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  1. Book ; Online: 90% F1 Score in Relational Triple Extraction

    Saini, Pratik / Pal, Samiran / Nayak, Tapas / Bhattacharya, Indrajit

    Is it Real ?

    2023  

    Abstract: Extracting relational triples from text is a crucial task for constructing knowledge bases. Recent advancements in joint entity and relation extraction models have demonstrated remarkable F1 scores ($\ge 90\%$) in accurately extracting relational triples ...

    Abstract Extracting relational triples from text is a crucial task for constructing knowledge bases. Recent advancements in joint entity and relation extraction models have demonstrated remarkable F1 scores ($\ge 90\%$) in accurately extracting relational triples from free text. However, these models have been evaluated under restrictive experimental settings and unrealistic datasets. They overlook sentences with zero triples (zero-cardinality), thereby simplifying the task. In this paper, we present a benchmark study of state-of-the-art joint entity and relation extraction models under a more realistic setting. We include sentences that lack any triples in our experiments, providing a comprehensive evaluation. Our findings reveal a significant decline (approximately 10-15\% in one dataset and 6-14\% in another dataset) in the models' F1 scores within this realistic experimental setup. Furthermore, we propose a two-step modeling approach that utilizes a simple BERT-based classifier. This approach leads to overall performance improvement in these models within the realistic experimental setting.

    Comment: Accepted in GenBench workshop @ EMNLP 2023
    Keywords Computer Science - Computation and Language
    Subject code 006
    Publishing date 2023-02-20
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Do the Benefits of Joint Models for Relation Extraction Extend to Document-level Tasks?

    Saini, Pratik / Nayak, Tapas / Bhattacharya, Indrajit

    2023  

    Abstract: Two distinct approaches have been proposed for relational triple extraction - pipeline and joint. Joint models, which capture interactions across triples, are the more recent development, and have been shown to outperform pipeline models for sentence- ... ...

    Abstract Two distinct approaches have been proposed for relational triple extraction - pipeline and joint. Joint models, which capture interactions across triples, are the more recent development, and have been shown to outperform pipeline models for sentence-level extraction tasks. Document-level extraction is a more challenging setting where interactions across triples can be long-range, and individual triples can also span across sentences. Joint models have not been applied for document-level tasks so far. In this paper, we benchmark state-of-the-art pipeline and joint extraction models on sentence-level as well as document-level datasets. Our experiments show that while joint models outperform pipeline models significantly for sentence-level extraction, their performance drops sharply below that of pipeline models for the document-level dataset.

    Comment: Accepted in IJCNLP-AACL 2023 (Short)
    Keywords Computer Science - Computation and Language
    Subject code 006
    Publishing date 2023-10-01
    Publishing country us
    Document type Book ; Online
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  3. Article: Diaphragm disease in emergency surgery.

    Sarma, Diwakar R / Bhattacharya, Pratik

    British journal of hospital medicine (London, England : 2005)

    2020  Volume 81, Issue 3, Page(s) 1–6

    Abstract: Background/aims: Diaphragm disease of the small bowel has been described in the literature over the last three decades. The pathognomonic characteristic of multiple circumferential stenosis is noted on gross examination of the bowel. It is a severe form ...

