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Article: In-vitro

Patil, P / Alagarasu, K / Chowdhury, D / Kakade, M / Cherian, S / Kaushik, S / Yadav, J P / Parashar, D

2022 Volume 8, Issue 12, Page(s) e11879

Abstract: Dengue and chikungunya are diseases of global health significance and currently, no antivirals are available to treat these arboviral diseases. ...

Abstract	Dengue and chikungunya are diseases of global health significance and currently, no antivirals are available to treat these arboviral diseases.
Language	English
Publishing date	2022-11-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2022.e11879
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Article ; Online: Malignant pleural effusion from a case of squamous-cell carcinoma of the oral cavity: Cytological detection of a rare outcome.

Paul, Pranoy / Kaushik, Bhoomika / Kumar, Arvind / Sharma, Prakhar / Rajput, Deepak / Chowdhury, Nilotpal

Diagnostic cytopathology

2023 Volume 51, Issue 5, Page(s) E161–E163

Abstract: Distant metastases from carcinomas of the oral cavity are rare. Detection of these metastasis are essential for staging and management of the patient. These tumours may metastasize to lung, liver, brain and bone; but pleural involvement by squamous-cell ... ...

Abstract	Distant metastases from carcinomas of the oral cavity are rare. Detection of these metastasis are essential for staging and management of the patient. These tumours may metastasize to lung, liver, brain and bone; but pleural involvement by squamous-cell carcinoma is distinctly rare. We present a case of bilateral pleural effusion arising from distant metastasis of squamous-cell carcinoma detected on cytology.
MeSH term(s)	Humans ; Pleural Effusion, Malignant/pathology ; Carcinoma, Squamous Cell/diagnosis ; Carcinoma, Squamous Cell/pathology ; Lung Neoplasms/pathology ; Pleural Effusion ; Mouth/pathology
Language	English
Publishing date	2023-01-31
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	632710-2
ISSN	1097-0339 ; 8755-1039
ISSN (online)	1097-0339
ISSN	8755-1039
DOI	10.1002/dc.25110
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Book ; Online: Towards Visual Syntactical Understanding

Chowdhury, Sayeed Shafayet / Chandra, Soumyadeep / Roy, Kaushik

2024

Abstract: Syntax is usually studied in the realm of linguistics and refers to the arrangement of words in a sentence. Similarly, an image can be considered as a visual 'sentence', with the semantic parts of the image acting as 'words'. While visual syntactic ... ...

Abstract	Syntax is usually studied in the realm of linguistics and refers to the arrangement of words in a sentence. Similarly, an image can be considered as a visual 'sentence', with the semantic parts of the image acting as 'words'. While visual syntactic understanding occurs naturally to humans, it is interesting to explore whether deep neural networks (DNNs) are equipped with such reasoning. To that end, we alter the syntax of natural images (e.g. swapping the eye and nose of a face), referred to as 'incorrect' images, to investigate the sensitivity of DNNs to such syntactic anomaly. Through our experiments, we discover an intriguing property of DNNs where we observe that state-of-the-art convolutional neural networks, as well as vision transformers, fail to discriminate between syntactically correct and incorrect images when trained on only correct ones. To counter this issue and enable visual syntactic understanding with DNNs, we propose a three-stage framework- (i) the 'words' (or the sub-features) in the image are detected, (ii) the detected words are sequentially masked and reconstructed using an autoencoder, (iii) the original and reconstructed parts are compared at each location to determine syntactic correctness. The reconstruction module is trained with BERT-like masked autoencoding for images, with the motivation to leverage language model inspired training to better capture the syntax. Note, our proposed approach is unsupervised in the sense that the incorrect images are only used during testing and the correct versus incorrect labels are never used for training. We perform experiments on CelebA, and AFHQ datasets and obtain classification accuracy of 92.10%, and 90.89%, respectively. Notably, the approach generalizes well to ImageNet samples which share common classes with CelebA and AFHQ without explicitly training on them.
Keywords	Computer Science - Computer Vision and Pattern Recognition
Subject code	006
Publishing date	2024-01-30
Publishing country	us
Document type	Book ; Online
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Article: Comparison of Serum Holotranscobalamin with Serum Vitamin B12 in Population Prone to Megaloblastic Anemia and their Correlation with Nerve Conduction Study.

