One-shot Localization and Segmentation of Medical Images with Foundation Models

Recent advances in Vision Transformers (ViT) and Stable Diffusion (SD) models with their ability to capture rich semantic features of the image have been used for image correspondence tasks on natural images. In this paper, we examine the ability of a variety of pre-trained ViT (DINO, DINOv2, SAM, CLIP) and SD models, trained exclusively on natural images, for solving the correspondence problems on medical images. While many works have made a case for in-domain training, we show that the models trained on natural images can offer good performance on medical images across different modalities (CT,MR,Ultrasound) sourced from various manufacturers, over multiple anatomical regions (brain, thorax, abdomen, extremities), and on wide variety of tasks. Further, we leverage the correspondence with respect to a template image to prompt a Segment Anything (SAM) model to arrive at single shot segmentation, achieving dice range of 62%-90% across tasks, using just one image as reference. We also show that our single-shot method outperforms the recently proposed few-shot segmentation method - UniverSeg (Dice range 47%-80%) on most of the semantic segmentation tasks(six out of seven) across medical imaging modalities.Comment: Accepted at NeurIPS 2023 R0-FoMo Worksho

Municipal solid waste management under Covid-19: Challenges and recommendations

Covid-19 is proving to be an unprecedented disaster for human health, social contacts and the economy worldwide. It is evident that SARS-CoV-2 may spread through municipal solid waste (MSW), if collected, bagged, handled, transported or disposed of inappropriately. Under the stress placed by the current pandemic on the sanitary performance across all MSW management (MSWM) chains, this industry needs to re-examine its infrastructure resilience with respect to all processes, from waste identification, classification, collection, separation, storage, transportation, recycling, treatment and disposal. The current paper provides an overview of the severe challenges placed by Covid-19 onto MSW systems, highlighting the essential role of waste management in public health protection during the ongoing pandemic. It also discusses the measures issued by various international organisations and countries for the protection of MSWM employees (MSWEs), identifying gaps, especially for developing countries, where personal protection equipment and clear guidelines to MSWEs may not have been provided, and the general public may not be well informed. In countries with high recycling rates of MSW, the need to protect MSWEs' health has affected the supply stream of the recycling industry. The article concludes with recommendations for the MSW industry operating under public health crisis conditions

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

An Ontological approach towards retrieval of video semantically

Recent era there is an increase in the use of videobased applications which revealed the need for extracting the content in videos and how semantically they are interrelated. In this paper we propose a semantic content extraction system that allows users to query and retrieve objects, events, and concepts that are extracted automatically by building the ontology with respect to events and related interest. This paper discusses retrieval techniques of multimedia content using ontology semantically

Design, synthesis, and discovery of novel non-peptide inhibitor of Caspase-3 using ligand based and structure based virtual screening approach

Caspase-3 belonging to a family of cysteine proteases is main executioner of apoptotic cascade pathway. The inhibitors of this protein are useful in the treatment of cardiomyopathy and neurodegenerative diseases. For the discovery of novel Caspase-3 non-peptide inhibitors from Maybridge database, ligand based and structure based virtual screening methods were used. Quantitative 3D pharmacophore models were generated using 25 known inhibitors of Caspase-3 and it was used as initial screen to retrieve the hits from the database. These compounds with high estimated activity were analyzed for drug like properties and docking studies were performed, to study the interaction between new hits and active site. One of the hits (AW01208), with good predictions was selected for synthesis and biological screening. This compound showed an inhibition activity against Caspase-3 in SKNH cell lines

Prognostic plasma biomarkers of early complications and graft‐versus‐host disease in patients undergoing allogeneic hematopoietic stem cell transplantation

Abstract Early complications post hematopoietic stem cell transplantation (HSCT) such as sinusoidal obstruction syndrome (SOS) and graft versus host disease (GVHD) can be life threatening. Although several biomarkers have been identified to correlate with these complications and their response to treatment, these are yet to be used in clinical practice. Here, we evaluated circulating endothelial cells (CECs) (n = 26) and plasma biomarkers (ST2, REG3α, VCAM1, ICAM1, TIM3) (N = 210) at early time points, to determine their association with early complications post‐HSCT. Elevated CEC counts at the end of conditioning was associated with GVHD, indicating endothelial damage during HSCT. Plasma levels of REG3α, VCAM1, ICAM1, and TIM3 on day 14 (D14) and D14 ICAM1 and D28 ST2 were significantly higher in patients with SOS and aGVHD, respectively. Upon sub‐group analysis, D28 ST2, D14/D28 REG3α, and D14 ICAM1 levels were significantly higher in patients with gastrointestinal GVHD, while D28 ST2 was higher in those with skin/liver GVHD. High ST2 levels on D28 was significantly associated with non‐relapse mortality (NRM) and overall survival. Our results suggest that elevated ST2 levels on D28 could predict the likelihood of developing aGVHD and could influence NRM and OS

Abstracts of National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020

This book presents the abstracts of the papers presented to the Online National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020 (RDMPMC-2020) held on 26th and 27th August 2020 organized by the Department of Metallurgical and Materials Science in Association with the Department of Production and Industrial Engineering, National Institute of Technology Jamshedpur, Jharkhand, India. Conference Title: National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020Conference Acronym: RDMPMC-2020Conference Date: 26–27 August 2020Conference Location: Online (Virtual Mode)Conference Organizer: Department of Metallurgical and Materials Engineering, National Institute of Technology JamshedpurCo-organizer: Department of Production and Industrial Engineering, National Institute of Technology Jamshedpur, Jharkhand, IndiaConference Sponsor: TEQIP-