187 results on '"Shaham S"'
Search Results
2. Nutritional intake comparison of vegan and non-vegan pregnant women
- Author
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Paz Dubinsky, E., primary, Shaham, S., additional, Zelber-Sagi, S., additional, Avnon, T., additional, Yogev, Y., additional, and Anbar, R., additional
- Published
- 2023
- Full Text
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3. When Machine Learning Meets Privacy
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Liu, B, Ding, M, Shaham, S, Rahayu, W, Farokhi, F, and Lin, Z
- Subjects
08 Information and Computing Sciences ,Information Systems - Abstract
The newly emerged machine learning (e.g., deep learning) methods have become a strong driving force to revolutionize a wide range of industries, such as smart healthcare, financial technology, and surveillance systems. Meanwhile, privacy has emerged as a big concern in this machine learning-based artificial intelligence era. It is important to note that the problem of privacy preservation in the context of machine learning is quite different from that in traditional data privacy protection, as machine learning can act as both friend and foe. Currently, the work on the preservation of privacy and machine learning are still in an infancy stage, as most existing solutions only focus on privacy problems during the machine learning process. Therefore, a comprehensive study on the privacy preservation problems and machine learning is required. This article surveys the state of the art in privacy issues and solutions for machine learning. The survey covers three categories of interactions between privacy and machine learning: (i) private machine learning, (ii) machine learning-aided privacy protection, and (iii) machine learning-based privacy attack and corresponding protection schemes. The current research progress in each category is reviewed and the key challenges are identified. Finally, based on our in-depth analysis of the area of privacy and machine learning, we point out future research directions in this field.
- Published
- 2021
4. Privacy Preservation in Location-Based Services: A Novel Metric and Attack Model
- Author
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Shaham, S, Ding, M, Liu, B, Dang, S, Lin, Z, Li, J, Shaham, S, Ding, M, Liu, B, Dang, S, Lin, Z, and Li, J
- Published
- 2020
5. Privacy Preserving Location Data Publishing: A Machine Learning Approach
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Shaham, S, Ding, M, Liu, B, Dang, S, Lin, Z, Li, J, Shaham, S, Ding, M, Liu, B, Dang, S, Lin, Z, and Li, J
- Published
- 2020
6. Listeria monocytogenes MDR transporters and c-di-AMP that contribute to Type I interferons induction, play a role in cell wall stress
- Author
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58. Kaplan Zeevi, M, N. Shafir, S. Shaham, S. Friedman, N. Sigal, R. Nir Paz, I.G. Boneca and A. Herskovits, 58. Kaplan Zeevi, M., N. Shafir, S. Shaham, S. Friedman, N. Sigal, R. Nir Paz, I.G. Boneca, and A. Herskovits
- Published
- 2013
7. A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens
- Author
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Rangan, K. J., primary, Pedicord, V. A., additional, Wang, Y.-C., additional, Kim, B., additional, Lu, Y., additional, Shaham, S., additional, Mucida, D., additional, and Hang, H. C., additional
- Published
- 2016
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8. Impact of ambient air pollution on outdoor employees’ performance: Mediating role of anxiety
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Muhammad Waseem Bari, Shaham Saleem, Mohsin Bashir, and Bashir Ahmad
- Subjects
ambient air pollution ,processing efficiency theory ,anxiety ,employee performance ,pharmaceutical industry ,Psychology ,BF1-990 - Abstract
This paper aims to examine the direct and indirect impact of ambient air pollution (AAP) on employees’ performance. This study has used cross sectional survey design to collect the data from the outdoor employees of the pharmaceutical industry of Pakistan. The data were collected in time lags from 299. Partial least squares- structural equation modeling (PLS-SEM) approach was applied to analyze the data. The results show that AAP has a significant negative impact on the employees’ performance, and anxiety partially mediates the association between AAP and employees’ performance. This study reveals that AAP brings anxiety among outdoor employees, which in turn decreases their working performance. The implications, limitations, and future research directions are presented in the last section of this study.
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- 2022
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9. Listeria monocytogenes Multidrug Resistance Transporters and Cyclic Di-AMP, Which Contribute to Type I Interferon Induction, Play a Role in Cell Wall Stress
- Author
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Kaplan Zeevi, M., primary, Shafir, N. S., additional, Shaham, S., additional, Friedman, S., additional, Sigal, N., additional, Nir Paz, R., additional, Boneca, I. G., additional, and Herskovits, A. A., additional
- Published
- 2013
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10. Two Novel DEG/ENaC Channel Subunits Expressed in Glia Are Needed for Nose-Touch Sensitivity in Caenorhabditis elegans
- Author
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Han, L., primary, Wang, Y., additional, Sangaletti, R., additional, D'Urso, G., additional, Lu, Y., additional, Shaham, S., additional, and Bianchi, L., additional
- Published
- 2013
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11. C. elegans ced-13 can promote apoptosis and is induced in response to DNA damage.
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Schumacher, B, Schertel, C, Wittenburg, N, Tuck, S, Mitani, S, Gartner, A, Conradt, B, Shaham, S, Schumacher, B, Schertel, C, Wittenburg, N, Tuck, S, Mitani, S, Gartner, A, Conradt, B, and Shaham, S
- Published
- 2005
12. Functional genomics of the cilium, a sensory organelle
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Blacque, O E, Perens, E A, Boroevich, K A, Inglis, P N, Li, C M, Warner, A, Khattra, J, Holt, R A, Ou, G S, Mah, A K, McKay, S J, Huang, P, Swoboda, Peter, Jones, S J M, Marra, M A, Baillie, D L, Moerman, D G, Shaham, S, Leroux, M R, Blacque, O E, Perens, E A, Boroevich, K A, Inglis, P N, Li, C M, Warner, A, Khattra, J, Holt, R A, Ou, G S, Mah, A K, McKay, S J, Huang, P, Swoboda, Peter, Jones, S J M, Marra, M A, Baillie, D L, Moerman, D G, Shaham, S, and Leroux, M R
- Abstract
Cilia and flagella play important roles in many physiological processes, including cell and fluid movement, sensory perception, and development [1]. The biogenesis and maintenance of cilia depend on intraflagellar transport (IFT), a motility process that operates bidirectionally along the ciliary axoneme [1, 2]. Disruption in IFT and cilia function causes several human disorders, including polycystic kidneys, retinal dystrophy, neurosensory impairment, and Bardet-Bledl syndrome (BBS) [3-5]. To uncover new ciliary components, including IFT proteins, we compared C. elegans ciliated neuronal and nonciliated cells through serial analysis of gene expression (SAGE) and screened for genes potentially regulated by the cillogenic transcription factor, DAF-19 [6]. Using these complementary approaches, we identified numerous candidate ciliary genes and confirmed the ciliated-cell-specific expression of 14 novel genes. One of these, C27H5.7a, encodes a ciliary protein that undergoes IFT. As with other IFT proteins, its ciliary localization and transport is disrupted by mutations in IFT and bbs genes. Furthermore, we demonstrate that the ciliary structural defect of C. elegans dyf-13(mn396) mutants is caused by a mutation in C27H5.7a. Together, our findings help define a ciliary transcriptome and suggest that DYF-13, an evolutionarily conserved protein, is a novel core IFT component required for cilia function.
