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Terahertz Patch Antenna Microcavity Lasers with Integrated Beam Control
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyTerahertz (THz) refers to the region of the electromagnetic spectrum that lies in between the infrared and microwaves. This frequency range possesses great potential to host several applications in wide-ranging fields, such as wireless communications, astronomy, non-invasive imaging and security scanning. However, despite sustained progress over the past decade, THz technology has not yet reached the level of maturity and flexibility of the neighboring radio frequency (RF) and optical range. One missing key aspect is the ability to integrate advanced beam control functionalities within a monolithic platform. A promising approach to achieve this goal is to combine within a single device two features of the neighboring ranges: optical microcavities, that can sustain efficient lasing operation; and antenna arrays, providing a high level of beam control. In this thesis, we investigate via simulations fabrication and characterization the emission properties of arrays of patch antenna-coupled microcavities embedding quantum cascade active regions. The geometrical configuration of the array allows independent and simultaneous tuning of the losses governing the microcavities as well as beam shaping by constructive interference in the far-field. We show that optimized arrays emit THz with unprecedented low beam divergence and robust lasing in single frequency and spatial mode. Additionally, we demonstrate polarization functionalization by coupling the patch antenna microcavities with plasmonic wires. This feature introduces an additional degree of freedom to adjust the relative emission from the cross-polarized modes of the patch, allowing the device to radiate with any coherent polarization state from linear to circular. Finally, we discuss how this design can further enable other advanced functionalities such as active beam steering and control of THz non-linearities. The successful implementation of integrated advanced functionalities and sources on-a-chip demonstrates the ability of our platform to replicate in the THz range the beam control concepts used in the RF and optics, thus paving the way towards establishing a mature technology in this range of the electromagnetic spectrum
Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs
Get PDFIn the open ocean without terrain boundaries, marine invertebrates with pelagic larvae can migrate long distances using ocean currents, suggesting reduced genetic diversification. Contrary to this assumption, however, genetic differentiation is often observed in marine invertebrates. In the present study, we sought to explain how population structure is established in the western Pacific Ocean, where the strong Kuroshio Current maintains high levels of gene flow from south to north, presumably promoting genetic homogeneity. We determined the population structure of the pearl oyster, Pinctada fucata, in the Indo-Pacific Ocean using genome-wide genotyping data from multiple sampling localities. Cluster analysis showed that the western Pacific population is distinct from that of the Indian Ocean, and that it is divided into northern (Japanese mainland) and southern (Nansei Islands, China, and Cambodia) populations. Genetic differentiation of P. fucata can be explained by geographic barriers in the Indian Ocean and a local lagoon, and by environmental gradients of sea surface temperature (SST) and oxygen concentration in the western Pacific. A genome scan showed evidence of adaptive evolution in genomic loci, possibly associated with changes in environmental factors, including SST and oxygen concentration. Furthermore, Bayesian simulation demonstrated that the past population expansion and division are congruent with ocean warming after the last glacial period. It is highly likely that the environmental gradient forms a genetic barrier that diversifies P. fucata populations in the western Pacific. This hypothesis helps to explain genetic differentiation and possible speciation of marine invertebrates.journal articl
Supporting Japanese Mothers of Children at Risk for Attention Deficit Hyperactivity Disorder (ADHD): A Small Scale Randomized Control Trial of Well Parent Japan
Get PDFObjectives Guidelines recommend parent management training in the multi-modal treatment of attention deficit hyperactivity disorder (ADHD). The availability of such interventions in Japan is limited. This study evaluated the effects of Well Parent Japan, a hybrid intervention including a group Japanese language adaptation of the New Forest Parenting Programme for ADHD (NFPP) augmented with strategies to improve parent’s psychological wellbeing and enhance confidence in their ability to implement change.
Methods Mothers of children aged 6–12 years displaying marked symptoms of ADHD were randomly assigned to the intervention (n=28) or a waitlist control condition (n=24). Measures were completed at baseline and again 14 weeks later. Parenting stress was the primary outcome. Other outcomes included maternal depression, parenting self-efficacy, reported and observed parenting behaviour, and maternal ratings of child ADHD, oppositional defiant disorder (ODD) symptoms, and internalizing problems.
