Following our identification of adult Drosophila intestinal stem cells (ISCs), we used this system to characterize genes and pathways important for gut homeostasis and in particular, to analyze crosstalk among signaling pathways. Fun fact: Michelle is a huge Stephen King fan. The EMBO journal 20 (20), 5759-5768, 2001. Understanding how circadian rhythms are generated, maintained, and adapted to changing conditions is key, as several diseases such as cancer and depression are associated with misalignment of the circadian clock with the environment. Towards the end of her time as a PhD candidate, she became exceptionally interested in the intersect between cancer metabolism and oncogenic signaling, particularly the metabolic switches that support and drive adaptive resistance to cancer therapy. In the Bandopadhayay Lab, Maddie is working on efforts to identify resistance mechanisms in pediatric brain tumors. We are now using this tool to establish sensors of each signaling pathway involved in gut homeostasis, and will use these reagents to examine pathway crosstalk. He can also be found doing crossword puzzles at odd hours. * Corresponding authors. Adam grew up in Ethiopia and moved to Bremen, Germany where he received his B.Sc and M.Sci in Biochemistry and Cell Biology from Jacobs University which was his very first exposure to the exciting field of epigenetics. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. Moreover, all of these approachesCRISPR, CRISPRa, and CRISPRialso take advantage of the pooled screen format, which provides complementary cell biological readouts as compared with arrayed format screening. Rybak-Wolf A., Stottmeister C., Glazar P., Jens M., Pino N., Giusti S., Hanan M., Behm M., Bartok O., Ashwal R., Herzog M., Schreyer L., Papavasileiou P., Ivanov A., Ohman M., Refojo D., Kadener S. and Rajewsky N. Circular RNAs in the mammalian brain are highly abundant, conserved, dynamically expressed, and regulated by ADAR1. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. tested regenerative limb interventions to restore form and function to the amputated hindlimbs in adult African clawed frogs. In addition and most importantly, genome-wide libraries of transgenic RNAi lines are available that allow knockdown of any. Simchovitz A, Hanan M, Yayon N, Lee S, Bennett ER, Greenberg DS, Kadener S, Soreq H. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. Fun fact: Dana is a huge Philadelphia sports fan and is mentally preparing to be the only Eagles fan in Boston. Two of these RNAs act as miRNA sponges, but no function is known for the thousands of other circRNAs found in species across the animal kingdom. Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. in Physics. Selected for Faculty of 1000 (Factor 3 Recommended). Wnt/Wingless, Insulin Receptor, EGFR, INR, JNK, JAK/STAT, Notch, and Hippo pathways play roles in the division and differentiation of ISCs in the context of homeostasis and/or injury. Second, we identified 53 transcription factors, specifically expressed or enriched in the ISCs, and are characterizing how they cooperate to integrate signal inputs. Simchovitz A, Hanan M, Niederhoffer N, Madrer N, Yayon N, Bennett ER, Greenberg DS, Kadener S, Soreq H. Thermosensitive alternative splicing senses and mediates temperature adaptation in, Reconfiguration of a Multi-oscillator Network by Light in the. DIOPT has been well received by the scientific community and has been integrated into FlyBase, PomBase, MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) and AGR (Alliance of Genome Resources); integrates annotation information for orthologs of multiple species in unified interfaces; allows scientists to mine the validation and phenotype data for. Exonic circular RNAs (circRNAs) are mostly generated from exons of protein-coding genes and, in many cases, are more abundant that the linear . and Torres H.N. Nov, 2017. Bartok O., Teesalu M., Pandey V., Hanan M., Poukkula M., Havula E., Moussaieff A., Vodala S., Nahmias Y., Kadener S.* and Hietakangas V.* Cabut-dependent repressive branch of the sugar sensing transcriptional network regulates glyceroneogenesis. For example, we identified a number of ion channels that either directly or indirectly regulate stem cell proliferation. Fun fact: Maddie is a multimedia artist and during quarantine, Maddie collaged all of the wooden furniture in her apartment. Tattikota SG., Rathjen T., Hausser J., Khedkar A., Kabra UD., Pandey V., Sury M., Wessels HH., Mollet IG., Eliasson L., Selbach M., Zinzen RP., Zavolan M., Kadener S, Tschp MH, Jastroch M, Friedlnder MR., Poy MN. While at UMass Amherst, Marissa worked in the Facette Lab studyong asymmetric cell division in maize andArabidopsis thaliana. Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Last but not least, we recently showed that some circRNAs are translated. Additionally, they study the role of circular RNAs (circRNAs) at the molecular and neural levels as well as the mechanisms underlying circadian clocks. At the lab, I research the role of temperature in the synchronization of the Drosophila circadian clock. For example, little is understood about how the simultaneous growth and differentiation of different tissues and organs are coordinated and how the development of different cell types and tissues is integrated within an organ. One of these translated circRNAs is circMbl. Bartok O., Kyriacou C., Levine J., Sehgal A. and Kadener S. Adaptation of molecular circadian clockwork to environmental changes: a role for alternative splicing and miRNAs. Mouse-olfactory bulb, brain stem, and thalamus-Mock. Sebastian Kadener E-mail (s) skadener@gmail.com Organization name The Hebrew University of Jerusalem Street address SIlberman Institute of Life Sciences, Edmund J. Safra Campus City Jerusalem ZIP/Postal code 91904 Country Israel Platform ID GPL20301 Series (1) GSE154616 Mammalian circRNA Atlas Relations BioSample SAMN15566042 SRA SRX8753063 Brown S.A., Ripperger J., Kadener S., Fleury-Olela F., Vilbois F., Rosbash M. and Schibler U. Fun fact: Anna is a gardening nerd on hold, as she does not have a garden in Boston. . Jess hopes to pursue a career as a physician-scientist, taking care of children with brain tumors and other solid tumors and working hard to improve treatments for her patients. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. Biol., The University of Buenos Aires, Buenos Aires, Argentina, Ph.D., The University of Buenos Aires, Buenos Aires, Argentina, Undergraduate Departmental Representatives, Heller School for Social Policy and Management, Rabb School: Graduate Professional Studies, Graduate Professional Studies (Online Programs). These tools, which are available viaDRSC/TRiP Functional Genomics Resources, include: DIOPTDIOPT-DISTGene2FunctionGLADBioLitMineUP-TORR, RSVPSnapDragonFlyPrimerBankFind CRISPRSNP-CRISPRDGET. Ultimately, the knowledge gained from these studies will generate testable hypotheses related to disease states such as diabetes, aging, and cancer, i.e., how biological processes observed in one tissue/organ (e.g., decreased cellular metabolism, mitochondrial dysfunction) may influence processes observed in a different tissue/organ. He completed his internship and pediatric residency training at Childrens National Medical Center, before immersing himself in pediatric hematology/oncology training followed by subspecialty Pediatric Neuro-Oncology training at Childrens Hospital Los Angeles/University of Southern California. There, she studied the oncogenic role of certain signaling molecules in the Hedgehog signaling pathway, and became extremely interested in advancing cancer therapy research. Understanding how circadian rhythms are generated, maintained, and adapted to changing conditions is key, as several diseases such as cancer and depression are associated with misalignment of the circadian clock with the environment. For example, little is understood about how the simultaneous growth and differentiation of different tissues and organs are coordinated and how the development of different cell types and tissues is integrated within an organ. Riley was born and raised in Seoul, South Korea, and moved to the U.S when she was 11 years old. She is also working to evaluate the role of altered metabolic signaling to driving formation of pediatric tumors such as Diffuse Intrinsic Pontine Gliomas. Further, we have established new cell lines and methods for screening (primary muscle and neuronal cells, fluorescent protein-tagged cell lines, CRISPR mutant cell lines), and experimental and bioinformatics approaches methods for addressing off-target issues and other sources of false discovery. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. In addition to genetic screens, we are also using both transcriptomics and proteomics approaches to identify factors and understand their systemic effects. Associate Professor, Brandeis University. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. 178: We are using CRISPR to mutate or engineer cell lines that can be used for screening, and have developed efficient protocols in Drosophila cells, which are particularly challenging as they are polyploid and difficult to grow following single-cell isolation. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. What are the differences at the molecular level between the individual circadian neurons? I am a junior who is majoring in biochemistry. . General Biology Laboratory [ sn wi ] T 12:20 PM-5:00 PM Shapiro Science: 010 T,F 8:00 AM-9:20 AM . With this advance, we hope to enable the mosquito community to easily perform genome-wide loss- or gain-of-function screens in cells, for example to discover entry and infection mechanisms of pathogens and drugs, as well as to aid in the functional annotation of mosquito genomes. Dana joined the Bandopadhayay Lab in 2021 where is she working to apply single-cell methods to evaluate the heterogeneity of pediatric gliomas, and to understand spatial associations. Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays. 2012- Lab manager at Ami Citri laboratory at the Hebrew University of Jerusalem 2010- 2012 Postdoc at the Hebrew University of Jerusalem at Sebastian Kadener Lab; research topic-studying neodegenerative diseases using fruit flies as a model 2000-2003 Research assistant at QBI company; I was part of research in English and Anthropology from Washington University in St. Louis (22). Chen TC, Tallo-Parra M, Cao QM, Kadener S, Bttcher R, Prez-Vilar G, Boonchuen P, Somboonwiwat K, Dez J, Sarnow P. A lncRNA survey finds increases in neuroprotective LINC-PINT in Parkinson's disease substantia nigra. Metazoan MicroRNAs (2018) David P. Bartel CELL Non-canonical functions of microRNA pathway enzymes - Drosha, DGCR8, Dicer and Ago proteins An early ancestor in the evolution of splicing: a. Nogues G., Kadener S., Cramer P., de la Mata M., Fededa J.P., Blaustein M., Srebrow A. and Kornblihtt A.R. Working under the mentorship of Dr. Beth Lawlor, April focused on understanding how hijacking of normal developmental pathways lead to heterogeneity and cell state plasticity in Ewing sarcoma. Rosenstiel332781-736-4915skadener@brandeis.edu, Neuroscience Program Volen 206 Mailstop 013 Brandeis University 415 South Street Waltham, MA 02453 781-736-2352neuroscience@brandeis.edu. Community support Reagent. We previously developed a recombination-mediated cassette exchange (RMCE) system that enables pooled CRISPR screening in Drosophila cells, as well as bioinformatics tools for identifying sgRNA designs for mosquitos and mosquito cell lines. One of the key reagents to understand protein expression and function are antibodies. Now the stage is set for the most exciting questions, which we are currently working in the lab, by combining molecular, computational and RNA biology with advances techniques in genetics and neurosciences. . 178: Thisrobustnessis the result of multiple layers of regulation that extend beyond the single-cell level. 502. He plans to continue his career as a physician-scientist in pediatric oncology. Fun fact: Like many Swedish people, Eric has completed Vasaloppet, a 60-mile cross-country skiing race (twice!). Aaron received his medical degree from Thomas Jefferson University in 2011. We showed that their translation is mediated by IRES-like sequences, is enhanced in response to starvation and happens in association with membranes and in synapses. Cs. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. During her undergraduate studies, she studied the role of the soluble adenyl cyclase (sAC) pathway in pH homeostasis in Dr. Katie Barotts lab. Although Celiac disease put a damper on her plans to be a foodie, Dana loves to eat and is always on the hunt for new gluten-free restaurants. How do circRNAs work at the molecular level? Rabin A, Zaffagni M, Ashwal-Fluss R, Patop IL, Jajoo A, Shenzis S, Carmel L, Kadener S. Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. Strikingly, these phenotypes are reminiscent of the pathophysiology of cystic fibrosis (CF), as in CF the non-functional CF transmembrane conductance regulator (CFTR) increases ENaC activity resulting in chronic dehydration of the intraluminal surface liquid in organs such as kidney, colon, lung and sweat glands. 1 / 3 Looking for Postdoctoral researchers Mezan S., Feuz JD, Deplancke B. and Kadener S. PDF signaling is an integral part of the. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. Fun fact: Adams passions expand beyond the lab and include weightlifting, hot yoga, singing acappella, heading to the ballpark for a game, and visiting craft breweries. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. Jens received his BS in Molecular Medicine from the University of Tubingen Germany in 2021, where he studied synthetic lethal interactors of mTOR inhibition in glioblastoma in the labs of Prof. Ghazaleh Tabatabai and Dr. Daniel Merk. CRIMICs allow in particular easy production of a number of derivative fly stocks, such as with Gal4 or GFP, that can be used to document gene expression and for proteomic studies using GFP nanobodies. Fun fact: One of the first things Jens did when he arrived in Boston was to buy a bike. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. Avigayel Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Ines Lucia Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel and Sebastian Kadener (2021). A slow RNA polymerase II affects alternative splicing in vivo. Eric received his medical degree in 2016 and defended his PhD thesis in 2018. Bartok O., Teesalu M., Pandey V., Hanan M., Poukkula M., Havula E., Moussaieff A., Vodala S., Nahmias Y., Kadener S.* and Hietakangas V.* Cabut-dependent repressive branch of the sugar sensing transcriptional network regulates glyceroneogenesis. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. Gut tumors can be induced in adult flies by overexpressing an active form of the transcriptional co-activator yorkie/YAP using the intestinal stem cell driver escargot-GAL4. Site developed by Health Communication Core, April received her BS in Cellular and Molecular Biology from Beloit College in 2017, where she worked in the lab of Dr. Amy Briggs studying the role of. Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. Further, fat-derived adipokines leptin and adiponectin serve as inter-organ secreted metabolic regulators. These two short peptide tags and their nanobodies can be used for labeling and manipulating proteins. Organ-to-organ communication is critical to living systems and plays major roles in homeostasis. Genome-Wide Analysis of Light- and Temperature-Entrained . What is their mechanisms of action? What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? Pathways that are misregulated in animals that develop organ wasting in the context of these various tumor models are identified using a combination of transcriptomics, e.g. Eric joined the Bandopadhayay Lab in 2020 where he is working to characterize driver mutations found in pediatric brain tumors and developing new approaches to treat these children with targeted therapies. J. Biol. *, Bartok O. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, we developed tools based on. This dual reporter can be used in either fixed or live tissues to monitor spatio-temporal activity of signaling pathways at an unprecedented resolution. She then moved from the Bay Area to Boston where she completed her Pediatrics residency at the Boston Combined Residency Program at Boston Childrens Hospital and Boston Medical Center in 2018, before joining the Dana-Farber/Boston Childrens Cancer and Blood Disorders Center as a Pediatric Hematology/Oncology/Stem Cell Transplant Fellow. Moreover, in 2019, we were funded to function as the Drosophila Research and Screening Center-Biomedical Technology Research Resource (DRSC-BTRR), which focuses on development of new screening and other technologies. In response to tissue damage reagents such as paraquat and bleomycin, TrpA1 mediates calcium influx, which in turn activates Ras/MAPK pathway and induces stem cell proliferation. I am studying potential applications of the CRISPR/Cas13 system. My diverse. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? He then pursued a PhD in chemistry at Caltech (17) under the mentorship of Dr. Jackie Barton. More recently, we optimized Cas9 to perform either tissue-specific loss-of-function or gain-of-function screens in vivo, and have generated >5000 transgenic gRNA lines. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. * Corresponding authors. Acquiring answers to these fascinating questions requires a deep understanding of the mechanisms by which cells integrate signals received from their inner selves, neighboring cells, other organs and the environment. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. She immediately transitioned into a PhD program, still working with Dr. Swartling to continue her work on mouse models and medulloblastoma treatments. As a highly qualified biology researcher with a PhD in molecular biology and genetics, I bring independent and creative thinking as well as strong interpersonal skills to any team. Chikne V.*, Doniger T.*, Bartok O. Before joining the Bando Lab, John worked as a High Frequency Trader. 1, Artyomov M., Shishkin A., Kadri S., Zhu X., Gutman M., Garber M.* and Kadener S.* Defining the 5 and 3 landscape of theDrosophilatranscriptome with ExoCAGE and RNaseH-seq. Moreover, we also showed that the neural and molecular circadian systems compensate and interact with each other. Media. He is now very excited to use his skills to contribute to cancer research, specifically focusing on improving our understanding of childhood brain tumors and the development of more effective treatments. What are the differences at the molecular level between the individual circadian neurons? CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. Rosi is accepted to attend the Autumn Workshop in Structural Proteomics in Nurmes, Finland and was chosen to receive a COST scholarship. First, we developed a new method to visualize the dynamic activation of pathway activities. Our lab is interested in determining how molecular and neural circadian components regulate each other and generate a system that is both robust and plastic. Dr. Kadener studies the circadian clock -- a mechanism that controls the sleep/wake cycle -- and neurodegeneration in pre-clinical models . Adam then moved to Boston for his postdoc in the lab of Dr. Yang Shi where he grew interested in identifying epigenetic targets for pediatric brain cancers. Transcriptional feedback and definition of the circadian pacemaker in, Kadener S., Villella A., Kula E., Palm K., Pyza E., Botas J., Hall J.C. and Rosbash M. Neurotoxic protein expression reveals connections between the circadian clock and mating behavior in. Simchovitz A, Hanan M, Niederhoffer N, Madrer N, Yayon N, Bennett ER, Greenberg DS, Kadener S, Soreq H. Thermosensitive alternative splicing senses and mediates temperature adaptation in, Reconfiguration of a Multi-oscillator Network by Light in the. Fun fact:Almost all of Johns socks are Christmas themed! She lived in Oregon and Connecticut and move to Massachusetts, where she received her BA in Biochemistry from Wellesley College (22). 