Charles A. Herring, Bob Chen, Eliot T. McKinley, Ken S. Lau,
... Boutet S.C. Terry J.M. Belgrader P. Ziraldo S.B. Mikkelsen T.S. Wang F. von ... P. Ryvkin P. Bent Z.W. Wilson R. Ziraldo S.B. Wheeler T.D. McDermott G.P. ...
Tópico(s): Gene Regulatory Network Analysis
2018 - Elsevier BV | Cellular and Molecular Gastroenterology and Hepatology
Simone Ziraldo, Giuseppe E. Santoro,
... sudden quantum quench, extending the results of S. Ziraldo et al. [Phys. Rev. Lett. 109, 247205 (2012)]. ...
Tópico(s): Cold Atom Physics and Bose-Einstein Condensates
2013 - American Physical Society | Physical Review B
Cordelia Ziraldo, Alexey Solovyev, Ana Allegretti, Shilpa Krishnan, M. Kristi Henzel, Gwendolyn Sowa, David M. Brienza, Gary An, Qi Mi, Yoram Vodovotz,
© 2015 Ziraldo et al. People with spinal cord injury (SCI) are predisposed to pressure ulcers (PU). PU remain a ...
Tópico(s): Diabetic Foot Ulcer Assessment and Management
2012 - Elsevier BV | Journal of Critical Care
Sergiu A. Lucaciu, Stephanie E. Leighton, Alexandra Hauser, Ryan Yee, Dale W. Laird,
... Google Scholar, 47Kuang Y. Zorzi V. Buratto D. Ziraldo G. Mazzarda F. Peres C. et al.A ...
Tópico(s): Yersinia bacterium, plague, ectoparasites research
2023 - Elsevier BV | Journal of Biological Chemistry
Sorin Drăghici, Tuan‐Minh Nguyen, Larry A. Sonna, Cordelia Ziraldo, Radu Vanciu, Raef Fadel, Austin Morrison, Rachel M. Kenney, George Alangaden, Mayur Ramesh, Gil Mor,
COVID-19 has several distinct clinical phases: a viral replication phase, an inflammatory phase and in some patients, a hyper-inflammatory phase. High mortality is associated with patients developing cytokine storm syndrome. Treatment of hyper-inflammation in these patients using existing approved therapies with proven safety profiles could address the immediate need to reduce mortality.We analyzed the changes in the gene expression, pathways and putative mechanisms induced by SARS-CoV2 in NHBE, ...
Tópico(s): PARP inhibition in cancer therapy
2021 - Oxford University Press | Bioinformatics
Yuanyuan Kuang, Veronica Zorzi, Damiano Buratto, Gaia Ziraldo, Flavia Mazzarda, Chiara Peres, Chiara Nardin, Anna Maria Salvatore, Francesco Chiani, Ferdinando Scavizzi, Marcello Raspa, Min Qiang, Youjun Chu, Xiaojie Shi, Yu Li, Lili Liu, Yaru Shi, Francesco Zonta, Guang Yang, Richard A. Lerner, Fabio Mammano,
Numerous currently incurable human diseases have been causally linked to mutations in connexin (Cx) genes. In several instances, pathological mutations generate abnormally active Cx hemichannels, referred to also as "leaky" hemichannels. The goal of this study was to assay the in vivo efficacy of a potent antagonist antibody targeting Cx hemichannels.
Tópico(s): Erythrocyte Function and Pathophysiology
2020 - Elsevier BV | EBioMedicine
Flavia Mazzarda, Annunziata D’Elia, Roberto Massari, Adele De Ninno, Francesca Romana Bertani, Luca Businaro, Gaia Ziraldo, Veronica Zorzi, Chiara Nardin, Chiara Peres, Francesco Chiani, Abraham Tettey‐Matey, Marcello Raspa, Ferdinando Scavizzi, A. Soluri, Anna Maria Salvatore, Jun Yang, Fabio Mammano,
Using microfluidics, ATP biosensors, multiphoton microscopy and genetically targeted mice, we show that ATP release through connexin hemichannels, and not pannexin 1 channels, underlies spontaneous Ca 2+ wave propagation in the greater epithelial ridge of the developing cochlea.
Tópico(s): Neuroscience and Neuropharmacology Research
2020 - Royal Society of Chemistry | Lab on a Chip
Ameen A. Salahudeen, S. S. Choi, Arjun Rustagi, Junjie Zhu, Vincent van Unen, Sean de la O, Ryan A. Flynn, Mar Margalef-Català, António J. M. Santos, Jihang Ju, Arpit Batish, Tatsuya Usui, Grace Zheng, Caitlin E. Edwards, Lisa E. Wagar, Vincent C. Luca, Benedict Anchang, Monica Nagendran, Khanh Cong Nguyen, Daniel J. Hart, Jessica M. Terry, Phillip Belgrader, Solongo B. Ziraldo, Tarjei S. Mikkelsen, Pehr B. Harbury, Jeffrey S. Glenn, K. Christopher García, Mark M. Davis, Ralph S. Baric, Chiara Sabatti, Manuel R. Amieva, Catherine A. Blish, Tushar Desai, Calvin J. Kuo,
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate the investigation of pathologies such as interstitial lung disease, cancer and coronavirus disease 2019 (COVID-19) pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we describe the development of a long-term feeder-free, chemically defined culture system for distal lung progenitors as organoids ...