- Published
- 2005
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13. Three-Dimensional Reconstruction of Actin in a Sensory Glial Cell using Bi-Plane PALM
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Watanabe, S, primary, Ebeling, C, additional, Oikonomou, G, additional, Shaham, S, additional, Gerton, J, additional, and Jorgensen, E, additional
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- 2011
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14. Molecular Architecture of a Sensory Ending Using Correlative Fluorescence and Electron Microscopy
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Watanabe, S, primary, Oikonomou, G, additional, Shaham, S, additional, and Jorgensen, E, additional
- Published
- 2011
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15. Automated 3D Reconstruction of Serial Electron Microscopy Image Sequences Using Object Recognition
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Lu, Y, primary and Shaham, S, additional
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- 2008
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16. Noncanonical cell death programs in the nematode Caenorhabditis elegans
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Blum, E S, primary, Driscoll, M, additional, and Shaham, S, additional
- Published
- 2008
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17. Erratum: C. elegans ced-13 can promote apoptosis and is induced in response to DNA damage
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Schumacher, B, primary, Schertel, C, additional, Wittenburg, N, additional, Tuck, S, additional, Mitani, S, additional, Gartner, A, additional, Conradt, B, additional, and Shaham, S, additional
- Published
- 2005
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18. C. elegans ced-13 can promote apoptosis and is induced in response to DNA damage
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Schumacher, B, primary, Schertel, C, additional, Wittenburg, N, additional, Tuck, S, additional, Mitani, S, additional, Gartner, A, additional, Conradt, B, additional, and Shaham, S, additional
- Published
- 2004
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19. Nuclear export of Far1p in response to pheromones requires the export receptor Msn5p/Ste21p
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Blondel, M., primary, Alepuz, P. M., additional, Huang, L. S., additional, Shaham, S., additional, Ammerer, G., additional, and Peter, M., additional
- Published
- 1999
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20. The Caenorhabditis elegans cell-death protein CED-3 is a cysteine protease with substrate specificities similar to those of the human CPP32 protease.
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Xue, D, primary, Shaham, S, additional, and Horvitz, H R, additional
- Published
- 1996
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21. Developing Caenorhabditis elegans neurons may contain both cell-death protective and killer activities.
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Shaham, S, primary and Horvitz, H R, additional
- Published
- 1996
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22. The Genetics of Programmed Cell Death in the Nematode Caenorhabditis elegans
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Horvitz, H.R., primary, Shaham, S., additional, and Hengartner, M.O., additional
- Published
- 1994
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23. C. elegans ced-13 can promote apoptosis and is induced in response to DNA damage.
- Author
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Schumacher, B., Schertel, C., Wittenburg, N., Tuck, S., Mitani, S., Gartner, A., Conradt, B., and Shaham, S.
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CAENORHABDITIS elegans ,APOPTOSIS ,DNA damage ,CELL death ,MESSENGER RNA ,SOMATIC cells - Abstract
The p53 tumor suppressor promotes apoptosis in response to DNA damage. Here we describe the Caenorhabditis elegans gene ced-13, which encodes a conserved BH3-only protein. We show that ced-13 mRNA accumulates following DNA damage, and that this accumulation is dependent on an intact C. elegans cep-1/p53 gene. We demonstrate that CED-13 protein physically interacts with the antiapoptotic Bcl-2-related protein CED-9. Furthermore, overexpression of ced-13 in somatic cells leads to the death of cells that normally survive, and this death requires the core apoptotic pathway of C. elegans. Recent studies have implicated two BH3-only proteins, Noxa and PUMA, in p53-induced apoptosis in mammals. Our studies suggest that in addition to the BH3-only protein EGL-1, CED-13 might also promote apoptosis in the C. elegans germ line in response to p53 activation. We propose that an evolutionarily conserved pathway exists in which p53 promotes cell death by inducing expression of two BH3-only genes.Cell Death and Differentiation (2005) 12, 153-161. doi:10.1038/sj.cdd.4401539 Published online 17 December 2004 [ABSTRACT FROM AUTHOR]
- Published
- 2005
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24. Identification of multiple Caenorhabditis elegans caspases and their potential roles in proteolytic cascades.
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Shaham, S
- Abstract
Proteases of the caspase family play a central role in the execution of programmed cell death in all metazoans examined. The Caenorhabditis elegans caspase CED-3 is essential for programmed cell death in this organism. Three additional C. elegans caspase-related genes, csp-1 (caspase homolog-1), which encodes the csp-1A, csp-1B, and csp-1C RNA species; csp-2, which encodes the csp-2A and csp-2B RNA species; and csp-3 are identified. CSP-1A, CSP-1B, CSP-2A, and CSP-2B proteins are similar in sequence to caspase proproteins. CSP-1C is similar only to large caspase subunits, and CSP-3 is similar only to small caspase subunits. CSP-1B can be activated to become a cysteine protease by processing at internal aspartate residues. Activated CSP-1B can cleave the CSP-1B, CED-3, and CSP-2B proproteins, and activated CED-3 can cleave the CED-3 and CSP-2B proproteins. Inhibitor and synthetic substrate studies further suggest that activated CSP-1B and activated CED-3 have different substrate specificities. These results suggest that C. elegans encodes several caspases that might act in proteolytic cascades to regulate processes such as programmed cell death.
- Published
- 1998
25. C. elegans PPEF-type phosphatase (Retinal degeneration C ortholog) functions in diverse classes of cilia to regulate nematode behaviors.
