Osaka City University

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 thatthere 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 completeprocess 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 increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost 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 manycases, 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 forreviewers 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 multipleassays 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 autophagyrelated 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.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTPhotochromism of Diarylethene Molecules and Crystals: Memories, Switches, and ActuatorsMasahiro Irie*†, Tuyoshi Fukaminato‡, Kenji Matsuda§, and Seiya Kobatake∥View Author Information† Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo 171-8501, Japan‡ Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan§ Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan∥ Department of Applied Chemistry, Graduate School of Engineering, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka 558-8585, Japan*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 24, 12174–12277Publication Date (Web):December 16, 2014Publication History Received19 May 2014Published online16 December 2014Published inissue 24 December 2014https://pubs.acs.org/doi/10.1021/cr500249phttps://doi.org/10.1021/cr500249preview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views43769Altmetric-Citations2136LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Crystals,Electromagnetic radiation,Fluorescence,Irradiation,Molecular structure Get e-Alerts

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

We report the observation of a narrow charmoniumlike state produced in the exclusive decay process ${B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}{K}^{\ifmmode\pm\else\textpm\fi{}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$. This state, which decays into ${\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$, has a mass of $3872.0\ifmmode\pm\else\textpm\fi{}0.6\mathrm{(}\mathrm{s}\mathrm{t}\mathrm{a}\mathrm{t}\mathrm{)}\ifmmode\pm\else\textpm\fi{}0.5\mathrm{(}\mathrm{s}\mathrm{y}\mathrm{s}\mathrm{t}\mathrm{)}\text{ }\text{ }\mathrm{M}\mathrm{e}\mathrm{V}$, a value that is very near the ${M}_{{D}^{0}}+{M}_{{D}^{*0}}$ mass threshold. The results are based on an analysis of 152M $B$-$\overline{B}$ events collected at the $\ensuremath{\Upsilon}(4S)$ resonance in the Belle detector at the KEKB collider. The signal has a statistical significance that is in excess of $10\ensuremath{\sigma}$.

having a defect spinel‐framework structure was prepared and examined in non‐aqueous lithium cells. (white in color) was reduced to (dark blue) at a voltage of 1.55 V and the reaction was highly reversible. X‐ray diffraction measurements indicated that the lattice dimension did not change during the reaction

Dilated cardiomyopathy is a severe pathology of the heart with poorly understood etiology. Disruption of the gene encoding the negative immunoregulatory receptor PD-1 in BALB/c mice, but not in BALB/c RAG-2-/- mice, caused dilated cardiomyopathy with severely impaired contraction and sudden death by congestive heart failure. Affected hearts showed diffuse deposition of immunoglobulin G (IgG) on the surface of cardiomyocytes. All of the affected PD-1-/- mice exhibited high-titer circulating IgG autoantibodies reactive to a 33-kilodalton protein expressed specifically on the surface of cardiomyocytes. These results indicate that PD-1 may be an important factor contributing to the prevention of autoimmune diseases.

Abstract A general formula for the difference of solvent shifts of fluorescence and absorption spectra in the approximation of long range dipolar interaction was derived using Ooshika’s theory of light absorption in solution. Measurements of fluorescence and absorption spectra of some naphthalene derivatives in various organic solvents were undertaken, and the data were analysed by the theoretical formula. The formula reproduces the experimental data satisfactorily, and from this fact it was concluded that the most predominant factor which determines the difference of solvent shifts of fluorescence and absorption spectra of these molecules is the interaction energy between solute and solvent molecules due to orientation polarization. The incremental values of dipolemoments in the excited state were estimated, and those for α-, β-naphthols and β-naphthyl methyl ether were interpreted as due to the increase of electron migration from the substituent in the excited state.

