Showing papers by "Kyushu University published in 2016"

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

A century of trends in adult human height

Abstract: Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3–19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8–144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.

A Comparative Evaluation of Unsupervised Anomaly Detection Algorithms for Multivariate Data.

Abstract: Anomaly detection is the process of identifying unexpected items or events in datasets, which differ from the norm. In contrast to standard classification tasks, anomaly detection is often applied on unlabeled data, taking only the internal structure of the dataset into account. This challenge is known as unsupervised anomaly detection and is addressed in many practical applications, for example in network intrusion detection, fraud detection as well as in the life science and medical domain. Dozens of algorithms have been proposed in this area, but unfortunately the research community still lacks a comparative universal evaluation as well as common publicly available datasets. These shortcomings are addressed in this study, where 19 different unsupervised anomaly detection algorithms are evaluated on 10 different datasets from multiple application domains. By publishing the source code and the datasets, this paper aims to be a new well-funded basis for unsupervised anomaly detection research. Additionally, this evaluation reveals the strengths and weaknesses of the different approaches for the first time. Besides the anomaly detection performance, computational effort, the impact of parameter settings as well as the global/local anomaly detection behavior is outlined. As a conclusion, we give an advise on algorithm selection for typical real-world tasks.

International consensus guidance for management of myasthenia gravis: Executive summary

Abstract: Objective: To develop formal consensus-based guidance for the management of myasthenia gravis (MG). Methods: In October 2013, the Myasthenia Gravis Foundation of America appointed a Task Force to develop treatment guidance for MG, and a panel of 15 international experts was convened. The RAND/UCLA appropriateness methodology was used to develop consensus guidance statements. Definitions were developed for goals of treatment, minimal manifestations, remission, ocular MG, impending crisis, crisis, and refractory MG. An in-person panel meeting then determined 7 treatment topics to be addressed. Initial guidance statements were developed from literature summaries. Three rounds of anonymous e-mail votes were used to attain consensus on guidance statements modified on the basis of panel input. Results: Guidance statements were developed for symptomatic and immunosuppressive treatments, IV immunoglobulin and plasma exchange, management of impending and manifest myasthenic crisis, thymectomy, juvenile MG, MG associated with antibodies to muscle-specific tyrosine kinase, and MG in pregnancy. Conclusion: This is an international formal consensus of MG experts intended to be a guide for clinicians caring for patients with MG worldwide.

Aerosol and monsoon climate interactions over Asia

Abstract: The increasing severity of droughts/floods and worsening air quality from increasing aerosols in Asia monsoon regions are the two gravest threats facing over 60% of the world population living in Asian monsoon regions. These dual threats have fueled a large body of research in the last decade on the roles of aerosols in impacting Asian monsoon weather and climate. This paper provides a comprehensive review of studies on Asian aerosols, monsoons, and their interactions. The Asian monsoon region is a primary source of emissions of diverse species of aerosols from both anthropogenic and natural origins. The distributions of aerosol loading are strongly influenced by distinct weather and climatic regimes, which are, in turn, modulated by aerosol effects. On a continental scale, aerosols reduce surface insolation and weaken the land-ocean thermal contrast, thus inhibiting the development of monsoons. Locally, aerosol radiative effects alter the thermodynamic stability and convective potential of the lower atmosphere leading to reduced temperatures, increased atmospheric stability, and weakened wind and atmospheric circulations. The atmospheric thermodynamic state, which determines the formation of clouds, convection, and precipitation, may also be altered by aerosols serving as cloud condensation nuclei or ice nuclei. Absorbing aerosols such as black carbon and desert dust in Asian monsoon regions may also induce dynamical feedback processes, leading to a strengthening of the early monsoon and affecting the subsequent evolution of the monsoon. Many mechanisms have been put forth regarding how aerosols modulate the amplitude, frequency, intensity, and phase of different monsoon climate variables. A wide range of theoretical, observational, and modeling findings on the Asian monsoon, aerosols, and their interactions are synthesized. A new paradigm is proposed on investigating aerosol-monsoon interactions, in which natural aerosols such as desert dust, black carbon from biomass burning, and biogenic aerosols from vegetation are considered integral components of an intrinsic aerosol-monsoon climate system, subject to external forcing of global warming, anthropogenic aerosols, and land use and change. Future research on aerosol-monsoon interactions calls for an integrated approach and international collaborations based on long-term sustained observations, process measurements, and improved models, as well as using observations to constrain model simulations and projections.