Tópico(s): Congenital Diaphragmatic Hernia Studies
2020 - Nature Portfolio | Nature
... Boutet S.C. Terry J.M. Belgrader P. Ziraldo S.B. Mikkelsen T.S. Wang F. von ...
Tópico(s): Helicobacter pylori-related gastroenterology studies
2019 - Elsevier BV | Cellular and Molecular Gastroenterology and Hepatology
Gaia Ziraldo, Damiano Buratto, Yuanyuan Kuang, Liang Xu, Andrea Carrer, Chiara Nardin, Francesco Chiani, Anna Maria Salvatore, Gaetano Paludetti, Richard A. Lerner, Guang Yang, Francesco Zonta, Fabio Mammano,
ORIGINAL RESEARCH article Front. Physiol., 11 June 2019Sec. Membrane Physiology and Membrane Biophysics Volume 10 - 2019 | https://doi.org/10.3389/fphys.2019.00392
Tópico(s): Neuroscience of respiration and sleep
2019 - Frontiers Media | Frontiers in Physiology
Anna Rita Fetoni, Veronica Zorzi, Fabiola Paciello, Gaia Ziraldo, Chiara Peres, Marcello Raspa, Ferdinando Scavizzi, Anna Maria Salvatore, Giulia Crispino, Gabriella Tognola, Giulia Gentile, Antonio Gianmaria Spampinato, Denis Cuccaro, Maria Guarnaccia, Giovanna Morello, Guy Van Camp, Erik Fransén, Marco Brumat, Giorgia Girotto, Gaetano Paludetti, Paolo Gasparini, Sebastiano Cavallaro, Fabio Mammano,
Mutations in GJB2, the gene that encodes connexin 26 (Cx26), are the most common cause of sensorineural hearing impairment. The truncating variant 35delG, which determines a complete loss of Cx26 protein function, is the prevalent GJB2 mutation in several populations. Here, we generated and analyzed Gjb2
Tópico(s): Neuroscience of respiration and sleep
2018 - Elsevier BV | Redox Biology
Riccardo Ziraldo, Andreas Hanke, Stephen D. Levene,
The topological state of covalently closed, double-stranded DNA is defined by the knot type $K$ and the linking-number difference $\Delta Lk$ relative to unknotted relaxed DNA. DNA topoisomerases are essential enzymes that control the topology of DNA in all cells. In particular, type-II topoisomerases change both $K$ and $\Delta Lk$ by a duplex-strand-passage mechanism and have been shown to simplify the topology of DNA to levels below thermal equilibrium at the expense of ATP hydrolysis. It remains a ...
Tópico(s): Bioactive Compounds and Antitumor Agents
2018 - Oxford University Press | Nucleic Acids Research
Kelley S. Yan, Claudia Y. Janda, Junlei Chang, Grace Zheng, Kathryn A. Larkin, Vincent C. Luca, Luis A. Chia, Amanda T. Mah, Arnold Han, Jessica M. Terry, Akifumi Ootani, Kelly Roelf, Mark Lee, Jenny Yuan, Li Xiao, Christopher R. Bolen, Julie Wilhelmy, Paige S. Davies, Hiroo Ueno, Richard J. von Furstenberg, Phillip Belgrader, Solongo B. Ziraldo, Heather Ordonez, Susan Henning, Melissa H. Wong, M Snyder, Irving L. Weissman, Aaron J.W. Hsueh, Tarjei S. Mikkelsen, K. Christopher García, Calvin J. Kuo,
R-spondin and Wnt ligand families act non-redundantly and cooperatively within the same molecular pathway in the intestinal stem-cell niche to maintain stem-cell competency and drive stem-cell expansion. Wnt ligands interact with FZD and Lrp5/6-type receptors to influence diverse developmental, homeostatic and pathologic processes through β-catenin-dependent signalling. However, the promiscuity of Wnt ligands towards several receptors and the fact that Wnts can be hydrophobic make it difficult to ...
Tópico(s): Cancer Cells and Metastasis
2017 - Nature Portfolio | Nature
Liang Xu, Andrea Carrer, Francesco Zonta, Zhihu Qu, Peixiang Ma, Sheng Li, Federico Ceriani, Damiano Buratto, Giulia Crispino, Veronica Zorzi, Gaia Ziraldo, Francesca Bruno, Chiara Nardin, Chiara Peres, Flavia Mazzarda, Anna Maria Salvatore, Marcello Raspa, Ferdinando Scavizzi, Youjun Chu, Sichun Xie, Xuemei Yang, Jun Liao, Xiao Liu, Wei Wang, Shanshan Wang, Guang Yang, Richard A. Lerner, Fabio Mammano,
Background: Mutations leading to changes in properties, regulation or expression of connexin–made channels have been implicated in twenty-eight distinct human hereditary diseases. Eight of these result from variants of connexin 26 (Cx26), a protein critically involved in cell-cell signaling in the inner ear and skin. Lack of non-toxic drugs with defined mechanisms of action poses a serious obstacle to therapeutic interventions for diseases caused by mutant connexins. In particular, molecules that ...