BACKGROUND: Treatment with dasatinib, a highly potent BCR-ABL kinase inhibitor, has resulted in high rates of complete cytogenetic response and progression-free survival among patients with chronic myeloid leukemia (CML) in the chronic phase, after failure of imatinib treatment. We assessed the efficacy and safety of dasatinib, as compared with imatinib, for the first-line treatment of chronic-phase CML. METHODS: In a multinational study, 519 patients with newly diagnosed chronic-phase CML were randomly assigned to receive dasatinib at a dose of 100 mg once daily (259 patients) or imatinib at a dose of 400 mg once daily (260 patients). The primary end point was complete cytogenetic response by 12 months, confirmed on two consecutive assessments at least 28 days apart. Secondary end points, including major molecular response, were tested at a significance level of 0.0001 to adjust for multiple comparisons. RESULTS: After a minimum follow-up of 12 months, the rate of confirmed complete cytogenetic response was higher with dasatinib than with imatinib (77% vs. 66%, P=0.007), as was the rate of complete cytogenetic response observed on at least one assessment (83% vs. 72%, P=0.001). The rate of major molecular response was higher with dasatinib than with imatinib (46% vs. 28%, P<0.0001), and responses were achieved in a shorter time with dasatinib (P<0.0001). Progression to the accelerated or blastic phase of CML occurred in 5 patients who were receiving dasatinib (1.9%) and in 9 patients who were receiving imatinib (3.5%). The safety profiles of the two treatments were similar. CONCLUSIONS: Dasatinib, administered once daily, as compared with imatinib, administered once daily, induced significantly higher and faster rates of complete cytogenetic response and major molecular response. Since achieving complete cytogenetic response within 12 months has been associated with better long-term, progression-free survival, dasatinib may improve the long-term outcomes among patients with newly diagnosed chronic-phase CML. (ClinicalTrials.gov number, NCT00481247.)

We establish the existence of the top quark using a $67{\mathrm{pb}}^{\ensuremath{-}1}$ data sample of $\overline{p}p$ collisions at $\sqrt{s}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1.8\mathrm{TeV}$ collected with the Collider Detector at Fermilab (CDF). Employing techniques similar to those we previously published, we observe a signal consistent with $t\overline{t}$ decay to $\mathrm{WWb}\overline{b}$, but inconsistent with the background prediction by $4.8\ensuremath{\sigma}$. Additional evidence for the top quark is provided by a peak in the reconstructed mass distribution. We measure the top quark mass to be $176\ifmmode\pm\else\textpm\fi{}8(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}10(\mathrm{syst})\mathrm{GeV}{/c}^{2}$, and the $t\overline{t}$ production cross section to be ${6.8}_{\ensuremath{-}2.4}^{+3.6}\mathrm{pb}$.

The inflammatory process is usually tightly regulated, involving both signals that initiate and maintain inflammation and signals that shut the process down. An imbalance between the two signals leaves inflammation unchecked, resulting in cellular and tissue damage. Macrophages are a major component of the mononuclear phagocyte system that consists of closely related cells of bone marrow origin, including blood monocytes, and tissue macrophages. From the blood, monocytes migrate into various tissues and transform macrophages. In inflammation, macrophages have three major function; antigen presentation, phagocytosis, and immunomodulation through production of various cytokines and growth factors. Macrophages play a critical role in the initiation, maintenance, and resolution of inflammation. They are activated and deactivated in the inflammatory process. Activation signals include cytokines (interferon gamma, granulocyte-monocyte colony stimulating factor, and tumor necrosis factor alpha), bacterial lipopolysaccharide, extracellular matrix proteins, and other chemical mediators. Inhibition of inflammation by removal or deactivation of mediators and inflammatory effector cells permits the host to repair damages tissues. Activated macrophages are deactivated by anti-inflammatory cytokines (interleukin 10 and transforming growth factor beta) and cytokine antagonists that are mainly produced by macrophages. Macrophages participate in the autoregulatory loop in the inflammatory process. Because macrophages produce a wide range of biologically active molecules participated in both beneficial and detrimental outcomes in inflammation, therapeutic interventions targeted macrophages and their products may open new avenues for controlling inflammatory diseases.

