Showing papers by "Kyoto University published in 2013"

Sinkhorn Distances: Lightspeed Computation of Optimal Transport

Abstract: Optimal transport distances are a fundamental family of distances for probability measures and histograms of features. Despite their appealing theoretical properties, excellent performance in retrieval tasks and intuitive formulation, their computation involves the resolution of a linear program whose cost can quickly become prohibitive whenever the size of the support of these measures or the histograms' dimension exceeds a few hundred. We propose in this work a new family of optimal transport distances that look at transport problems from a maximum-entropy perspective. We smooth the classic optimal transport problem with an entropic regularization term, and show that the resulting optimum is also a distance which can be computed through Sinkhorn's matrix scaling algorithm at a speed that is several orders of magnitude faster than that of transport solvers. We also show that this regularized distance improves upon classic optimal transport distances on the MNIST classification problem.

Tunable Photoluminescence of Monolayer MoS2 via Chemical Doping

Abstract: We demonstrate the tunability of the photoluminescence (PL) properties of monolayer (1L)-MoS2 via chemical doping. The PL intensity of 1L-MoS2 was drastically enhanced by the adsorption of p-type dopants with high electron affinity but reduced by the adsorption of n-type dopants. This PL modulation results from switching between exciton PL and trion PL depending on carrier density in 1L-MoS2. Achievement of the extraction and injection of carriers in 1L-MoS2 by this solution-based chemical doping method enables convenient control of optical and electrical properties of atomically thin MoS2.

Essential biodiversity variables

Abstract: Reducing the rate of biodiversity loss and averting dangerous biodiversity change are international goals, reasserted by the Aichi Targets for 2020 by Parties to the United Nations (UN) Convention on Biological Diversity (CBD) after failure to meet the 2010 target (1, 2). However, there is no global, harmonized observation system for delivering regular, timely data on biodiversity change (3). With the first plenary meeting of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) soon under way, partners from the Group on Earth Observations Biodiversity Observation Network (GEO BON) (4) are developing—and seeking consensus around—Essential Biodiversity Variables (EBVs) that could form the basis of monitoring programs worldwide.

CXCL12 in early mesenchymal progenitors is required for haematopoietic stem-cell maintenance

Abstract: Haematopoietic stem cells (HSCs) primarily reside in the bone marrow where signals generated by stromal cells regulate their self-renewal, proliferation and trafficking. Endosteal osteoblasts and perivascular stromal cells including endothelial cells, CXCL12-abundant reticular cells, leptin-receptor-positive stromal cells, and nestin-green fluorescent protein (GFP)-positive mesenchymal progenitors have all been implicated in HSC maintenance. However, it is unclear whether specific haematopoietic progenitor cell (HPC) subsets reside in distinct niches defined by the surrounding stromal cells and the regulatory molecules they produce. CXCL12 (chemokine (C-X-C motif) ligand 12) regulates both HSCs and lymphoid progenitors and is expressed by all of these stromal cell populations. Here we selectively deleted Cxcl12 from candidate niche stromal cell populations and characterized the effect on HPCs. Deletion of Cxcl12 from mineralizing osteoblasts has no effect on HSCs or lymphoid progenitors. Deletion of Cxcl12 from osterix-expressing stromal cells, which include CXCL12-abundant reticular cells and osteoblasts, results in constitutive HPC mobilization and a loss of B-lymphoid progenitors, but HSC function is normal. Cxcl12 deletion from endothelial cells results in a modest loss of long-term repopulating activity. Strikingly, deletion of Cxcl12 from nestin-negative mesenchymal progenitors using Prx1-cre (Prx1 also known as Prrx1) is associated with a marked loss of HSCs, long-term repopulating activity, HSC quiescence and common lymphoid progenitors. These data suggest that osterix-expressing stromal cells comprise a distinct niche that supports B-lymphoid progenitors and retains HPCs in the bone marrow, and that expression of CXCL12 from stromal cells in the perivascular region, including endothelial cells and mesenchymal progenitors, supports HSCs.

