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747 results on '"Fernandez, Nicolas"'

2. The black box of the relationship between breast cancer patients and accompanying patients: the accompanied patients’ point of view

Author

Pomey, Marie-Pascale, Iliescu Nelea, Monica, Vialaron, Cécile, Normandin, Louise, Côté, Marie-Andrée, Desforges, Mado, Pomey-Carpentier, Pénélope, Adjtoutah, Nesrine, Fortin, Israël, Ganache, Isabelle, Régis, Catherine, Rosberger, Zeev, Charpentier, Danielle, Bélanger, Lynda, Dorval, Michel, Ghadiri, Djahanchah P., Lavoie-Tremblay, Mélanie, Boivin, Antoine, Pelletier, Jean-François, Fernandez, Nicolas, Danino, Alain M., and de Guise, Michèle

Published
2024
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4. Integrating accompanying patients into clinical oncology teams: limiting and facilitating factors

Author

Pomey, Marie-Pascale, Paquette, Jesseca, Nelea, Monica Iliescu, Vialaron, Cécile, Mourad, Rim, Bouchard, Karine, Normandin, Louise, Côté, Marie-Andrée, Desforges, Mado, Pomey-Carpentier, Pénélope, Fortin, Israël, Ganache, Isabelle, Régis, Catherine, Rosberger, Zeev, Charpentier, Danielle, Vachon, Marie-France, Bélanger, Lynda, Dorval, Michel, Ghadiri, Djahanchah P., Lavoie-Tremblay, Mélanie, Boivin, Antoine, Pelletier, Jean-François, Fernandez, Nicolas, Danino, Alain M., and de Guise, Michèle

Published
2024
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6. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

Author

Chen, Jonathan H., Nieman, Linda T., Spurrell, Maxwell, Jorgji, Vjola, Elmelech, Liad, Richieri, Peter, Xu, Katherine H., Madhu, Roopa, Parikh, Milan, Zamora, Izabella, Mehta, Arnav, Nabel, Christopher S., Freeman, Samuel S., Pirl, Joshua D., Lu, Chenyue, Meador, Catherine B., Barth, Jaimie L., Sakhi, Mustafa, Tang, Alexander L., Sarkizova, Siranush, Price, Colles, Fernandez, Nicolas F., Emanuel, George, He, Jiang, Van Raay, Katrina, Reeves, Jason W., Yizhak, Keren, Hofree, Matan, Shih, Angela, Sade-Feldman, Moshe, Boland, Genevieve M., Pelka, Karin, Aryee, Martin J., Mino-Kenudson, Mari, Gainor, Justin F., Korsunsky, Ilya, and Hacohen, Nir

Published
2024
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7. Circulating myeloid-derived MMP8 in stress susceptibility and depression

Author

Cathomas, Flurin, Lin, Hsiao-Yun, Chan, Kenny L., Li, Long, Parise, Lyonna F., Alvarez, Johana, Durand-de Cuttoli, Romain, Aubry, Antonio V., Muhareb, Samer, Desland, Fiona, Shimo, Yusuke, Ramakrishnan, Aarthi, Estill, Molly, Ferrer-Pérez, Carmen, Parise, Eric M., Wilk, C. Matthias, Kaster, Manuella P., Wang, Jun, Sowa, Allison, Janssen, William G., Costi, Sara, Rahman, Adeeb, Fernandez, Nicolas, Campbell, Matthew, Swirski, Filip K., Nestler, Eric J., Shen, Li, Merad, Miriam, Murrough, James W., and Russo, Scott J.

Published
2024
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8. DNA Methylation and RNA-DNA Hybrids Regulate the Single-Molecule Localization of a DNA Methyltransferase on the Bacterial Nucleoid.

