Indian Institute of Technology Guwahati

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.

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.

Increasingly ubiquitous communication networks and connectivity via portable devices have engendered a host of applications in which sources, for example people and environmental sensors, send updates of their status to interested recipients. These applications desire status updates at the recipients to be as timely as possible; however, this is typically constrained by limited network resources. In this paper, we employ a time-average age metric for the performance evaluation of status update systems. We derive general methods for calculating the age metric that can be applied to a broad class of service systems. We apply these methods to queue-theoretic system abstractions consisting of a source, a service facility and monitors, with the model of the service facility (physical constraints) a given. The queue discipline of first-come-first-served (FCFS) is explored. We show the existence of an optimal rate at which a source must generate its information to keep its status as timely as possible at all its monitors. This rate differs from those that maximize utilization (throughput) or minimize status packet delivery delay. While our abstractions are simpler than their real-world counterparts, the insights obtained, we believe, are a useful starting point in understanding and designing systems that support real time status updates.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent Advances in Transition Metal Catalyzed Oxidation of Organic Substrates with Molecular OxygenT. Punniyamurthy, Subbarayan Velusamy, and Javed IqbalView Author Information Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India, and Dr. Reddy's Research Foundation, Miyapur, Hyderabad 500050, India Cite this: Chem. Rev. 2005, 105, 6, 2329–2364Publication Date (Web):May 6, 2005Publication History Received7 January 2005Published online6 May 2005Published inissue 1 June 2005https://pubs.acs.org/doi/10.1021/cr050523vhttps://doi.org/10.1021/cr050523vresearch-articleACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views22251Altmetric-Citations1585LEARN 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:Catalysts,Hydrocarbons,Organic reactions,Oxidation,Oxygen Get e-Alerts

The rapid depletion of conventional fossil fuels and day-by-day growth of environmental pollution due to use of extensive use of fossil fuels have raised concerns over the use of the fossil fuels; and thus search for alternate renewable and sustainable sources for fuels has started in the last few decades. In this context biomass derived fuels seems to be the promising path; and various routes are available for the biomass processing such as pyrolysis, transesterification, hydrothermal liquefaction, steam reforming, etc.; and the hydrothermal liquefaction (HTL) of wet biomass seems to be the promising route. Therefore, this article briefly enlightened a few concepts of HTL such as the elemental composition of bio-crude obtained by HTL, different types of feedstock adopted for HTL, mechanism of HTL processes, possible process flow diagrams for HTL of both wet and dry biomass and energy efficiency of the process. In addition, this article also enlisted possible future research scope for concerned researchers and a few of them are setting up HTL plant suitable for both wet and dry biomass feedstock; analysing influence of parameters such as temperature, pressure, residence time, catalytic effects, etc.; deriving optimized pathways for better conversion; and development of theoretical models representing the process to the best possible accuracy depending on nature of feedstock.

Nuclear segmentation in digital microscopic tissue images can enable extraction of high-quality features for nuclear morphometrics and other analysis in computational pathology. Conventional image processing techniques, such as Otsu thresholding and watershed segmentation, do not work effectively on challenging cases, such as chromatin-sparse and crowded nuclei. In contrast, machine learning-based segmentation can generalize across various nuclear appearances. However, training machine learning algorithms requires data sets of images, in which a vast number of nuclei have been annotated. Publicly accessible and annotated data sets, along with widely agreed upon metrics to compare techniques, have catalyzed tremendous innovation and progress on other image classification problems, particularly in object recognition. Inspired by their success, we introduce a large publicly accessible data set of hematoxylin and eosin (H&E)-stained tissue images with more than 21000 painstakingly annotated nuclear boundaries, whose quality was validated by a medical doctor. Because our data set is taken from multiple hospitals and includes a diversity of nuclear appearances from several patients, disease states, and organs, techniques trained on it are likely to generalize well and work right out-of-the-box on other H&E-stained images. We also propose a new metric to evaluate nuclear segmentation results that penalizes object- and pixel-level errors in a unified manner, unlike previous metrics that penalize only one type of error. We also propose a segmentation technique based on deep learning that lays a special emphasis on identifying the nuclear boundaries, including those between the touching or overlapping nuclei, and works well on a diverse set of test images.