    Abstract Background/aims: Diaphragm disease of the small bowel has been described in the literature over the last three decades. The pathognomonic characteristic of multiple circumferential stenosis is noted on gross examination of the bowel. It is a severe form of non-steroidal anti-inflammatory drug-induced enteropathy, often presenting as acute small bowel obstruction. A systematic review was performed to identify risk factors and patient outcomes in histologically-proven diaphragm disease of the small intestine in patients undergoing emergency operation for small bowel obstruction.
    Methods: A comprehensive search was performed between January 1975 and March 2019 using relevant MeSH terms. Studies were chosen based on predefined inclusion criteria. Diaphragm disease of the small intestine was defined as macroscopically detected thin diaphragm-like mucosal folding inside the lumen of the bowel. The parameters assessed included patient characteristics, duration of use of non-steroidal anti-inflammatory drugs, type of emergency surgery performed, complications, recurrence, presentation and diagnosis of diaphragm disease.
    Results: A total of 21 studies were analysed which included 17 case reports, one case series, and three retrospective comparative studies. Overall 29 patients with diaphragm disease of the small bowel were reported following emergency laparotomy for small bowel obstruction. Use of non-steroidal anti-inflammatory drugs was noted in all cases with an average duration of 3-5 years. All patients presented acutely with features of small bowel obstruction and had emergency laparotomy, except one who underwent laparoscopic resection. In the comparative studies patients were more likely to be female and to have been taking non-steroidal anti-inflammatory drugs for more than 7 years.
    Conclusions: This is a rare disease, difficult to diagnose and often confirmed by the intra-operative macroscopic appearance of circumferential stenosis of the bowel. Risk factors for developing small bowel diaphragm disease include long-term use of non-steroidal anti-inflammatory drugs, and female gender. Patients with this disease are at increased risk of developing acute small bowel obstruction, so early identification is important.
    MeSH term(s) Anti-Inflammatory Agents, Non-Steroidal/adverse effects ; Emergencies ; Humans ; Intestinal Obstruction/chemically induced ; Intestinal Obstruction/diagnosis ; Intestinal Obstruction/surgery ; Intestine, Small/pathology ; Intestine, Small/surgery ; Postoperative Complications/epidemiology ; Risk Factors
    Chemical Substances Anti-Inflammatory Agents, Non-Steroidal
    Language English
    Publishing date 2020-03-11
    Publishing country England
    Document type Journal Article ; Systematic Review
    ISSN 1750-8460
    ISSN 1750-8460
    DOI 10.12968/hmed.2019.0409
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Tumor-derived small extracellular vesicles in cancer invasion and metastasis: molecular mechanisms, and clinical significance.

    Zhang, Chi / Qin, Chaoying / Dewanjee, Saikat / Bhattacharya, Hiranmoy / Chakraborty, Pratik / Jha, Niraj Kumar / Gangopadhyay, Moumita / Jha, Saurabh Kumar / Liu, Qing

    Molecular cancer

    2024  Volume 23, Issue 1, Page(s) 18

    Abstract: The production and release of tumor-derived small extracellular vesicles (TDSEVs) from cancerous cells play a pivotal role in the propagation of cancer, through genetic and biological communication with healthy cells. TDSEVs are known to orchestrate the ... ...

    Abstract The production and release of tumor-derived small extracellular vesicles (TDSEVs) from cancerous cells play a pivotal role in the propagation of cancer, through genetic and biological communication with healthy cells. TDSEVs are known to orchestrate the invasion-metastasis cascade via diverse pathways. Regulation of early metastasis processes, pre-metastatic niche formation, immune system regulation, angiogenesis initiation, extracellular matrix (ECM) remodeling, immune modulation, and epithelial-mesenchymal transition (EMT) are among the pathways regulated by TDSEVs. MicroRNAs (miRs) carried within TDSEVs play a pivotal role as a double-edged sword and can either promote metastasis or inhibit cancer progression. TDSEVs can serve as excellent markers for early detection of tumors, and tumor metastases. From a therapeutic point of view, the risk of cancer metastasis may be reduced by limiting the production of TDSEVs from tumor cells. On the other hand, TDSEVs represent a promising approach for in vivo delivery of therapeutic cargo to tumor cells. The present review article discusses the recent developments and the current views of TDSEVs in the field of cancer research and clinical applications.
    MeSH term(s) Humans ; Clinical Relevance ; Neoplasms/pathology ; Extracellular Vesicles ; MicroRNAs/genetics ; Cell Communication ; Epithelial-Mesenchymal Transition ; Tumor Microenvironment ; Neoplasm Metastasis/pathology
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2024-01-19
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2091373-4
    ISSN 1476-4598 ; 1476-4598
    ISSN (online) 1476-4598
    ISSN 1476-4598
    DOI 10.1186/s12943-024-01932-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation.

