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1. The Role of TIM-1 and CD300a in Zika Virus Infection Investigated with Cell-Based Electrical Impedance

Author

Merel Oeyen, Clément J. F. Heymann, Maarten Jacquemyn, Dirk Daelemans, and Dominique Schols

Subjects
zika virus, impedance, TIM-1, CD300a, phosphatidylserine receptor, Biotechnology, TP248.13-248.65
Abstract

Orthoflaviviruses cause a major threat to global public health, and no antiviral treatment is available yet. Zika virus (ZIKV) entry, together with many other viruses, is known to be enhanced by phosphatidylserine (PS) receptors such as T-cell immunoglobulin mucin domain protein 1 (TIM-1). In this study, we demonstrate for the first time, using cell-based electrical impedance (CEI) biosensing, that ZIKV entry is also enhanced by expression of CD300a, another PS receptor. Furthermore, inhibiting CD300a in immature monocyte-derived dendritic cells partially but significantly inhibits ZIKV replication. As we have previously demonstrated that CEI is a useful tool to study Orthoflavivirus infection in real time, we now use this technology to determine how these PS receptors influence the kinetics of in vitro ZIKV infection. Results show that ZIKV entry is highly sensitive to minor changes in TIM-1 expression, both after overexpression of TIM-1 in infection-resistant HEK293T cells, as well as after partial knockout of TIM-1 in susceptible A549 cells. These results are confirmed by quantification of viral copy number and viral infectivity, demonstrating that CEI is highly suited to study and compare virus-host interactions. Overall, the results presented here demonstrate the potential of targeting this universal viral entry pathway.

Published
2024
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2. Anaerobutyricum soehngenii Reduces Hepatic Lipogenic Pathways and Increases Intestinal Gluconeogenic Gene Expression in Metabolic-Dysfunction-Associated Steatotic Liver Disease (MASLD) Mice

Author

Anne Linde Mak, Quinten J. J. Augustijn, Clément J. F. Heymann, Stefan Havik, Xanthe Verdoes, Melany Rios-Morales, Laura A. Bosmans, Joanne Verheij, Abraham S. Meijnikman, Patrick A. de Jonge, Hilde Herrema, Willem M. de Vos, Max Nieuwdorp, Aldo Grefhorst, and Adriaan G. Holleboom

Subjects
MASLD, gut microbiome, short-chain fatty acids, mice, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

Metabolic-dysfunction-associated steatotic liver disease (MASLD) is a growing health problem for which no therapy exists to date. The modulation of the gut microbiome may have treatment potential for MASLD. Here, we investigated Anaerobutyricum soehngenii, a butyrate-producing anaerobic bacterium with beneficial effects in metabolic syndrome, in a diet-induced MASLD mouse model. Male C57BL/6J mice received a Western-type high-fat diet and water with 15% fructose (WDF) to induce MASLD and were gavaged with A. soehngenii (108 or 109 colony-forming units (CFU) 3 times per week) or a placebo for 6 weeks. The A. soehngenii gavage increased the cecal butyrate concentrations. Although there was no effect on histological MASLD scores, A. soehngenii improved the glycemic response to insulin. In the liver, the WDF-associated altered expression of three genes relevant to the MASLD pathophysiology was reversed upon treatment with A. soehngenii: Lipin-1 (Lpin1), insulin-like growth factor binding protein 1 (Igfbp1) and Interleukin 1 Receptor Type 1 (Il1r1). A. soehngenii administration also increased the intestinal expression of gluconeogenesis and fructolysis genes. Although these effects did not translate into significant histological improvements in MASLD, these results provide a basis for combined gut microbial approaches to induce histological improvements in MASLD.