Benefiting from the capability of building interdependencies among channels or spatial locations, attention mechanisms have been extensively studied and broadly used in a variety of computer vision tasks recently. In this paper, we investigate light-weight but effective attention mechanisms and present triplet attention, a novel method for computing attention weights by capturing crossdimension interaction using a three-branch structure. For an input tensor, triplet attention builds inter-dimensional dependencies by the rotation operation followed by residual transformations and encodes inter-channel and spatial information with negligible computational overhead. Our method is simple as well as efficient and can be easily plugged into classic backbone networks as an add-on module. We demonstrate the effectiveness of our method on various challenging tasks including image classification on ImageNet-1k and object detection on MSCOCO and PASCAL VOC datasets. Furthermore, we provide extensive insight into the performance of triplet attention by visually inspecting the GradCAM and GradCAM++ results. The empirical evaluation of our method supports our intuition on the importance of capturing dependencies across dimensions when computing attention weights. Code for this paper can be publicly accessed at https://github.com/LandskapeAI/triplet-attention.

Curcumin, a yellow pigment in the Indian spice Turmeric (Curcuma longa), which is chemically known as diferuloylmethane, was first isolated exactly two centuries ago in 1815 by two German Scientists, Vogel and Pelletier. However, according to the pubmed database, the first study on its biological activity as an antibacterial agent was published in 1949 in Nature and the first clinical trial was reported in The Lancet in 1937. Although the current database indicates almost 9000 publications on curcumin, until 1990 there were less than 100 papers published on this nutraceutical. At the molecular level, this multitargeted agent has been shown to exhibit anti-inflammatory activity through the suppression of numerous cell signalling pathways including NF-κB, STAT3, Nrf2, ROS and COX-2. Numerous studies have indicated that curcumin is a highly potent antimicrobial agent and has been shown to be active against various chronic diseases including various types of cancers, diabetes, obesity, cardiovascular, pulmonary, neurological and autoimmune diseases. Furthermore, this compound has also been shown to be synergistic with other nutraceuticals such as resveratrol, piperine, catechins, quercetin and genistein. To date, over 100 different clinical trials have been completed with curcumin, which clearly show its safety, tolerability and its effectiveness against various chronic diseases in humans. However, more clinical trials in different populations are necessary to prove its potential against different chronic diseases in humans. This review's primary focus is on lessons learnt about curcumin from clinical trials. LINKED ARTICLES: This article is part of a themed section on Principles of Pharmacological Research of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.11/issuetoc.

In response to the 2013 Update of the European Strategy for Particle Physics, the Future Circular Collider (FCC) study was launched, as an international collaboration hosted by CERN. This study covers a highest-luminosity high-energy lepton collider (FCC-ee) and an energy-frontier hadron collider (FCC-hh), which could, successively, be installed in the same 100 km tunnel. The scientific capabilities of the integrated FCC programme would serve the worldwide community throughout the 21st century. The FCC study also investigates an LHC energy upgrade, using FCC-hh technology. This document constitutes the second volume of the FCC Conceptual Design Report, devoted to the electron-positron collider FCC-ee. After summarizing the physics discovery opportunities, it presents the accelerator design, performance reach, a staged operation scenario, the underlying technologies, civil engineering, technical infrastructure, and an implementation plan. FCC-ee can be built with today's technology. Most of the FCC-ee infrastructure could be reused for FCC-hh. Combining concepts from past and present lepton colliders and adding a few novel elements, the FCC-ee design promises outstandingly high luminosity. This will make the FCC-ee a unique precision instrument to study the heaviest known particles (Z, W and H bosons and the top quark), offering great direct and indirect sensitivity to new physics.