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Barbelanne M, Lu Y, Kumar K, Zhang X, Li C, Park K, Warner A, Xu XZS, Shaham S, and Leroux MR
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- Animals, Retinal Degeneration metabolism, Retinal Degeneration genetics, Retinal Degeneration pathology, Behavior, Animal, Cilia metabolism, Caenorhabditis elegans metabolism, Caenorhabditis elegans genetics, Caenorhabditis elegans Proteins metabolism, Caenorhabditis elegans Proteins genetics
- Abstract
Primary (non-motile) cilia represent structurally and functionally diverse organelles whose roles as specialized cellular antenna are central to animal cell signaling pathways, sensory physiology and development. An ever-growing number of ciliary proteins, including those found in vertebrate photoreceptors, have been uncovered and linked to human disorders termed ciliopathies. Here, we demonstrate that an evolutionarily-conserved PPEF-family serine-threonine phosphatase, not functionally linked to cilia in any organism but associated with rhabdomeric (non-ciliary) photoreceptor degeneration in the Drosophila rdgC (retinal degeneration C) mutant, is a bona fide ciliary protein in C. elegans. The nematode protein, PEF-1, depends on transition zone proteins, which make up a 'ciliary gate' in the proximal-most region of the cilium, for its compartmentalization within cilia. Animals lacking PEF-1 protein function display structural defects to several types of cilia, including potential degeneration of microtubules. They also exhibit anomalies to cilium-dependent behaviors, including impaired responses to chemical, temperature, light, and noxious CO
2 stimuli. Lastly, we demonstrate that PEF-1 function depends on conserved myristoylation and palmitoylation signals. Collectively, our findings broaden the role of PPEF proteins to include cilia, and suggest that the poorly-characterized mammalian PPEF1 and PPEF2 orthologs may also have ciliary functions and thus represent ciliopathy candidates., Competing Interests: Declarations Competing interests The authors declare no competing interests., (© 2024. The Author(s).)- Published
- 2024
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26. Apoptotic and Nonapoptotic Cell Death in Caenorhabditis elegans Development.
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Horowitz LB and Shaham S
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- Animals, Cell Death genetics, Autophagy genetics, Signal Transduction, Phagocytosis genetics, Caenorhabditis elegans genetics, Caenorhabditis elegans growth & development, Apoptosis genetics, Caenorhabditis elegans Proteins genetics, Caenorhabditis elegans Proteins metabolism, Caspases metabolism, Caspases genetics
- Abstract
Programmed cell death (PCD) is an essential component of animal development, and aberrant cell death underlies many disorders. Understanding mechanisms that govern PCD during development can provide insight into cell death programs that are disrupted in disease. Key steps mediating apoptosis, a highly conserved cell death program employing caspase proteases, were first uncovered in the nematode Caenorhabditis elegans , a powerful model system for PCD research. Recent studies in C. elegans also unearthed conserved nonapoptotic caspase-independent cell death programs that function during development. Here, we discuss recent advances in understanding cell death during C. elegans development. We review insights expanding the molecular palette behind the execution of apoptotic and nonapoptotic cell death, as well as new discoveries revealing the mechanistic underpinnings of dying cell engulfment and clearance. A number of open questions are also discussed that will continue to propel the field over the coming years.
- Published
- 2024
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27. Impact of serous fluid volume on next-generation sequencing: a significant step forward for optimization of serous fluid sample collection.
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Beg S, Xu K, Solomon JP, Alperstein SA, and Siddiqui MT
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- Humans, Female, Middle Aged, Aged, Male, Adult, Aged, 80 and over, Specimen Handling methods, Ascitic Fluid pathology, Ascitic Fluid cytology, Neoplasms genetics, Neoplasms pathology, Neoplasms diagnosis, Pleural Effusion, Malignant genetics, Pleural Effusion, Malignant pathology, Pleural Effusion, Malignant diagnosis, Mutation, Biomarkers, Tumor genetics, Adenocarcinoma genetics, Adenocarcinoma pathology, Adenocarcinoma diagnosis, High-Throughput Nucleotide Sequencing methods
- Abstract
Introduction: Current literature lacks data regarding the influence of serous fluid volume (SFV) on next-generation sequencing (NGS) performed on malignant cases. In this study, we highlight the impact of SFV and other parameters influencing the outcome of NGS analysis., Materials and Methods: We evaluated 827 samples of serous fluids from 607 patients. Of these, 72 samples underwent NGS analysis. Effusion volume, tumor cellularity, DNA, and RNA quality metrics, as well as clinicopathologic and molecular data were evaluated. Pleural fluid accounted for 56.3% of the fluid samples collected. The most common primary tumor site was gastrointestinal/pancreatobiliary, adenocarcinoma was the most common histologic type. Overall mean volume was 293 mL. The mean Qubit DNA of the 72 effusion samples that underwent NGS analysis was 14.3 ng/μL and mean Qubit RNA was 28.2 ng/μL. The mean Qubit DNA concentration increases in SFV up to 100 mL only., Results: No correlation exists between SFV and mean tumor cellularity. In addition, 74.6% (50 of 67) of sequenced samples showed oncogenic drivers; KRAS was the most common driver followed by EGFR. Three cases displayed ALK fusions, and 1 case displayed NTRK1 fusion. The DNA yield is higher in SFV of 100 mL as a cutoff. Beyond 100 mL, there is no impact of SFV on DNA yield. SFV does not impact RNA yield and mean tumor cellularity. Effusion samples should be submitted for molecular testing despite low tumor cellularity., Conclusions: Our results as a pilot study are important in optimization of SFV for both diagnosis as well as NGS analysis for improving management., (Copyright © 2024 American Society of Cytopathology. Published by Elsevier Inc. All rights reserved.)
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- 2024
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28. Diagnostic interobserver agreement for thyroid fine-needle aspirates: Effects of reviewer experience and molecular diagnostics.