Published
2024
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3. Detection of tumor‐derived cell‐free DNA from colorectal cancer peritoneal metastases in plasma and peritoneal fluid

Author

Iris van't Erve, Koen P Rovers, Alexander Constantinides, Karen Bolhuis, Emma CE Wassenaar, Robin J Lurvink, Clément J Huysentruyt, Petur Snaebjornsson, Djamila Boerma, Daan van denBroek, Tineke E Buffart, Max J Lahaye, Arend GJ Aalbers, Niels FM Kok, Gerrit A Meijer, Cornelis JA Punt, Onno Kranenburg, Ignace HJT deHingh, and Remond JA Fijneman

Subjects
colorectal neoplasms, liquid biopsy, circulating tumor DNA, peritoneum, ascitic fluid, plasma, Pathology, RB1-214
Abstract

Abstract Tumor‐derived cell‐free DNA (cfDNA) is an emerging biomarker for guiding the personalized treatment of patients with metastatic colorectal cancer (CRC). While patients with CRC liver metastases (CRC‐LM) have relatively high levels of plasma cfDNA, little is known about patients with CRC peritoneal metastases (CRC‐PM). This study evaluated the presence of tumor‐derived cfDNA in plasma and peritoneal fluid (i.e. ascites or peritoneal washing) in 20 patients with isolated CRC‐PM and in the plasma of 100 patients with isolated CRC‐LM. Among tumor tissue KRAS/BRAF mutation carriers, tumor‐derived cfDNA was detected by droplet digital polymerase chain reaction (ddPCR) in plasma of 93% of CRC‐LM and 20% of CRC‐PM patients and in peritoneal fluid in all CRC‐PM patients. Mutant allele fraction (MAF) and mutant copies per ml (MTc/ml) were lower in CRC‐PM plasma than in CRC‐LM plasma (median MAF = 0.28 versus 18.9%, p

Published
2021
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4. Reclassification of Appendiceal Mucinous Neoplasms and Associated Pseudomyxoma Peritonei According to the Peritoneal Surface Oncology Group International Consensus: Clinicopathological Reflections of a Two-Center Cohort Study

Author

Rauwerdink, Paulien, Al-Toma, Dania, Wassenaar, Emma C. E., Raicu, Mihaela G., Laclé, Miangela M., Milne, Anya N., Kuijpers, Karel C., Huysentruyt, Clément J. R., Poelmann, Floris B., van Ramshorst, Bert, Elias, Sjoerd G., Kranenburg, Onno, Borel Rinkes, Inne H. M., Witkamp, Arjen J., Wiezer, Marinus J., van Grevenstein, Helma M. U., and Boerma, Djamila

Published
2024
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5. Cortical dendritic activity correlates with spindle-rich oscillations during sleep in rodents

Author

Julie Seibt, Clément J. Richard, Johanna Sigl-Glöckner, Naoya Takahashi, David I. Kaplan, Guy Doron, Denis de Limoges, Christina Bocklisch, and Matthew E. Larkum

Subjects
Science
Abstract

Different stages of sleep, marked by particular electroencephalographic (EEG) signatures, have been linked to memory consolidation, but underlying mechanisms are poorly understood. Here, the authors show that dendritic calcium synchronisation correlates with spindle-rich sleep phases.

Published
2017
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6. Salvage endoscopic resection in patients with esophageal adenocarcinoma after chemoradiotherapy

Author

Irma C. Noordzij, Wouter L. Curvers, Clément J. Huysentruyt, Grard A.P. Nieuwenhuijzen, Geert-Jan Creemers, Maurice J.C. van der Sangen, and Erik J. Schoon

Subjects
Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

Background and study aims For early esophageal adenocarcinoma, endoscopic resection is an accepted curative treatment with an excellent long-term prognosis. Case series from Japan have reported endoscopic resection of residual esophageal squamous cell carcinoma after chemoradiotherapy. This is the first report describing endoscopic resection of residual esophageal adenocarcinoma after chemoradiotherapy. Two patients with advanced esophageal adenocarcinoma had been treated with chemoradiotherapy because comorbidity precluded esophageal resection. When residual tumor was observed endoscopically, complete remission was achieved by salvage endoscopic therapy alone or in combination with argon plasma coagulation (APC). Both patients achieved long-term sustained remission and died of non-tumor-related causes.

