A Randomized Crossover Study in Single-Sided Deafness Comparing a Cartilage Conduction CROS System and an Air-Conduction CROS System.

OBJECTIVE: To investigate if cartilage conduction (CC) rerouting devices are noninferior to air-conduction (AC) rerouting devices for single-sided deafness (SSD) patients by measuring objective and subjective performance using speech-in-noise tests that resemble a realistic hearing environment, sound localization tests, and standardized questionnaires. STUDY DESIGN: Prospective, single-subject randomized, crossover study. SETTING: Anechoic room inside a university. PATIENTS: Nine adults between 21 and 58 years of age with severe or profound unilateral sensorineural hearing loss. INTERVENTIONS: Patients' baseline hearing was assessed; they then used both the cartilage conduction contralateral routing of signals device (CC-CROS) and an air-conduction CROS hearing aid (AC-CROS). Patients wore each device for 2 weeks in a randomly assigned order. MAIN OUTCOME MEASURES: Three main outcome measures were 1) speech-in-noise tests, measuring speech reception thresholds; 2) proportion of correct sound localization responses; and 3) scores on the questionnaires, "Abbreviated Profile of Hearing Aid Benefit" (APHAB) and "Speech, Spatial, and Qualities of Hearing Scale" with 12 questions (SSQ-12). RESULTS: Speech reception threshold improved significantly when noise was ambient, and speech was presented from the front or the poor-ear side with both CC-CROS and AC-CROS. When speech was delivered from the better-ear side, AC-CROS significantly improved performance, whereas CC-CROS had no significant effect. Both devices mainly worsened sound localization, whereas the APHAB and SSQ-12 scores showed benefits. CONCLUSION: CC-CROS has noninferior hearing-in-noise performance except when the speech was presented to the better ear under ambient noise. Subjective measures showed that the patients realized the effectiveness of both devices.

Chromosome-scale Genome Assembly and Characterization of Top-quality Japanese Green Tea Cultivar 'Seimei'.

Japanese green tea, an essential beverage in Japanese culture, is characterized by the initial steaming of freshly harvested leaves during production. This process efficiently inactivates endogenous enzymes such as polyphenol oxidases, resulting in the production of sencha, gyokuro, and matcha that preserves the vibrant green color of young leaves. Although genome sequences of several tea cultivars and germplasms have been published, no reference genome sequences are available for Japanese green tea cultivars. Here, we constructed a reference genome sequence of the cultivar 'Seimei', which is used to produce high-quality Japanese green tea. Using the PacBio HiFi and Hi-C technologies for chromosome-scale genome assembly, we obtained 15 chromosome sequences with a total genome size of 3.1 Gb and an N50 of 214.9 Mb. By analyzing the genomic diversity of 23 Japanese tea cultivars and lines, including the leading green tea cultivars 'Yabukita' and 'Saemidori', revealed several candidate genes that could be related to the characteristics of Japanese green tea. The reference genome of 'Seimei' and information on genomic diversity of Japanese green tea cultivars should provide crucial information for effective breeding of such cultivars in the future.

Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy.

Plant hybridization is a pathway for the evolution of adaptive traits. However, hybridization between adapted and nonadapted populations may affect the persistence of combinations of adaptive alleles evolved through natural selection. Seed dormancy is an adaptive trait for weedy rice because it regulates the timing of seed germination and the persistence of the soil seed bank. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. Here, we explored the influence of hybridization on the conservation of adaptive allele combinations by evaluating natural variation and genetic structure in seed dormancy-associated genomic regions. Based on sequence variation in the genomic regions associated with seed dormancy, hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, hybrid-derived weedy rice strains were more dormant than their parental weedy rice strains, and this trait was strongly influenced by the environment. This study suggests that hybridization between weedy rice (adaptive allelic combinations for seed dormancy) and cultivated rice (nonadaptive combinations) generates weedy rice strains expressing deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and nonadapted populations appears to be reinforcing the trajectory towards the evolution of adaptive traits.