Dynamic molecular crystals with switchable physical properties

Abstract: The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials.

Extended Clavien-Dindo classification of surgical complications: Japan Clinical Oncology Group postoperative complications criteria

Abstract: Prior to publication of the Clavien-Dindo classification in 2004, there were no grading definitions for surgical complications in either clinical practice or surgical trials. This report establishes supplementary criteria for this classification to standardize the evaluation of postoperative complications in clinical trials. The Japan Clinical Oncology Group (JCOG) commissioned a committee. Members from nine surgical study groups (gastric, esophageal, colorectal, lung, breast, gynecologic, urologic, bone and soft tissue, and brain) specified postoperative complications experienced commonly in their fields and defined more detailed grading criteria for each complication in accordance with the general grading rules of the Clavien-Dindo classification. We listed 72 surgical complications experienced commonly in surgical trials, focusing on 17 gastroenterologic complications, 13 infectious complications, six thoracic complications, and several other complications. The grading criteria were defined simply and were optimized for surgical complications. The JCOG postoperative complications criteria (JCOG PC criteria) aim to standardize the terms used to define adverse events (AEs) and provide detailed grading guidelines based on the Clavien-Dindo classification. We believe that the JCOG PC criteria will allow for more precise comparisons of the frequency of postoperative complications among trials across many different surgical fields.

Pose Estimation for Augmented Reality: A Hands-On Survey

Abstract: Augmented reality (AR) allows to seamlessly insert virtual objects in an image sequence. In order to accomplish this goal, it is important that synthetic elements are rendered and aligned in the scene in an accurate and visually acceptable way. The solution of this problem can be related to a pose estimation or, equivalently, a camera localization process. This paper aims at presenting a brief but almost self-contented introduction to the most important approaches dedicated to vision-based camera localization along with a survey of several extension proposed in the recent years. For most of the presented approaches, we also provide links to code of short examples. This should allow readers to easily bridge the gap between theoretical aspects and practical implementations.

The quiescent intracluster medium in the core of the Perseus cluster

Abstract: The Hitomi collaboration reports X-ray observations of the core of the Perseus cluster of galaxies the brightest X-ray-emitting cluster in the sky. Such clusters typically consist of tens to thousands of galaxies bound together by gravity and are studied as models of both small-scale cosmology and large-scale astrophysical processes. The data reveal a remarkably quiescent atmosphere, where gas velocities are quite low, with a line-of-sight velocity dispersion of about 164 kilometres per second at a distance of 3060 kiloparsecs from the central nucleus.

Muon reconstruction performance of the ATLAS detector in proton–proton collision data at √ s =13 TeV

Abstract: This article documents the performance of the ATLAS muon identification and reconstruction using the first LHC dataset recorded at s√ = 13 TeV in 2015. Using a large sample of J/ψ→μμ and Z→μμ decays from 3.2 fb−1 of pp collision data, measurements of the reconstruction efficiency, as well as of the momentum scale and resolution, are presented and compared to Monte Carlo simulations. The reconstruction efficiency is measured to be close to 99% over most of the covered phase space (|η| 2.2, the pT resolution for muons from Z→μμ decays is 2.9% while the precision of the momentum scale for low-pT muons from J/ψ→μμ decays is about 0.2%.

Reconstitution in vitro of the entire cycle of the mouse female germ line

Abstract: The female germ line undergoes a unique sequence of differentiation processes that confers totipotency to the egg. The reconstitution of these events in vitro using pluripotent stem cells is a key achievement in reproductive biology and regenerative medicine. Here we report successful reconstitution in vitro of the entire process of oogenesis from mouse pluripotent stem cells. Fully potent mature oocytes were generated in culture from embryonic stem cells and from induced pluripotent stem cells derived from both embryonic fibroblasts and adult tail tip fibroblasts. Moreover, pluripotent stem cell lines were re-derived from the eggs that were generated in vitro, thereby reconstituting the full female germline cycle in a dish. This culture system will provide a platform for elucidating the molecular mechanisms underlying totipotency and the production of oocytes of other mammalian species in culture.

