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  1. Article ; Online: "Stop scaring the children": a call for resilient and tenacious optimism.

    Banerjee, Abhik K

    The Journal of clinical investigation

    2020  Volume 130, Issue 6, Page(s) 2733–2737

    MeSH term(s) COVID-19 ; Child ; Female ; Humans ; Male ; Optimism ; Pandemics ; SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-06-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3067-3
    ISSN 1558-8238 ; 0021-9738
    ISSN (online) 1558-8238
    ISSN 0021-9738
    DOI 10.1172/JCI139537
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  3. Article ; Online: "Stop scaring the children"

    Banerjee, Abhik K.

    a call for resilient and tenacious optimism

    2020  

    Abstract: ... APSA). My name is Abhik Banerjee, and I serve as the 2019–2020 President for the organization ...

    Abstract Welcome everyone to the 2020 Business Meeting of the American Physician Scientists Association (APSA). My name is Abhik Banerjee, and I serve as the 2019–2020 President for the organization. As you are aware because of the COVID-19 pandemic, we had been forced to cancel our 2020 Association of American Physician (AAP)/American Society for Clinical Investigation (ASCI)/APSA Joint Meeting at the Fairmont Chicago, originally scheduled on April 3 to 5, 2020. The safety of our membership is our top priority, and our organization is currently navigating through the aftermath of the cancelled meeting. Despite not being able to facilitate an in-person meeting for trainees of all stages of their physician-scientist career development, we are committed to continue to be the student physician-scientist’s leading voice for improving educational opportunities, advancing patient-oriented research, and advocating for the future of translational medicine. In keeping with our organization’s mission and based on several trainee requests, APSA has elected to provide Annual Meeting–related content online via the GoToMeeting platform over the originally scheduled weekend. Despite the rapidly changing public health crisis our country faces, our organization remains steadfast in our commitment to advocate for trainees’ needs, and we hope you take advantage of the excellent programming our volunteers have coordinated over these next two days.
    Keywords covid19
    Subject code 020
    Publishing date 2020-06-01
    Publisher American Society for Clinical Investigation
    Publishing country us
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: An AI based smart-phone system for asbestos identification.

    Rolfe, Michael / Hayes, Samantha / Smith, Meaghan / Owen, Matthew / Spruth, Michael / McCarthy, Chris / Forkan, Abdur / Banerjee, Abhik / Hocking, Rosalie K

    Journal of hazardous materials

    2023  Volume 463, Page(s) 132853

    Abstract: Asbestos identification is a complex environmental and economic challenge. Typical commercial identification of asbestos involves sending samples to a laboratory where someone learned in the field uses light microscopy and specialized mounting to ... ...

    Abstract Asbestos identification is a complex environmental and economic challenge. Typical commercial identification of asbestos involves sending samples to a laboratory where someone learned in the field uses light microscopy and specialized mounting to identify the morphologically distinct signatures of Asbestos. In this work we investigate the use of a portable (30x) microscope which works with a smart phone camera to develop an image recognition system. 7328 images from over 1000 distinct samples of cement sheet from Melbourne, Australia were used to train a phone-based image recognition system for Asbestos identification. Three common CNN's were tested ResNet101, InceptionV3 and VGG_16 with ResNet101 achieving the best result. The distinctiveness of Asbestos was found to be identified correctly 90% of the time using a phone-based system and no specialized mounting. The image recognition system was trained with ResNet101 a convolutional neural network deep learning model which weights layers with a residual function. Resulting in an accuracy of 98.46% and loss of 3.8% ResNet101 was found to produce a more accurate model for this use-case than other deep learning neural networks.
    Language English
    Publishing date 2023-10-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2023.132853
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  5. Article ; Online: Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo.

    Guo, Jimmy K / Blanco, Mario R / Walkup, Ward G / Bonesteele, Grant / Urbinati, Carl R / Banerjee, Abhik K / Chow, Amy / Ettlin, Olivia / Strehle, Mackenzie / Peyda, Parham / Amaya, Enrique / Trinh, Vickie / Guttman, Mitchell

    Molecular cell

    2024  Volume 84, Issue 7, Page(s) 1271–1289.e12

    Abstract: Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence ... ...

    Abstract Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
    MeSH term(s) Animals ; Mice ; Humans ; Polycomb Repressive Complex 2/genetics ; Polycomb Repressive Complex 2/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Chromatin/genetics ; Binding Sites
    Chemical Substances Polycomb Repressive Complex 2 (EC 2.1.1.43) ; RNA, Long Noncoding ; Chromatin
    Language English
    Publishing date 2024-02-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.01.026
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  6. Article ; Online: Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome.

    Jachowicz, Joanna W / Strehle, Mackenzie / Banerjee, Abhik K / Blanco, Mario R / Thai, Jasmine / Guttman, Mitchell

    Nature structural & molecular biology

    2022  Volume 29, Issue 3, Page(s) 239–249

    Abstract: Although thousands of long non-coding RNAs (lncRNAs) are encoded in mammalian genomes, their mechanisms of action are poorly understood, in part because they are often expressed at lower levels than their proposed targets. One such lncRNA is Xist, which ... ...