Author

Fernandez, Nicolas, Chen, Ziyuan, Fuller, David, van Gijtenbeek, Lieke, Nye, Taylor, Biteen, Julie, and Simmons, Lyle

Subjects
Bacillus subtilis, epigenetic, replisome, restriction modification, superresolution microscopy, Methyltransferases, DNA Methylation, RNA, DNA, Bacterial, DNA Restriction-Modification Enzymes, Bacteriophages
Abstract

Bacterial DNA methyltransferases (MTases) function in restriction modification systems, cell cycle control, and the regulation of gene expression. DnmA is a recently described DNA MTase that forms N6-methyladenosine at nonpalindromic 5-GACGAG-3 sites in Bacillus subtilis, yet how DnmA activity is regulated is unknown. To address DnmA regulation, we tested substrate binding in vitro and found that DnmA binds poorly to methylated DNA and to an RNA-DNA hybrid with the DNA recognition sequence. Further, DnmA variants with amino acid substitutions that disrupt cognate sequence recognition or catalysis also bind poorly to DNA. Using superresolution fluorescence microscopy and single-molecule tracking of DnmA-PAmCherry, we characterized the subcellular DnmA diffusion and detected its preferential localization to the replisome region and the nucleoid. Under conditions where the chromosome is highly methylated, upon RNA-DNA hybrid accumulation, or with a DnmA variant with severely limited DNA binding activity, DnmA is excluded from the nucleoid, demonstrating that prior methylation or accumulation of RNA-DNA hybrids regulates the association of DnmA with the chromosome in vivo. Furthermore, despite the high percentage of methylated recognition sites and the proximity to putative endonuclease genes conserved across bacterial species, we find that DnmA fails to protect B. subtilis against phage predation, suggesting that DnmA is functionally an orphan MTase involved in regulating gene expression. Our work explores the regulation of a bacterial DNA MTase and identifies prior methylation and RNA-DNA hybrids as regulators of MTase localization. These MTase regulatory features could be common across biology. IMPORTANCE DNA methyltransferases (MTases) influence gene expression, cell cycle control, and host defense through DNA modification. Predicted MTases are pervasive across bacterial genomes, but the vast majority remain uncharacterized. Here, we show that in the soil microorganism Bacillus subtilis, the DNA MTase dnmA and neighboring genes are remnants of a phage defense system that no longer protects against phage predation. This result suggests that portions of the bacterial methylome may originate from inactive restriction modification systems that have maintained methylation activity. Analysis of DnmA movement in vivo shows that active DnmA localizes in the nucleoid, suggesting that DnmA can search for recognition sequences throughout the nucleoid region with some preference for the replisome. Our results further show that prior DNA methylation and RNA-DNA hybrids regulate DnmA dynamics and nucleoid localization, providing new insight into how DNA methylation is coordinated within the cellular environment.

Published
2023

16. Gravitational wave and CMB probes of axion kination

Author

Co, Raymond T, Dunsky, David, Fernandez, Nicolas, Ghalsasi, Akshay, Hall, Lawrence J, Harigaya, Keisuke, and Shelton, Jessie

Subjects
Nuclear and Plasma Physics, Particle and High Energy Physics, Astronomical Sciences, Physical Sciences, Cosmology of Theories beyond the SM, Beyond Standard Model, Supersymmetric Standard Model, Mathematical Physics, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Quantum Physics, Nuclear & Particles Physics, Mathematical physics, Nuclear and plasma physics, Particle and high energy physics
Abstract

Abstract : Rotations of an axion field in field space provide a natural origin for an era of kination domination, where the energy density is dominated by the kinetic term of the axion field, preceded by an early era of matter domination. Remarkably, no entropy is produced at the end of matter domination and hence these eras of matter and kination domination may occur even after Big Bang Nucleosynthesis. We derive constraints on these eras from both the cosmic microwave background and Big Bang Nucleosynthesis. We investigate how this cosmological scenario affects the spectrum of possible primordial gravitational waves and find that the spectrum features a triangular peak. We discuss how future observations of gravitational waves can probe the viable parameter space, including regions that produce axion dark matter by the kinetic misalignment mechanism or the baryon asymmetry by axiogenesis. For QCD axion dark matter produced by the kinetic misalignment mechanism, a modification to the inflationary gravitational wave spectrum occurs above 0.01 Hz and, for high values of the energy scale of inflation, the prospects for discovery are good. We briefly comment on implications for structure formation of the universe.