Salient Object Detection: A Discriminative Regional Feature Integration Approach

Abstract: Salient object detection has been attracting a lot of interest, and recently various heuristic computational models have been designed. In this paper, we regard saliency map computation as a regression problem. Our method, which is based on multi-level image segmentation, uses the supervised learning approach to map the regional feature vector to a saliency score, and finally fuses the saliency scores across multiple levels, yielding the saliency map. The contributions lie in two-fold. One is that we show our approach, which integrates the regional contrast, regional property and regional background ness descriptors together to form the master saliency map, is able to produce superior saliency maps to existing algorithms most of which combine saliency maps heuristically computed from different types of features. The other is that we introduce a new regional feature vector, background ness, to characterize the background, which can be regarded as a counterpart of the objectness descriptor [2]. The performance evaluation on several popular benchmark data sets validates that our approach outperforms existing state-of-the-arts.

The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43

Abstract: The gut microbiota affects nutrient acquisition and energy regulation of the host, and can influence the development of obesity, insulin resistance, and diabetes. During feeding, gut microbes produce short-chain fatty acids, which are important energy sources for the host. Here we show that the short-chain fatty acid receptor GPR43 links the metabolic activity of the gut microbiota with host body energy homoeostasis. We demonstrate that GPR43-deficient mice are obese on a normal diet, whereas mice overexpressing GPR43 specifically in adipose tissue remain lean even when fed a high-fat diet. Raised under germ-free conditions or after treatment with antibiotics, both types of mice have a normal phenotype. We further show that short-chain fatty acid-mediated activation of GPR43 suppresses insulin signalling in adipocytes, which inhibits fat accumulation in adipose tissue and promotes the metabolism of unincorporated lipids and glucose in other tissues. These findings establish GPR43 as a sensor for excessive dietary energy, thereby controlling body energy utilization while maintaining metabolic homoeostasis.

Sequence-controlled polymers.

Abstract: Background During the last few decades, progress has been made in manipulating the architecture of synthetic polymer materials. However, the primary structure—that is, the sequential arrangement of monomer units in a polymer chain—is generally poorly controlled in synthetic macromolecules. Common synthetic polymers are usually homopolymers, made of the same monomer unit, or copolymers with simple chain microstructures, such as random or block copolymers. These polymers are used in many areas but do not have the structural and functional complexity of sequence-defined biopolymers, such as nucleic acids or proteins. Indeed, monomer sequence regulation plays a key role in biology and is a prerequisite for crucial features of life, such as heredity, self-replication, complex self-assembly, and molecular recognition. In this context, developing synthetic polymers containing controlled monomer sequences is an important area for research. Precise molecular encoding of synthetic polymer chains. In most synthetic copolymers, monomer units (represented here as colored square boxes A, B, C, and D) are distributed randomly along the polymer chains (left). In sequence-controlled polymers, they are arranged in a specific order in all of the chains (right). Monomer sequence regularity strongly influences the molecular, supramolecular, andmacroscopic properties of polymer materials. Advances Various synthetic methods for controlling monomer sequences in polymers have been identified, and two major trends in the field of sequence-controlled polymers have emerged. Some approaches use biological concepts that have been optimized by nature for sequence regulation. For instance, DNA templates, enzymes, or even living organisms can be used to prepare sequence-defined polymers. These natural mechanisms can be adapted to tolerate nonnatural monomers. The other trend is the preparation of sequence-controlled polymers by synthetic chemistry. In the most popular approach, monomer units are attached one by one to a support, which is an efficient method but demanding in practice. Recently, some strategies have been proposed for controlling sequences in chain-growth and step-growth polymerizations. These mechanisms usually allow fast and large-scale synthesis of polymers. Specific kinetics and particular catalytic or template conditions allow sequence regulation in these processes. Outlook The possibility of controlling monomer sequences in synthetic macromolecules has many scientific and technological implications. Information can be controlled at the molecular level in synthetic polymer chains. This opens up interesting perspectives for the field of data storage. In addition, having power over monomer sequences could mean structural control of the resulting polymer, as it strongly influences macromolecular folding and self-assembly. For instance, functional synthetic assemblies that mimic the properties of globular proteins, such as enzymes and transporters, can be foreseen. Moreover, monomer sequence control influences some macroscopic properties. For example, bulk properties such as conductivity, rigidity, elasticity, or biodegradability can be finely tuned in sequence-controlled polymers. The behavior of polymers in solution, particularly in water, is also strongly dependent on monomer sequences. Thus, sequence regulation may enable a more effective control of structure-property relations in tomorrow’s polymer materials.