A review on high-pressure torsion (HPT) from 1935 to 1988

Abstract: High-pressure torsion (HPT) method currently receives much attention as a severe plastic deformation (SPD) technique mainly because of the reports of Prof. Ruslan Z. Valiev and his co-workers in 1988. They reported the efficiency of the method in creating ultrafine-grained (UFG) structures with predominantly high-angle grain boundaries, which started the new age of nanoSPD materials with novel properties. The HPT method was first introduced by Prof. Percy W. Bridgman in 1935. Bridgman pioneered application of high torsional shearing stress combined with high hydrostatic pressure to many different kinds of materials such as pure elements, metallic materials, glasses, geological materials (rocks and minerals), biological materials, polymers and many different kinds of organic and inorganic compounds. This paper reviews the findings of Bridgman and his successors from 1935 to 1988 using the HPT method and summarizes their historical importance in recent advancement of materials, properties, phase transformations and HPT machine designs.

Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions

Abstract: Despite the importance of DNA methylation in health and disease, technologies to readily manipulate methylation of specific sequences for functional analysis and therapeutic purposes are lacking. Here we adapt the previously described dCas9-SunTag for efficient, targeted demethylation of specific DNA loci. The original SunTag consists of ten copies of the GCN4 peptide separated by 5-amino-acid linkers. To achieve efficient recruitment of an anti-GCN4 scFv fused to the ten-eleven (TET) 1 hydroxylase, which induces demethylation, we changed the linker length to 22 amino acids. The system attains demethylation efficiencies >50% in seven out of nine loci tested. Four of these seven loci showed demethylation of >90%. We demonstrate targeted demethylation of CpGs in regulatory regions and demethylation-dependent 1.7- to 50-fold upregulation of associated genes both in cell culture (embryonic stem cells, cancer cell lines, primary neural precursor cells) and in vivo in mouse fetuses.

Performance of $b$-Jet Identification in the ATLAS Experiment

Abstract: The identification of jets containing b hadrons is important for the physics programme of the ATLAS experiment at the Large Hadron Collider. Several algorithms to identify jets containing b hadrons are described, ranging from those based on the reconstruction of an inclusive secondary vertex or the presence of tracks with large impact parameters to combined tagging algorithms making use of multi-variate discriminants. An independent b-tagging algorithm based on the reconstruction of muons inside jets as well as the b-tagging algorithm used in the online trigger are also presented. The b-jet tagging efficiency, the c-jet tagging efficiency and the mistag rate for light flavour jets in data have been measured with a number of complementary methods. The calibration results are presented as scale factors defined as the ratio of the efficiency (or mistag rate) in data to that in simulation. In the case of b jets, where more than one calibration method exists, the results from the various analyses have been combined taking into account the statistical correlation as well as the correlation of the sources of systematic uncertainty.

Producing Bulk Ultrafine-Grained Materials by Severe Plastic Deformation: Ten Years Later

Abstract: It is now well established that the processing of bulk solids through the application of severe plastic deformation (SPD) leads to exceptional grain refinement to the submicrometer or nanometer level. Extensive research over the last decade has demonstrated that SPD processing also produces unusual phase transformations and leads to the introduction of a range of nanostructural features, including nonequilibrium grain boundaries, deformation twins, dislocation substructures, vacancy agglomerates, and solute segregation and clustering. These many structural changes provide new opportunities for fine tuning the characteristics of SPD metals to attain major improvements in their physical, mechanical, chemical, and functional properties. This review provides a summary of some of these recent developments. Special emphasis is placed on the use of SPD processing in achieving increased electrical conductivity, superconductivity, and thermoelectricity, an improved hydrogen storage capability, materials for use in biomedical applications, and the fabrication of high-strength metal-matrix nanocomposites.

Afterglow Organic Light-Emitting Diode

Abstract: An afterglow organic light-emitting diode (OLED) that displays electroluminescence with long transient decay after it is turned off is demonstrated. This OLED exhibits blue and green dual emission originating from fluorescence and phosphorescence, respectively. A phosphorescence lifetime of 4.3 s is achieved.