Verma, Abhishek / Aggarwal, Sunita / Garg, Sandeep / Kaushik, Smita / Chowdhury, Debashish

Indian journal of clinical biochemistry : IJCB

2022 Volume 38, Issue 1, Page(s) 42–50

Abstract: Early detection of megaloblastic anemia and associated neurological complications is crucial for management. This study was conducted to compare serum holotranscobalamin level with serum vitamin B12 level as early biomarker in people prone to ... ...

Abstract	Early detection of megaloblastic anemia and associated neurological complications is crucial for management. This study was conducted to compare serum holotranscobalamin level with serum vitamin B12 level as early biomarker in people prone to megaloblastic anemia and to evaluate co-relation between these biomarkers and nerve conduction study in study patients. 83 adult patients (Hb > 12 gm/dl) prone to megaloblastic anemia were studied for basic haematological investigations, random blood sugar, thyroid function test, liver function test, kidney function test, serum vitamin B12, serum holotranscobalamin and serum folic acid levels. 45 patients among them underwent nerve conduction studies. All study patients were classified in 6 groups on the basis of risk factors for megaloblastic anemia. 29 patients (34.9%) were on antiepileptic drugs, 26 (31.3%) were chronic alcoholic, 10 patients (12%) each, had malabsorption and ileal tuberculosis, 6 (7.22%) had chronic pancreatitis and 2 (2.4%) had ileal resection. 30 patients (36.14%) had low serum holotranscobalamin, including 7 patients (8.43%) with low serum vitamin B12 level also, unmasking vitamin B12 deficiency in 23 patients (27.7%). 7 patients (8.43%) had mean corpuscular volume (MCV) > 100fL and 8 patients (9.63%) had vitamin B12 deficiency related changes on peripheral smear. Serum vitamin B12 and holotranscobalamin levels were significantly low in patients with peripheral smear changes, with p value 0.039 and 0.041 respectively, while no such association seen with MCV. Subclinical peripheral neuropathy was detected in 18 (40%) out of 45 patients on nerve conduction study. Serum holotranscobalamin levels were significantly lower (
Language	English
Publishing date	2022-03-17
Publishing country	India
Document type	Journal Article
ZDB-ID	1033583-3
ISSN	0974-0422 ; 0970-1915
ISSN (online)	0974-0422
ISSN	0970-1915
DOI	10.1007/s12291-022-01027-x
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Article ; Online: Modulation of VEGFA Signaling During Heart Regeneration in Zebrafish.

Chowdhury, Kaushik / Lai, Shih-Lei / Marín-Juez, Rubén

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2475, Page(s) 297–312

Abstract: Over the last decades, myocardial infarction and heart failure have accounted every year for millions of deaths worldwide. After a coronary occlusion, the lack of blood supply to downstream muscle leads to cell death and scarring. To date, several pro- ... ...

