance through the mediation of employee human capital and perceived organizational support and was positively related to individual knowledge-intensive service performance through the mediation of employee human capital and psychological empowerment. At the same time, management perspective of HPWSs was related to employee human capital and both types of service performance. Finally, a branch's overall knowledge-intensive service performance was positively associated with customer overall satisfaction with the branch's service.

Influence of low Arctic sea‐ice minima in early autumn on the wintertime climate over Eurasia is investigated. Observational evidence shows that significant cold anomalies over the Far East in early winter and zonally elongated cold anomalies from Europe to Far East in late winter are associated with the decrease of the Arctic sea‐ice cover in the preceding summer‐to‐autumn seasons. Results from numerical experiments using an atmospheric general circulation model support these notions. The remote response in early winter is regarded as a stationary Rossby wave generated thermally through an anomalous turbulent heat fluxes as a result of anomalous ice‐cover over the Barents‐Kara Seas in late autumn, which tends to induce an amplification of the Siberian high causing colder conditions over the Far East. The late‐winter cold anomalies over Eurasia are also reproduced in our experiment, which is associated with the negative phase of the North Atlantic Oscillation.

We propose a new model of knowledge creation in purposeful, loosely coordinated, distributed systems, as an alternative to a firm-based one. Specifically, using the case of the Linux kernel development project, we build a model of community-based, evolutionary knowledge creation to study how thousands of talented volunteers, dispersed across organizational and geographical boundaries, collaborate via the Internet to produce a knowledge-intensive, innovative product of high quality. By comparing and contrasting the Linux model with the traditional/commercial model of software development and firmbased knowledge creation efforts, we show how the proposed model of knowledge creation expands beyond the boundary of the firm. Our model suggests that the product development process can be effectively organized as an evolutionary process of learning driven by criticism and error correction. We conclude by offering some theoretical implications of our community-based model of knowledge creation for the literature of organizational learning, community life, and the uses of knowledge in society.

This paper discusses production systems with a focus on the relationships between product supply and customer demand in the context of Industry 2.0–4.0. One driver of production evolution is changes in customer demand over time, which is categorised into several dimensions. Major production systems – flow line, Toyota production system (TPS), job shop, cell, flexible manufacturing system and seru – have been developed and applied to supplies to match different demand dimensions over time. For each production system, two questions are addressed: what and how. Comparisons between seru with TPS and cell are given. The possibilities of a future smart factory equipped with internet of things are discussed. The demand dimensions of Industry 4.0, the product architecture change in the automobile industry and the impact of 3D printing are elaborated. Potential applications of lean and seru principles for Industry 4.0 are presented.

BACKGROUND: Corneal endothelial cell (CEC) disorders, such as Fuchs's endothelial corneal dystrophy, induce abnormal corneal hydration and result in corneal haziness and vision loss known as bullous keratopathy. We investigated whether injection of cultured human CECs supplemented with a rho-associated protein kinase (ROCK) inhibitor into the anterior chamber could increase CEC density. METHODS: passaged cells were supplemented with a ROCK inhibitor (final volume, 300 μl) and injected into the anterior chamber of the eye that was selected for treatment. After the procedure, patients were placed in a prone position for 3 hours. The primary outcome was restoration of corneal transparency, with a CEC density of more than 500 cells per square millimeter at the central cornea at 24 weeks after cell injection. Secondary outcomes were a corneal thickness of less than 630 μm and an improvement in best corrected visual acuity equivalent to two lines or more on a Landolt C eye chart at 24 weeks after cell injection. RESULTS: At 24 weeks after cell injection, we recorded a CEC density of more than 500 cells per square millimeter (range, 947 to 2833) in 11 of the 11 treated eyes (100%; 95% confidence interval [CI], 72 to 100), of which 10 had a CEC density exceeding 1000 cells per square millimeter. A corneal thickness of less than 630 μm (range, 489 to 640) was attained in 10 of the 11 treated eyes (91%; 95% CI, 59 to 100), and an improvement in best corrected visual acuity of two lines or more was recorded in 9 of the 11 treated eyes (82%; 95% CI, 48 to 98). CONCLUSIONS: Injection of human CECs supplemented with a ROCK inhibitor was followed by an increase in CEC density after 24 weeks in 11 persons with bullous keratopathy. (Funded by the Japan Agency for Medical Research and Development and others; UMIN number, UMIN000012534 .).