Aggregation-Induced Delayed Fluorescence Based on Donor/Acceptor-Tethered Janus Carborane Triads: Unique Photophysical Properties of Nondoped OLEDs.

Abstract: Luminescent materials consisting of boron clusters, such as carboranes, have attracted immense interest in recent years. In this study, luminescent organic-inorganic conjugated systems based on o-carboranes directly bonded to electron-donating and electron-accepting π-conjugated units were elaborated as novel optoelectronic materials. These o-carborane derivatives simultaneously possessed aggregation-induced emission (AIE) and thermally activated delayed fluorescence (TADF) capabilities, and showed strong yellow-to-red emissions with high photoluminescence quantum efficiencies of up to 97 % in their aggregated states or in solid neat films. Organic light-emitting diodes utilizing these o-carborane derivatives as a nondoped emission layer exhibited maximum external electroluminescence quantum efficiencies as high as 11 %, originating from TADF.

ENETS Consensus Guidelines Update for Gastroduodenal Neuroendocrine Neoplasms.

Abstract: a Department of Digestive and Liver Disease, Ospedale Sant’Andrea, Rome , Italy; b NET Centre, St. Vincent’s University and Department of Clinical Medicine, St. James Hospital and Trinity College, Dublin , Ireland; c Department of Radiology, Section for Molecular Imaging, University Hospital, Uppsala , Sweden; d Netherlands Cancer Centre, Lijnden , The Netherlands; e NET Centre, Umbria Regional Cancer Network, Università degli Studi di Perugia, Perugia , Italy; f Gastroenterology Department, Hampshire Hospitals NHS Trust, Hampshire , UK; g Department of Endocrine and Metabolic Sciences, University of Genoa, Genoa , Italy; h Pancreatic Diseases Branch, Kyushu University Hospital, Fukuoka , Japan; i Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, N.Y. , USA; j Department of Endocrinology, Peking Union Medical College Hospital, Beijing , China; k Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam , The Netherlands; l Department of Visceral and Transplant Surgery, Campus Virchow Klinikum, Charité Universitätsmedizin Berlin, Berlin , Germany; m Department of Gastroenterology, Beaujon Hospital, Clichy , France

Multiphase lattice Boltzmann simulations for porous media applications : a review

Abstract: Over the last two decades, lattice Boltzmann methods have become an increasingly popular tool to compute the flow in complex geometries such as porous media. In addition to single phase simulations allowing, for example, a precise quantification of the permeability of a porous sample, a number of extensions to the lattice Boltzmann method are available which allow to study multiphase and multicomponent flows on a pore scale level. In this article we give an extensive overview on a number of these diffuse interface models and discuss their advantages and disadvantages. Furthermore, we shortly report on multiphase flows containing solid particles, as well as implementation details and optimization issues.

Performance of pile-up mitigation techniques for jets in pp collisions at √s = 8 TeV using the ATLAS detector

Abstract: The large rate of multiple simultaneous protonproton interactions, or pile-up, generated by the Large Hadron Collider in Run 1 required the development of many new techniques to mitigate the advers ...

Hemodynamic changes under balloon occlusion of hepatic artery: predictor of the short-term therapeutic effect of balloon-occluded transcatheter arterial chemolipiodolization using miriplatin for hepatocellular carcinoma

Abstract: To clarify the hemodynamic changes under balloon occlusion of the hepatic artery and to identify predictors of the short-term therapeutic effect (TE) after balloon-occluded transcatheter arterial chemoembolization using miriplatin (B-TACE) for hepatocellular carcinoma (HCC). Tumor variables and angiographic data were collected for 35 nodules (29 patients) with a B-TACE for HCC. Lesions were classified into three groups based on the balloon-occluded CT hepatic arteriography (BO-CTHA) results: Group A, presence of corona enhancement; Group B, absence of corona enhancement; Group C, decreased perfusion or perfusion defect compared to standard CTHA. Objective response was defined as TE3/4, and poor TE as TE1/2, evaluated by response evaluation criteria in cancer of the liver at 1–4 months after the procedure. Univariate analysis revealed that proximal level of balloon occlusion, intratumoral lower CT values immediately after treatment and BO-CTHA findings were significantly correlated with poor TE (p = 0.034, 0.037, and 0.003, respectively). Multivariate logistic analysis identified the Group C as a significant factor associated with the worse short term TE (odds ratio 8.34; 95 % confidence interval 1.49–68.8). Partial or complete perfusion defect on BO-CTHA was an independent factor associated with poor therapeutic effect.