Based on the full BABAR data sample, we report improved measurements of the ratios $\mathcal{R}({D}^{(*)})=\mathcal{B}(\overline{B}\ensuremath{\rightarrow}{D}^{(*)}{\ensuremath{\tau}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\tau}})/\mathcal{B}(\overline{B}\ensuremath{\rightarrow}{D}^{(*)}{\ensuremath{\ell}}_{\ensuremath{\ell}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\ell}})$, where $\ensuremath{\ell}$ is either $e$ or $\ensuremath{\mu}$. These ratios are sensitive to new physics contributions in the form of a charged Higgs boson. We measure $\mathcal{R}(D)=0.440\ifmmode\pm\else\textpm\fi{}0.058\ifmmode\pm\else\textpm\fi{}0.042$ and $\mathcal{R}({D}^{*})=0.332\ifmmode\pm\else\textpm\fi{}0.024\ifmmode\pm\else\textpm\fi{}0.018$, which exceed the standard model expectations by $2.0\ensuremath{\sigma}$ and $2.7\ensuremath{\sigma}$, respectively. Taken together, our results disagree with these expectations at the $3.4\ensuremath{\sigma}$ level. This excess cannot be explained by a charged Higgs boson in the type II two-Higgs-doublet model.

Staining and scanning of tissue samples for microscopic examination is fraught with undesirable color variations arising from differences in raw materials and manufacturing techniques of stain vendors, staining protocols of labs, and color responses of digital scanners. When comparing tissue samples, color normalization and stain separation of the tissue images can be helpful for both pathologists and software. Techniques that are used for natural images fail to utilize structural properties of stained tissue samples and produce undesirable color distortions. The stain concentration cannot be negative. Tissue samples are stained with only a few stains and most tissue regions are characterized by at most one effective stain. We model these physical phenomena that define the tissue structure by first decomposing images in an unsupervised manner into stain density maps that are sparse and non-negative. For a given image, we combine its stain density maps with stain color basis of a pathologist-preferred target image, thus altering only its color while preserving its structure described by the maps. Stain density correlation with ground truth and preference by pathologists were higher for images normalized using our method when compared to other alternatives. We also propose a computationally faster extension of this technique for large whole-slide images that selects an appropriate patch sample instead of using the entire image to compute the stain color basis.

The cross section for ${e}^{+}{e}^{\ensuremath{-}}\ensuremath{\rightarrow}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$ between 3.8 and 5.5 GeV is measured with a $967\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ data sample collected by the Belle detector at or near the $\ensuremath{\Upsilon}(nS)$ ($n=1,2,\dots{},5$) resonances. The $Y(4260)$ state is observed, and its resonance parameters are determined. In addition, an excess of ${\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$ production around 4 GeV is observed. This feature can be described by a Breit-Wigner parametrization with properties that are consistent with the $Y(4008)$ state that was previously reported by Belle. In a study of $Y(4260)\ensuremath{\rightarrow}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$ decays, a structure is observed in the $M({\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}}J/\ensuremath{\psi})$ mass spectrum with $5.2\ensuremath{\sigma}$ significance, with mass $M=(3894.5\ifmmode\pm\else\textpm\fi{}6.6\ifmmode\pm\else\textpm\fi{}4.5)\text{ }\text{ }\mathrm{MeV}/{c}^{2}$ and width $\ensuremath{\Gamma}=(63\ifmmode\pm\else\textpm\fi{}24\ifmmode\pm\else\textpm\fi{}26)\text{ }\text{ }\mathrm{MeV}/{c}^{2}$, where the errors are statistical and systematic, respectively. This structure can be interpreted as a new charged charmoniumlike state.