- Author
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Gokozan HN, Mostyka M, Scognamiglio T, Solomon JP, Beg S, Stern E, Goyal A, Siddiqui MT, and Heymann JJ
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- Humans, Biopsy, Fine-Needle, Thyroid Nodule pathology, Thyroid Nodule genetics, Thyroid Nodule diagnosis, Pathology, Molecular, Mutation, Proto-Oncogene Proteins B-raf genetics, Observer Variation, Thyroid Gland pathology, Thyroid Neoplasms genetics, Thyroid Neoplasms pathology, Thyroid Neoplasms diagnosis
- Abstract
Objectives: Few cytologically indeterminate thyroid fine-needle aspirations (FNAs) harbor BRAF V600E. Here, we assess interobserver agreement for The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) category III (atypia of undetermined significance [AUS]) FNAs harboring BRAF V600E and contrast their features with those harboring non-BRAF V600E alterations, with attention to cytopathology experience., Methods: Seven reviewers evaluated 5 AUS thyroid FNAs harboring BRAF V600E. To blind reviewers, cases were intermixed with 19 FNAs falling within other TBSRTC categories and in which genetic alterations other than BRAF V600E had been identified (24 FNAs total). Interobserver agreement against both "index" and most popular ("mode") diagnoses was calculated. Four additional BRAF V600E cases were independently reviewed., Results: Reviewers included 3 trainees and 3 American Board of Pathology (board)-certified cytopathologists. Board-certified cytopathologists, whose experience ranged from 2 to more than 15 subspecialty practice years, had known AUS rates. BRAF V600E was identified in 5 of 260 (2%) AUS FNAs. Interobserver agreement was higher among cytopathologists with more experience. Mode diagnosis differed from index diagnosis in 6 of 11 cases harboring RAS-like alterations; mode diagnosis was AUS in 4 of 5 BRAF V600E FNAs., Conclusions: Atypia of undetermined significance of thyroid FNAs harboring BRAF V600E is uncommon yet relatively reproducible, particularly among pathologists with experience. It is advisable to sequence BRAF across V600 in such cases., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society for Clinical Pathology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
- Published
- 2024
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29. Glia Development and Function in the Nematode Caenorhabditis elegans .
- Author
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Singhvi A, Shaham S, and Rapti G
- Abstract
The nematode Caenorhabditis elegans is a powerful experimental setting for uncovering fundamental tenets of nervous system organization and function. Its nearly invariant and simple anatomy, coupled with a plethora of methodologies for interrogating single-gene functions at single-cell resolution in vivo, have led to exciting discoveries in glial cell biology and mechanisms of glia-neuron interactions. Findings over the last two decades reinforce the idea that insights from C. elegans can inform our understanding of glial operating principles in other species. Here, we summarize the current state-of-the-art, and describe mechanistic insights that have emerged from a concerted effort to understand C. elegans glia. The remarkable acceleration in the pace of discovery in recent years paints a portrait of striking molecular complexity, exquisite specificity, and functional heterogeneity among glia. Glial cells affect nearly every aspect of nervous system development and function, from generating neurons, to promoting neurite formation, to animal behavior, and to whole-animal traits, including longevity. We discuss emerging questions where C. elegans is poised to fill critical knowledge gaps in our understanding of glia biology., (Copyright © 2024 Cold Spring Harbor Laboratory Press; all rights reserved.)
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- 2024
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30. Boosting Thermoelectric Performance in Nanocrystalline Ternary Skutterudite Thin Films through Metallic CoTe 2 Integration.
- Author
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Jarwal B, Abbas S, Chou TL, Vailyaveettil SM, Kumar A, Quadir S, Ho TT, Wong DP, Chen LC, and Chen KH
- Abstract
Metal-semiconductor nanocomposites have emerged as a viable strategy for concurrently tailoring both thermal and electronic transport properties of established thermoelectric materials, ultimately achieving synergistic performance. In this investigation, a series of nanocomposite thin films were synthesized, embedding metallic cobalt telluride (CoTe
2 ) nanophase within the nanocrystalline ternary skutterudite (Co(Ge1.22 Sb0.22 )Te1.58 or CGST) matrix. Our approach harnessed composition fluctuation-induced phase separation and in situ growth during thermal annealing to seamlessly integrate the metallic phase. The distinctive band structures of both materials have developed an ohmic-type contact characteristic at the interface, which raised carrier density considerably yet negligibly affected the mobility counterpart, leading to a substantial improvement in electrical conductivity. The intricate balance in transport properties is further influenced by the metallic CoTe2 phase's role in diminishing lattice thermal conductivity. The presence of the metallic phase instigates enhanced phonon scattering at the interface boundaries. Consequently, a 2-fold enhancement in the thermoelectric figure of merit (zT ∼ 1.30) is attained with CGST-7 wt. % CoTe2 nanocomposite film at 655 K compared to that of pristine CGST.- Published
- 2024
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31. The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis.
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Ohara K, Rendeiro AF, Bhinder B, Eng KW, Ravichandran H, Nguyen D, Pisapia D, Vosoughi A, Fernandez E, Shohdy KS, Manohar J, Beg S, Wilkes D, Robinson BD, Khani F, Bareja R, Tagawa ST, Ouseph MM, Sboner A, Elemento O, Faltas BM, and Mosquera JM
- Subjects
- Humans, Genomics methods, Gene Expression Profiling, Transcriptome, Carcinoma, Transitional Cell genetics, Carcinoma, Transitional Cell pathology, Urinary Bladder Neoplasms genetics, Urinary Bladder Neoplasms pathology
- Abstract
The molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are not well understood, and there is a lack of knowledge regarding the genomic and transcriptomic differences between primary and metastatic UTUC. To address these gaps, we integrate whole-exome sequencing, RNA sequencing, and Imaging Mass Cytometry using lanthanide metal-conjugated antibodies of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. We perform a spatially-resolved single-cell analysis of cancer, immune, and stromal cells to understand the evolution of primary to metastatic UTUC. We discover that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature are stable across primary and matched metastatic UTUC. Molecular and immune subtypes are consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single cells. Molecular subtypes at the single-cell level are highly conserved between primary and metastatic UTUC tumors within the same patient., (© 2024. The Author(s).)
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- 2024
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32. LET-381/FoxF and its target UNC-30/Pitx2 specify and maintain the molecular identity of C. elegans mesodermal glia that regulate motor behavior.
- Author
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Stefanakis N, Jiang J, Liang Y, and Shaham S
- Subjects
- Animals, Gene Expression Regulation, Neuroglia metabolism, Transcription Factors genetics, Transcription Factors metabolism, Caenorhabditis elegans metabolism, Caenorhabditis elegans Proteins genetics, Caenorhabditis elegans Proteins metabolism, Forkhead Transcription Factors metabolism, Homeodomain Proteins metabolism
- Abstract
While most glial cell types in the central nervous system (CNS) arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which envelop the brain neuropil and separate it from the circulatory system cavity. Transcriptome analysis shows that GLR glia combine astrocytic and endothelial characteristics, which are relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor also expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, the UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naive cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and promotes salt-induced paralysis, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neuronal differentiation, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate., (© 2024. The Author(s).)
- Published
- 2024
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33. Fair Spatial Indexing: A paradigm for Group Spatial Fairness.