Published
2018
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7. OSNR Monitoring for QPSK and QAM in Fiber-Optic Networks Using Machine Learning

Author

Sahu, Shakrajit, Clement, J. Christopher, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Nanda, Umakanta, editor, Tripathy, Asis Kumar, editor, Sahoo, Jyoti Prakash, editor, Sarkar, Mahasweta, editor, and Li, Kuan-Ching, editor

Published
2024
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8. Identification of constrained sequence elements across 239 primate genomes

Author

Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N. F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, and Farh, Kyle Kai-How

Published
2024
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9. Publisher Correction: Cortical dendritic activity correlates with spindle-rich oscillations during sleep in rodents

Author

Julie Seibt, Clément J. Richard, Johanna Sigl-Glöckner, Naoya Takahashi, David I. Kaplan, Guy Doron, Denis de Limoges, Christina Bocklisch, and Matthew E. Larkum

Subjects
Science
Abstract

Abstract In the originally published version of this Article, incorrect references were cited on two occasions in the Results section. Under the subheading ‘Ca2+ activity in single dendrites and somata of L5 neurons’, the final sentence of the second paragraph incorrectly cited reference 29 instead of reference 31. Under the subheading ‘Spiking of L5 cell bodies is not influenced by spindles’, the first sentence cited reference 30 instead of reference 29. These errors have now been corrected in both the PDF and HTML versions of the Article.

Published
2017
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14. Real-Time Rainfall Prediction System Using IoT and Machine Learning

Author

Sharma, Shreya Atul, Gangopadhyay, Abantee, Koushik, K. T., Sriharipriya, K. C., Clement, J. Christopher, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Arunachalam, V., editor, and Sivasankaran, K., editor

Published
2022
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21. Electronic Health Records

Author

Melton, Genevieve B., McDonald, Clement J., Tang, Paul C., Hripcsak, George, Shortliffe, Edward H., editor, Cimino, James J., editor, and Chiang, Michael F., Section Editor

Published
2021
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23. Anaerobutyricum soehngenii Reduces Hepatic Lipogenic Pathways and Increases Intestinal Gluconeogenic Gene Expression in Metabolic-Dysfunction-Associated Steatotic Liver Disease (MASLD) Mice

Author

Mak, Anne Linde, primary, Augustijn, Quinten J. J., additional, Heymann, Clément J. F., additional, Havik, Stefan, additional, Verdoes, Xanthe, additional, Rios-Morales, Melany, additional, Bosmans, Laura A., additional, Verheij, Joanne, additional, Meijnikman, Abraham S., additional, de Jonge, Patrick A., additional, Herrema, Hilde, additional, de Vos, Willem M., additional, Nieuwdorp, Max, additional, Grefhorst, Aldo, additional, and Holleboom, Adriaan G., additional

Published
2024
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27. Pressurized Intraperitoneal Aerosol Chemotherapy (Oxaliplatin) for Unresectable Colorectal Peritoneal Metastases: A Multicenter, Single-Arm, Phase II Trial (CRC-PIPAC)

Author

Rovers, Koen P., Wassenaar, Emma C. E., Lurvink, Robin J., Creemers, Geert-Jan M., Burger, Jacobus W. A., Los, Maartje, Huysentruyt, Clément J. R., van Lijnschoten, Gesina, Nederend, Joost, Lahaye, Max J., Deenen, Maarten J., Wiezer, Marinus J., Nienhuijs, Simon W., Boerma, Djamila, and de Hingh, Ignace H. J. T.

