記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Plant Phenomics  

Leaves, crucial for plant physiology, exhibit various morphological traits that meet diverse functional needs. Traditional leaf morphology quantification, largely 2-dimensional (2D), has not fully captured the 3-dimensional (3D) aspects of leaf function. Despite improvements in 3D data acquisition, accurately depicting leaf morphologies, particularly at the edges, is difficult. This study proposes a method for 3D leaf edge reconstruction, combining 2D image segmentation with curve-based 3D reconstruction. Utilizing deep-learning-based instance segmentation for 2D edge detection, structure from motion for estimation of camera positions and orientations, leaf correspondence identification for matching leaves among images, and curve-based 3D reconstruction for estimating 3D curve fragments, the method assembles 3D curve fragments into a leaf edge model through B-spline curve fitting. The method's performances were evaluated on both virtual and actual leaves, and the results indicated that small leaves and high camera noise pose greater challenges to reconstruction. We developed guidelines for setting a reliability threshold for curve fragments, considering factors occlusion, leaf size, the number of images, and camera error; the number of images had a lesser impact on this threshold compared to others. The method was effective for lobed leaves and leaves with fewer than 4 holes. However, challenges still existed when dealing with morphologies exhibiting highly local variations, such as serrations. This nondestructive approach to 3D leaf edge reconstruction marks an advancement in the quantitative analysis of plant morphology. It is a promising way to capture whole-plant architecture by combining 2D and 3D phenotyping approaches adapted to the target anatomical structures.

DOI： 10.34133/plantphenomics.0181

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記述言語：その他   掲載種別：研究論文（学術雑誌）   出版者・発行元：MDPI AG  

The present study collected a larger set of three-dimensional data on human crania from the Kofun period (as well as from previous periods, i.e., the Jomon and Yayoi periods) in the Japanese archipelago (AD 250 to around 700) than previous studies. Three-dimensional geometric morphometrics were employed to investigate human migration patterns in finer-grained phases. These results are consistent with those of previous studies, although some new patterns were discovered. These patterns were interpreted in terms of demic diffusion, archaeological findings, and historical evidence. In particular, the present results suggest the presence of a gradual geological cline throughout the Kofun period, although the middle period did not display such a cline. This discrepancy might reflect social changes in the middle Kofun period, such as the construction of keyhole-shaped mounds in the peripheral regions. The present study implies that a broader investigation with a larger sample of human crania is essential to elucidating macro-level cultural evolutionary processes.

DOI： 10.3390/humans4020008

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記述言語：その他   掲載種別：研究論文（学術雑誌）   出版者・発行元：Human Behavior and Evolution Society of Japan  

The present study examines the 3-dimensional data of human crania from the Yayoi period (800 BC to AD 250) of the Japanese archipelago by geometric morphometrics to investigate demic diffusion patterns. This is the first study on the Yayoi crania using their 3D data and geometric morphometrics with a much larger number of skeletal remains outside of the Kyushu regions than previous studies. The comparative results between the Jōmon and Yayoi samples show that the Yayoi people not only in the eastern parts but also in the western parts of the archipelago are significantly different from the final Jōmon people and the Yayoi people were not strongly affected by the Jōmon people. A relatively gradual geological cline is also found among the Yayoi population, suggesting that the immigrants from the continental East Asia moved from the western parts to the eastern parts of the archipelago though the causes of the morphological changes are unclear.

DOI： 10.5178/lebs.2023.111

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記述言語：その他   掲載種別：研究論文（学術雑誌）   出版者・発行元：PLoS Computational Biology  

Despite substantial variation in leaf vein architectures among angiosperms, a typical hierarchical network pattern is shared within clades. Functional demands (e.g., hydraulic conductivity, transpiration efficiency, and tolerance to damage and blockage) constrain the network structure of leaf venation, generating a biased distribution in the morphospace. Although network structures and their diversity are crucial for understanding angiosperm venation, previous studies have relied on simple morphological measurements (e.g., length, diameter, branching angles, and areole area) and their derived statistics to quantify phenotypes. To better understand the morphological diversities and constraints on leaf vein networks, we developed a simple, high-throughput phenotyping workflow for the quantification of vein networks and identified leaf venation-specific morphospace patterns. The proposed method involves four processes: leaf image acquisition using a feasible system, leaf vein segmentation based on a deep neural network model, network extraction as an undirected graph, and network feature calculation. To demonstrate the proposed method, we applied it to images of non-chemically treated leaves of five species for classification based on network features alone, with an accuracy of 90.6%. By dimensionality reduction, a one-dimensional morphospace, along which venation shows variation in loopiness, was identified for both untreated and cleared leaf images. Because the one-dimensional distribution patterns align with the Pareto front that optimizes transport efficiency, construction cost, and robustness to damage, as predicted by the earlier theoretical study, our findings suggested that venation patterns are determined by a functional trade-off. The proposed network feature-based method is a useful morphological descriptor, providing a quantitative representation of the topological aspects of venation and enabling inverse mapping to leaf vein structures. Accordingly, our approach is promising for analyses of the functional and structural properties of veins.