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Shaham S, Ghinita G, and Shahabi C
- Abstract
Machine learning (ML) is playing an increasing role in decision-making tasks that directly affect individuals, e.g., loan approvals, or job applicant screening. Significant concerns arise that, without special provisions, individuals from under-privileged backgrounds may not get equitable access to services and opportunities. Existing research studies fairness with respect to protected attributes such as gender, race or income, but the impact of location data on fairness has been largely overlooked. With the widespread adoption of mobile apps, geospatial attributes are increasingly used in ML, and their potential to introduce unfair bias is significant, given their high correlation with protected attributes. We propose techniques to mitigate location bias in machine learning. Specifically, we consider the issue of miscalibration when dealing with geospatial attributes. We focus on spatial group fairness and we propose a spatial indexing algorithm that accounts for fairness. Our KD-tree inspired approach significantly improves fairness while maintaining high learning accuracy, as shown by extensive experimental results on real data.
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- 2024
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34. HTF: Homogeneous Tree Framework for Differentially-Private Release of Large Geospatial Datasets with Self-Tuning Structure Height.
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Shaham S, Ghinita G, Ahuja R, Krumm J, and Shahabi C
- Abstract
Mobile apps that use location data are pervasive, spanning domains such as transportation, urban planning and healthcare. Important use cases for location data rely on statistical queries, e.g., identifying hotspots where users work and travel. Such queries can be answered efficiently by building histograms. However, precise histograms can expose sensitive details about individual users. Differential privacy (DP) is a mature and widely-adopted protection model, but most approaches for DP-compliant histograms work in a data-independent fashion, leading to poor accuracy. The few proposed data-dependent techniques attempt to adjust histogram partitions based on dataset characteristics, but they do not perform well due to the addition of noise required to achieve DP. In addition, they use ad-hoc criteria to decide the depth of the partitioning. We identify density homogeneity as a main factor driving the accuracy of DP-compliant histograms, and we build a data structure that splits the space such that data density is homogeneous within each resulting partition. We propose a self-tuning approach to decide the depth of the partitioning structure that optimizes the use of privacy budget. Furthermore, we provide an optimization that scales the proposed split approach to large datasets while maintaining accuracy. We show through extensive experiments on large-scale real-world data that the proposed approach achieves superior accuracy compared to existing approaches.
- Published
- 2023
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35. Glia detect and mount a protective response to loss of dendrite substructure integrity in C. elegans .
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Varandas KC, Hodges BM, Lubeck L, Farinas A, Liang Y, Lu Y, and Shaham S
- Abstract
Neurons have elaborate structures that determine their connectivity and functions. Changes in neuronal structure accompany learning and memory formation and are hallmarks of neurological disease. Here we show that glia monitor dendrite structure and respond to dendrite perturbation. In C. elegans mutants with defective sensory-organ dendrite cilia, adjacent glia accumulate extracellular matrix-laden vesicles, secrete excess matrix around cilia, alter gene expression, and change their secreted protein repertoire. Inducible cilia disruption reveals that this response is acute. DGS-1, a 7-transmembrane domain neuronal protein, and FIG-1, a multifunctional thrombospondin-domain glial protein, are required for glial detection of cilia integrity, and exhibit mutually-dependent localization to and around cilia, respectively. While inhibiting glial secretion disrupts dendritic cilia properties, hyperactivating the glial response protects against dendrite damage. Our studies uncover a homeostatic protective dendrite-glia interaction and suggest that similar signaling occurs at other sensory structures and at synapses, which resemble sensory organs in architecture and molecules.
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- 2023
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36. Generating Realistic and Representative Trajectories with Mobility Behavior Clustering.
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Lin H, Shaham S, Chiang YY, and Shahabi C
- Abstract
Accessing realistic human movements (aka trajectories) is essential for many application domains, such as urban planning, transportation, and public health. However, due to privacy and commercial concerns, real-world trajectories are not readily available, giving rise to an important research area of generating synthetic but realistic trajectories. Inspired by the success of deep neural networks (DNN), data-driven methods learn the underlying human decision-making mechanisms and generate synthetic trajectories by directly fitting real-world data. However, these DNN-based approaches do not exploit people's moving behaviors (e.g., work commute, shopping purpose), significantly influencing human decisions during the generation process. This paper proposes MBP-GAIL, a novel framework based on generative adversarial imitation learning that synthesizes realistic trajectories that preserve moving behavior patterns in real data. MBP-GAIL models temporal dependencies by Recurrent Neural Networks (RNN) and combines the stochastic constraints from moving behavior patterns and spatial constraints in the learning process. Through comprehensive experiments, we demonstrate that MBP-GAIL outperforms state-of-the-art methods and can better support decision making in trajectory simulations.
- Published
- 2023
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37. Optimal fluid volume for detecting malignancy in serous effusions: a single institution experience.
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Beg S, Zanettini C, Queiroz L, Marchionni L, Alperstein SA, and Siddiqui MT
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- Humans, Exudates and Transudates, Peritoneum pathology, Cytodiagnosis, Neoplasms diagnosis, Neoplasms pathology
- Abstract
Introduction: Detection of malignant cells in serous fluids is an indicator of advanced stage of malignancy and is critical in clinical management decisions and prompt treatment initiation. The minimum volume which is ideal for detecting malignancy in serous fluid is not well established. In this study, we aim to identify optimal volume that will be ideal for adequate cytopathological diagnosis., Materials and Methods: A total of 1597 samples of serous fluids from 1134 patients were included in the study. Samples were diagnosed based on International System for Reporting Serous Fluid Cytopathology (ISRSFC). Clinicopathologic results from different diagnostic groups were compared and statistically analyzed., Results: Pleural fluids comprised 890 (55.7%) specimens, followed by 456 (28.6%) peritoneal, 128 (8%) ascites, and 123 (7.7%) pericardial fluid specimens. The majority were negative for malignancy (1138, 71.3%), followed by malignant (376, 23.5%), atypical (59, 3.7%), and suspicious for malignancy (24, 1.5%). Malignancy was identified in sample with volumes from 5 mL to 5000 mL. Rate of detection of malignant cells increased significantly with higher sample volumes. For malignancy detection the optimal volume for overall serous fluid is 70 mL. Pericardial fluid is an exception, with lower mean volume and significantly lower proportion of cases with malignant diagnosis., Conclusions: Our study indicates that higher fluid volumes have a higher rate of malignancy detection and a low false-negative rate. We recommend a minimum of 70 mL of serous fluid for optimal cytopathologic examination and malignancy detection. Pericardial fluid is an exception, with lower mean volume and thus lower requirement., (Copyright © 2023 American Society of Cytopathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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38. Nucleus-independent transgenerational small RNA inheritance in Caenorhabditis elegans .