Abstract	Over the last decades, myocardial infarction and heart failure have accounted every year for millions of deaths worldwide. After a coronary occlusion, the lack of blood supply to downstream muscle leads to cell death and scarring. To date, several pro-angiogenic factors have been tested to stimulate reperfusion of the affected myocardium, VEGFA being one of the most extensively studied. Given the unsuccessful outcomes of clinical trials, understanding how cardiac revascularization takes place in models with endogenous regenerative capacity holds the key to devising more efficient therapies. Here, we summarize the main findings on VEGFA's role during cardiac repair and regeneration, with a particular focus on zebrafish as a regenerative model. Moreover, we provide a comprehensive overview of available tools to modulate Vegfa expression and action in zebrafish regeneration studies. Understanding the role of Vegfa during zebrafish heart regeneration may help devise efficient therapies and circumvent current limitations in using VEGFA for therapeutic angiogenesis approaches.
MeSH term(s)	Animals ; Heart/physiology ; Myocardial Infarction/metabolism ; Myocardium/metabolism ; Myocytes, Cardiac/metabolism ; Zebrafish/metabolism ; Zebrafish Proteins/metabolism
Chemical Substances	Zebrafish Proteins
Language	English
Publishing date	2022-04-22
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2217-9_22
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Article ; Online: Comparative Study in Zebrafish and Medaka Unravels the Mechanisms of Tissue Regeneration

Kaushik Chowdhury / Shi Lin / Shih-Lei Lai

Frontiers in Ecology and Evolution, Vol

2022 Volume 10

Abstract: Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over ... ...

Abstract	Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over evolution. Organisms with variable regenerative capacity are usually distinct in phylogeny, anatomy, and physiology. This phenomenon hinders the feasibility of studying tissue regeneration by directly comparing regenerative with non-regenerative animals, such as zebrafish (Danio rerio) and mice (Mus musculus). Medaka (Oryzias latipes) is a fish model with a complete reference genome and shares a common ancestor with zebrafish approximately 110–200 million years ago (compared to 650 million years with mice). Medaka shares similar features with zebrafish, including size, diet, organ system, gross anatomy, and living environment. However, while zebrafish regenerate almost every organ upon experimental injury, medaka shows uneven regenerative capacity. Their common and distinct biological features make them a unique platform for reciprocal analyses to understand the mechanisms of tissue regeneration. Here we summarize current knowledge about tissue regeneration in these fish models in terms of injured tissues, repairing mechanisms, available materials, and established technologies. We further highlight the concept of inter-species and inter-organ comparisons, which may reveal mechanistic insights and hint at therapeutic strategies for human diseases.
Keywords	zebrafish ; medaka (Oryzias latipes) ; tissue regeneration ; heart ; retina ; fin ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Subject code	590
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: A novel seasonal index-based machine learning approach for air pollution forecasting.

Khan, Adeel / Sharma, Sumit / Chowdhury, Kaushik Roy / Sharma, Prateek

Environmental monitoring and assessment

2022 Volume 194, Issue 6, Page(s) 429

Abstract: Novel machine learning models (MLMs) using the seasonal indexing approach that captures the variation in air quality caused due to meteorological changes have been used to provide short-term, real-time forecasts of ... ...

Abstract	Novel machine learning models (MLMs) using the seasonal indexing approach that captures the variation in air quality caused due to meteorological changes have been used to provide short-term, real-time forecasts of PM
MeSH term(s)	Air Pollutants/analysis ; Air Pollution/analysis ; Environmental Monitoring ; Forecasting ; Machine Learning ; Particulate Matter/analysis ; Seasons
Chemical Substances	Air Pollutants ; Particulate Matter
Language	English
Publishing date	2022-05-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	782621-7
ISSN	1573-2959 ; 0167-6369
ISSN (online)	1573-2959
ISSN	0167-6369
DOI	10.1007/s10661-022-10092-x
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Article ; Online: Child Neurology: Allgrove Syndrome: An Intriguing Etiology of Motor Neuron Disease in Children

Gupta, Juhi / Chowdhury, Sayoni Roy / Jauhari, Prashant / Ragunathan, Kaushik / Chakrabarty, Biswaroop / Jain, Vandana / Gulati, Sheffali

Neurology

2024 Volume 102, Issue 4, Page(s) e208049

Abstract: Motor neuron diseases are a rare group of neurodegenerative disorders with considerable phenotypic heterogeneity and a multitude of etiologies in the pediatric population. In this study, we report 2 unrelated adolescents (a boy and a girl) who presented ... ...