Based on the full BABAR data sample, we report improved measurements of the ratios $\mathcal{R}(D)=\mathcal{B}(\overline{B}\ensuremath{\rightarrow}D{\ensuremath{\tau}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\tau}})/\mathcal{B}(\overline{B}\ensuremath{\rightarrow}D{\ensuremath{\ell}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\ell}})$ and $\mathcal{R}({D}^{*})=\mathcal{B}(\overline{B}\ensuremath{\rightarrow}{D}^{*}{\ensuremath{\tau}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\tau}})/\mathcal{B}(\overline{B}\ensuremath{\rightarrow}{D}^{*}{\ensuremath{\ell}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\ell}})$, where $\ensuremath{\ell}$ refers to either an electron or muon. These ratios are sensitive to new physics contributions in the form of a charged Higgs boson. We measure $\mathcal{R}(D)=0.440\ifmmode\pm\else\textpm\fi{}0.058\ifmmode\pm\else\textpm\fi{}0.042$ and $\mathcal{R}({D}^{*})=0.332\ifmmode\pm\else\textpm\fi{}0.024\ifmmode\pm\else\textpm\fi{}0.018$, which exceed the standard model expectations by $2.0\ensuremath{\sigma}$ and $2.7\ensuremath{\sigma}$, respectively. Taken together, the results disagree with these expectations at the $3.4\ensuremath{\sigma}$ level. This excess cannot be explained by a charged Higgs boson in the type II two-Higgs-doublet model. Kinematic distributions presented here exclude large portions of the more general type III two-Higgs-doublet model, but there are solutions within this model compatible with the results.

Abiotic stresses like heavy metals, drought, salt, low temperature, etc. are the major factors that limit crop productivity and yield. These stresses are associated with production of certain deleterious chemical entities called reactive oxygen species (ROS), which include hydrogen peroxide (H₂O₂), superoxide radical (O₂(-)), hydroxyl radical (OH(-)), etc. ROS are capable of inducing cellular damage by degradation of proteins, inactivation of enzymes, alterations in the gene and interfere in various pathways of metabolic importance. Our understanding on ROS in response to abiotic stress is revolutionized with the advancements in plant molecular biology, where the basic understanding on chemical behavior of ROS is better understood. Understanding the molecular mechanisms involved in ROS generation and its potential role during abiotic stress is important to identify means by which plant growth and metabolism can be regulated under acute stress conditions. ROS mediated oxidative stress, which is the key to understand stress related toxicity have been widely studied in many plants and the results in those studies clearly revealed that oxidative stress is the main symptom of toxicity. Plants have their own antioxidant defense mechanisms to encounter ROS that is of enzymic and non-enzymic nature . Coordinated activities of these antioxidants regulate ROS detoxification and reduces oxidative load in plants. Though ROS are always regarded to impart negative impact on plants, some reports consider them to be important in regulating key cellular functions; however, such reports in plant are limited. Molecular approaches to understand ROS metabolism and signaling have opened new avenues to comprehend its critical role in abiotic stress. ROS also acts as secondary messenger that signals key cellular functions like cell proliferation, apoptosis and necrosis. In higher eukaryotes, ROS signaling is not fully understood. In this review we summarize our understanding on ROS and its signaling behavior in plants under abiotic stress.

We report a measurement of the branching fraction ratios $R({D}^{(*)})$ of $\overline{B}\ensuremath{\rightarrow}{D}^{(*)}{\ensuremath{\tau}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\tau}}$ relative to $\overline{B}\ensuremath{\rightarrow}{D}^{(*)}{\ensuremath{\ell}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\ell}}$ (where $\ensuremath{\ell}=e$ or $\ensuremath{\mu}$) using the full Belle data sample of $772\ifmmode\times\else\texttimes\fi{}{10}^{6}B\overline{B}$ pairs collected at the $\mathrm{\ensuremath{\Upsilon}}(4S)$ resonance with the Belle detector at the KEKB asymmetric-energy ${e}^{+}{e}^{\ensuremath{-}}$ collider. The measured values are $R(D)=0.375\ifmmode\pm\else\textpm\fi{}0.064(\text{stat})\ifmmode\pm\else\textpm\fi{}0.026(\text{syst})$ and $R({D}^{*})=0.293\ifmmode\pm\else\textpm\fi{}0.038(\text{stat})\ifmmode\pm\else\textpm\fi{}0.015(\text{syst})$. The analysis uses hadronic reconstruction of the tag-side $B$ meson and purely leptonic $\ensuremath{\tau}$ decays. The results are consistent with earlier measurements and do not show a significant deviation from the standard model prediction.