The T2K experiment observes indications of ν(μ) → ν(e) appearance in data accumulated with 1.43×10(20) protons on target. Six events pass all selection criteria at the far detector. In a three-flavor neutrino oscillation scenario with |Δm(23)(2)| = 2.4×10(-3) eV(2), sin(2)2θ(23) = 1 and sin(2)2θ(13) = 0, the expected number of such events is 1.5±0.3(syst). Under this hypothesis, the probability to observe six or more candidate events is 7×10(-3), equivalent to 2.5σ significance. At 90% C.L., the data are consistent with 0.03(0.04) < sin(2)2θ(13) < 0.28(0.34) for δ(CP) = 0 and a normal (inverted) hierarchy.

The synthesis and characterization of for a 4 V secondary lithium cell was done. The was prepared by ten different methods and characterized by x‐ray diffraction and electrochemical methods. prepared from and [or ] exhibited more than 150 mAh · g−1 of rechargeable capacity in the voltage range between 2.5 and 4.2 V in 1M propylene carbonate solution. The reaction mechanism was also examined and explained in terms of topotactic reaction. Lithium nickelate(III) (R3m; , in hexagonal setting) was oxidized to nickel dioxide (R3m; , ) via having a monoclinic lattice (C2/m). The nickel dioxide could be reversibly reduced to lithium nickelate(III). Factors affecting the electrochemical reactivity of are given and the possibility of using for 4 V secondary lithium cells is described.

Abstract Layered LiCo1/3Ni1/3Mn1/3O2 was prepared by a solid state reaction at 1000 °C in air and examined in nonaqueous lithium cells. LiCo1/3Ni1/3Mn1/3O2 showed a rechargeable capacity of 150 mAh g−1 in 3.5–4.2 V or 200 mAh g−1 in 3.5–5.0 V. Operating voltage of Li / LiCo1/3Ni1/3Mn1/3O2 was by 0.2–0.25 V lower than that of a cell with LiCoO2 or LiMn2O4 and by 0.15–0.3 V higher than that with LiNiO2 or LiCo1/2Ni1/2O2 due to a complex solid solution mechanism.

Fully mapped tree census plots of large area, 25 to 52 hectares, have now been completed at six different sites in tropical forests, including dry deciduous to wet evergreen forest on two continents. One of the main goals of these plots has been to evaluate spatial patterns in tropical tree populations. Here the degree of aggregation in the distribution of 1768 tree species is examined based on the average density of conspecific trees in circular neighborhoods around each tree. When all individuals larger than 1 centimeter in stem diameter were included, nearly every species was more aggregated than a random distribution. Considering only larger trees (>/= 10 centimeters in diameter), the pattern persisted, with most species being more aggregated than random. Rare species were more aggregated than common species. All six forests were very similar in all the particulars of these results.

PURPOSE Enzalutamide, a potent androgen-receptor inhibitor, has demonstrated significant benefits in metastatic and nonmetastatic castration-resistant prostate cancer. We evaluated the efficacy and safety of enzalutamide in metastatic hormone-sensitive prostate cancer (mHSPC). METHODS ARCHES (ClinicalTrials.gov identifier: NCT02677896 ) is a multinational, double-blind, phase III trial, wherein 1,150 men with mHSPC were randomly assigned 1:1 to enzalutamide (160 mg/day) or placebo, plus androgen deprivation therapy (ADT), stratified by disease volume and prior docetaxel chemotherapy. The primary end point was radiographic progression-free survival. RESULTS As of October 14, 2018, the risk of radiographic progression or death was significantly reduced with enzalutamide plus ADT versus placebo plus ADT (hazard ratio, 0.39; 95% CI, 0.30 to 0.50; P &lt; .001; median not reached v 19.0 months). Similar significant improvements in radiographic progression-free survival were reported in prespecified subgroups on the basis of disease volume and prior docetaxel therapy. Enzalutamide plus ADT significantly reduced the risk of prostate-specific antigen progression, initiation of new antineoplastic therapy, first symptomatic skeletal event, castration resistance, and reduced risk of pain progression. More men achieved an undetectable prostate-specific antigen level and/or an objective response with enzalutamide plus ADT ( P &lt; .001). Patients in both treatment groups reported a high baseline level of quality of life, which was maintained over time. Grade 3 or greater adverse events were reported in 24.3% of patients who received enzalutamide plus ADT versus 25.6% of patients who received placebo plus ADT, with no unexpected adverse events. CONCLUSION Enzalutamide with ADT significantly reduced the risk of metastatic progression or death over time versus placebo plus ADT in men with mHSPC, including those with low-volume disease and/or prior docetaxel, with a safety analysis that seems consistent with the safety profile of enzalutamide in previous clinical trials in castration-resistant prostate cancer.