Integrated molecular analysis of clear-cell renal cell carcinoma.

Abstract: Clear-cell renal cell carcinoma (ccRCC) is the most prevalent kidney cancer and its molecular pathogenesis is incompletely understood. Here we report an integrated molecular study of ccRCC in which ≥100 ccRCC cases were fully analyzed by whole-genome and/or whole-exome and RNA sequencing as well as by array-based gene expression, copy number and/or methylation analyses. We identified a full spectrum of genetic lesions and analyzed gene expression and DNA methylation signatures and determined their impact on tumor behavior. Defective VHL-mediated proteolysis was a common feature of ccRCC, which was caused not only by VHL inactivation but also by new hotspot TCEB1 mutations, which abolished Elongin C-VHL binding, leading to HIF accumulation. Other newly identified pathways and components recurrently mutated in ccRCC included PI3K-AKT-mTOR signaling, the KEAP1-NRF2-CUL3 apparatus, DNA methylation, p53-related pathways and mRNA processing. This integrated molecular analysis unmasked new correlations between DNA methylation, gene mutation and/or gene expression and copy number profiles, enabling the stratification of clinical risks for patients with ccRCC.

The second fermi large area telescope catalog of gamma-ray pulsars

Abstract: This catalog summarizes 117 high-confidence > 0.1 GeV gamma-ray pulsar detections using three years of data acquired by the Large Area Telescope (LAT) on the Fermi satellite. Half are neutron stars discovered using LAT data, through periodicity searches in gamma-ray and radio data around LAT unassociated source positions. The 117 pulsars are evenly divided into three groups: millisecond pulsars, young radio-loud pulsars, and young radio-quiet pulsars. We characterize the pulse profiles and energy spectra and derive luminosities when distance information exists. Spectral analysis of the off-peak phase intervals indicates probable pulsar wind nebula emission for four pulsars, and off-peak magnetospheric emission for several young and millisecond pulsars. We compare the gamma-ray properties with those in the radio, optical, and X-ray bands. We provide flux limits for pulsars with no observed gamma-ray emission, highlighting a small number of gamma-faint, radio-loud pulsars. The large, varied gamma-ray pulsar sample constrains emission models. Fermi's selection biases complement those of radio surveys, enhancing comparisons with predicted population distributions.

Terminology of metal–organic frameworks and coordination polymers (IUPAC Recommendations 2013)

Abstract: A set of terms, definitions, and recommendations is provided for use in the classi- fication of coordination polymers, networks, and metal-organic frameworks (MOFs). A hier- archical terminology is recommended in which the most general term is coordination poly- mer. Coordination networks are a subset of coordination polymers and MOFs a further subset of coordination networks. One of the criteria an MOF needs to fulfill is that it contains poten- tial voids, but no physical measurements of porosity or other properties are demanded per se. The use of topology and topology descriptors to enhance the description of crystal structures of MOFs and 3D-coordination polymers is furthermore strongly recommended.

Resonant and nonresonant control over matter and light by intense terahertz transients

Abstract: This article provides an overview and illustrative examples of how the electric and magnetic fields of intense terahertz transients can be used to resonantly, and even nonresonantly, control matter and light. It discusses the fundamental interaction mechanisms of intense terahertz radiation with matter.

Detection of the characteristic pion-decay signature in supernova remnants

Abstract: Cosmic rays are particles (mostly protons) accelerated to relativistic speeds. Despite wide agreement that supernova remnants (SNRs) are the sources of galactic cosmic rays, unequivocal evidence for the acceleration of protons in these objects is still lacking. When accelerated protons encounter interstellar material, they produce neutral pions, which in turn decay into gamma rays. This offers a compelling way to detect the acceleration sites of protons. The identification of pion-decay gamma rays has been difficult because high-energy electrons also produce gamma rays via bremsstrahlung and inverse Compton scattering. We detected the characteristic pion-decay feature in the gamma-ray spectra of two SNRs, IC 443 and W44, with the Fermi Large Area Telescope. This detection provides direct evidence that cosmic-ray protons are accelerated in SNRs.