Published
2021
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28. Identification of constrained sequence elements across 239 primate genomes

Author

Natural Environment Research Council (UK), UK Research and Innovation, National Human Genome Research Institute (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, Ministry of Science and Technology of Vietnam, Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Wenner-Gren Foundation, Leakey Foundation, National Science Foundation (US), National Geographic Society, National Institute on Aging (US), Swedish Research Council, National Research Foundation Singapore, European Research Council, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Farh, Kyle Kai-How, Natural Environment Research Council (UK), UK Research and Innovation, National Human Genome Research Institute (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, Ministry of Science and Technology of Vietnam, Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Wenner-Gren Foundation, Leakey Foundation, National Science Foundation (US), National Geographic Society, National Institute on Aging (US), Swedish Research Council, National Research Foundation Singapore, European Research Council, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marqués-Bonet, Tomàs, and Farh, Kyle Kai-How

Abstract

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Published
2024

29. Identification of constrained sequence elements across 239 primate genomes

Author

Kuderna, Lukas F.K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, Farh, Kyle Kai How, Kuderna, Lukas F.K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, and Farh, Kyle Kai How

Abstract

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals., Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3–9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Published
2024

30. A CubeSat for Calibrating Ground-Based and Sub-Orbital Millimeter-Wave Polarimeters (CalSat)

Author

Johnson, Bradley R., Vourch, Clement J., Drysdale, Timothy D., Kalman, Andrew, Fujikawa, Steve, Keating, Brian, and Kaufman, Jon

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

We describe a low-cost, open-access, CubeSat-based calibration instrument that is designed to support ground-based and sub-orbital experiments searching for various polarization signals in the cosmic microwave background (CMB). All modern CMB polarization experiments require a robust calibration program that will allow the effects of instrument-induced signals to be mitigated during data analysis. A bright, compact, and linearly polarized astrophysical source with polarization properties known to adequate precision does not exist. Therefore, we designed a space-based millimeter-wave calibration instrument, called CalSat, to serve as an open-access calibrator, and this paper describes the results of our design study. The calibration source on board CalSat is composed of five "tones" with one each at 47.1, 80.0, 140, 249 and 309 GHz. The five tones we chose are well matched to (i) the observation windows in the atmospheric transmittance spectra, (ii) the spectral bands commonly used in polarimeters by the CMB community, and (iii) The Amateur Satellite Service bands in the Table of Frequency Allocations used by the Federal Communications Commission. CalSat would be placed in a polar orbit allowing visibility from observatories in the Northern Hemisphere, such as Mauna Kea in Hawaii and Summit Station in Greenland, and the Southern Hemisphere, such as the Atacama Desert in Chile and the South Pole. CalSat also would be observable by balloon-borne instruments launched from a range of locations around the world. This global visibility makes CalSat the only source that can be observed by all terrestrial and sub-orbital observatories, thereby providing a universal standard that permits comparison between experiments using appreciably different measurement approaches.

Published
2015
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31. The Role of TIM-1 and CD300a in Zika Virus Infection Investigated with Cell-Based Electrical Impedance.

Author

Oeyen, Merel, Heymann, Clément J. F., Jacquemyn, Maarten, Daelemans, Dirk, and Schols, Dominique

Subjects
HEPATITIS A virus cellular receptors, ZIKA virus infections, ELECTRIC impedance, ZIKA virus, IMMUNOGLOBULIN receptors
Abstract

Orthoflaviviruses cause a major threat to global public health, and no antiviral treatment is available yet. Zika virus (ZIKV) entry, together with many other viruses, is known to be enhanced by phosphatidylserine (PS) receptors such as T-cell immunoglobulin mucin domain protein 1 (TIM-1). In this study, we demonstrate for the first time, using cell-based electrical impedance (CEI) biosensing, that ZIKV entry is also enhanced by expression of CD300a, another PS receptor. Furthermore, inhibiting CD300a in immature monocyte-derived dendritic cells partially but significantly inhibits ZIKV replication. As we have previously demonstrated that CEI is a useful tool to study Orthoflavivirus infection in real time, we now use this technology to determine how these PS receptors influence the kinetics of in vitro ZIKV infection. Results show that ZIKV entry is highly sensitive to minor changes in TIM-1 expression, both after overexpression of TIM-1 in infection-resistant HEK293T cells, as well as after partial knockout of TIM-1 in susceptible A549 cells. These results are confirmed by quantification of viral copy number and viral infectivity, demonstrating that CEI is highly suited to study and compare virus-host interactions. Overall, the results presented here demonstrate the potential of targeting this universal viral entry pathway. [ABSTRACT FROM AUTHOR]