DOI： 10.1371/journal.pcbi.1010581

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記述言語：その他   掲載種別：研究論文（学術雑誌）  

DOI： 10.1093/evolut/qpad110

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1111/1348-0421.13034

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Despite the morphological diversity of organisms, they only occupy a fraction of the theoretically possible spectrum (i.e., morphospace) and have been studied on several taxa. Such morphospace occupation patterns are formed through evolutionary processes under multiple constraints. In this study, we discovered a differential morphospace occupation pattern between terrestrial and aquatic gastropods and subsequently attempted to quantitatively understand these differences through morphospace analysis. These differential occupation patterns between terrestrial and aquatic species were observed in the morphospace of spire height and aperture inclination, including a bimodal distribution of shell height in terrestrial species alongside the absence of high-spired shells with high aperture inclination. Although terrestrial species were distributed along optimal lines of shell instability and shell hindrance to locomotion, aquatic species were distributed not only along this line but also within a suboptimal region of the low spire with low inclination. Based on numerical simulation and biometric analysis, here we propose the hypothesis that this difference was caused by the aquatic species being able to adopt a posture with the growth direction perpendicular to the substrate due to reduced functional demands. Our results provided an ultimate explanation for the differential occupation patterns between habitats alongside an overview of the morphospace.

DOI： 10.1093/evolut/qpad110

担当区分：筆頭著者,　責任著者   出版者・発行元：株式会社医学書院  

DOI： 10.11477/mf.2425201656

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記述言語：英語   出版者・発行元：John Wiley & Sons Australia, Ltd  

喫煙歴とSARS-Cov-2感染性との関係性について検討した。2013年1月～2019年12月までの期間内に、著者等の医療施設で外科治療で採取した肺組織試料を用い、喫煙者、喫煙歴ありの非喫煙者、非喫煙者肺から検出されるアンジオテンシン変換酵素2(ACE2)の遺伝子発現を調査した。その結果、禁煙期間6ヵ月未満の患者ではACE2遺伝子発現量が、非喫煙者や禁煙期間6ヵ月以上の患者から検出された発現量に比べ高発現であった。また、SARS-Cov-2の感染効率はACE2発現量に依存して亢進し、喫煙者肺のRNA-seq解析では、炎症シグナル伝達に関与する遺伝子発現がACE2遺伝子発現と相関することが明らかにされた。なかでも、過去に喫煙歴がある患者では、禁煙期間が長いほどACE2遺伝子発現量のみならず、炎症シグナル伝達に関与する遺伝子発現量でも低下が認められた。以上より、喫煙はACE2遺伝子と炎症シグナル伝達に関与する遺伝子発現量を亢進させ、SARS-Cov-2への感染効率は、喫煙を介したACE2遺伝子発現量のアップレギュレーションにより増強されることが示唆された。

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Scientific Reports  

<jats:title>Abstract</jats:title><jats:p>Trees are thought to have acquired a mechanically optimized shape through evolution, but a scientific methodology to investigate the mechanical rationality of tree morphology remains to be established. The aim of this study was to develop a new method for 3D reconstruction of actual tree shape and to establish a theoretical formulation for elucidating the structure and function of tree branches. We obtained 3D point cloud data of tree shape of Japanese zelkova (<jats:italic>Zelkova serrata</jats:italic>) and Japanese larch (<jats:italic>Larix kaempferi</jats:italic>) using the NavVis Lidar scanner, then applied a cylinder structure extraction from point cloud data with error estimation. We then formulated the mechanical stress of branches under gravity using the elastic theory, and performed finite element method simulations to evaluate the mechanical characteristics. Subsequently, we constructed a mechanics-based theoretical formulation of branch development that ensures constant bending stress produces various branching patterns depending on growth properties. The derived theory recapitulates the trade-off among branch growth anisotropy, stress-gravity length, and branch shape, which may open the quantitative way to evaluate mechanical and morphological rationality of tree branches.</jats:p>

DOI： 10.1038/s41598-022-08030-5

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その他リンク： https://www.nature.com/articles/s41598-022-08030-5