    Singh, Pratik N P / Gu, Wei / Madha, Shariq / Lynch, Allen W / Cejas, Paloma / He, Ruiyang / Bhattacharya, Swarnabh / Gomez, Miguel M / Oser, Matthew G / Brown, Myles / Long, Henry W / Meyer, Clifford A / Zhou, Qiao / Shivdasani, Ramesh A

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Enteroendocrine cells (EECs), which secrete serotonin (enterochromaffin cells, EC) or a dominant peptide hormone, serve vital physiologic functions. As with any adult human lineage, the basis for terminal cell diversity remains obscure. We replicated ... ...

    Abstract Enteroendocrine cells (EECs), which secrete serotonin (enterochromaffin cells, EC) or a dominant peptide hormone, serve vital physiologic functions. As with any adult human lineage, the basis for terminal cell diversity remains obscure. We replicated human EEC differentiation
    Language English
    Publishing date 2024-01-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.09.574746
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Surgical valvotomy versus balloon dilatation for children with severe aortic valve stenosis: a systematic review.

    Elhedai, Huzeifa / S Mohamed, Salma Saeed / Idriss, Hamid / Bhattacharya, Pratik / Y Mohamedahmed, Ali Yasen

    Future cardiology

    2022  Volume 18, Issue 11, Page(s) 901–913

    Abstract: Aim: ...

    Abstract Aim:
    MeSH term(s) Child ; Humans ; Dilatation ; Aortic Valve Stenosis/surgery ; Aortic Valve/surgery ; Aortic Valve Insufficiency ; Catheterization ; Treatment Outcome
    Language English
    Publishing date 2022-09-05
    Publishing country England
    Document type Systematic Review ; Journal Article ; Review
    ZDB-ID 2274267-0
    ISSN 1744-8298 ; 1479-6678
    ISSN (online) 1744-8298
    ISSN 1479-6678
    DOI 10.2217/fca-2022-0053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Stroke after trauma in children and young adults: Some opportunity for primary prevention.

    Jordan, Lori C / Bhattacharya, Pratik D

    Neurology

    2017  Volume 89, Issue 23, Page(s) 2306–2307

    MeSH term(s) Brain Ischemia ; Child ; Humans ; Ischemia ; Primary Prevention ; Risk Factors ; Stroke ; Young Adult
    Language English
    Publishing date 2017-11-08
    Publishing country United States
    Document type Editorial ; Comment
    ZDB-ID 207147-2
    ISSN 1526-632X ; 0028-3878
    ISSN (online) 1526-632X
    ISSN 0028-3878
    DOI 10.1212/WNL.0000000000004723
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  8. Article ; Online: Robotic vs. Laparoscopic Splenectomy in Management of Non-traumatic Splenic Pathologies: A Systematic Review and Meta-Analysis.

    Bhattacharya, Pratik / Phelan, Liam / Fisher, Simon / Hajibandeh, Shahab / Hajibandeh, Shahin

    The American surgeon

    2021  Volume 88, Issue 1, Page(s) 38–47

    Abstract: We aimed to evaluate comparative outcomes of robotic and laparoscopic splenectomy in patients with non-traumatic splenic pathologies. A systematic search of electronic databases and bibliographic reference lists were conducted, and a combination of free ... ...

    Abstract We aimed to evaluate comparative outcomes of robotic and laparoscopic splenectomy in patients with non-traumatic splenic pathologies. A systematic search of electronic databases and bibliographic reference lists were conducted, and a combination of free text and controlled vocabulary search adapted to thesaurus headings, search operators and limits in electronic databases were applied. Intraoperative and post-operative complications, wound infection, haematoma, conversion to open procedure, return to theatre, volume of blood loss, procedure time and length of hospital stay were the evaluated outcome parameters. We identified 8 comparative studies reporting a total of 560 patients comparing outcomes of robotic (
    MeSH term(s) Adult ; Bias ; Blood Loss, Surgical/statistics & numerical data ; Child ; Conversion to Open Surgery/statistics & numerical data ; Hematoma/epidemiology ; Humans ; Intraoperative Complications/epidemiology ; Laparoscopy/adverse effects ; Laparoscopy/statistics & numerical data ; Length of Stay ; Observational Studies as Topic ; Operative Time ; Postoperative Complications/epidemiology ; Reoperation/statistics & numerical data ; Retrospective Studies ; Robotic Surgical Procedures/adverse effects ; Robotic Surgical Procedures/statistics & numerical data ; Splenectomy/adverse effects ; Splenectomy/methods ; Splenic Diseases/surgery ; Surgical Wound Infection/epidemiology
    Language English
    Publishing date 2021-02-17
    Publishing country United States
    Document type Journal Article ; Meta-Analysis ; Systematic Review
    ZDB-ID 202465-2
    ISSN 1555-9823 ; 0003-1348
    ISSN (online) 1555-9823
    ISSN 0003-1348
    DOI 10.1177/0003134821995057
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  9. Article ; Online: Comparison of the Colonic J-Pouch Versus Side-To-End Anastomosis Following Low Anterior Resection: A Systematic Review and Meta-Analysis.