Published
2022

24. Intratumoral dendritic cell–CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma

Author

Magen, Assaf, Hamon, Pauline, Fiaschi, Nathalie, Soong, Brian Y., Park, Matthew D., Mattiuz, Raphaël, Humblin, Etienne, Troncoso, Leanna, D’souza, Darwin, Dawson, Travis, Kim, Joel, Hamel, Steven, Buckup, Mark, Chang, Christie, Tabachnikova, Alexandra, Schwartz, Hara, Malissen, Nausicaa, Lavin, Yonit, Soares-Schanoski, Alessandra, Giotti, Bruno, Hegde, Samarth, Ioannou, Giorgio, Gonzalez-Kozlova, Edgar, Hennequin, Clotilde, Le Berichel, Jessica, Zhao, Zhen, Ward, Stephen C., Fiel, Isabel, Kou, Baijun, Dobosz, Michael, Li, Lianjie, Adler, Christina, Ni, Min, Wei, Yi, Wang, Wei, Atwal, Gurinder S., Kundu, Kunal, Cygan, Kamil J., Tsankov, Alexander M., Rahman, Adeeb, Price, Colles, Fernandez, Nicolas, He, Jiang, Gupta, Namita T., Kim-Schulze, Seunghee, Gnjatic, Sacha, Kenigsberg, Ephraim, Deering, Raquel P., Schwartz, Myron, Marron, Thomas U., Thurston, Gavin, Kamphorst, Alice O., and Merad, Miriam

Published
2023
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25. Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis

Author

Amadori, Letizia, Calcagno, Claudia, Fernandez, Dawn M., Koplev, Simon, Fernandez, Nicolas, Kaur, Ravneet, Mury, Pauline, Khan, Nayaab S, Sajja, Swathy, Shamailova, Roza, Cyr, Yannick, Jeon, Minji, Hill, Christopher A., Chong, Peik Sean, Naidu, Sonum, Sakurai, Ken, Ghotbi, Adam Ali, Soler, Raphael, Eberhardt, Natalia, Rahman, Adeeb, Faries, Peter, Moore, Kathryn J., Fayad, Zahi A., Ma’ayan, Avi, and Giannarelli, Chiara

Published
2023
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26. Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon

Author

Fokam, Joseph, Essomba, Rene Ghislain, Njouom, Richard, Okomo, Marie-Claire A., Eyangoh, Sara, Godwe, Celestin, Tegomoh, Bryan, Otshudiema, John O., Nwobegahay, Julius, Ndip, Lucy, Akenji, Blaise, Takou, Desire, Moctar, Mohamed M. M., Mbah, Cleophas Kahtita, Ndze, Valantine Ngum, Maidadi-Foudi, Martin, Kouanfack, Charles, Tonmeu, Sandrine, Ngono, Dorine, Nkengasong, John, Ndembi, Nicaise, Bissek, Anne-Cecile Z. K., Mouangue, Christian, Ndongo, Chanceline B., Epée, Emilienne, Mandeng, Nadia, Kamso Belinga, Sandrine, Ayouba, Ahidjo, Fernandez, Nicolas, Tongo, Marcel, Colizzi, Vittorio, Halle-Ekane, Gregory-Edie, Perno, Carlo-Federico, Ndjolo, Alexis, Ndongmo, Clement B., Shang, Judith, Esso, Linda, de-Tulio, Oliviera, Diagne, Moussa Moise, Boum, II, Yap, Mballa, Georges A. E., and Njock, Louis R.