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Smoking is one of the risk factors most closely related to the severity of coronavirus disease 2019 (COVID-19). However, the relationship between smoking history and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is unknown. In this study, we evaluated the ACE2 expression level in the lungs of current smokers, ex-smokers, and nonsmokers. The ACE2 expression level of ex-smokers who smoked cigarettes until recently (cessation period shorter than 6 months) was higher than that of nonsmokers and ex-smokers with a long history of nonsmoking (cessation period longer than 6 months). We also showed that the efficiency of SARS-CoV-2 infection was enhanced in a manner dependent on the angiotensin-converting enzyme 2 (ACE2) expression level. Using RNA-seq analysis on the lungs of smokers, we identified that the expression of inflammatory signaling genes was correlated with ACE2 expression. Notably, with increasing duration of smoking cessation among ex-smokers, not only ACE2 expression level but also the expression levels of inflammatory signaling genes decreased. These results indicated that smoking enhances the expression levels of ACE2 and inflammatory signaling genes. Our data suggest that the efficiency of SARS-CoV-2 infection is enhanced by smoking-mediated upregulation of ACE2 expression level.

DOI： 10.1111/1348-0421.13034

記述言語：日本語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1371/journal.pone.0270660

記述言語：その他   掲載種別：研究論文（学術雑誌）  

SfM/MVS photogrammetry has received increasing attention due to its convenience, broadening the range of its applications into archaeology and anthropology. Because the accuracy of SfM/MVS depends on photography, one important issue is that incorrect or low-density point clouds are found in 3D models due to poor overlapping between images. A systematic way of taking photographs solve these problems, though it has not been well established and the accuracy has not been examined either, with some exceptions. The present study aims to (i) develop an efficient method for recording pottery using an automated turntable and (ii) assess its accuracy through a comparison with 3D models made by laser scanning. We recorded relatively simple pottery manufactured by prehistoric farmers in the Japanese archipelago using SfM/MVS photogrammetry and laser scanning. Further, by measuring the Hausdorff distance between 3D models made using these two methods, we show that their difference is negligibly small, suggesting that our method is sufficiently accurate to record pottery.

DOI： 10.1371/journal.pone.0270660

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CiNii Research

記述言語：英語   掲載種別：研究論文（学術雑誌）  

<title>Abstract</title>Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F₁ individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92&#37; of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.

DOI： 10.1038/s41438-021-00485-3

記述言語：その他   掲載種別：研究論文（学術雑誌）  

<sec id="sec001"><title>Background</title>Development of an effective antiviral drug for Coronavirus Disease 2019 (COVID-19) is a global health priority. Although several candidate drugs have been identified through in vitro and in vivo models, consistent and compelling evidence from clinical studies is limited. The lack of evidence from clinical trials may stem in part from the imperfect design of the trials. We investigated how clinical trials for antivirals need to be designed, especially focusing on the sample size in randomized controlled trials.</sec><sec id="sec002"><title>Methods and findings</title>A modeling study was conducted to help understand the reasons behind inconsistent clinical trial findings and to design better clinical trials. We first analyzed longitudinal viral load data for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) without antiviral treatment by use of a within-host virus dynamics model. The fitted viral load was categorized into 3 different groups by a clustering approach. Comparison of the estimated parameters showed that the 3 distinct groups were characterized by different virus decay rates (<italic>p</italic>-value < 0.001). The mean decay rates were 1.17 d⁻¹ (95&amp;#37; CI: 1.06 to 1.27 d⁻¹), 0.777 d⁻¹ (0.716 to 0.838 d⁻¹), and 0.450 d⁻¹ (0.378 to 0.522 d⁻¹) for the 3 groups, respectively. Such heterogeneity in virus dynamics could be a confounding variable if it is associated with treatment allocation in compassionate use programs (i.e., observational studies).Subsequently, we mimicked randomized controlled trials of antivirals by simulation. An antiviral effect causing a 95&amp;#37; to 99&amp;#37; reduction in viral replication was added to the model. To be realistic, we assumed that randomization and treatment are initiated with some time lag after symptom onset. Using the duration of virus shedding as an outcome, the sample size to detect a statistically significant mean difference between the treatment and placebo groups (1:1 allocation) was 13,603 and 11,670 (when the antiviral effect was 95&amp;#37; and 99&amp;#37;, respectively) per group if all patients are enrolled regardless of timing of randomization. The sample size was reduced to 584 and 458 (when the antiviral effect was 95&amp;#37; and 99&amp;#37;, respectively) if only patients who are treated within 1 day of symptom onset are enrolled. We confirmed the sample size was similarly reduced when using cumulative viral load in log scale as an outcome.We used a conventional virus dynamics model, which may not fully reflect the detailed mechanisms of viral dynamics of SARS-CoV-2. The model needs to be calibrated in terms of both parameter settings and model structure, which would yield more reliable sample size calculation.</sec><sec id="sec003"><title>Conclusions</title>In this study, we found that estimated association in observational studies can be biased due to large heterogeneity in viral dynamics among infected individuals, and statistically significant effect in randomized controlled trials may be difficult to be detected due to small sample size. The sample size can be dramatically reduced by recruiting patients immediately after developing symptoms. We believe this is the first study investigated the study design of clinical trials for antiviral treatment using the viral dynamics model.</sec>