Artificial selection in the expansion of rice cultivation.

KEY MESSAGE: Gene distributions and population genomics suggest artificial selection of ghd7 osprr37, for extremely early heading date of rice, in the Tohoku region of Japan. The ranges of cultivated crops expanded into various environmental conditions around the world after their domestication. Hokkaido, Japan, lies at the northern limit of cultivation of rice, which originated in the tropics. Novel genotypes for extremely early heading date in Hokkaido are controlled by loss-of-function of both Grain number, plant height and heading date 7 (Ghd7) and Oryza sativa Pseudo-Response Regulator 37 (OsPRR37). We traced genotypes for extremely early heading date and analyzed the phylogeny of rice varieties grown historically in Japan. The mutations in Ghd7 and OsPRR37 had distinct local distributions. Population genomics revealed that varieties collected from the Tohoku region of northern Japan formed three clusters. Mutant alleles of Ghd7 and OsPRR37 appear to have allowed rice cultivation to spread into Hokkaido. Our results show that the mutations of two genes might be occurred in the process of artificial selection during early rice cultivation in the Tohoku region.

Comparative analyses of Stvb-allelic genes reveal japonica specificity of rice stripe resistance in Oryza sativa.

Rice stripe, a viral disease, causes widespread damage to japonica rice (Oryza sativa ssp. japonica). A rice stripe virus (RSV) bioassay revealed that many indica and japonica upland varieties exhibit resistance, whereas japonica paddy varieties are susceptible. However, the genetic background for this subspecies-dependent resistance is unclear. Herein, we focused on rice stripe resistance genes located at the Stvb locus. Three resistant alleles, Stvb-i (indica), Stvb (japonica upland), and Stvb-o (Oryza officinalis) were compared with the susceptible allele, stvb-j (japonica paddy). The expression of the resistance genes was higher than that of stvb-j. Sequence comparison revealed that the resistant and susceptible alleles had different 5'-end sequences and 61-bp element(s) in the fourth intron. The insertion of an LTR-retrotransposon modified the exon 1 sequence of stvb-j. We then developed four DNA markers based on gene structure information and genotyped resistant and susceptible varieties. The LTR-retrotransposon insertion was detected only in susceptible varieties. Resistant genotypes were primarily found in indica and upland japonica, whereas paddy japonica carried the susceptible genotype. Our results characterize the genetic differences associated with RSV resistance and susceptibility in O. sativa and provide insights on the application of DNA markers in rice stripe disease management.

Insect wing 3D printing.

Insects have acquired various types of wings over their course of evolution and have become the most successful terrestrial animals. Consequently, the essence of their excellent environmental adaptability and locomotive ability should be clarified; a simple and versatile method to artificially reproduce the complex structure and various functions of these innumerable types of wings is necessary. This study presents a simple integral forming method for an insect-wing-type composite structure by 3D printing wing frames directly onto thin films. The artificial venation generation algorithm based on the centroidal Voronoi diagram, which can be observed in the wings of dragonflies, was used to design the complex mechanical properties of artificial wings. Furthermore, we implemented two representative functions found in actual insect wings: folding and coupling. The proposed crease pattern design software developed based on a beetle hindwing enables the 3D printing of foldable wings of any shape. In coupling-type wings, the forewing and hindwing are connected to form a single large wing during flight; these wings can be stored compactly by disconnecting and stacking them like cicada wings.

Blower-Powered Soft Inflatable Joints for Physical Human-Robot Interaction.