We present possible observing scenarios for the Advanced LIGO, Advanced Virgo and KAGRA gravitational-wave detectors over the next decade, with the intention of providing information to the astronomy community to facilitate planning for multi-messenger astronomy with gravitational waves. We estimate the sensitivity of the network to transient gravitational-wave signals, and study the capability of the network to determine the sky location of the source. We report our findings for gravitational-wave transients, with particular focus on gravitational-wave signals from the inspiral of binary neutron star systems, which are the most promising targets for multi-messenger astronomy. The ability to localize the sources of the detected signals depends on the geographical distribution of the detectors and their relative sensitivity, and [Formula: see text] credible regions can be as large as thousands of square degrees when only two sensitive detectors are operational. Determining the sky position of a significant fraction of detected signals to areas of 5-[Formula: see text] requires at least three detectors of sensitivity within a factor of [Formula: see text] of each other and with a broad frequency bandwidth. When all detectors, including KAGRA and the third LIGO detector in India, reach design sensitivity, a significant fraction of gravitational-wave signals will be localized to a few square degrees by gravitational-wave observations alone.

BACKGROUND: Previous studies on the effect of interferon therapy on the incidence of hepatocellular carcinoma have not sufficiently assessed degree of liver fibrosis, a major risk factor for hepatocellular carcinoma. OBJECTIVE: To evaluate the effect of interferon therapy on incidence of hepatocellular carcinoma, adjusting for risk factors, including the degree of liver fibrosis. DESIGN: Retrospective cohort study. SETTING: Seven university hospitals and one regional core hospital in Japan. PATIENTS: 2890 patients with chronic hepatitis C who had undergone liver biopsy since 1986. Of these patients, 2400 received interferon and 490 were untreated. MEASUREMENTS: The degree of liver fibrosis was assessed from stage F0 (no fibrosis) to stage F4 (cirrhosis). Response to interferon was determined virologically and biochemically. Screening for development of hepatocellular carcinoma was performed periodically during an average follow-up of 4.3 years. Effect of interferon therapy on the risk for hepatocellular carcinoma was analyzed by using Cox proportional hazards regression. RESULTS: Hepatocellular carcinoma developed in 89 interferon-treated patients and in 59 untreated patients. Among untreated patients, the annual incidence of hepatocellular carcinoma increased with the degree of liver fibrosis, from 0.5% among patients with stage F0 or F1 fibrosis to 7.9% among patients with stage F4 fibrosis. The cumulative incidence in treated and untreated patients differed significantly for patients with stage F2 fibrosis (P = 0.0128) and for those with stage F3 fibrosis (P = 0.0011). In multivariate analysis, interferon therapy was associated with a reduced risk for hepatocellular carcinoma (adjusted risk ratio, 0.516 [95% CI, 0.358 to 0.742]; P < 0.001), especially among patients with sustained virologic response (risk ratio, 0.197 [CI, 0.099 to 0.392]), among those with persistently normal serum alanine aminotransferase levels (risk ratio, 0.197 [CI, 0.104 to 0.375]), and among those with alanine aminotransferase levels less than two times the upper limit of normal (risk ratio, 0.358 [CI, 0.206 to 0.622]). CONCLUSIONS: Interferon therapy significantly reducesthe risk for hepatocellular carcinoma, especially among virologic or biochemical responders.