DOI： 10.1371/journal.pmed.1003660

記述言語：その他   掲載種別：研究論文（学術雑誌）  

Recent advances in unmanned aerial vehicle (UAV) remote sensing and image analysis provide large amounts of plant canopy data, but there is no method to integrate the large imagery datasets with the much smaller manually collected datasets. A simple geographic information system (GIS)-based analysis for a UAV-supported field study (GAUSS) analytical framework was developed to integrate these datasets. It has three steps: developing a model for predicting sample values from UAV imagery, field gridding and trait value prediction, and statistical testing of predicted values. A field cultivation experiment was conducted to examine the effectiveness of the GAUSS framework, using a soybean–wheat crop rotation as the model system Fourteen soybean cultivars and subsequently a single wheat cultivar were grown in the same field. The crop rotation benefits of the soybeans for wheat yield were examined using GAUSS. Combining manually sampled data (n = 143) and pixel-based UAV imagery indices produced a large amount of high-spatial-resolution predicted wheat yields (n = 8,756). Significant differences were detected among soybean cultivars in their effects on wheat yield, and soybean plant traits were associated with the increases. This is the first reported study that links traits of legume plants with rotational benefits to the subsequent crop. Although some limitations and challenges remain, the GAUSS approach can be applied to many types of field-based plant experimentation, and has potential for extensive use in future studies.

DOI： 10.3389/fpls.2021.637694

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The pelagic snail Limacina helicina Phipps, 1774 is widely distributed in high-latitude seas and is a sensitive bioindicator of ocean acidification. It is known that the response patterns to ocean acidification differ among populations within or among species. Thus, it is important to understand their genetic population structure and identify the cryptic species. L. helicina displays different shell morphotypes, called "formae," in different regions (North Atlantic, L. helicina forma helicina Phipps, 1774; Northwest Pacific, L. helicina f. acuta Spoel, 1967; Northeast Pacific, L. helicina f. pacifica Dall, 1871; Okhotsk Sea, L. helicina f. ochotensis Shkoldina, 1999: Spoel, 1967, pp. 257, 349). A recent study by Shimizu et al. (Journal of Molluscan Studies 84:30-37, 2018) showed clear genetic differentiation between two formae, L. helicina forma helicina (Svalbard in the Arctic Ocean) and L. helicina f. acuta (station K2 in the western North Pacific) (phi CT = 0.59282), using partial mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. However, whether other formae of this species are genetically distinct remain unknown. Here we focused on L. helicina f. ochotensis, which inhabits the Sea of Okhotsk, and compared its shell morphology and partial mitochondrial COI gene sequences with another forma, L. helicina f. acuta, which is found in the western North Pacific. We found differences in the shell morphology of L. helicina f. ochotensis collected from the Sea of Okhotsk (off the coast of Monbetsu, Hokkaido, Japan) and L. helicina f. acuta collected from the western North Pacific (station K2). However, molecular analysis of an mtDNA COI region (503 bp) revealed that most individuals collected from Monbetsu (Sea of Okhotsk) were haplotype 1 (75.5&#37;), which is also the major haplotype found in L. helicina f. acuta (western North Pacific). Our results suggest that individuals of L. helicina are frequently dispersed between the Sea of Okhotsk and the western North Pacific by ocean currents. Thus, the two formae, L. helicina f. acuta and L. helicina f. ochotensis, are more likely to be attributable to phenotypic plasticity in response to different environmental parameters, such as temperature and salinity, than to differences in their genetic backgrounds.

DOI： 10.1007/s12526-021-01166-z

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Plants require water, but a deficit or excess of water can negatively impact their growth and functioning. Soil flooding, in which root-zone is filled with excess water, restricts oxygen diffusion into the soil. Global climate change is increasing the risk of crop yield loss caused by flooding, and the development of flooding tolerant crops is urgently needed. Root anatomical traits are essential for plants to adapt to drought and flooding, as they determine the balance between the rates of water and oxygen transport. The stele contains xylem and the cortex contains aerenchyma (gas spaces), which respectively contribute to water uptake from the soil and oxygen supply to the roots; this implies that there is a trade-off between the ratio of cortex and stele sizes with respect to adaptation to drought or flooding. In this review, we analyze recent advances in the understanding of root anatomical traits that confer drought and/or flooding tolerance to plants and illustrate the trade-off between cortex and stele sizes. Moreover, we introduce the progress that has been made in modelling and fully automated analyses of root anatomical traits and discuss how key root anatomical traits can be used to improve crop tolerance to soil flooding.