Inflatables are safe and lightweight structures even at the human scale. Inflatable robots are expected to be applied to physical human-robot interaction (pHRI). Although active joint mechanisms are essential for developing inflatable robots, the existing mechanisms are complex in structure and it is difficult to integrate actuators, which diminish the advantages of inflatables. This study proposes blower-powered soft inflatable joints that are easy to fabricate and contain enough space for an actuation inside. The joints are driven by tendon wires pulled by linear actuators. We derived a theoretical model for both unilateral and bilateral joints and demonstrated a hugging robot with multiple joints as an application of the proposed joint mechanism. The novelty of the proposed joint mechanism and the inflatable robot is that rigid parts have been thoroughly eliminated and the tendons for actuation have been successfully hidden inside. Moreover, the active control of the internal pressure makes inflatables resistant to punctures. We expect that the contact safety of inflatable robots will facilitate advancement of the pHRI field.

Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution.

Agricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.

Translation of continuous artificial selection on phenotype into genotype during rice breeding programs.

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.

Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing.

The Rice Core Collection of Japanese Landraces (JRC) consisting of 50 accessions was developed by the genebank at the National Agriculture and Food Research Organization (NARO) in 2008. As a Japanese landrace core collection, the JRC has been used for many research projects, including screening for different phenotypes and allele mining for target genes. To understand the genetic diversity of Japanese Landraces, we performed whole-genome resequencing of these 50 accessions and obtained a total of 2,145,095 single nucleotide polymorphism (SNPs) and 317,832 insertion-deletions (indels) by mapping against the Oryza sativa ssp. japonica Nipponbare genome. A JRC phylogenetic tree based on 1,394 representative SNPs showed that JRC accessions were divided into two major groups and one small group. We used the multiple genome browser, TASUKE+, to examine the haplotypes of flowering genes and detected new mutations in these genes. Finally, we performed genome-wide association studies (GWAS) for agronomical traits using the JRC and another core collection, the World Rice Core Collection (WRC), comprising 69 accessions also provided by the NARO genebank. In leaf blade width, a strong peak close to NAL1, a key gene for the regulation of leaf width, and, in heading date, a peak near HESO1 involved in flowering regulation were observed in GWAS using the JRC. They were also detected in GWAS using the combined JRC + WRC. Thus, JRC and JRC + WRC are suitable populations for GWAS of particular traits.

Hydrogel Glucose Sensor with In Vivo Stable Fluorescence Intensity Relying on Antioxidant Enzymes for Continuous Glucose Monitoring.

Hydrogel glucose sensors with boronic acid-based fluorescence intensity theoretically hold promise to improve in vivo continuous glucose monitoring (CGM) by facilitating long-lasting accuracy. However, these sensors generally degrade after implantation and the fluorescence intensity decreases immediately over time. Herein, we describe a hydrogel glucose sensor with in vivo stability based on boronic acid-based fluorescence intensity, integrating two antioxidant enzymes, superoxide dismutase (SOD), and catalase. These protected the arylboronic acid from being degraded by hydrogen peroxide in vitro and preserved the boronic acid-based fluorescence intensity of the hydrogel glucose sensors in rats for 28 days. These antioxidant enzymes also allowed the hydrogel glucose sensor attached to a homemade semi-implantable CGM device to trace blood glucose concentrations in rats for 5 h with the accuracy required for clinical settings. Hydrogel glucose sensors with boronic acid-based fluorescence intensity containing SOD and catalase could comprise a new strategy for in vivo CGM.

Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding.

Citrus species are some of the most valuable and widely consumed fruits globally. The genome sequences of representative citrus (e.g., Citrus clementina, C. sinensis, C. grandis) species have been released but the research base for mandarin molecular breeding is still poor. We assembled the genomes of Citrus unshiu and Poncirus trifoliata, two important species for citrus industry in Japan, using hybrid de novo assembly of Illumina and PacBio sequence data, and developed the Mikan Genome Database (MiGD). The assembled genome sizes of C. unshiu and P. trifoliata are 346 and 292 Mb, respectively, similar to those of citrus species in public databases; they are predicted to possess 41,489 and 34,333 protein-coding genes in their draft genome sequences, with 9,642 and 8,377 specific genes when compared to C. clementina, respectively. MiGD is an integrated database of genome annotation, genetic diversity, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information, with these contents being mutually linked by genes. MiGD facilitates access to genome sequences of interest from previously reported linkage maps through CAPS markers and obtains polymorphism information through the multiple genome browser TASUKE. The genomic resources in MiGD (https://mikan.dna.affrc.go.jp) could provide valuable information for mandarin molecular breeding in Japan.

Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat.

Crop cultivars with larger root systems have an increased ability to absorb water and nutrients under conditions of water deficit. To unravel the molecular mechanism of water-stress tolerance in wheat, we performed RNA-seq analysis on the two genotypes, Colotana 296-52 (Colotana) and Tincurrin, contrasting the root growth under polyethylene-glycol-induced water-stress treatment. Out of a total of 35,047 differentially expressed genes, 3692 were specifically upregulated in drought-tolerant Colotana under water stress. Transcription factors, pyrroline-5-carboxylate reductase and late-embryogenesis-abundant proteins were among upregulated genes in Colotana. Variant calling between Colotana and Tincurrin detected 15,207 SNPs and Indels, which may affect protein function and mediate the contrasting root length phenotype. Finally, the expression patterns of five triads in response to water, high-salinity, heat, and cold stresses were analyzed using qRT-PCR to see if there were differences in homoeologous gene expression in response to those conditions. The five examined triads showed variation in the contribution of homoeologous genes to water, high-salinity, heat, and cold stresses in the two genotypes. The variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.

Continuum Robotic Caterpillar with Wirelessly Powered Shape Memory Alloy Actuators.

Wireless power transfer (WPT) has the significant potential for soft-bodied continuum robots to extend the operational time limitlessly and reduce weight. However, rigid power receiver coils, widely used in WPT, hinder the continuum deformation of the robot, and as a result, the function realization using the continuum deformation (e.g., locomotion) is impaired. Therefore, this article introduces that a soft-bodied continuum robot can be designed by using thin film receiver coils and an inductively coupled wireless powering solution without sacrificing the continuum deformation and locomotion ability. A system is described for powering and controlling a soft robotic caterpillar consisting of nothing more than its continuum structure, actuators, and thin/flexible power receiving coils.

Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley.

The high toxicity of cadmium (Cd) and its ready uptake by plants has become a major agricultural problem. To investigate the genetic architecture and genetic regulation of Cd tolerance in barley, we conducted quantitative trait loci (QTL) analysis in the phenotypically polymorphic Oregon Wolfe Barley (OWB) mapping population, derived from a cross between Rec and Dom parental genotypes. Through evaluating the Cd tolerance of 87 available doubled haploid lines of the OWB mapping population at the seedling stage, one minor and one major QTL were detected on chromosomes 2H and 6H, respectively. For chlorosis and necrosis traits, the major QTL explained 47.24% and 38.59% of the phenotypic variance, respectively. RNA-Seq analysis of the parental seedlings under Cd treatment revealed 542 differentially expressed genes between Cd-tolerant Rec and Cd-susceptible Dom genotypes. By analyzing sequence variations in transcribed sequences of the parental genotypes, 155,654 SNPs and 1,525 InDels were identified between the two contrasting genotypes and may contribute to Cd tolerance. Finally, by integrating the data from the identified QTLs and RNA-Seq analysis, 16 Cd tolerance-related candidate genes were detected, nine of which were metal ion transporters. These results provide promising candidate genes for further gene cloning and improving Cd tolerance in barley.

Infants Show Physiological Responses Specific to Parental Hugs.

Caregivers hug their infants to express affection and joy. However, it remains unknown how infants react to being hugged. Here we examined heart rate responses in first-year infants during a hug, hold, and tight hug from parents. Infants older than four months showed an increased R-R interval (RRI) during a hug, indicating reduced heart rates and pronounced parasympathetic activity. Few head movements predicted a higher RRI increase in infants during a parental hug compared with that during a hold and tight hug. Infants did not show an increased RRI during a hug from a female stranger. Infants younger than four months did not show RRI increase during parental hug but exhibited a decreased RRI correlated with contact pressure. Parents showed an increased RRI during hugging their infants. These results suggest the parent-infant hug underlies the parent-infant bonding and psychophysiological development of infants.