Published
2024
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34. The response to re-emergence of yellow fever in Nigeria, 2017

Author

Nwachukwu, William E., Yusuff, H., Nwangwu, U., Okon, A., Ogunniyi, A., Imuetinyan-Clement, J., Besong, M., Ayo-Ajayi, P., Nikau, J., Baba, A., Dogunro, F., Akintunde, B., Oguntoye, M., Kamaldeen, K., Fakayode, O., Oyebanji, O., Emelife, O., Oteri, J., Aruna, O., Ilori, E., Ojo, O., Mba, N., Nguku, P., and Ihekweazu, C.

Published
2020
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36. Principios del tratamiento quirúrgico de los traumatismos anorrectales y de los órganos genitales

Author

Clément, J., Chiron, P., Arvieux, C., and Hornez, E.

Abstract

Este artículo es una actualización del tratamiento quirúrgico urgente de los traumatismos del recto subperitoneal, del ano y de los órganos genitales internos y externos en adultos. Estas lesiones se inscriben en el marco de los traumatismos pelviperineales, cuyos mecanismos son múltiples, la mayoría de las veces penetrantes. Su tratamiento es complejo, debido a la proximidad a los distintos tractos digestivo, urinario y ginecológico. Las posibles lesiones asociadas del marco óseo y de las estructuras vasculares próximas se añadan aún más a la complejidad del tratamiento inicial. La presentación inicial puede estar dominada por el carácter hemorrágico de las lesiones, pero el riesgo principal es sobre todo séptico, en particular para las lesiones digestivas. El tratamiento urgente requiere en primer lugar realizar una evaluación meticulosa, clínica y con pruebas de laboratorio, para no pasar por alto una lesión. Los objetivos del tratamiento son primero inmediatos, con el control de la hemorragia y de la sepsis, y después tardíos, con la prevención de las secuelas funcionales a medio plazo. El tratamiento de las heridas del recto intraperitoneal (idéntico al de las heridas del colon), de las lesiones hemorrágicas de la pelvis, así como de las secuelas de los traumatismos del ano y de los órganos genitales no se aborda en este artículo.

Published
2024
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37. Investigating the agreement between force platform and plantar pressure insole data in barefoot and skating-specific footwear conditions across four different movement patterns.

Author

Dunne, C., Hsu, T., Lockwood, K., Holmes, M., Wagnac, E., and Clément, J.

Abstract

Conducting applied sport research in real-world settings is challenged by the lack of portable instrumentation capable of producing valid and reliable data that is collected without interfering with the athletes' movement and is meaningful to sport performance. The purpose of this study was to compare and contrast data collected simultaneously from a force platform and a plantar pressure insole to provide support for the use of the XSENSOR® plantar pressure insoles in a skating-performance application. Data was collected in two conditions. The barefoot condition consisted of the insole on a force platform in isolation and the in-skate condition consisted of the insole inside a speed skate boot on a force platform. A single-participant design was conducted whereby an injury-free female completed multiple trials in both conditions. A P6000 Force Platform (BTS Bioengineering Corp., MI, Italy) was used to collect force data and an X4 Foot and Gait Measurement Systems plantar pressure insole (XSENSOR® Technology Corporation, AB, Canada) was used to collect pressure data in the two conditions across four movement patterns; static stance (SS), anterior-posterior sway (AP), medial-lateral sway (ML), and lateral jump (LJ). Intraclass correlation coefficients (ICC) and Bland-Altman plots revealed excellent agreement between the cumulative centre of pressure path length (mm) measured from the force platform and insole in the barefoot condition and moderate to excellent agreement between impulse (Ns) measured from the force platform and insole, in both conditions. These outcomes provide researchers and practitioners with empirical support and confidence to employ the XSENSOR® plantar pressure insoles outside of a laboratory setting in a real-world skating environment to collect and analyse in-skate kinetic data during on ice performance. [ABSTRACT FROM AUTHOR]