Drp1-Dependent Mitochondrial Autophagy Plays a Protective Role Against Pressure Overload-Induced Mitochondrial Dysfunction and Heart Failure.

Abstract: Background—Mitochondrial autophagy is an important mediator of mitochondrial quality control in cardiomyocytes. The occurrence of mitochondrial autophagy and its significance during cardiac hypertr...

Substantial nitrogen pollution embedded in international trade

Abstract: Anthropogenic emissions of reactive nitrogen have had severe environmental impacts. An analysis of reactive nitrogen emissions from the production, consumption and transport of commodities attributes roughly a quarter to international trade. Anthropogenic emissions of reactive nitrogen to the atmosphere and water bodies can damage human health and ecosystems1,2. As a measure of a nation’s contribution to this potential damage, a country’s nitrogen footprint has been defined as the quantity of reactive nitrogen emitted during the production, consumption and transportation of commodities consumed within that country, whether those commodities are produced domestically or internationally3. Here we use global emissions databases4,5, a global nitrogen cycle model6, and a global input–output database of domestic and international trade7,8 to calculate the nitrogen footprints for 188 countries as the sum of emissions of ammonia, nitrogen oxides and nitrous oxide to the atmosphere, and of nitrogen potentially exportable to water bodies. Per-capita footprints range from under 7 kg N yr−1 in some developing countries to over 100 kg N yr−1 in some wealthy nations. Consumption in China, India, the United States and Brazil is responsible for 46% of global emissions. Roughly a quarter of the global nitrogen footprint is from commodities that were traded across country borders. The main net exporters have significant agricultural, food and textile exports, and are often developing countries, whereas important net importers are almost exclusively developed economies. We conclude that substantial local nitrogen pollution is driven by demand from consumers in other countries.

Abnormal asymmetries in subcortical brain volume in schizophrenia.

Abstract: Subcortical structures, which include the basal ganglia and parts of the limbic system, have key roles in learning, motor control and emotion, but also contribute to higher-order executive functions. Prior studies have reported volumetric alterations in subcortical regions in schizophrenia. Reported results have sometimes been heterogeneous, and few large-scale investigations have been conducted. Moreover, few large-scale studies have assessed asymmetries of subcortical volumes in schizophrenia. Here, as a work completely independent of a study performed by the ENIGMA consortium, we conducted a large-scale multisite study of subcortical volumetric differences between patients with schizophrenia and controls. We also explored the laterality of subcortical regions to identify characteristic similarities and differences between them. T1-weighted images from 1680 healthy individuals and 884 patients with schizophrenia, obtained with 15 imaging protocols at 11 sites, were processed with FreeSurfer. Group differences were calculated for each protocol and meta-analyzed. Compared with controls, patients with schizophrenia demonstrated smaller bilateral hippocampus, amygdala, thalamus and accumbens volumes as well as intracranial volume, but larger bilateral caudate, putamen, pallidum and lateral ventricle volumes. We replicated the rank order of effect sizes for subcortical volumetric changes in schizophrenia reported by the ENIGMA consortium. Further, we revealed leftward asymmetry for thalamus, lateral ventricle, caudate and putamen volumes, and rightward asymmetry for amygdala and hippocampal volumes in both controls and patients with schizophrenia. Also, we demonstrated a schizophrenia-specific leftward asymmetry for pallidum volume. These findings suggest the possibility of aberrant laterality in neural pathways and connectivity patterns related to the pallidum in schizophrenia.

Luminosity determination in pp collisions at √s = 8 TeV using the ATLAS detector at the LHC

Abstract: The luminosity determination for the ATLAS detector at the LHC during pp collisions at s√= 8 TeV in 2012 is presented. The evaluation of the luminosity scale is performed using several luminometers ...