Abstract	Motor neuron diseases are a rare group of neurodegenerative disorders with considerable phenotypic heterogeneity and a multitude of etiologies in the pediatric population. In this study, we report 2 unrelated adolescents (a boy and a girl) who presented with 4-6 years of progressive difficulty in walking, thinning of limbs, and gradually progressive darkening of the skin. Examination revealed generalized hyperpigmentation of skin and features suggestive of motor neuron involvement such as tongue atrophy, wasting of distal extremities, and brisk deep tendon reflexes. On detailed exploration for systemic involvement, history of dysphagia, inability to produce tears, and Addisonian crises were evident. An etiologic diagnosis of Allgrove syndrome, which is characterized by a triad of achalasia, alacrimia, and adrenal insufficiency was considered. Next-generation sequencing revealed pathogenic variants in the
MeSH term(s)	Male ; Female ; Adolescent ; Humans ; Child ; Esophageal Achalasia/complications ; Esophageal Achalasia/diagnosis ; Adrenal Insufficiency/complications ; Adrenal Insufficiency/diagnosis ; Motor Neuron Disease/genetics ; Motor Neuron Disease/complications ; Neurology
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	207147-2
ISSN	1526-632X ; 0028-3878
ISSN (online)	1526-632X
ISSN	0028-3878
DOI	10.1212/WNL.0000000000208049
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Article: Comparison of Serum Holotranscobalamin with Serum Vitamin B12 in People Prone to Megaloblastic Anemia and Correlation with Nerve Conduction Study.

Verma, Abhishek / Aggarwal, Sunita / Garg, Sandeep / Kaushik, Smita / Chowdhury, Debashish

The Journal of the Association of Physicians of India

2020 Volume 68, Issue 1, Page(s) 101

MeSH term(s)	Anemia, Megaloblastic ; Humans ; Neural Conduction ; Neurologic Examination ; Vitamin B 12 ; Vitamin B 12 Deficiency
Chemical Substances	Vitamin B 12 (P6YC3EG204)
Language	English
Publishing date	2020-01-23
Publishing country	India
Document type	Journal Article
ZDB-ID	800766-4
ISSN	0004-5772
ISSN	0004-5772
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Book ; Online: Segmented Recurrent Transformer

Long, Yinghan / Chowdhury, Sayeed Shafayet / Roy, Kaushik

An Efficient Sequence-to-Sequence Model

2023

Abstract: Transformers have shown dominant performance across a range of domains including language and vision. However, their computational cost grows quadratically with the sequence length, making their usage prohibitive for resource-constrained applications. To ...

Abstract	Transformers have shown dominant performance across a range of domains including language and vision. However, their computational cost grows quadratically with the sequence length, making their usage prohibitive for resource-constrained applications. To counter this, our approach is to divide the whole sequence into segments and use local attention mechanism on the individual segments. We propose a segmented recurrent transformer (SRformer) that combines segmented (local) attention with recurrent attention. The loss caused by reducing the attention window length is compensated by aggregating information across segments with recurrent attention. SRformer leverages Recurrent Accumulate-and-Fire (RAF) neurons' inherent memory to update the cumulative product of keys and values. The segmented attention and lightweight RAF neurons ensure the efficiency of the proposed transformer. Such an approach leads to models with sequential processing capability at a lower computation/memory cost. We apply the proposed method to T5 and BART transformers. The modified models are tested on summarization datasets including CNN-dailymail, XSUM, ArXiv, and MediaSUM. Notably, using segmented inputs of varied sizes, the proposed model achieves $6-22\%$ higher ROUGE1 scores than a segmented transformer and outperforms other recurrent transformer approaches. Furthermore, compared to full attention, the proposed model reduces the computational complexity of cross attention by around $40\%$. Comment: Findings of EMNLP 2023
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence ; Computer Science - Machine Learning
Subject code	006
Publishing date	2023-05-23
Publishing country	us
Document type	Book ; Online
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