Severe plastic deformation (SPD) is effective in producing bulk ultrafine-grained and nanostructured materials with large densities of lattice defects. This field, also known as NanoSPD, experienced a significant progress within the past two decades. Beside classic SPD methods such as high-pressure torsion, equal-channel angular pressing, accumulative roll-bonding, twist extrusion, and multi-directional forging, various continuous techniques were introduced to produce upscaled samples. Moreover, numerous alloys, glasses, semiconductors, ceramics, polymers, and their composites were processed. The SPD methods were used to synthesize new materials or to stabilize metastable phases with advanced mechanical and functional properties. High strength combined with high ductility, low/room-temperature superplasticity, creep resistance, hydrogen storage, photocatalytic hydrogen production, photocatalytic CO2 conversion, superconductivity, thermoelectric performance, radiation resistance, corrosion resistance, and biocompatibility are some highlighted properties of SPD-processed materials. This article reviews recent advances in the NanoSPD field and provides a brief history regarding its progress from the ancient times to modernity. Abbreviations: ARB: Accumulative Roll-Bonding; BCC: Body-Centered Cubic; DAC: Diamond Anvil Cell; EBSD: Electron Backscatter Diffraction; ECAP: Equal-Channel Angular Pressing (Extrusion); FCC: Face-Centered Cubic; FEM: Finite Element Method; FSP: Friction Stir Processing; HCP: Hexagonal Close-Packed; HPT: High-Pressure Torsion; HPTT: High-Pressure Tube Twisting; MDF: Multi-Directional (-Axial) Forging; NanoSPD: Nanomaterials by Severe Plastic Deformation; SDAC: Shear (Rotational) Diamond Anvil Cell; SEM: Scanning Electron Microscopy; SMAT: Surface Mechanical Attrition Treatment; SPD: Severe Plastic Deformation; TE: Twist Extrusion; TEM: Transmission Electron Microscopy; UFG: Ultrafine Grained. © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

Amyloid beta protein (Abeta), a pathogenic molecule associated with Alzheimer's disease, is produced by gamma-secretase, which cleaves the beta-carboxyl terminal fragment (betaCTF) of beta-amyloid precursor protein in the middle of its transmembrane domain. How the cleavage proceeds within the membrane has long been enigmatic. We hypothesized previously that betaCTF is cleaved first at the membrane-cytoplasm boundary, producing two long Abetas, Abeta(48) and Abeta(49), which are processed further by releasing three residues at each step to produce Abeta(42) and Abeta(40), respectively. To test this hypothesis, we used liquid chromatography tandem mass spectrometry (LC-MS/MS) to quantify the specific tripeptides that are postulated to be released. Using CHAPSO (3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxyl-1-propanesulfonate)-reconstituted gamma-secretase system, we confirmed that Abeta(49) is converted to Abeta(43/40) by successively releasing two or three tripeptides and that Abeta(48) is converted to Abeta(42/38) by successively releasing two tripeptides or these plus an additional tetrapeptide. Most unexpectedly, LC-MS/MS quantification revealed an induction period, 3-4 min, in the generation of peptides. When extrapolated, each time line for each tripeptide appears to intercept the same point on the x-axis. According to numerical simulation based on the successive reaction kinetics, the induction period exists. These results strongly suggest that Abeta is generated through the stepwise processing of betaCTF by gamma-secretase.

Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite) stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in understanding the biology of this unusual parasite.