DOI： 10.1270/jsbbs.20119

記述言語：その他   掲載種別：研究論文（学術雑誌）  

DOI： 10.1002/ece3.6861

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1002/ece3.6861

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Water lilies (Nymphaeaspp.) have diverse floral morphologies. Water lilies are not only commonly used as ornamental plants, but they are also important for understanding the diversification of basal angiosperms. Although the diversity in floral morphology of water lily provides useful information for evolutionary biology, horticulture, and horticultural science, it is difficult to describe and analyze the three-dimensional morphology of flowers. In this study, we propose a method to describe the floral morphology of water lily using a three-dimensional theoretical morphological model. The theoretical model was constructed based on three components, i.e., (1) the gradual change in size of floral organs, (2) spiral phyllotaxis, and (3) the interpolation of elevation angles, which were integrated into the model. We generated three-dimensional representation of water lily flowers and visualized theoretical morphospaces by varying each morphological parameter. The theoretical morphospace is a mathematical space of morphological spectrum generated by a theoretical morphological model. These morphospaces seems to display the large part of morphological variations of water lily. We measured morphological parameters of real flowers based on our theoretical model and display the occupation pattern of morphological parameters. We also surveyed the relation between morphological parameters and flower shape descriptions found in a catalog. In some parameters, we found breeders' description can link to our morphological model. In addition, the relationship between the global features of floral morphology and the parameters of the theoretical model was calculated with flower silhouettes simulated with a range of parameter values and the global features of the silhouette. We used two simple indices to assess the global morphological features, which were calculated with the convex hull. The results indicated that our method can effectively provide an objective and quantitative overview of the diversity in the floral morphology of water lily.

DOI： 10.1371/journal.pone.0239781

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS.

DOI： 10.1371/journal.pone.0224695

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1539/sangyoeisei.2018-040-C

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Progress in remote sensing and robotic technologies decreases the hardware costs of phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, and present a trade-off between investment and manpower costs. We then discuss the structure of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) major costs arise from plant handling and manpower; (ii) the total costs per plant/microplot are similar in robotized platform or field experiments with drones, hand-held or robotized ground vehicles; (iii) the cost of vehicles carrying sensors represents only 5–26% of the total costs. These conclusions depend on the context, in particular for labor cost, the quantitative demand of phenotyping and the number of days available for phenotypic measurements due to climatic constraints. Data analysis represents 10–20% of total cost if pipelines have already been developed. A trade-off exists between the initial high cost of pipeline development and labor cost of manual operations. Overall, depending on the context and objsectives, “cost-effective” phenotyping may involve either low investment (“affordable phenotyping”), or initial high investments in sensors, vehicles and pipelines that result in higher quality and lower operational costs.

DOI： 10.1016/j.plantsci.2018.06.015

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Accumulating evidence indicates that plants are capable of self/non-self and kin/stranger discrimination. Plants increase biomass of and resource allocation to roots when they encounter roots of conspecific non-self-neighbors, but not when they encounter self roots. Root proliferation usually occurs at the expense of reproductive investment. Therefore, if clonal crops are capable of self/non-self-discrimination, spatially aggregated planting with seedlings of the same genotype may decrease root proliferation and produce a higher yield than planting without considering seedling genotype. To test this idea, we grew Helianthus tuberosus (Jerusalem artichoke) in pot and field conditions and examined self/non-self-discrimination and the effectiveness of genotype-aggregated planting. Plants grown in self pairs allocated less to root biomass than plants grown in non-self pairs in both pot and field conditions; in field conditions, the self pairs produced 40% more tubers by weight than the non-self pairs. When six sprouts from seed tuber of two different genotypes were grown together, with the two genotypes planted aggregately (AGG) or alternately (ALT), plants in the AGG group produced 14% more tubers than plants in the ALT group. These results suggest that spatial aggregation of genotypes increases tuber production in H. tuberosus. Because we found no evidence for trade-offs between root biomass and tuber production, suppression of root proliferation may not be the only mechanism behind the benefits of genotype aggregation. By applying the concept of self/non-self-discrimination, farmers can increase crop production without additional external inputs or expansion of agricultural land use.