Results Analysis of covariance (ANCOVA) compared the groups post intervention. Intervention mothers reported significantly less parenting stress, higher parenting self-esteem and use of more effective parenting strategies compared with controls, including a reduction in observed negative parenting, post intervention. These mothers also reported lower levels of child aggression and internalizing problems post intervention together with a trend (p<0.05) toward reduced symptoms of inattention.
Conclusions Well Parent Japan is an effective psychosocial intervention for parents of children with ADHD in Japan. The group format and the session content is well tolerated. This is the first randomized control trial (RCT) of a psychosocial intervention targeting ADHD in Japan.journal articl
Primary orthologs from local sequence context
Get PDFBackground
The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don't code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to gene-, centric modes of inferring paths of sequence evolution are increasingly relevant. Customarily, homologous sequences derived from the same direct ancestor, whose ancestral position in two genomes is usually conserved, are termed "primary" (or "positional") orthologs. Methods based solely on similarity don't reliably distinguish primary orthologs from other homologs; for this, genomic context is often essential. Context-dependent identification of orthologs traditionally relies on genomic context over length scales characteristic of conserved gene order or whole-genome sequence alignment, and can be computationally intensive.
Results
We demonstrate that short-range sequence context-as short as a single "maximal" match- distinguishes primary orthologs from other homologs across whole genomes. On mammalian whole genomes not preprocessed by repeat-masker, potential orthologs are extracted by genome intersection as "non-nested maximal matches:" maximal matches that are not nested into other maximal matches. It emerges that on both nucleotide and gene scales, non-nested maximal matches recapitulate primary or positional orthologs with high precision and high recall, while the corresponding computation consumes less than one thirtieth of the computation time required by commonly applied whole-genome alignment methods. In regions of genomes that would be masked by repeat-masker, non-nested maximal matches recover orthologs that are inaccessible to Lastz net alignment, for which repeat-masking is a prerequisite. mmRBHs, reciprocal best hits of genes containing non-nested maximal matches, yield novel putative orthologs, e.g. around 1000 pairs of genes for human-chimpanzee.
Conclusions
We describe an intersection-based method that requires neither repeat-masking nor alignment to infer evolutionary history of sequences based on short-range genomic sequence context. Ortholog identification based on non-nested maximal matches is parameter-free, and less computationally intensive than many alignment-based methods. It is especially suitable for genome-wide identification of orthologs, and may be applicable to unassembled genomes. We are agnostic as to the reasons for its effectiveness, which may reflect local variation of mean mutation rate.journal articl
Unsupervised Learning Facilitates Neural Coordination Across the Functional Clusters of the C. elegans Connectome
Get PDFModeling of complex adaptive systems has revealed a still poorly understood benefit of unsupervised learning: when neural networks are enabled to form an associative memory of a large set of their own attractor configurations, they begin to reorganize their connectivity in a direction that minimizes the coordination constraints posed by the initial network architecture. This self-optimization process has been replicated in various neural network formalisms, but it is still unclear whether it can be applied to biologically more realistic network topologies and scaled up to larger networks. Here we continue our efforts to respond to these challenges by demonstrating the process on the connectome of the widely studied nematode worm C. elegans. We extend our previous work by considering the contributions made by hierarchical partitions of the connectome that form functional clusters, and we explore possible beneficial effects of inter-cluster inhibitory connections. We conclude that the self-optimization process can be applied to neural network topologies characterized by greater biological realism, and that long-range inhibitory connections can facilitate the generalization capacity of the process.journal articl
Spo0J and SMC are required for normal chromosome segregation in Staphylococcus aureus