0. Fun fact:April does not drink coffee or tea (which perplexes Mimi) and loves milk and the whole lab likes to make fun of her for it. In college, he minored in art history and loves spending hours at art museums. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. Third, we found that the stretch activated calcium channel Piezzo regulates ISC proliferation and differentiation. Gene activation is triggered by co-expression of catalytically dead Cas9 (dCas9) fused to an activator domain. We have also generated stable nuclease-dead Cas9 activator (dCas9a) cell lines that can be used, after transfection with gRNAs, to perform overexpression screens - thus complementing loss of function screens. Nucleic Acids Research47(11): e95; 1-16 (2017). *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. Portal D., Lobo G.S., Kadener S., Prasad J., Espinosa J.M., Pereira C.A., Tang Z., Lin R.J., Manley J.L., Kornblihtt A.R., Flawia M.M. Previously, Kadener was a Professor in the Biological Chemistry department at the Hebrew University of Jerusalem. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. In this context, the most important question looking forward are: Afik S. 1, Bartok O. BOX 39.4 CHRONOPHARMACOLOGY Many drugs, toxins, and, Academic Degrees - Dartmouth Medical School, BOX 39.2 MOLECULAR MECHANISMS OF CIRCADIAN, Evolutionary mechanisms underlying the functional divergence of, Trainee Professional Development Day Session Information, Naslov projekta: Defining the role of circadian genes in behavioral, Supplementary Information - Word file (66 KB ), INTRODUCTION TO CHRONOPHARMACOLOGY - Copy, Fall 2012 Application for Associate Editors, BOX 39.1 NEURONAL CONTROL OF DROSOPHILA CIRCADIAN, Biological Rhythms - Cornell University Ergonomics Web. Stelzer Y., Bar S., Bartok O., Afik S., Ronen D., Kadener S.* and Benvenisty N.* Studying the differentiation of human parthenogenetic cells reveals novel tissue and isoform dependent imprinted transcripts. One point of focus for DRSC-BTRR efforts is establishment of CRISPR pooled screening in cell lines from mosquito vectors of infectious diseases. She also loves bagels and is always on the hunt for the best bagel. Acquiring answers to these fascinating questions requires a deep understanding of the mechanisms by which cells integrate signals received from their inner selves, neighboring cells, other organs and the environment. During his time at Dickinson, Sher worked in Dr. Michael Roberts lab, investigating gene targets for potential Acute Myeloid Leukemia therapies. We generated a dual reporter with a destabilized fast folding GFP (dsGFP) protein and a stable RFP reporter. This collection is available to the community through the Bloomington Drosophila Stock Center. In the past 50 years, studies using genetically tractable model systems have led to a detailed understanding of genetic mechanisms involved in the control of developmental events, as illustrated by our knowledge of patterning and morphogenesis. Interestingly, mechanical stress caused by overfeeding flies with 10% methylcellulose, which distorts the gut, induces ISC proliferation. PubMed ID: 31702556 The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, we developed tools based on APEX, an engineered ascorbate peroxidase derived from plants, and BioID, a mutant form of the biotin ligase BirA from E coli and demonstrated their use for in vivo studies. Levels change at synapses and whether they are modulated by neuronal activity ( ). Attend the Autumn Workshop in Structural proteomics in Nurmes, Finland and was chosen to a! 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Cell lines, in combination with RNAi, provide a robust platform for combinatorial screening for RNA II... 12:20 PM-5:00 PM Shapiro Science: 010 T, F 8:00 AM-9:20 am College. The general mechanism of the key reagents to understand protein expression and function antibodies! And manipulating proteins that circRNAs can function incisas RNA traps RNA traps Omnibus ( GEO ) is a database of... The dynamic activation of pathway activities 5759-5768, 2001 number of ion channels that directly... She immediately transitioned into a target genomic location at an unprecedented resolution move to Massachusetts, where she her... Either directly or indirectly regulate stem cell proliferation CRISPR pooled screening in cell,... Determine behavior with special emphasis on RNA metabolism Boston was to buy a bike is mentally preparing to the! Cell proliferation of alternative splicing by a transcriptional enhancer through RNA pol II elongation physician-scientist pediatric.
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