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Rieger I, Weintraub G, Lev I, Goldstein K, Bar-Zvi D, Anava S, Gingold H, Shaham S, and Rechavi O
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- Animals, RNA, Small Interfering genetics, RNA Interference, Gene Silencing, RNA, Double-Stranded genetics, Caenorhabditis elegans genetics, Caenorhabditis elegans metabolism, Caenorhabditis elegans Proteins genetics
- Abstract
In Caenorhabditis elegans worms, epigenetic information transmits transgenerationally. Still, it is unknown whether the effects transfer to the next generation inside or outside of the nucleus. Here, we use the tractability of gene-specific double-stranded RNA-induced silencing to demonstrate that RNA interference can be inherited independently of any nuclear factors via mothers that are genetically engineered to transmit only their ooplasm but not the oocytes' nuclei to the next generation. We characterize the mechanisms and, using RNA sequencing, chimeric worms, and sequence polymorphism between different isolates, identify endogenous small RNAs which, similarly to exogenous siRNAs, are inherited in a nucleus-independent manner. From a historical perspective, these results might be regarded as partial vindication of discredited cytoplasmic inheritance theories from the 19th century, such as Darwin's "pangenesis" theory.
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- 2023
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39. LET-381/FoxF and UNC-30/Pitx2 control the development of C. elegans mesodermal glia that regulate motor behavior.
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Stefanakis N, Jiang J, Liang Y, and Shaham S
- Abstract
While most CNS glia arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which ensheath the brain neuropil and separate it from the circulatory-system cavity. Transcriptome analysis suggests GLR glia merge astrocytic and endothelial characteristics relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naïve cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and induces salt hypersensitivity, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neurons, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
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- 2023
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40. Shai Shaham.
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Shaham S
- Subjects
- Humans, Animals, Neurons, Universities, Caenorhabditis elegans, Neuroglia
- Abstract
Interview with Shai Shaham, who studies glia-neuron interactions in C. elegans at The Rockefeller University., Competing Interests: Declaration of interests The author declares no competing interests., (Copyright © 2023.)
- Published
- 2023
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41. Analysis of a pre-2017 follicular variant papillary thyroid carcinoma cohort reclassified as noninvasive follicular thyroid neoplasm with papillary-like features (NIFTP): an 11-year retrospective single institution experience.
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Beg S, Khan SI, Cui I, Scognamiglio T, and Rao R
- Subjects
- Humans, Proto-Oncogene Proteins B-raf genetics, Retrospective Studies, Adenocarcinoma, Follicular classification, Adenocarcinoma, Follicular diagnostic imaging, Adenocarcinoma, Follicular genetics, Adenocarcinoma, Follicular surgery, Thyroid Cancer, Papillary classification, Thyroid Cancer, Papillary diagnosis, Thyroid Cancer, Papillary genetics, Thyroid Cancer, Papillary surgery, Thyroid Neoplasms classification, Thyroid Neoplasms diagnostic imaging, Thyroid Neoplasms genetics, Thyroid Neoplasms surgery
- Abstract
Introduction: Noninvasive follicular thyroid neoplasm with papillary-like features (NIFTP), represents a distinct class of thyroid neoplasms with very low risk of adverse outcome and a set of strict histologic criteria. Introduction of NIFTP as a non-cancer has had an appreciable decrease in risk of malignancy and body of literature on this entity continues to grow. In this study, we reviewed clinical, fine-needle aspiration cytology (FNAC), imaging, and molecular findings of histologically proven NIFTPs at our institution., Materials and Methods: Thyroid resections during an 11-year period, with histologic diagnosis of follicular variant of papillary thyroid carcinoma (FVPTC), were retrospectively reviewed to identify NIFTP. Ultrasonographic appearance, FNA findings, and molecular findings were also reviewed., Results: Of 244 cases of FVPTC identified, 74 (30%) cases were reclassified as NIFTP. Mean tumor size was 2.5 cm. Of 33 patients with lymph node dissection, none had lymph node metastases. On imaging, 36 NIFTP (49%) showed vascularity, 25 (33%) were isoechoic to hypoechoic, there were calcifications in 14 cases (19%), and 7 cases (9%) showed a hypoechoic rim. Bethesda III/IV was the most common interpretation rendered on FNAC (31%). Seven cases had NRAS mutations and 1 case had BRAF V600E mutation. The remaining cases were either negative for BRAF V600E or had no identifiable molecular alterations., Conclusions: A significant percentage of tumors previously diagnosed as FVPTC were reclassified as NIFTP. This tumor cannot be reliably diagnosed preoperatively on FNAC, shows no characteristic features on ultrasound and has low suspicion of malignancy. BRAF V600E mutations are infrequent in NIFTP., (Copyright © 2022 American Society of Cytopathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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42. Models and Mechanisms for Spatial Data Fairness.
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Shaham S, Ghinita G, and Shahabi C
- Abstract
Fairness in data-driven decision-making studies scenarios where individuals from certain population segments may be unfairly treated when being considered for loan or job applications, access to public resources, or other types of services. In location-based applications, decisions are based on individual whereabouts, which often correlate with sensitive attributes such as race, income, and education. While fairness has received significant attention recently, e.g., in machine learning, there is little focus on achieving fairness when dealing with location data. Due to their characteristics and specific type of processing algorithms, location data pose important fairness challenges. We introduce the concept of spatial data fairness to address the specific challenges of location data and spatial queries. We devise a novel building block to achieve fairness in the form of fair polynomials . Next, we propose two mechanisms based on fair polynomials that achieve individual spatial fairness, corresponding to two common location-based decision-making types: distance-based and zone-based . Extensive experimental results on real data show that the proposed mechanisms achieve spatial fairness without sacrificing utility.
- Published
- 2022
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- View/download PDF
43. Impact of ambient air pollution on outdoor employees' performance: Mediating role of anxiety.
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Bari MW, Saleem S, Bashir M, and Ahmad B
- Abstract
This paper aims to examine the direct and indirect impact of ambient air pollution (AAP) on employees' performance. This study has used cross sectional survey design to collect the data from the outdoor employees of the pharmaceutical industry of Pakistan. The data were collected in time lags from 299. Partial least squares- structural equation modeling (PLS-SEM) approach was applied to analyze the data. The results show that AAP has a significant negative impact on the employees' performance, and anxiety partially mediates the association between AAP and employees' performance. This study reveals that AAP brings anxiety among outdoor employees, which in turn decreases their working performance. The implications, limitations, and future research directions are presented in the last section of this study., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bari, Saleem, Bashir and Ahmad.)