Get PDFBacterial chromosome segregation is an essential cellular process that is particularly elusive in spherical bacteria such as the opportunistic human pathogen Staphylococcus aureus. In this study, we examined the functional significance of a ParB homologue, Spo0J, in staphylococcal chromosome segregation and investigated the role of the structural maintenance of chromosomes (SMC) bacterial condensin in this process. We show that neither spo0J nor smc is essential in S. aureus; however, their absence causes abnormal chromosome segregation. We demonstrate that formation of complexes containing Spo0J and SMC is required for efficient S. aureus chromosome segregation and that SMC localization is dependent on Spo0J. Furthermore, we found that cell division and cell cycle progression are unaffected by the absence of spo0J or smc. Our results verify the role of Spo0J and SMC in ensuring accurate staphylococcal chromosome segregation and also imply functional redundancy or the involvement of additional mechanisms that might contribute to faithful chromosome inheritance.journal articl
Fano-Resonant, Asymmetric, Metamaterial-Assisted Tweezers for Single Nanoparticle Trapping
Get PDFPlasmonic nanostructures overcome Abbe’s diffraction limit to create strong gradient electric fields, enabling efficient optical trapping of nanoparticles. However, it remains challenging to achieve stable trapping with low incident laser intensity. Here, we demonstrate Fano resonance-assisted plasmonic optical tweezers for single nanoparticle trapping in an array of asymmetrical split nanoapertures on a 50 nm gold thin film. A large normalized trap stiffness of 8.65 fN/nm/mW for 20 nm polystyrene particles at a near-resonance trapping wavelength of 930 nm was achieved. The trap stiffness on-resonance is enhanced by a factor of 63 compared to that of off-resonance due to the ultrasmall mode volume, enabling large near-field strengths and a cavity effect contribution. These results facilitate trapping with low incident laser intensity, thereby providing new options for studying transition paths of single molecules such as proteins.journal articl
Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome
Get PDFIntronic regions of eukaryotic genomes accumulate many Transposable Elements (TEs). Intronic TEs often trigger the formation of transcriptionally repressive heterochromatin, even within transcription-permissive chromatin environments. Although TE-bearing introns are widely observed in eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, remain poorly understood. In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. We found that over 10% of rice genes contain intronic heterochromatin, most of which are associated with TEs and repetitive sequences. These heterochromatic introns are longer and highly enriched in promoter-proximal positions. On the other hand, introns also accumulate hypomethylated short TEs. Genes with heterochromatic introns are implicated in various biological functions. Transcription of genes bearing intronic heterochromatin is regulated by an epigenetic mechanism involving the conserved factor OsIBM2, mutation of which results in severe developmental and reproductive defects. Furthermore, we found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study demonstrates that heterochromatin is a common epigenetic feature associated with actively transcribed genes in the rice genome.journal articl
細胞創傷治癒の分子基盤とその帰結
Get PDFこの世界で最初の細胞は、遺伝情報を司る核酸とそれ を包み込み環境変化から守る膜の成立により誕生した。したがって、細胞膜の傷を修復する「細胞創傷治癒」の仕組みは生命誕生の瞬間から必要とされただろう。細胞創傷治癒の欠損は筋ジストロフィー症など、さまざまな疾病に関与するが、そのメカニズムは未だ不明な点が多く残されている。筆者らは出芽酵母を用いて細胞創傷治 癒に関与する遺伝子を網羅的に同定した結果、プロテア ソームによるタンパク質分解が修復反応の開始に必須であること、細胞膜損傷が細胞周期チェックポイントを活性化すること、分裂寿命の短縮を誘導することなどを明らかにした。また細胞膜損傷チェックポイントや分裂寿命の短縮はヒト培養細胞まで進化的に保存されていることなどが明らかになりつつある。journal articl
Generation of homogeneous midbrain organoids with in vivo-like cellular composition facilitates neurotoxin-based Parkinson's disease modeling
Get PDFRecent studies have demonstrated the generation of midbrain-like organoids (MOs) from human pluripotent stem cells. However, the low efficiency of MO generation and the relatively immature and heterogeneous structures of the MOs hinder the translation of these organoids from the bench to the clinic. Here we describe the robust generation of MOs with homogeneous distribution of midbrain dopaminergic (mDA) neurons. Our MOs contain not only mDA neurons but also other neuronal subtypes as well as functional glial cells including astrocytes and oligodendrocytes. Furthermore, our MOs exhibit mDA neuron-specific cell death upon treatment with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, indicating that MOs could be a proper human model system for studying the in vivo pathology of Parkinson's disease (PD). Our optimized conditions for producing homogeneous and mature MOs might provide an advanced patient-specific platform for in vitro disease modeling as well as for drug screening for PD.journal articl