The importance of correcting for sampling bias in MaxEnt species distribution models

Abstract: Aim Advancement in ecological methods predicting species distributions is a crucial precondition for deriving sound management actions. Maximum entropy (MaxEnt) models are a popular tool to predict species distributions, as they are considered able to cope well with sparse, irregularly sampled data and minor location errors. Although a fundamental assumption of MaxEnt is that the entire area of interest has been systematically sampled, in practice, MaxEnt models are usually built from occurrence records that are spatially biased towards better-surveyed areas. Two common, yet not compared, strategies to cope with uneven sampling effort are spatial filtering of occurrence data and background manipulation using environmental data with the same spatial bias as occurrence data. We tested these strategies using simulated data and a recently collated dataset on Malay civet Viverra tangalunga in Borneo. Location Borneo, Southeast Asia. Methods We collated 504 occurrence records of Malay civets from Borneo of which 291 records were from 2001 to 2011 and used them in the MaxEnt analysis (baseline scenario) together with 25 environmental input variables. We simulated datasets for two virtual species (similar to a range-restricted highland and a lowland species) using the same number of records for model building. As occurrence records were biased towards north-eastern Borneo, we investigated the efficacy of spatial filtering versus background manipulation to reduce overprediction or underprediction in specific areas. Results Spatial filtering minimized omission errors (false negatives) and commission errors (false positives). We recommend that when sample size is insufficient to allow spatial filtering, manipulation of the background dataset is preferable to not correcting for sampling bias, although predictions were comparatively weak and commission errors increased. Main Conclusions We conclude that a substantial improvement in the quality of model predictions can be achieved if uneven sampling effort is taken into account, thereby improving the efficacy of species conservation planning.

SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction

Abstract: This technical report describes a method to clear fixed brain tissues while allowing for fluorescent dye tracing and retaining cellular morphology. The authors demonstrate the utility of the technique by obtaining a wiring diagram for sister mitral cells.

A rheostat for immune responses: the unique properties of PD-1 and their advantages for clinical application.

Abstract: PD-1, a negative coreceptor expressed on antigen-stimulated T cells and B cells, seems to serve as a 'rheostat' of the immune response. The molecular mechanisms of the functions of PD-1, in conjunction with the mild, chronic and strain-specific autoimmune phenotypes of PD-1-deficient mice, in contrast to the devastating fatal autoimmune disease of mice deficient in the immunomodulatory receptor CTLA-4, suggest that immunoregulation by PD-1 is rather antigen specific and is mainly cell intrinsic. Such unique properties make PD-1 a powerful target for immunological therapy, with highly effective clinical applications for cancer treatment.

Molecular understanding of sulphuric acid-amine particle nucleation in the atmosphere

Abstract: Nucleation of aerosol particles from trace atmospheric vapours is thought to provide up to half of global cloud condensation nuclei(1). Aerosols can cause a net cooling of climate by scattering sun ...

Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell–derived neocortex

Abstract: Here, using further optimized 3D culture that allows highly selective induction and long-term growth of human ES cell (hESC)-derived cortical neuroepithelium, we demonstrate unique aspects of self-organization in human neocorticogenesis. Self-organized cortical tissue spontaneously forms a polarity along the dorsocaudal-ventrorostral axis and undergoes region-specific rolling morphogenesis that generates a semispherical structure. The neuroepithelium self-forms a multilayered structure including three neuronal zones (subplate, cortical plate, and Cajal-Retzius cell zones) and three progenitor zones (ventricular, subventricular, and intermediate zones) in the same apical-basal order as seen in the human fetal cortex in the early second trimester. In the cortical plate, late-born neurons tend to localize more basally to early-born neurons, consistent with the inside-out pattern seen in vivo. Furthermore, the outer subventricular zone contains basal progenitors that share characteristics with outer radial glia abundantly found in the human, but not mouse, fetal brain. Thus, human neocorticogenesis involves intrinsic programs that enable the emergence of complex neocortical features.

Ion conductivity and transport by porous coordination polymers and metal-organic frameworks.