Electrochemical reduction of natural graphite was carried out in 1M ethylene carbonate (EC)/1,2‐dimethoxyethane (DME) (1:1 by volume) solution at 30°C. Natural graphite was reduced stepwise to (golden yellow in color). The staging phenomenon was observed by x‐ray diffraction (XRD). The first stage (; ) and the second stage (; ) compounds were identified as a commensurate structure in which lithium atoms form a close‐packed two‐dimensional array. A second‐stage compound with a different in‐plane lithium ordering based on a two‐dimensional packing in lithium intercalated sheets also was observed; also third (; ), fourth‐(; ), and eighth‐(; ) stage compounds were identified. The electrochemical oxidation of the first‐stage compound was examined and shown to be reversible over the entire range, i.e., . The reaction mechanism for the reduction of graphite and the oxidation of the first‐stage compound are discussed in relation to the staging phenomenon from the detailed open‐circuit voltage and XRD data. The chemical potential of was estimated to be −3.6 kcal · mol−1 from the observed reversible potential. The feasibility of using a lithium‐graphite intercalation compound in lithium ion (shuttlecock) cells is described, and the innovative secondary systems, and fabricated in discharged states, are demonstrated.

We have isolated and characterized a cDNA for a novel Per-Arnt/AhR-Sim basic helix-loop-helix (bHLH-PAS) factor that interacts with the Ah receptor nuclear translocator (Arnt), and its predicted amino acid sequence exhibits significant similarity to the hypoxia-inducible factor 1alpha (HIF1alpha) and Drosophila trachealess (dTrh) gene product. The HIF1alpha-like factor (HLF) encoded by the isolated cDNA bound the hypoxia-response element (HRE) found in enhancers of genes for erythropoietin, vascular endothelial growth factor (VEGF), and various glycolytic enzymes, and activated transcription of a reporter gene harboring the HRE. Although transcription-activating properties of HLF were very similar to those reported for HIF1alpha, their expression patterns were quite different between the two factors; HLF mRNA was most abundantly expressed in lung, followed by heart, liver, and other various organs under normoxic conditions, whereas HIF1alpha mRNA was ubiquitously expressed at much lower levels. In lung development around parturition, HLF mRNA expression was markedly enhanced, whereas that of HIF1alpha mRNA remained apparently unchanged at a much lower level. Moreover, HLF mRNA expression was closely correlated with that of VEGF mRNA. Whole mount in situ hybridization experiments demonstrated that HLF mRNA was expressed in vascular endothelial cells at the middle stages (9.5 and 10.5 days postcoitus) of mouse embryo development, where HIF1alpha mRNA was almost undetectable. The high expression level of HLF mRNA in the O2 delivery system of developing embryos and adult organs suggests that in a normoxic state, HLF regulates gene expression of VEGF, various glycolytic enzymes, and others driven by the HRE sequence, and may be involved in development of blood vessels and the tubular system of lung.

A new temperature measurement procedure using phase mapping was developed that makes use of the temperature dependence of the water proton chemical shift. Highly accurate and fast measurements were obtained during phantom and in vivo experiments. In the pure water phantom experiments, an accuracy of more than +/- 0.5 degrees C was obtained within a few seconds/slice using a field echo pulse sequence (TR/TE = 115/13 ms, matrix = 128 x 128, number of slices = 5). The temperature dependence of the water proton chemical shift was found to be almost the same for different materials with a chemical composition similar to living tissues (water, glucide, protein). Using this method, the temperature change inside a cat's brain was obtained with an accuracy of more than +/- 1 degree C and an in-plane resolution of 0.6 x 0.6 mm. The temperature measurement error was affected by several factors in the living system (B0 shifts caused by position shifts of the sample, blood flow, etc.), the position shift effect being the most serious.