DOI： 10.1111/eva.12735

記述言語：英語   掲載種別：研究論文（学術雑誌）  

In orchards, measuring crown characteristics is essential for monitoring the dynamics of tree growth and optimizing farm management. However, it lacks a rapid and reliable method of extracting the features of trees with an irregular crown shape such as trained peach trees. Here, we propose an efficient method of segmenting the individual trees and measuring the crown width and crown projection area (CPA) of peach trees with time-series information, based on gathered images. The images of peach trees were collected by unmanned aerial vehicles in an orchard in Okayama, Japan, and then the digital surface model was generated by using a Structure from Motion (SfM) and Multi-View Stereo (MVS) based software. After individual trees were identified through the use of an adaptive threshold and marker-controlled watershed segmentation in the digital surface model, the crown widths and CPA were calculated, and the accuracy was evaluated against manual delineation and field measurement, respectively. Taking manual delineation of 12 trees as reference, the root-mean-square errors of the proposed method were 0.08 m (R
²
= 0.99) and 0.15 m (R
²
= 0.93) for the two orthogonal crown widths, and 3.87 m
²
for CPA (R
²
= 0.89), while those taking field measurement of 44 trees as reference were 0.47 m (R
²
= 0.91), 0.51 m (R
²
= 0.74), and 4.96 m
²
(R
²
= 0.88). The change of growth rate of CPA showed that the peach trees grew faster from May to July than from July to September, with a wide variation in relative growth rates among trees. Not only can this method save labour by replacing field measurement, but also it can allow farmers to monitor the growth of orchard trees dynamically.

DOI： 10.1038/s41438-018-0097-z

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1539/sangyoeisei.2018-022-C

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The genetic diversity of one of the most abundant species in the Arctic and subarctic oceans, the pelagic snail Limacina helicina, has not yet been characterized in the north Pacific. This species has different â €? forma' (L. helicina forma helicina, acuta, pacifica and ochotensis), but whether or not the morphological differences between these forma are caused by phenotypic plasticity or genetic differentiation remains unclear. Here, we analysed partial nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I gene in L. helicina from the subarctic western North Pacific Ocean (SWNP; L. helicina f. acuta) and compared them with those from Svalbard (L. helicina f. helicina) and other localities (Beaufort Sea, eastern Pacific, northern Sea of Japan and western Atlantic). The results show clear genetic differentiation between populations in the SWNP and Svalbard (? ▪ CT = 0.59282, P < 0.001). These genetic differences are consistent with the previous description of the two forma L. h. f. acuta (SWNP) and L. h. f. helicina (Svalbard) based on shell morphology.

DOI： 10.1093/mollus/eyx040

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Sorghum (Sorghum bicolor L. Moench) is a C4 tropical grass that plays an essential role in providing nutrition to humans and livestock, particularly in marginal rainfall environments. The timing of head development and the number of heads per unit area are key adaptation traits to consider in agronomy and breeding but are time consuming and labor intensive to measure. We propose a two-step machine-based image processing method to detect and count the number of heads from high-resolution images captured by unmanned aerial vehicles (UAVs) in a breeding trial. To demonstrate the performance of the proposed method, 52 images were manually labeled; the precision and recall of head detection were 0.87 and 0.98, respectively, and the coefficient of determination (R
²
) between the manual and new methods of counting was 0.84. To verify the utility of the method in breeding programs, a geolocation-based plot segmentation method was applied to pre-processed ortho-mosaic images to extract >1000 plots from original RGB images. Forty of these plots were randomly selected and labeled manually; the precision and recall of detection were 0.82 and 0.98, respectively, and the coefficient of determination between manual and algorithm counting was 0.56, with the major source of error being related to the morphology of plants resulting in heads being displayed both within and outside the plot in which the plants were sown, i.e., being allocated to a neighboring plot. Finally, the potential applications in yield estimation from UAV-based imagery from agronomy experiments and scouting of production fields are also discussed.

DOI： 10.3389/fpls.2018.01544

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Heart failure is a complex clinical syndrome characterized by insufficient cardiac function. In addition to abnormalities intrinsic to the heart, dysfunction of other organs and dysregulation of systemic factors greatly affect the development and consequences of heart failure. Here we show that the heart and kidneys function cooperatively in generating an adaptive response to cardiac pressure overload. In mice subjected to pressure overload in the heart, sympathetic nerve activation led to activation of renal collecting-duct (CD) epithelial cells. Cell-cell interactions among activated CD cells, tissue macrophages and endothelial cells within the kidney led to secretion of the cytokine CSF2, which in turn stimulated cardiac-resident Ly6C lo macrophages, which are essential for the myocardial adaptive response to pressure overload. The renal response to cardiac pressure overload was disrupted by renal sympathetic denervation, adrenergic β2-receptor blockade or CD-cell-specific deficiency of the transcription factor KLF5. Moreover, we identified amphiregulin as an essential cardioprotective mediator produced by cardiac Ly6C lo macrophages. Our results demonstrate a dynamic interplay between the heart, brain and kidneys that is necessary for adaptation to cardiac stress, and they highlight the homeostatic functions of tissue macrophages and the sympathetic nervous system.