- Published
- 2022
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44. A developmental pathway for epithelial-to-motoneuron transformation in C. elegans.
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Rashid A, Tevlin M, Lu Y, and Shaham S
- Subjects
- Animals, Cell Differentiation, Motor Neurons metabolism, Nerve Growth Factors metabolism, Nerve Tissue Proteins metabolism, Transcription Factors metabolism, Caenorhabditis elegans metabolism, Caenorhabditis elegans Proteins metabolism
- Abstract
Motoneurons and motoneuron-like pancreatic β cells arise from radial glia and ductal cells, respectively, both tube-lining progenitors that share molecular regulators. To uncover programs underlying motoneuron formation, we studied a similar, cell-division-independent transformation of the C. elegans tube-lining Y cell into the PDA motoneuron. We find that lin-12/Notch acts through ngn-1/Ngn and its regulator hlh-16/Olig to control transformation timing. lin-12 loss blocks transformation, while lin-12(gf) promotes precocious PDA formation. Early basal expression of ngn-1/Ngn and hlh-16/Olig depends on sem-4/Sall and egl-5/Hox. Later, coincident with Y cell morphological changes, ngn-1/Ngn expression is upregulated in a sem-4/Sall and egl-5/Hox-dependent but hlh-16/Olig-independent manner. Subsequently, Y cell retrograde extension forms an anchored process priming PDA axon extension. Extension requires ngn-1-dependent expression of the cytoskeleton organizers UNC-119, UNC-44/ANK, and UNC-33/CRMP, which also activate PDA terminal-gene expression. Our findings uncover cell-division-independent regulatory events leading to motoneuron generation, suggesting a conserved pathway for epithelial-to-motoneuron/motoneuron-like cell differentiation., Competing Interests: Declaration of interests S.S. is a member of the Cell Reports advisory board., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
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45. Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer.
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Raman R, Villefranc JA, Ullmann TM, Thiesmeyer J, Anelli V, Yao J, Hurley JR, Pauli C, Bareja R, Wha Eng K, Dorsaint P, Wilkes DC, Beg S, Kudman S, Shaw R, Churchill M, Ahmed A, Keefer L, Misner I, Nichol D, Gumpeni N, Scognamiglio T, Rubin MA, Grandori C, Solomon JP, Song W, Mosquera JM, Dephoure N, Sboner A, Elemento O, and Houvras Y
- Subjects
- Animals, Cytoskeletal Proteins genetics, Humans, Proteomics, Proto-Oncogene Proteins c-ret genetics, Receptors, Fibroblast Growth Factor, Lung Neoplasms pathology, Thyroid Neoplasms drug therapy, Thyroid Neoplasms genetics
- Abstract
Genetic alterations in RET lead to activation of ERK and AKT signaling and are associated with hereditary and sporadic thyroid cancer and lung cancer. Highly selective RET inhibitors have recently entered clinical use after demonstrating efficacy in treating patients with diverse tumor types harboring RET gene rearrangements or activating mutations. In order to understand resistance mechanisms arising after treatment with RET inhibitors, we performed a comprehensive molecular and genomic analysis of a patient with RET-rearranged thyroid cancer. Using a combination of drug screening and proteomic and biochemical profiling, we identified an adaptive resistance to RET inhibitors that reactivates ERK signaling within hours of drug exposure. We found that activation of FGFR signaling is a mechanism of adaptive resistance to RET inhibitors that activates ERK signaling. Combined inhibition of FGFR and RET prevented the development of adaptive resistance to RET inhibitors, reduced cell viability, and decreased tumor growth in cellular and animal models of CCDC6-RET-rearranged thyroid cancer., (© 2022 Raman et al.)
- Published
- 2022
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46. Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets.
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Tang F, Xu D, Wang S, Wong CK, Martinez-Fundichely A, Lee CJ, Cohen S, Park J, Hill CE, Eng K, Bareja R, Han T, Liu EM, Palladino A, Di W, Gao D, Abida W, Beg S, Puca L, Meneses M, de Stanchina E, Berger MF, Gopalan A, Dow LE, Mosquera JM, Beltran H, Sternberg CN, Chi P, Scher HI, Sboner A, Chen Y, and Khurana E
- Subjects
- Cell Line, Tumor, Gene Expression Profiling, Humans, Male, Neoplastic Stem Cells classification, Neoplastic Stem Cells metabolism, Organoids metabolism, Organoids pathology, Receptors, Androgen genetics, Receptors, Androgen metabolism, Transcription Factor AP-1 genetics, Transcription Factor AP-1 metabolism, Chromatin genetics, Molecular Targeted Therapy, Prostatic Neoplasms, Castration-Resistant classification, Prostatic Neoplasms, Castration-Resistant drug therapy, Prostatic Neoplasms, Castration-Resistant genetics
- Abstract
In castration-resistant prostate cancer (CRPC), the loss of androgen receptor (AR) dependence leads to clinically aggressive tumors with few therapeutic options. We used ATAC-seq (assay for transposase-accessible chromatin sequencing), RNA-seq, and DNA sequencing to investigate 22 organoids, six patient-derived xenografts, and 12 cell lines. We identified the well-characterized AR-dependent and neuroendocrine subtypes, as well as two AR-negative/low groups: a Wnt-dependent subtype, and a stem cell-like (SCL) subtype driven by activator protein-1 (AP-1) transcription factors. We used transcriptomic signatures to classify 366 patients, which showed that SCL is the second most common subtype of CRPC after AR-dependent. Our data suggest that AP-1 interacts with the YAP/TAZ and TEAD proteins to maintain subtype-specific chromatin accessibility and transcriptomic landscapes in this group. Together, this molecular classification reveals drug targets and can potentially guide therapeutic decisions.
- Published
- 2022
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47. Combining molecular testing and the Bethesda category III:VI ratio for thyroid fine-needle aspirates: A quality-assurance metric for evaluating diagnostic performance in a cytopathology laboratory.