Published
2023
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27. RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Author

Komatsu, Jun, Cico, Alba, Poncin, Raya, Le Bohec, Maël, Morf, Jörg, Lipin, Stanislav, Graindorge, Antoine, Eckert, Hélène, Saffarian, Azadeh, Cathaly, Léa, Guérin, Frédéric, Majello, Sara, Ulveling, Damien, Vayaboury, Anaïs, Fernandez, Nicolas, Dimitrova, Dilyana, Bussell, Xavier, Fourne, Yannick, Chaumat, Pierre, André, Barbara, Baldivia, Elodie, Godet, Ulysse, Guinin, Mathieu, Moretto, Vivien, Ismail, Joy, Caille, Olivier, Roblot, Natacha, Beaupère, Carine, Liboz, Alexandrine, Guillemain, Ghislaine, Blondeau, Bertrand, Walrafen, Pierre, and Edelstein, Stuart

Published
2023
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28. An exploratory cross-sectional study of the effects of ongoing relationships with accompanying patients on cancer care experience, self-efficacy, and psychological distress

Author

Pomey, Marie-Pascale, Nelea, Monica Iliescu, Normandin, Louise, Vialaron, Cécile, Bouchard, Karine, Côté, Marie-Andrée, Duarte, Maria Alejandra Rodriguez, Ghadiri, Djahanchah Philip, Fortin, Israël, Charpentier, Danielle, Lavoie-Tremblay, Mélanie, Fernandez, Nicolas, Boivin, Antoine, Dorval, Michel, Desforges, Mado, Régis, Catherine, Ganache, Isabelle, Bélanger, Lynda, Rosberger, Zeev, Danino, Michel Alain, Pelletier, Jean-François, Vu, Thi Trinh Thuc, and de Guise, Michèle

Published
2023
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29. Lepto-axiogenesis

Author

Co, Raymond T, Fernandez, Nicolas, Ghalsasi, Akshay, Hall, Lawrence J, and Harigaya, Keisuke

Subjects
Nuclear and Plasma Physics, Particle and High Energy Physics, Physical Sciences, Cosmology of Theories beyond the SM, Beyond Standard Model, Supersymmetric Standard Model, Mathematical Physics, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Quantum Physics, Nuclear & Particles Physics, Mathematical physics, Nuclear and plasma physics, Particle and high energy physics
Abstract

We propose a baryogenenesis mechanism that uses a rotating condensate of a Peccei-Quinn (PQ) symmetry breaking field and the dimension-five operator that gives Majorana neutrino masses. The rotation induces charge asymmetries for the Higgs boson and for lepton chirality through sphaleron processes and Yukawa interactions. The dimension-five interaction transfers these asymmetries to the lepton asymmetry, which in turn is transferred into the baryon asymmetry through the electroweak sphaleron process. QCD axion dark matter can be simultaneously produced by dynamics of the same PQ field via kinetic misalignment or parametric resonance, favoring an axion decay constant fa ≲ 1010 GeV, or by conventional misalignment and contributions from strings and domain walls with fa ∼ 1011 GeV. The size of the baryon asymmetry is tied to the mass of the PQ field. In simple supersymmetric theories, it is independent of UV parameters and predicts the supersymmtry breaking mass scale to be O(10 − 104) TeV, depending on the masses of the neutrinos and whether the condensate is thermalized during a radiation or matter dominated era. The high supersymmetry breaking mass scale may be free from cosmological and flavor/CP problems. We also construct a theory where TeV scale supersymmetry is possible. Parametric resonance may give warm axions, and the radial component of the PQ field may give signals in rare kaon decays from mixing with the Higgs and in dark radiation.