    Abstract Although thousands of long non-coding RNAs (lncRNAs) are encoded in mammalian genomes, their mechanisms of action are poorly understood, in part because they are often expressed at lower levels than their proposed targets. One such lncRNA is Xist, which mediates chromosome-wide gene silencing on one of the two X chromosomes (X) to achieve gene expression balance between males and females. How a limited number of Xist molecules can mediate robust silencing of a much larger number of target genes while maintaining specificity exclusively to genes on the X within each cell is not well understood. Here, we show that Xist drives non-stoichiometric recruitment of the essential silencing protein SHARP (also known as SPEN) to amplify its abundance across the inactive X, including at regions not directly occupied by Xist. This amplification is achieved through concentration-dependent homotypic assemblies of SHARP on the X and is required for chromosome-wide silencing. Expression of Xist at higher levels leads to increased localization at autosomal regions, demonstrating that low levels of Xist are critical for ensuring its specificity to the X. We show that Xist (through SHARP) acts to suppress production of its own RNA which may act to constrain overall RNA levels and restrict its ability to spread beyond the X. Together, our results demonstrate a spatial amplification mechanism that allows Xist to achieve two essential but countervailing regulatory objectives: chromosome-wide gene silencing and specificity to the X. This suggests a more general mechanism by which other low-abundance lncRNAs could balance specificity to, and robust control of, their regulatory targets.
    MeSH term(s) Animals ; Female ; Gene Silencing ; Male ; Mammals/genetics ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; X Chromosome/genetics ; X Chromosome/metabolism ; X Chromosome Inactivation
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2022-03-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-022-00739-1
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    Zs.A 4101: Show issues Location:
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  7. Article ; Online: Identification of two novel thiophene analogues as inducers of autophagy mediated cell death in breast cancer cells.

    Gain, Chandrima / Sarkar, Aparna / Bural, Shrea / Rakshit, Moumita / Banerjee, Jeet / Dey, Ankita / Biswas, Nabendu / Kar, Gandhi K / Saha, Abhik

    Bioorganic & medicinal chemistry

    2021  Volume 37, Page(s) 116112

    Abstract: Natural compounds isolated from different medicinal plants remain one of the major resources of anticancer drugs due to their enormous chemical diversity. Studies suggested therapeutic potential for various tanshinones, key bioactive lipophilic compounds ...

    Abstract Natural compounds isolated from different medicinal plants remain one of the major resources of anticancer drugs due to their enormous chemical diversity. Studies suggested therapeutic potential for various tanshinones, key bioactive lipophilic compounds from the root extracts of Salvia miltiorrhiza Bunge, against multiple cancers including breast carcinoma. We designed, synthesized and evaluated anti-cancer properties of a series of condensed and doubly condensed furophenanthraquinones of tanshinone derivatives on two breast cancer lines - MCF7 and MDA-MB-231. We identified two thiophene analogues - compounds 48 and 52 with greater anti-proliferative efficiency (~4 fold) as compared to the natural tanshinones. Mechanistically, we showed that both compounds induced autophagy mediated cell death and partial but significant restoration of cell death in the presence of autophagy inhibitor further supported this notion. Both compounds transcriptionally activated several autophagy genes responsible for autophagosome formation along with two death regulators - GADD34 and CHOP for inducing cell death. Altogether, our studies provide strong evidence to support compounds 48 and 52 as promising leads for further development as anticancer agents through modulating autophagy mechanism.
    MeSH term(s) Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/pharmacology ; Apoptosis/drug effects ; Autophagy/drug effects ; Breast Neoplasms/drug therapy ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Drug Screening Assays, Antitumor ; Humans ; Thiophenes/chemical synthesis ; Thiophenes/pharmacology ; Unfolded Protein Response/drug effects
    Chemical Substances Antineoplastic Agents ; Thiophenes
    Language English
    Publishing date 2021-03-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1161284-8
    ISSN 1464-3391 ; 0968-0896
    ISSN (online) 1464-3391
    ISSN 0968-0896
    DOI 10.1016/j.bmc.2021.116112
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    Zs.A 3815: Show issues Location:
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  8. Article ; Online: Xist nucleates local protein gradients to propagate silencing across the X chromosome.

    Markaki, Yolanda / Chong, Johnny Gan / Wang, Yuying / Jacobson, Elsie C / Luong, Christy / Tan, Shawn Y X / Jachowicz, Joanna W / Strehle, Mackenzie / Maestrini, Davide / Banerjee, Abhik K / Mistry, Bhaven A / Dror, Iris / Dossin, Francois / Schӧneberg, Johannes / Heard, Edith / Guttman, Mitchell / Chou, Tom / Plath, Kathrin

    Cell

    2021  Volume 184, Issue 25, Page(s) 6212

    Language English
    Publishing date 2021-12-10
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.11.028
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    Zs.A 1167: Show issues Location:
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  9. Article ; Online: Search for New Anode Materials for High Performance Li-Ion Batteries.