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Gokozan HN, Dilcher TL, Alperstein SA, Qiu Y, Mostyka M, Scognamiglio T, Solomon JP, Song W, Rennert H, Beg S, Stern E, Goyal A, Siddiqui MT, and Heymann JJ
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Biopsy, Fine-Needle, Child, Female, Humans, Male, Middle Aged, Molecular Diagnostic Techniques, Mutation, Young Adult, Adenocarcinoma, Follicular diagnosis, Adenocarcinoma, Follicular genetics, Adenocarcinoma, Follicular pathology, Thyroid Neoplasms diagnosis, Thyroid Neoplasms genetics, Thyroid Neoplasms pathology, Thyroid Nodule diagnosis, Thyroid Nodule genetics, Thyroid Nodule pathology
- Abstract
Background: Molecular testing (MT) of thyroid fine-needle aspiration (FNA)-derived genetic material is commonly used to assess malignancy risk for indeterminate cases. The Bethesda System for Reporting Thyroid Cytopathology (TBS) provides limited guidance for the appropriate use of category III (atypia of undetermined significance [AUS]). The authors combined MT with cytomorphology to monitor AUS diagnoses in a cytopathology laboratory., Methods: Neoplasia-associated genetic alterations (NGAs) were determined by MT of preoperative FNA biopsies or resected malignancies and were categorized as BRAF V600E mutations, RAS-like mutations (HRAS, NRAS, or KRAS mutations or non-V600E BRAF mutations), or other mutations., Results: Among 7382 thyroid FNA biopsies, the AUS rate was 9.3% overall and ranged from 4.3% to 24.2% among 6 cytopathologists (CPs) who evaluated >150 cases. The ratio of specimens falling into TBS category III to specimens falling into category VI (malignant) (the III:VI ratio) was 2.4 overall (range, 1.1-8.1), and the ratio of specimens falling into TBS categories III and IV (follicular neoplasm or suspicious for follicular neoplasm) combined (III+IV) to specimens falling into category VI (the [III+IV]:VI ratio) was 2.9 overall (range, 1.4-9.5). MT was performed on 588 cases from 560 patients (79% women) with a median age of 56 years (range, 8-89 years). BRAF V600E mutation was the most common (76% of cases) in TBS category VI and was rare (3%) in category III. RAS-like mutations were most common in TBS categories III (13%), IV (25%), and V (suspicious for malignancy) (17.5%). The NGA rate in AUS cases fell between 5% and 20% for 5 of 6 CPs and did not correlate with the III:VI ratio or the (III+IV):VI ratio., Conclusions: Lack of correlation between the NGA rate and easily calculable diagnostic ratios enables the calibration of diagnostic thresholds, even for CPs who have normal metrics. Specifically, calculation of the NGA rate and the III:VI ratio may allow individual CPs to determine whether they are overcalling or undercalling cases that other CPs might otherwise recategorize., (© 2021 American Cancer Society.)
- Published
- 2022
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48. Publisher Correction: Atomistic insights into highly active reconstructed edges of monolayer 2H-WSe 2 photocatalyst.
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Qorbani M, Sabbah A, Lai YR, Kholimatussadiah S, Quadir S, Huang CY, Shown I, Huang YF, Hayashi M, Chen KH, and Chen LC
- Published
- 2022
- Full Text
- View/download PDF
49. Atomistic insights into highly active reconstructed edges of monolayer 2H-WSe 2 photocatalyst.
- Author
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Qorbani M, Sabbah A, Lai YR, Kholimatussadiah S, Quadir S, Huang CY, Shown I, Huang YF, Hayashi M, Chen KH, and Chen LC
- Abstract
Ascertaining the function of in-plane intrinsic defects and edge atoms is necessary for developing efficient low-dimensional photocatalysts. We report the wireless photocatalytic CO
2 reduction to CH4 over reconstructed edge atoms of monolayer 2H-WSe2 artificial leaves. Our first-principles calculations demonstrate that reconstructed and imperfect edge configurations enable CO2 binding to form linear and bent molecules. Experimental results show that the solar-to-fuel quantum efficiency is a reciprocal function of the flake size. It also indicates that the consumed electron rate per edge atom is two orders of magnitude larger than the in-plane intrinsic defects. Further, nanoscale redox mapping at the monolayer WSe2 -liquid interface confirms that the edge is the most preferred region for charge transfer. Our results pave the way for designing a new class of monolayer transition metal dichalcogenides with reconstructed edges as a non-precious co-catalyst for wired or wireless hydrogen evolution or CO2 reduction reactions., (© 2022. The Author(s).)- Published
- 2022
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50. RET Fusion-Positive Papillary Thyroid Cancers are Associated with a More Aggressive Phenotype.
- Author
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Ullmann TM, Thiesmeyer JW, Lee YJ, Beg S, Mosquera JM, Elemento O, Fahey TJ 3rd, Scognamiglio T, and Houvras Y
- Abstract
Background: It is unclear if different genetic drivers in papillary thyroid cancer (PTC) confer different phenotypic tumor behavior leading to more aggressive disease. We hypothesized that RET-driven cancers are more aggressive., Patients and Methods: We reviewed records of consecutive patients treated for newly diagnosed PTC at this single institution from 2015 to 2016. Tumor samples from these patients were genotyped to identify RET-translocated, BRAF
V600E mutant, and HRAS, KRAS, and NRAS mutant tumors. Patient demographic, clinicopathologic, and outcomes data were compared to identify genotype-specific patterns of disease., Results: Of the 327 patients who underwent initial surgery for PTC during the study period, 192 (58.7%) had BRAFV600E mutant tumors (BRAF), 14 (4.3%) had RET-rearranged tumors (RET), 46 (14.1%) had RAS mutant tumors (RAS), and 75 (22.9%) had BRAF, RET, and RAS wildtype tumors. RET-driven tumors were more likely to have extrathyroidal extension (50.0% versus 27.0% for BRAF and 2.2% for RAS, P < 0.001), multifocal disease (85.7% versus 60.3%, and 44.4%, respectively, P = 0.017), and distant metastases (14.3% versus 1.1%, and 0%, respectively, P = 0.019). RET and BRAF patients also had worse disease-free survival than RAS patients (Kaplan-Meier log rank, P = 0.027)., Conclusions: Patients with RET-driven PTCs had higher rates of extrathyroidal extension, multifocal disease, and distant metastases than patients whose tumors had BRAFV600E or RAS mutations. Patients with RET-rearranged tumors had similar disease-free survival to patients with BRAFV600E mutant tumors. RET rearrangement may confer an aggressive phenotype in PTC., (© 2022. Society of Surgical Oncology.)- Published
- 2022
- Full Text
- View/download PDF
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