Published
2021

34. Abdominoscrotal hydrocele: excision of sac may not be necessary

Author

Xu, Weichen, Ko, Joan, Fernandez, Nicolas, Koyle, Martin, Canning, Douglas A, and Kurzrock, Eric A

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, 6.4 Surgery, Evaluation of treatments and therapeutic interventions, Biometry, Child, Humans, Infant, Male, Operative Time, Retrospective Studies, Scrotum, Testicular Hydrocele, Pediatric hydrocele, Abdominoscrotal hydrocele, Paediatrics and Reproductive Medicine, Urology & Nephrology, Clinical sciences, Paediatrics
Abstract

IntroductionAbdominoscrotal hydroceles (ASH) are uncommon occurrences in boys and usually treated similarly to a hernia with the assumption that there is an associated patent processus vaginalis. Treatment in this manner may be challenging due to sac size, extension and adherence to the spermatic cord. Due to the rarity of ASH, the literature is mostly limited to small, single-institution case studies.ObjectiveOur goal was to evaluate two techniques in large number. We hypothesized a simplified scrotal technique with eversion, Jaboulay procedure, would demonstrate less complications and equivalent efficacy to standard excision.MethodsWe retrospectively reviewed medical records at three tertiary children's hospitals to identify boys who underwent surgical repair of ASH between 1998 and 2018. Group 1 had excision and/or ligation of the hydrocele sac. Group 2 had a scrotal incision with limited excision and then eversion of the hydrocele sac (Jaboulay procedure). Variables that were analyzed included preoperative imaging, surgical technique, surgical findings, length of follow up, complications and recurrence of swelling.ResultsWe identified 61 boys, who had 77 abdominoscrotal hydroceles. Group 1 included 38 patients with 48 hydroceles. Group 2 included 23 patients with 29 hydroceles. Complications were more common in Group 1 patients (18% vs 0%) but complication rate and operative time were not statistically associated with surgery type or age. No patient in either group had recurrence of hydrocele.DiscussionAlthough this is a large study for this rare condition, the analysis is limited by number and its retrospective nature.ConclusionFor the rare and difficult to treat abdominoscrotal hydrocele, we were unable to prove with statistical significance that a simplified technique of eversion via the scrotum is safer. However, this large series did demonstrate that the simplified procedure provides equal efficacy as excision.

Published
2020

35. Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects.

Author

Edwards, Jonathan J, Rouillard, Andrew D, Fernandez, Nicolas F, Wang, Zichen, Lachmann, Alexander, Shankaran, Sunita S, Bisgrove, Brent W, Demarest, Bradley, Turan, Nahid, Srivastava, Deepak, Bernstein, Daniel, Deanfield, John, Giardini, Alessandro, Porter, George, Kim, Richard, Roberts, Amy E, Newburger, Jane W, Goldmuntz, Elizabeth, Brueckner, Martina, Lifton, Richard P, Seidman, Christine E, Chung, Wendy K, Tristani-Firouzi, Martin, Yost, H Joseph, Ma'ayan, Avi, and Gelb, Bruce D

Subjects
CHD, congenital heart disease, CORUM, Comprehensive Resource of Mammalian Protein Complexes, CRISPR, clustered regularly interspaced short palindromic repeats, CTD, conotruncal defect, GOBP, Gene Ontology biological processes, HHE, high heart expression, HLHS, hypoplastic left heart syndrome, HTX, heterotaxy, LVOTO, left ventricular outflow tract obstruction, MGI, Mouse Genome Informatics, PCGC, Pediatric Cardiac Genomics Consortium, PPI, protein-protein interaction, congenital heart disease, systems biology, translational genomics, CHD, CORUM, Comprehensive Resource of Mammalian Protein Complexes, CRISPR, clustered regularly interspaced short palindromic repeats, CTD, conotruncal defect, GOBP, Gene Ontology biological processes, HHE, high heart expression, HLHS, hypoplastic left heart syndrome, HTX, heterotaxy, LVOTO, left ventricular outflow tract obstruction, MGI, Mouse Genome Informatics, PCGC, Pediatric Cardiac Genomics Consortium, PPI, protein-protein interaction, Cardiorespiratory Medicine and Haematology, Clinical Sciences
Abstract

Genetic variants are the primary driver of congenital heart disease (CHD) pathogenesis. However, our ability to identify causative variants is limited. To identify causal CHD genes that are associated with specific molecular functions, the study used prior knowledge to filter de novo variants from 2,881 probands with sporadic severe CHD. This approach enabled the authors to identify an association between left ventricular outflow tract obstruction lesions and genes associated with the WAVE2 complex and regulation of small GTPase-mediated signal transduction. Using CRISPR zebrafish knockdowns, the study confirmed that WAVE2 complex proteins brk1, nckap1, and wasf2 and the regulators of small GTPase signaling cul3a and racgap1 are critical to cardiac development.