Published
2024
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38. Identification of constrained sequence elements across 239 primate genomes

Author

Kuderna, Lukas F. K., primary, Ulirsch, Jacob C., additional, Rashid, Sabrina, additional, Ameen, Mohamed, additional, Sundaram, Laksshman, additional, Hickey, Glenn, additional, Cox, Anthony J., additional, Gao, Hong, additional, Kumar, Arvind, additional, Aguet, Francois, additional, Christmas, Matthew J., additional, Clawson, Hiram, additional, Haeussler, Maximilian, additional, Janiak, Mareike C., additional, Kuhlwilm, Martin, additional, Orkin, Joseph D., additional, Bataillon, Thomas, additional, Manu, Shivakumara, additional, Valenzuela, Alejandro, additional, Bergman, Juraj, additional, Rouselle, Marjolaine, additional, Silva, Felipe Ennes, additional, Agueda, Lidia, additional, Blanc, Julie, additional, Gut, Marta, additional, de Vries, Dorien, additional, Goodhead, Ian, additional, Harris, R. Alan, additional, Raveendran, Muthuswamy, additional, Jensen, Axel, additional, Chuma, Idriss S., additional, Horvath, Julie E., additional, Hvilsom, Christina, additional, Juan, David, additional, Frandsen, Peter, additional, Schraiber, Joshua G., additional, de Melo, Fabiano R., additional, Bertuol, Fabrício, additional, Byrne, Hazel, additional, Sampaio, Iracilda, additional, Farias, Izeni, additional, Valsecchi, João, additional, Messias, Malu, additional, da Silva, Maria N. F., additional, Trivedi, Mihir, additional, Rossi, Rogerio, additional, Hrbek, Tomas, additional, Andriaholinirina, Nicole, additional, Rabarivola, Clément J., additional, Zaramody, Alphonse, additional, Jolly, Clifford J., additional, Phillips-Conroy, Jane, additional, Wilkerson, Gregory, additional, Abee, Christian, additional, Simmons, Joe H., additional, Fernandez-Duque, Eduardo, additional, Kanthaswamy, Sree, additional, Shiferaw, Fekadu, additional, Wu, Dongdong, additional, Zhou, Long, additional, Shao, Yong, additional, Zhang, Guojie, additional, Keyyu, Julius D., additional, Knauf, Sascha, additional, Le, Minh D., additional, Lizano, Esther, additional, Merker, Stefan, additional, Navarro, Arcadi, additional, Nadler, Tilo, additional, Khor, Chiea Chuen, additional, Lee, Jessica, additional, Tan, Patrick, additional, Lim, Weng Khong, additional, Kitchener, Andrew C., additional, Zinner, Dietmar, additional, Gut, Ivo, additional, Melin, Amanda D., additional, Guschanski, Katerina, additional, Schierup, Mikkel Heide, additional, Beck, Robin M. D., additional, Karakikes, Ioannis, additional, Wang, Kevin C., additional, Umapathy, Govindhaswamy, additional, Roos, Christian, additional, Boubli, Jean P., additional, Siepel, Adam, additional, Kundaje, Anshul, additional, Paten, Benedict, additional, Lindblad-Toh, Kerstin, additional, Rogers, Jeffrey, additional, Marques Bonet, Tomas, additional, and Farh, Kyle Kai-How, additional