Interest in the analysis of wave propagation characteristics and transients associated with cable systems has rapidly increased. In order to answer the need of the analyst, impedances and admittances of various cables have to be known. This paper describes a general formulation of impedances and admittances of single-core coaxial and pipe-type cables. The formulation presented here can handle a coaxial cable consisting of a core, sheath and armor, a pipe-type cable of which the pipe thickness is finite and an overhead cable, which has not been discussed in the literature heretofore.

The acoustic properties of bovine cancellous (spongy) bone have been experimentally studied in vitro by the pulse transmission technique. Fast and slow longitudinal waves have been clearly identified when the acoustic wave propagates parallel to the direction of the trabeculae. Propagation speeds and attenuation of the fast and slow waves were observed in the frequency range of 0.5-5 MHz. Theoretical discussion is given to Biot's theory and the propagation of sound waves in fluid-saturated porous media.

Pacific salmon and other anadromous salmonids represent a major vector for transporting marine nutrients across ecosystem boundaries (i.e., from marine to freshwater and terrestrial ecosystems). Salmon carcasses provide nutrients and energy to biota within aquatic and terrestrial ecosystems through various pathways. In this paper we review and synthesize the growing number of studies documenting this process in different localities. We also discuss the implications for maintaining the nutrient feedback system. Our findings show that future management will need to view spawning salmon and their carcasses as important habitat components for sustaining the production of fish as well as other salmon-dependent species within watersheds.

OBJECTIVE: Several epidemiological studies have shown that regular exercise can prevent the onset of colon cancer, although the underlying mechanism is unclear. Myokines are secreted skeletal muscle proteins responsible for some exercise-induced health benefits including metabolic improvement and anti-inflammatory effects in organs. The purpose of this study was to identify new myokines that contribute to the prevention of colon tumorigenesis. METHODS: To identify novel secreted muscle-derived proteins, DNA microarrays were used to compare the transcriptome of muscle tissue in sedentary and exercised young and old mice. The level of circulating secreted protein acidic and rich in cysteine (SPARC) was measured in mice and humans that performed a single bout of exercise. The effect of SPARC on colon tumorigenesis was examined using SPARC-null mice. The secretion and function of SPARC was examined in culture experiments. RESULTS: A single bout of exercise increased the expression and secretion of SPARC in skeletal muscle in both mice and humans. In addition, in an azoxymethane-induced colon cancer mouse model, regular low-intensity exercise significantly reduced the formation of aberrant crypt foci in wild-type mice but not in SPARC-null mice. Furthermore, regular exercise enhanced apoptosis in colon mucosal cells and increased the cleaved forms of caspase-3 and caspase-8 in wild-type mice but not in SPARC-null mice. Culture experiments showed that SPARC secretion from myocytes was induced by cyclic stretch and inhibited proliferation with apoptotic effect of colon cancer cells. CONCLUSIONS: These findings suggest that exercise stimulates SPARC secretion from muscle tissues and that SPARC inhibits colon tumorigenesis by increasing apoptosis.