Abstract: We review the physics opportunities of the Future Circular Collider, covering its e+e-, pp, ep and heavy ion programmes. We describe the measurement capabilities of each FCC component, addressing the study of electroweak, Higgs and strong interactions, the top quark and flavour, as well as phenomena beyond the Standard Model. We highlight the synergy and complementarity of the different colliders, which will contribute to a uniquely coherent and ambitious research programme, providing an unmatchable combination of precision and sensitivity to new physics.

Abstract: In response to the 2013 Update of the European Strategy for Particle Physics (EPPSU), the Future Circular Collider (FCC) study was launched as a world-wide international collaboration hosted by CERN. The FCC study covered an energy-frontier hadron collider (FCC-hh), a highest-luminosity high-energy lepton collider (FCC-ee), the corresponding 100 km tunnel infrastructure, as well as the physics opportunities of these two colliders, and a high-energy LHC, based on FCC-hh technology. This document constitutes the third volume of the FCC Conceptual Design Report, devoted to the hadron collider FCC-hh. It summarizes the FCC-hh physics discovery opportunities, presents the FCC-hh accelerator design, performance reach, and staged operation plan, discusses the underlying technologies, the civil engineering and technical infrastructure, and also sketches a possible implementation. Combining ingredients from the Large Hadron Collider (LHC), the high-luminosity LHC upgrade and adding novel technologies and approaches, the FCC-hh design aims at significantly extending the energy frontier to 100 TeV. Its unprecedented centre of-mass collision energy will make the FCC-hh a unique instrument to explore physics beyond the Standard Model, offering great direct sensitivity to new physics and discoveries.

Water contamination is an escalating emergency confronting communities worldwide. While traditional adsorbents have laid the groundwork for effective water purification, their selectivity, capacity, and sustainability limitations have driven the search for more advanced solutions. Despite many technological advancements, economic, environmental, and regulatory hurdles challenge the practical application of advanced adsorption techniques in large-scale water treatment. Integrating nanotechnology, advanced material fabrication techniques, and data-driven design enabled by artificial intelligence (AI) and machine learning (ML) have led to a new generation of optimized, high-performance adsorbents. These advanced materials leverage properties like high surface area, tailored pore structures, and functionalized surfaces to capture diverse water contaminants efficiently. With a focus on sustainability and effectiveness, this review highlights the transformative potential of these advanced materials in setting new benchmarks for water purification technologies. This article delivers an in-depth exploration of the current landscape and future directions of adsorbent technology for water remediation, advocating for a multidisciplinary approach to overcome existing barriers in large-scale water treatment applications.

In the original version of this manuscript, an error was introduced on pp352. '2.7nb:1.6nb' has been corrected to '2.4nb:1.3nb' in the current online and printed version. doi:10.1093/ptep/ptz106.

In milk caseins exists a natural nanostructure, which can be exploited as a carrier of hydrophobic drugs. Here we investigated the complex formation of curcumin with bovine casein micelles (CMs) and its use as a vehicle for drug delivery to cancer cells. DLS studies of the CM suspension that was stable in buffer solution (pH 7.4) showed an average size distribution of <200 nm. SEM and AFM studies showed that the particles were roughly spherical in shape. Steady-state fluorescence spectroscopy of the CM-curcumin complex formation revealed that curcumin molecules formed complexes with CMs (CM-curcumin complex) through hydrophobic interactions. The binding constant for the CM-curcumin interaction was calculated to be 1.48 x 10(4) M(-1), as determined by the curcumin fluorescence. Fluorescence quenching showed that curcumin molecules quench the intrinsic fluorescence of caseins upon binding. We evaluated the utility of CMs as carriers of curcumin by using in vitro cultured HeLa cells. Cytotoxicity studies of HeLa cells revealed that the IC50 of free curcumin and the CM-curcumin complex was 14.85 and 12.69 microM, respectively.