    Roy, Kingshuk / Banerjee, Abhik / Ogale, Satishchandra

    ACS applied materials & interfaces

    2022  Volume 14, Issue 18, Page(s) 20326–20348

    Abstract: Owing to an unmatched combination of power and energy density along with cyclic stability, the Li-ion battery has qualified itself to be the highest performing rechargeable battery. Taking both transportable and stationary energy storage requirements ... ...

    Abstract Owing to an unmatched combination of power and energy density along with cyclic stability, the Li-ion battery has qualified itself to be the highest performing rechargeable battery. Taking both transportable and stationary energy storage requirements into consideration, Li-ion batteries indeed stand tall in comparison to any other existing rechargeable battery technologies. However, graphite, which is still one of the best performing Li-ion anodes, has specific drawbacks in fulfilling the ever-increasing energy and power density requirements of the modern world. Therefore, further research on alternative anode materials is absolutely essential. Equally important is the search for and enhanced use of right earth abundant materials for battery electrodes so as to bring down the costs of the battery systems. In this spotlight article, we discuss the current research progress in the area of alternative anode materials for Li-ion battery, putting our own research work over the past several years into perspective. Starting from conversion anode systems like oxides and sulfides, to insertion cum alloying systems like transition metal carbides, to molecularly engineered open framework systems like metal organic frameworks (MOFs), covalent organic frameworks (COFs), and organic-inorganic hybrid perovskites (OIHPs), this spotlight provides a complete essence of the recent developments in the area of alternative anodes. The possible and potential impact of these new anode materials is detailed and discussed here.
    Language English
    Publishing date 2022-04-12
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.1c25262
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  10. Article ; Online: Association of rare variants in genes of immune regulation with pediatric autoimmune CNS diseases.

    Jafarpour, Saba / Banerjee, Abhik / Boyd, Natalie K / Vogel, Benjamin N / Paulsen, Kelli C / Ahsan, Nusrat / Mitchell, Wendy G / Jeste, Shafali S / Santoro, Jonathan D

    Journal of neurology

    2022  Volume 269, Issue 12, Page(s) 6512–6529

    Abstract: Background: There is a gap in the literature regarding genetic underpinnings of pediatric autoimmune CNS diseases. This study explored rare gene variants implicated in immune dysregulation within these disorders.: Methods: This was a single-center ... ...

    Abstract Background: There is a gap in the literature regarding genetic underpinnings of pediatric autoimmune CNS diseases. This study explored rare gene variants implicated in immune dysregulation within these disorders.
    Methods: This was a single-center observational study of children with inflammatory CNS disorder who had genetic testing through next generation focused exome sequencing targeting 155 genes associated with innate or adaptive immunity. For in silico prediction of functional effects of single-nucleotide variants, Polymorphism Phenotyping v2, and Sorting Intolerant from Tolerant were used, and Combined Annotation Dependent Depletion (CADD) scores were calculated. Identified genes were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.
    Results: Of 54 patients, 42 (77.8%) carried variant(s), among which 12 (22.2%) had 3-8 variants. Eighty-eight unique single-nucleotide variants of 55 genes were identified. The most variants were detected in UNC13D, LRBA, LYST, NOD2, DOCK8, RNASEH2A, STAT5B, and AIRE. The majority of variants (62, 70.4%) had CADD > 10. KEGG pathway analysis revealed seven genes associated with primary immunodeficiency (Benjamini 1.40E - 06), six genes with NOD-like receptor signaling (Benjamini 4.10E - 04), five genes with Inflammatory Bowel Disease (Benjamini 9.80E - 03), and five genes with NF-kappa B signaling pathway (Benjamini 1.90E - 02).
    Discussion: We observed a high rate of identification of rare and low-frequency variants in immune regulatory genes in pediatric neuroinflammatory CNS disorders. We identified 88 unique single-nucleotide variants of 55 genes with pathway analysis revealing an enrichment of NOD2-receptor signaling, consistent with involvement of the pathway within other autoinflammatory conditions and warranting further investigation.
    MeSH term(s) Humans ; Child ; Whole Exome Sequencing ; Genetic Testing ; Autoimmune Diseases ; Central Nervous System Diseases ; Nucleotides ; Genetic Predisposition to Disease/genetics ; Adaptor Proteins, Signal Transducing/genetics ; Membrane Proteins/genetics ; Guanine Nucleotide Exchange Factors/genetics
    Chemical Substances Nucleotides ; LRBA protein, human (EC 2.7.10.-) ; Adaptor Proteins, Signal Transducing ; UNC13D protein, human ; Membrane Proteins ; DOCK8 protein, human ; Guanine Nucleotide Exchange Factors
    Language English
    Publishing date 2022-08-12
    Publishing country Germany
    Document type Observational Study ; Journal Article
    ZDB-ID 187050-6
    ISSN 1432-1459 ; 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
    ISSN (online) 1432-1459
    ISSN 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
    DOI 10.1007/s00415-022-11325-2
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