Published
2023
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44. A global catalog of whole-genome diversity from 233 primate species

Author

Kuderna, Lukas F. K., primary, Gao, Hong, additional, Janiak, Mareike C., additional, Kuhlwilm, Martin, additional, Orkin, Joseph D., additional, Bataillon, Thomas, additional, Manu, Shivakumara, additional, Valenzuela, Alejandro, additional, Bergman, Juraj, additional, Rousselle, Marjolaine, additional, Silva, Felipe Ennes, additional, Agueda, Lidia, additional, Blanc, Julie, additional, Gut, Marta, additional, de Vries, Dorien, additional, Goodhead, Ian, additional, Harris, R. Alan, additional, Raveendran, Muthuswamy, additional, Jensen, Axel, additional, Chuma, Idrissa S., additional, Horvath, Julie E., additional, Hvilsom, Christina, additional, Juan, David, additional, Frandsen, Peter, additional, Schraiber, Joshua G., additional, de Melo, Fabiano R., additional, Bertuol, Fabrício, additional, Byrne, Hazel, additional, Sampaio, Iracilda, additional, Farias, Izeni, additional, Valsecchi, João, additional, Messias, Malu, additional, da Silva, Maria N. F., additional, Trivedi, Mihir, additional, Rossi, Rogerio, additional, Hrbek, Tomas, additional, Andriaholinirina, Nicole, additional, Rabarivola, Clément J., additional, Zaramody, Alphonse, additional, Jolly, Clifford J., additional, Phillips-Conroy, Jane, additional, Wilkerson, Gregory, additional, Abee, Christian, additional, Simmons, Joe H., additional, Fernandez-Duque, Eduardo, additional, Kanthaswamy, Sree, additional, Shiferaw, Fekadu, additional, Wu, Dongdong, additional, Zhou, Long, additional, Shao, Yong, additional, Zhang, Guojie, additional, Keyyu, Julius D., additional, Knauf, Sascha, additional, Le, Minh D., additional, Lizano, Esther, additional, Merker, Stefan, additional, Navarro, Arcadi, additional, Nadler, Tilo, additional, Khor, Chiea Chuen, additional, Lee, Jessica, additional, Tan, Patrick, additional, Lim, Weng Khong, additional, Kitchener, Andrew C., additional, Zinner, Dietmar, additional, Gut, Ivo, additional, Melin, Amanda D., additional, Guschanski, Katerina, additional, Schierup, Mikkel Heide, additional, Beck, Robin M. D., additional, Umapathy, Govindhaswamy, additional, Roos, Christian, additional, Boubli, Jean P., additional, Rogers, Jeffrey, additional, Farh, Kyle Kai-How, additional, and Marques Bonet, Tomas, additional

Published
2023
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45. The landscape of tolerated genetic variation in humans and primates