Published
2020

40. Superradiance and the Spins of Black Holes from LIGO and X-ray binaries

Author

Fernandez, Nicolas, Ghalsasi, Akshay, and Profumo, Stefano

Subjects
hep-ph, astro-ph.CO, gr-qc
Abstract

Measurements of the spin of stellar mass black holes (BHs) are now possibleboth through LIGO observations of binary BH mergers and for BHs in X-ray binarysystems. The spins of BHs as inferred from LIGO observations suggest that BHspins are on the lower end of what is expected for a ``flat'' distribution ofspins, while those from BHs in X-ray binaries tend to be large. Superradiance,a process that can effectively reduce the spin of BHs before they merge, couldexplain the lower observed spins in binary BH mergers for a nonself-interacting light boson. In this paper, we use Bayesian analysis to inferthe posterior probability distribution for the mass of a light boson that couldfit LIGO data. We also analyze spins of BHs from X-ray binaries, and find thatthe X-ray binary data can be explained by superradiance due to a light bosonwith large self-interactions. We infer the mass range for such a boson that isconsistent with the X-ray binary data.

Published
2019

41. Unraveling the origin of black holes from effective spin measurements with LIGO-Virgo

Author

Fernandez, Nicolas and Profumo, Stefano

Subjects
Astronomical Sciences, Physical Sciences, GR black holes, gravitational waves/sources, primordial black holes, astro-ph.HE, astro-ph.CO, gr-qc, hep-ph, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics, Astronomical sciences, Particle and high energy physics
Abstract

We investigate how to use information on the effective spin parameter ofbinary black hole mergers from the LIGO-Virgo gravitational wave detections todiscriminate the origin of the merging black holes. We calculate the expectedprobability distribution function for the effective spin parameter forprimordial black holes. Using LIGO-Virgo observations, we then calculate oddsratios for different models for the distribution of black holes' spin magnitudeand alignment. We evaluate the posterior probability density for a possiblemixture of astrophysical and primordial black holes as emerging from currentdata, and calculate the number of future merger events needed to discriminatedifferent spin and alignment models at a given level of statisticalsignificance.

Published
2019

42. Comment on "keV neutrino dark matter in a fast expanding universe" by Biswas et al.

Author

Fernandez, Nicolas and Profumo, Stefano

Subjects
hep-ph, astro-ph.CO, astro-ph.HE, Mathematical Physics, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics
Abstract

Biswas et al. found that the thermal relic density of a dark matter particlefreezing out while the universe's energy density is dominated by a non-standardextra component $\phi$, whose energy density redshifts faster than radiation,can be greatly suppressed. Here we show that this result, which contradictsextensive previous literature, is incorrect: the mistake lies with theassumption that the (decoupled) extra component $\phi$ contributes to theentropic degrees of freedom relevant for dark matter freeze out. If this werethe case, a completely different approach would be needed to calculate the darkmatter relic abundance, with dramatically different results.

Published
2019

50. Vasa nucleates asymmetric translation along the mitotic spindle during unequal cell divisions

Author

Ana Fernandez-Nicolas, Alicia Uchida, Jessica Poon, and Mamiko Yajima

Subjects
Science
Abstract

Association of mRNA translation with the mitotic spindle is thought to be involved in localized production of cell fate determinants. Here, the authors show Vasa facilitates asymmetric translation, which contributes to differential regulation during sea urchin embryogenesis.

Published
2022
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