Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

Dynamic physiological imaging and quantification of tumor microcirculation

In this project, we have developed parametric and non-parametric methods for analysis of Dynamic Contrast-Enhanced (DCE) imaging data, with the aim of studying tumor microcirculation. These include a generalized mamillary distributed- parameter model for capillary-tissue exchange, a regression approach to regularization using both conventional and generalized Singular Value Decomposition (SVD), and the use of piecewise continuous regression models for the automatic estimation of bolus arrival times. The generalized mamillary model can be used to study possible kinetic heterogeneity in tumors, and does not assume instantaneous diffusion in the interacting compartments. The advantages of the proposed regression regularization approach for SVD deconvolution, as compared with previous methods, include its efficiency of computation, the ability to achieve adequate regularization to reproduce less noisy solutions, and that it does not require prior knowledge of the noise condition

EXCITON SCATTERING IN QUANTUM STRUCTURES

Ph.DDOCTOR OF PHILOSOPH

An Introduction to MR Perfusion Imaging of the Liver

This article introduces the basic principles of magnetic resonance (MR) perfusion imaging of liver and summarized the currently available literature. Perfusion magnetic resonance imaging (MRI) is a functional imaging technique that quantifies the microcirculatory status of liver parenchyma and liver lesions such as flow, permeability, fractional intravascular volume and fractional interstitial volume. It potentially allows one to (i) detect liver metastases, (ii) assess effectiveness of anti-angiogenic therapy, (iii) assess viable tumour after therapy or ablation, and (iv) diagnose cirrhosis and assess its severity. Further work is required to establish and validate perfusion MRI as a clinical modality