DOI： 10.1038/nm.4326

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The morphology of gastropod shells provides a record of the growth rate at the aperture of the shell, and molecular biological studies have shown that the growth rate gradient along the aperture of a gastropod shell can be closely related to gene expression at the aperture. Here, we develop a novel method for deriving microscopic growth rates from the macroscopic shapes of gastropod shells. The growth vector map of a shell provides information on the growth rate gradient as a vector field along the aperture, over the growth history. However, it is difficult to estimate the growth vector map directly from the macroscopic shape of a specimen, because the degree of freedom of the growth vector map is very high. In order to overcome this difficulty, we develop a method of estimating the growth vector map based on a growing tube model, where the latter includes fewer parameters to be estimated. In addition, we calculate an aperture map specifying the magnitude of the growth vector at each location, which can be compared with the expression levels of several genes or proteins that are important in morphogenesis. Finally, we show a concrete example of how macroscopic shell shapes evolve in a morphospace when microscopic growth rate gradient changes.

DOI： 10.1016/j.jtbi.2015.10.011

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The morphology of gastropod shells has been a focus of analyses in ecology and evolution. It has recently emerged as an important issue in developmental biology, thanks to recent advancements in molecular biological techniques. The growing tube model is a theoretical morphological model for describing various coiling patterns of molluscan shells, and it is a useful theoretical tool to relate local tissue growth with global shell morphology. However, the growing tube model has rarely been adopted in empirical research owing to the difficulty in estimating the parameters of the model from morphological data. In this article, I solve this problem by developing methods of parameter estimation when (1) 3D Computed Tomography (CT) data are available and (2) only 2D image data (such as photographs) are available. When 3D CT data are available, the parameters can be estimated by fitting an analytical solution of the growing tube model to the data. When only 2D image data are available, we first fit Raup's model to the 2D image data and then convert the parameters of Raup's model to those of the growing tube model. To illustrate the use of these methods, I apply them to data generated by a computer simulation of the model. Both methods work well, except when shells grow without coiling. I also demonstrate the effectiveness of the methods by applying the model to actual 3D CT data and 2D image data of land snails. I conclude that the method proposed in this article can reconstruct the coiling pattern from observed data.

DOI： 10.1016/j.jtbi.2014.08.010

記述言語：英語   掲載種別：研究論文（学術雑誌）  

We studied the morphological diversity of gastropod shell forms from the viewpoint of theoretical morphology, emphasizing the relationships of shell form to postural stability and the available space for soft body, which we assessed in terms of the moment of force and soft-tissue ratio calculations, respectively. The results of computer simulations suggest a functional trade-off between postural stability and available space for soft body: a compact shell possessing a low spire and small umbilicus exhibits high postural stability, whereas a less overlapped shell form with a high spire and large umbilicus makes available space for soft body. A functional morphospace analysis using theoretical models reveals that outward and downward inclination of the aperture moderates the functional trade-off between these parameter values and permits compatibility between stable posture and efficient shell construction. The hypothetical optimum that realizes this compatibility is consistent with the observed range of forms estimated from 359 extant gastropod species. The biometric results also suggest that land snails are more highly constrained than marine species in achieving a balance between postural stability and available space for soft body.

DOI： 10.1666/10060.1

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The Spiral Shell Form was developed as an original computer software package designed for theoretical morphological analysis of gastropod shell forms using the Raup's model. It is composed of the following three programs. Spiral Shell Measure is a software for capturing coordinate data of the points of interest on computer image files of a specimen. Raup's Parameter Calculator is a Mathematica program for calculation of Raup's parameters from coordinate data that were collected using the Spiral Shell Measure. Spiral Shell Properties is a Mathematica program for computing physical properties of a theoretical model such as shell volume, area of the aperture, center of gravity, soft-body ratio and length of trajectory of centroid of aperture.

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：日本育種学会  

The morphological traits of plants contribute to many important functional features such as radiation inter-ception, lodging tolerance, gas exchange efficiency, spatial competition between individuals and/or species, and disease resistance. Although the importance of plant phenotyping techniques is increasing with advances in molecular breeding strategies, there are barriers to its advancement, including the gap between measured data and phenotypic values, low quantitativity, and low throughput caused by the lack of models for repre-senting morphological traits. In this review, we introduce morphological descriptors that can be used for pheno-typing plant morphological traits. Geometric morphometric approaches pave the way to a general-purpose method applicable to single units. Hierarchical structures composed of an indefinite number of multiple elements, which is often observed in plants, can be quantified in terms of their multi-scale topological characteristics using topological data analysis. Theoretical morphological models capture specific anatomical structures, if recognized. These morphological descriptors provide us with the advantages of model-based plant phenotyping, including robust quantification of limited datasets. Moreover, we discuss the future possi-bilities that a system of model-based measurement and model refinement would solve the lack of morphological models and the difficulties in scaling out the phenotyping processes.