    Zaman, Shafquat / Peterknecht, Elizabeth / Bhattacharya, Pratik / Ayeni, Adewale A / Gilbody, Helen / Ahmad, Adil N / Mohamedahmed, Ali Y-Y / Akingboye, Akinfemi

    The American surgeon

    2023  Volume 90, Issue 1, Page(s) 92–110

    Abstract: Background: The aim of this systematic review and meta-analysis is to evaluate clinical, functional, and anorectal physiology outcomes of the side-to-end vs colonic J-pouch (CJP) anastomosis following anterior resection for rectal cancer.: Methods: A ...

    Abstract Background: The aim of this systematic review and meta-analysis is to evaluate clinical, functional, and anorectal physiology outcomes of the side-to-end vs colonic J-pouch (CJP) anastomosis following anterior resection for rectal cancer.
    Methods: A PRISMA-compliant systematic review and meta-analysis was conducted using multiple electronic databases and clinical trial registers and all studies comparing side-to-end vs CJP anastomosis were included. Peri-operative complications, mortality rate, functional bowel, and anorectal outcomes were evaluated.
    Results: Eight randomized controlled trials (RCTs) and two observational studies with 1125 patients (side-to-end: n = 557; CJP: n = 568) were included. Of the entire functional bowel outcome parameters analyzed, only the sensation of incomplete bowel evacuation was significant in the CJP group at 6 months [OR: 2.07; 95% CI 1.06 - 4.02,
    Discussion: Clinical and functional outcomes following CJP surgery and side-to-end coloanal anastomosis are comparable. Neither technique appears to proffer solution to low anterior resection syndrome in the short term but future well-designed; high-quality RCTs with long term follow-up are required.
    MeSH term(s) Humans ; Anal Canal/surgery ; Anastomosis, Surgical/methods ; Colon/surgery ; Colonic Pouches ; Proctectomy ; Proctocolectomy, Restorative ; Rectal Neoplasms/surgery ; Rectum/surgery ; Treatment Outcome
    Language English
    Publishing date 2023-07-28
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Meta-Analysis ; Systematic Review
    ZDB-ID 202465-2
    ISSN 1555-9823 ; 0003-1348
    ISSN (online) 1555-9823
    ISSN 0003-1348
    DOI 10.1177/00031348231191769
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  10. Article ; Online: Corrigendum to "Carnosic acid attenuates doxorubicin-induced cardiotoxicity by decreasing oxidative stress and its concomitant pathological consequences" [Food Chem. Toxicol. 166 (2022) 113205].

    Manna, Prasenjit / Dewanjee, Saikat / Joardar, Swarnalata / Chakraborty, Pratik / Bhattacharya, Hiranmoy / Bhanja, Shrestha / Bhattacharyya, Chiranjib / Bhowmik, Manas / Bhowmick, Shovonlal / Saha, Achintya / Das, Joydeep / Sil, Parames C

    Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association

    2023  Volume 181, Page(s) 114099

    Language English
    Publishing date 2023-10-19
    Publishing country England
    Document type Published Erratum
    ZDB-ID 782617-5
    ISSN 1873-6351 ; 0278-6915
    ISSN (online) 1873-6351
    ISSN 0278-6915
    DOI 10.1016/j.fct.2023.114099
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