Author

Gao, Hong, primary, Hamp, Tobias, additional, Ede, Jeffrey, additional, Schraiber, Joshua G., additional, McRae, Jeremy, additional, Singer-Berk, Moriel, additional, Yang, Yanshen, additional, Dietrich, Anastasia S. D., additional, Fiziev, Petko P., additional, Kuderna, Lukas F. K., additional, Sundaram, Laksshman, additional, Wu, Yibing, additional, Adhikari, Aashish, additional, Field, Yair, additional, Chen, Chen, additional, Batzoglou, Serafim, additional, Aguet, Francois, additional, Lemire, Gabrielle, additional, Reimers, Rebecca, additional, Balick, Daniel, additional, Janiak, Mareike C., additional, Kuhlwilm, Martin, additional, Orkin, Joseph D., additional, Manu, Shivakumara, additional, Valenzuela, Alejandro, additional, Bergman, Juraj, additional, Rousselle, Marjolaine, additional, Silva, Felipe Ennes, additional, Agueda, Lidia, additional, Blanc, Julie, additional, Gut, Marta, additional, de Vries, Dorien, additional, Goodhead, Ian, additional, Harris, R. Alan, additional, Raveendran, Muthuswamy, additional, Jensen, Axel, additional, Chuma, Idriss S., additional, Horvath, Julie E., additional, Hvilsom, Christina, additional, Juan, David, additional, Frandsen, Peter, additional, de Melo, Fabiano R., additional, Bertuol, Fabrício, additional, Byrne, Hazel, additional, Sampaio, Iracilda, additional, Farias, Izeni, additional, do Amaral, João Valsecchi, additional, Messias, Mariluce, additional, da Silva, Maria N. F., additional, Trivedi, Mihir, additional, Rossi, Rogerio, additional, Hrbek, Tomas, additional, Andriaholinirina, Nicole, additional, Rabarivola, Clément J., additional, Zaramody, Alphonse, additional, Jolly, Clifford J., additional, Phillips-Conroy, Jane, additional, Wilkerson, Gregory, additional, Abee, Christian, additional, Simmons, Joe H., additional, Fernandez-Duque, Eduardo, additional, Kanthaswamy, Sree, additional, Shiferaw, Fekadu, additional, Wu, Dongdong, additional, Zhou, Long, additional, Shao, Yong, additional, Zhang, Guojie, additional, Keyyu, Julius D., additional, Knauf, Sascha, additional, Le, Minh D., additional, Lizano, Esther, additional, Merker, Stefan, additional, Navarro, Arcadi, additional, Bataillon, Thomas, additional, Nadler, Tilo, additional, Khor, Chiea Chuen, additional, Lee, Jessica, additional, Tan, Patrick, additional, Lim, Weng Khong, additional, Kitchener, Andrew C., additional, Zinner, Dietmar, additional, Gut, Ivo, additional, Melin, Amanda, additional, Guschanski, Katerina, additional, Schierup, Mikkel Heide, additional, Beck, Robin M. D., additional, Umapathy, Govindhaswamy, additional, Roos, Christian, additional, Boubli, Jean P., additional, Lek, Monkol, additional, Sunyaev, Shamil, additional, O’Donnell-Luria, Anne, additional, Rehm, Heidi L., additional, Xu, Jinbo, additional, Rogers, Jeffrey, additional, Marques-Bonet, Tomas, additional, and Farh, Kyle Kai-How, additional

Published
2023
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50. Functionalisation of natural fibers using ionizing radiations

Author

Brendlé, Clément, El Hage, Roland, Sonnier, Rodolphe, Otazaghine, Belkacem, Rouif, Sophie, Clément, J-C, Polymères Composites et Hybrides (PCH - IMT Mines Alès), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Ionisos SAS, Aix-Marseille Université - Faculté des Sciences (AMU SCI), Aix Marseille Université (AMU), and Projet SABRES

Subjects
[SPI.MAT]Engineering Sciences [physics]/Materials
Abstract

International audience; Plant products arouse great interest in many fields (construction, automotive, textiles, etc …).However, some of their characteristics as their flammability represent major disadvantagesfor some applications. Research is now being conducted in academia and industry to developeffective methods of functionalizing or modifying the surface of these fibers to improve theirperformance. In this respect, radiation-grafting, based on the use of ionizing radiation(gamma or e-beam), represents an interesting method compared to chemical or enzymaticmethods. This technique makes it possible to generate radicals on the fibers allowing thegrafting of molecules of interest, thus offering a large spectrum of possibilities for themodification of the fibers [1][2]. Two ways for grafting under ionizing conditions can beused (Figure 1), pre irradiation and mutual irradiation. In any case, many factors conditionthe success of grafting reactions. In particular, the structure and the composition of thesubstrate influence the nature of the active species formed, and therefore, the feasibility ofthe grafting reaction. Some techniques, such as Electronic Paramagnetic Resonance (EPR),helps us to better understand these parameters, which will be the subject of this presentation.

Published
2023

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