DOI： 10.1270/jsbbs.21078

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担当ページ：総ページ数：xxiv, 500p   記述言語：日本語  

担当ページ：pp. 83-93.   記述言語：日本語   著書種別：学術書

DOI： 10.1007/978-981-13-1002-7_9

記述言語：日本語   著書種別：学術書

開催年月日： 2023年6月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：Wageningen, Nederland   国名：日本国  

開催年月日： 2023年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：オンライン，ホスト：明治大学   国名：日本国  

開催年月日： 2023年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：九州大学 馬出キャンパス，福岡   国名：日本国  

開催年月日： 2021年10月

記述言語：日本語   会議種別：シンポジウム・ワークショップ パネル（公募）  

開催地：名古屋大学   国名：日本国  

開催年月日： 2021年10月

記述言語：日本語   会議種別：シンポジウム・ワークショップ パネル（公募）  

国名：日本国  

開催年月日： 2021年9月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：オンライン，ホスト：宮崎大学   国名：日本国  

開催年月日： 2021年9月

記述言語：日本語   会議種別：シンポジウム・ワークショップ パネル（公募）  

開催地：オンライン，ホスト：東京都立大学   国名：日本国  

開催年月日： 2021年8月

記述言語：英語   会議種別：シンポジウム・ワークショップ パネル（公募）  

開催地：online   国名：日本国  

開催年月日： 2021年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：オンライン   国名：日本国  

開催年月日： 2021年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：京都大学 数理解析研究所   国名：日本国  

開催年月日： 2021年6月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：Tucson, AZ   国名：アメリカ合衆国  

開催年月日： 2021年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：オンライン，ホスト：名古屋大学   国名：日本国  

開催年月日： 2021年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：オンライン，ホスト：横浜国立大学   国名：日本国  

開催年月日： 2021年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：オンライン，ホスト：岡山   国名：日本国  

開催年月日： 2021年5月

記述言語：日本語   会議種別：シンポジウム・ワークショップ パネル（公募）  

開催地：オンライン   国名：日本国  

開催年月日： 2019年11月

記述言語：日本語   会議種別：口頭発表（一般）  

国名：日本国  

開催年月日： 2019年11月

記述言語：日本語  

開催地：北海道   国名：日本国  

開催年月日： 2019年10月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：Nanjing   国名：中華人民共和国  

開催年月日： 2019年10月

記述言語：英語  

開催地：Nanjing   国名：中華人民共和国  

開催年月日： 2019年9月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：Tokyo   国名：日本国  

開催年月日： 2019年9月

記述言語：日本語   会議種別：シンポジウム・ワークショップ パネル（公募）  

開催地：東京   国名：日本国  

開催年月日： 2019年6月

記述言語：日本語   会議種別：口頭発表（一般）  

開催地：神戸   国名：日本国  

開催年月日： 2019年6月

記述言語：英語  

開催地：Town & Country Hotel, San Diego, CA   国名：アメリカ合衆国  

開催年月日： 2019年6月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：Ehime Univ.   国名：日本国  

開催年月日： 2019年6月

記述言語：日本語   会議種別：公開講演，セミナー，チュートリアル，講習，講義等  

国名：日本国  

開催年月日： 2019年6月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：University of Sydney, Sydney   国名：オーストラリア連邦  

開催年月日： 2019年6月

記述言語：日本語  

国名：日本国  

開催年月日： 2019年6月

記述言語：英語  

開催地：National Wine Centre of Australia, Adelaide   国名：オーストラリア連邦  

開催年月日： 2019年6月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：UGA, Athens, GA   国名：アメリカ合衆国  

記述言語：日本語  

Application of AI in the field of social medicine

記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）  

DOI： 10.24480/bsj-review.11c2.00191

記述言語：日本語  

AI research in the field of social medicine

記述言語：日本語  

AI research in the field of social medicine

記述言語：日本語  

AI in social medicine

記述言語：日本語  

DOI： 10.24480/bsj-review.10b7.00160

記述言語：日本語  

3D reconstruction of crop architecture under field environment

記述言語：日本語  

記述言語：日本語  

Spiral shell form: a computer software package for theoretical morphological analysis of spiral shell form

DOI： 10.14945/00005294

対象：社会人・一般,　学術団体,　企業,　市民団体,　行政機関

種別：セミナー・ワークショップ

対象：社会人・一般,　学術団体,　企業,　市民団体,　行政機関

種別：講演会