The self-aggregation of cationic porphyrins in aqueous solution has been studied by means of absorption, 1H NMR, and resonance light scattering spectroscopy. The aim of the present study is clarification of the factors which most influence porphyrin self-aggregation in water. Cationic 5,10,15,20-tetrasubstituted porphyrins [PorSub4: PC3Py (Sub = −(CH2)3-Py+Cl-), PC5Py (Sub = −(CH2)5-Py+Cl-), PC7Py (Sub = −(CH2)7-Py+Cl-), TPPOC2Py (Sub = p-C6H4-O(CH2)2-Py+Br-), and TPPOC3Py (Sub = p-C6H4-O(CH2)3-Py+Br-), where Py+ = N-alkylpyridinium] were used. PC3Py forms a dimer in aqueous solution with or without an added inorganic salt. In the presence of KNO3, dimer formation of PC3Py is dominated by a large and negative enthalpy change. The entropy change for aggregation increases with increasing concentrations of added KNO3, while enthalpy changes are almost constant. The thermodynamic parameters suggest that dimer formation of PC3Py is the result of a large enthalpic gain due to extended van der Waals interactions, in cooperation with enhanced hydrophobic interactions. Electrostatic repulsion suppresses further association. However, other cationic porphyrins studied show evidence of higher self-aggregate formation. X-ray crystallographic studies of PC5Cl (Sub = −(CH2)5-Cl), a precursor of PC5Py, show the formation of a slipped face-to-face dimer as the basic unit for forming a crystal lattice, while that of TPP (Sub = −C6H5) indicates the absence of face-to-face stacking interaction in the crystals. Judging from these results, it is assumed that the slipped face-to-face dimer is the unit of the higher self-aggregates of PC5Py or PC7Py in water with or without KNO3. Elongated alkyl chains of PC5Py and PC7Py may be responsible by enhancing hydrophobic interaction of the porphyrins studied. TPPOC2Py alone forms a J-aggregate, characterized by a sharp and red-shifted Soret band and a strongly enhanced resonance light scattering signal. Higher self-aggregates having face-to-face arrangement are formed with TPPOC3Py; these provide no enhanced RLS feature. The present study reveals the dependence of aggregate formation of water-soluble porphyrins on the peripheral meso-substituents.

Polycrystalline n-ZnO/p-Cu2O heterojunctions have been fabricated by low-temperature eletrodepositions of ZnO and Cu2O layers in aqueous solutions. The condition for forming the Cu2O layer significantly reflected the electrical rectification characteristic and the photovoltaic performance, and the heterojunction fabricated under optimized conditions showed an excellent electrical rectification characteristic and a photovoltaic performance of 1.28% in conversion efficiency under an AM 1.5 illumination.

We describe a secure communication scheme that uses the random fluctuation of the natural environment of communication channels. Only the transmitter and the receiver share the communication channel characteristics. From reciprocity between a transmitter and a receiver, it is possible for them to share one-time information of their fluctuating channel. This can provide a secret key agreement scheme without key management and key distribution processes. In this paper, we propose a new secret key generation and agreement scheme that uses the fluctuation of channel characteristics with an electronically steerable parasitic array radiator (ESPAR) antenna. This antenna, which has been proposed and prototyped, is a smart antenna designed for consumers. Using the beam-forming technique of the ESPAR antenna, we can increase the fluctuation of the channel characteristics. From experimental results, we conclude that the proposed scheme has the ability to generate secret keys from the received signal strength indicator (RSSI) profile with sufficient independence.

Abnormal α-synuclein aggregation is a key pathological feature of a group of neurodegenerative diseases known as synucleinopathies, which include Parkinson's disease (PD), dementia with Lewy bodies and multiple system atrophy (MSA). The pathogenic β-sheet seed conformation of α-synuclein is found in various tissues, suggesting potential as a biomarker, but few studies have been able to reliably detect these seeds in serum samples. In this study, we developed a modified assay system, called immunoprecipitation-based real-time quaking-induced conversion (IP/RT-QuIC), which enables the detection of pathogenic α-synuclein seeds in the serum of individuals with synucleinopathies. In our internal first and second cohorts, IP/RT-QuIC showed high diagnostic performance for differentiating PD versus controls (area under the curve (AUC): 0.96 (95% confidence interval (CI) 0.95-0.99)/AUC: 0.93 (95% CI 0.84-1.00)) and MSA versus controls (AUC: 0.64 (95% CI 0.49-0.79)/AUC: 0.73 (95% CI 0.49-0.98)). IP/RT-QuIC also showed high diagnostic performance in differentiating individuals with PD (AUC: 0.86 (95% CI 0.74-0.99)) and MSA (AUC: 0.80 (95% CI 0.65-0.97)) from controls in a blinded external cohort. Notably, amplified seeds maintained disease-specific properties, allowing the differentiation of samples from individuals with PD versus MSA. In summary, here we present a novel platform that may allow the detection of individuals with synucleinopathies using serum samples.