Abstract: Ion conduction and transport in solids are both interesting and useful and are found in widely distinct materials, from those in battery-related technologies to those in biological systems. Scientists have approached the synthesis of ion-conductive compounds in a variety of ways, in the areas of organic and inorganic chemistry. Recently, based on their ion-conducting behavior, porous coordination polymers (PCPs) and metal–organic frameworks (MOFs) have been recognized for their easy design and the dynamic behavior of the ionic components in the structures. These PCP/MOFs consist of metal ions (or clusters) and organic ligands structured via coordination bonds. They could have highly concentrated mobile ions with dynamic behavior, and their characteristics have inspired the design of a new class of ion conductors and transporters.In this Account, we describe the state-of-the-art of studies of ion conductivity by PCP/MOFs and nonporous coordination polymers (CPs) and offer future perspectives. PCP/MOF struc...

Autophagy deficiency leads to protection from obesity and insulin resistance by inducing Fgf21 as a mitokine

Abstract: Despite growing interest and a recent surge in papers, the role of autophagy in glucose and lipid metabolism is unclear. We produced mice with skeletal muscle–specific deletion of Atg7 (encoding autophagy-related 7). Unexpectedly, these mice showed decreased fat mass and were protected from diet-induced obesity and insulin resistance; this phenotype was accompanied by increased fatty acid oxidation and browning of white adipose tissue (WAT) owing to induction of fibroblast growth factor 21 (Fgf21). Mitochondrial dysfunction induced by autophagy deficiency increased Fgf21 expression through induction of Atf4, a master regulator of the integrated stress response. Mitochondrial respiratory chain inhibitors also induced Fgf21 in an Atf4-dependent manner. We also observed induction of Fgf21, resistance to diet-induced obesity and amelioration of insulin resistance in mice with autophagy deficiency in the liver, another insulin target tissue. These findings suggest that autophagy deficiency and subsequent mitochondrial dysfunction promote Fgf21 expression, a hormone we consequently term a 'mitokine', and together these processes promote protection from diet-induced obesity and insulin resistance.

An Efficient Nonviral Method to Generate Integration-Free Human-Induced Pluripotent Stem Cells from Cord Blood and Peripheral Blood Cells†‡§

Abstract: The generation of induced pluripotent stem cells (iPSCs) provides the opportunity to use patient-specific somatic cells, which are a valuable source for disease modeling and drug discovery. To promote research involving these cells, it is important to make iPSCs from easily accessible and less invasive tissues, like blood. We have recently reported the efficient generation of human iPSCs from adult fibroblasts using a combination of plasmids encoding OCT3/4, SOX2, KLF4, L-MYC, LIN28, and shRNA for TP53. We herein report a modified protocol enabling efficient iPSC induction from CD34+ cord blood cells and from peripheral blood isolated from healthy donors using these plasmid vectors. The original plasmid mixture could induce iPSCs; however, the efficiency was low. The addition of EBNA1, an essential factor for episomal amplification of the vectors, by an extra plasmid greatly increased the efficiency of iPSC induction, especially when the induction was performed from αβT cells. This improvement enabled the establishment of blood-derived iPSCs from seven healthy donors ranging in age from their 20s to their 60s. This induction method will be useful for the derivation of patient-specific integration-free iPSCs and would also be applicable to the generation of clinical-grade iPSCs in the future.

Efficient Persistent Room Temperature Phosphorescence in Organic Amorphous Materials under Ambient Conditions

Abstract: Persistent emission with a long lifetime (>1 s) from organic materials can only be observed at a low temperature, because of the significant nonradiative deactivation pathway that occurs at room-temperature (RT). If organic materials with persistent RT emission in air could be developed, they could potentially be utilized for a variety of applications. Here, organic host-guest materials with efficient persistent RT phosphorescence (RTP) are developed by minimizing the nonradiative deactivation pathway of triplet excitons. The nonradiative deactivation pathway is dependent on both nonradiative deactivation of the guest and quenching by diffusional motion of the host. The rigidity and oxygen barrier properties of the steroidal compound used as the host suppressed the quenching, and the aromatic hydrocarbon used as the guest is highly deuterated to minimize nonradiative deactivation of the guest. Red-green-blue persistent RTP with a lifetime >1 s and a quantum yield >10% in air is realized for a pure organic material.