TASUKE+: a web-based platform for exploring genome-wide association studies results and large-scale resequencing data.

Recent revolutionary advancements in sequencing technologies have made it possible to obtain mass quantities of genome-scale sequence data in a cost-effective manner and have drastically altered molecular biological studies. To utilize these sequence data, genome-wide association studies (GWASs) have become increasingly important. Hence, there is an urgent need to develop a visualization tool that enables efficient data retrieval, integration of GWAS results with diverse information and rapid public release of such large-scale genotypic and phenotypic data. We developed a web-based genome browser TASUKE+ (https://tasuke.dna.affrc.go.jp/), which is equipped with the following functions: (i) interactive GWAS results visualization with genome resequencing data and annotation information, (ii) PCR primer design, (iii) phylogenetic tree reconstruction and (iv) data sharing via the web. GWAS results can be displayed in parallel with polymorphism data, read depths and annotation information in an interactive and scalable manner. Users can design PCR primers for polymorphic sites of interest. In addition, a molecular phylogenetic tree of any region can be reconstructed so that the overall relationship among the examined genomes can be understood intuitively at a glance. All functions are implemented through user-friendly web-based interfaces so that researchers can easily share data with collaborators in remote places without extensive bioinformatics knowledge.

Exploring Behaviors of Caterpillar-Like Soft Robots with a Central Pattern Generator-Based Controller and Reinforcement Learning.

Due to their flexibility, soft-bodied robots can potentially achieve rich and various behaviors within a single body. However, to date, no methodology has effectively harnessed these robots to achieve such diverse desired functionalities. Controllers that accomplish only a limited range of behaviors in such robots have been handcrafted. Moreover, the behaviors of these robots should be determined through body-environment interactions because an appropriate behavior may not always be manifested even if the body dynamics are given. Therefore, we have proposed SenseCPG-PGPE, a method for automatically designing behaviors for caterpillar-like soft-bodied robots. This method optimizes mechanosensory feedback to a central pattern generator (CPG)-based controller, which controls actuators in a robot, using policy gradients with parameter-based exploration (PGPE). In this article, we deeply investigated this method. We found that PGPE can optimize a CPG-based controller for soft-bodied robots that exhibit viscoelasticity and large deformation, whereas other popular policy gradient methods, such as trust region policy optimization and proximal policy optimization, cannot. Scalability of the method was confirmed using simulation as well. Although SenseCPG-PGPE uses a CPG-based controller, it can achieve nonsteady motion such as climbing a step in a simulated robot. The approach also resulted in distinctive behaviors depending on different body-environment conditions. These results demonstrate that the proposed method enables soft robots to explore a variety of behaviors automatically.

Gene expression of rice seeds surviving 13- and 20-month exposure to space environment.

Rice seeds were exposed outside of the international space station to assess the risk of space environment exposure on gene expression associated with seed germination. The germination percentages of the space-stored and ground-stored seeds exposed for 13 months were 48 and 96% respectively. Those for 20 months were 7 and 76%, respectively. Germination was defined 3 days after imbibition, except for the space-stored seeds exposed for 20 months, which germinated 5 days after imbibition. Subsequent RNA-seq analyses of the dry seeds, germinated seeds, and roots and shoots of seedlings revealed that the mutation rates of mRNA sequences were not significantly different between space-stored and ground-stored samples exposed for 13 months and 20 months. In all, 4 and 16 transcripts of glycolysis-related genes were increased in the germinated seeds after 13-month and 20-month exposure, respectively. Also, 2 and 39 transcripts of long-lived mRNA required for germination were decreased more than 2-fold in the dry seeds after 13-month and 20-month exposure, respectively. These results suggest that damage to long-lived mRNA in seeds by a space environment delays and reduces germination.