Tópico(s): Nicotinic Acetylcholine Receptors Study
2017 - Frontiers Media | Frontiers in Molecular Neuroscience
Veronica Zorzi, Fabiola Paciello, Gaia Ziraldo, Chiara Peres, Flavia Mazzarda, Chiara Nardin, Miriam Pasquini, Francesco Chiani, Marcello Raspa, Ferdinando Scavizzi, Andrea Carrer, Giulia Crispino, Catalin D. Ciubotaru, Hannah Monyer, Anna Rita Fetoni, Anna Maria Salvatore, Fabio Mammano,
Panx1 forms plasma membrane channels in brain and several other organs, including the inner ear. Biophysical properties, activation mechanisms and modulators of Panx1 channels have been characterized in detail, however the impact of Panx1 on auditory function is unclear due to conflicts in published results. To address this issue, hearing performance and cochlear function of the Panx1-/- mouse strain, the first with a reported global ablation of Panx1, were scrutinized. Male and female homozygous ( ...
Tópico(s): Hearing, Cochlea, Tinnitus, Genetics
2017 - Frontiers Media | Frontiers in Molecular Neuroscience
Kelley S. Yan, Olivier Gevaert, Grace Zheng, Benedict Anchang, C Probert, Kathryn A. Larkin, Paige S. Davies, Zhuan-fen Cheng, John S. Kaddis, Arnold Han, Kelly Roelf, Ruben I. Calderon, Esther Cynn, Xiaoyi Hu, Komal Mandleywala, Julie Wilhelmy, Susan M. Grimes, David C. Corney, Stéphane C. Boutet, Jessica M. Terry, Phillip Belgrader, Solongo B. Ziraldo, Tarjei S. Mikkelsen, Fengchao Wang, Richard J. von Furstenberg, Nicholas R. Smith, Parthasarathy Chandrakesan, Randal May, Mary Ann S. Chrissy, Rishee K. Jain, Christine A. Cartwright, Joyce C. Niland, Young-Kwon Hong, Jill L. Carrington, David T. Breault, Jonathan A. Epstein, Courtney W. Houchen, John P. Lynch, Martı́n G. Martı́n, Sylvia K. Plevritis, Christina Curtis, Hanlee P. Ji, Linheng Li, Susan Henning, Melissa H. Wong, Calvin J. Kuo,
Several cell populations have been reported to possess intestinal stem cell (ISC) activity during homeostasis and injury-induced regeneration. Here, we explored inter-relationships between putative mouse ISC populations by comparative RNA-sequencing (RNA-seq). The transcriptomes of multiple cycling ISC populations closely resembled Lgr5+ ISCs, the most well-defined ISC pool, but Bmi1-GFP+ cells were distinct and enriched for enteroendocrine (EE) markers, including Prox1. Prox1-GFP+ cells exhibited ...
Tópico(s): Pancreatic function and diabetes
2017 - Elsevier BV | Cell stem cell
Grace Zheng, Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary Bent, Ryan J. Wilson, Solongo B. Ziraldo, Tobias D. Wheeler, Geoff P. McDermott, Junjie Zhu, Mark Gregory, Joe Shuga, Luz Montesclaros, Jason G. Underwood, Donald A Masquelier, Stefanie Y. Nishimura, Michael Schnall-Levin, Paul W. Wyatt, Christopher M. Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D. Ness, Lan Beppu, H. Joachim Deeg, Christopher McFarland, Keith R. Loeb, William J. Valente, Nolan G. Ericson, Emily A. Stevens, Jerald P. Radich, Tarjei S. Mikkelsen, Benjamin J. Hindson, Jason H. Bielas,
Abstract Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system’s technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the ...
Tópico(s): Gene Regulatory Network Analysis
2017 - Nature Portfolio | Nature Communications
Cordelia Ziraldo, Chang Gong, Denise E. Kirschner, Jennifer J. Linderman,
Lack of an effective vaccine results in 9 million new cases of tuberculosis (TB) every year and 1.8 million deaths worldwide. Although many infants are vaccinated at birth with BCG (an attenuated M. bovis), this does not prevent infection or development of TB after childhood. Immune responses necessary for prevention of infection or disease are still unknown, making development of effective vaccines against TB challenging. Several new vaccines are ready for human clinical trials, but these trials ...
Tópico(s): T-cell and B-cell Immunology
2016 - Frontiers Media | Frontiers in Microbiology
Ian Ziraldo, Kristen E. Watts, Arnold Luk, Anthony F. Lagalante, Richard Wolbers,
It has often been observed anecdotally and implied through experimentation that acrylic emulsion paintings accumulate and entrain soils over time due to the inherent mechanical softness in artist's acrylic paint films, through the presence of hydrophilic film components, and by virtue of the ubiquitous presence of surfactant moieties on these film surfaces once they dry. In the present study, it has been this last effect that we have sought to describe more fully in terms of surfactant responsiveness ...
Tópico(s): Analytical Chemistry and Chromatography
2015 - Taylor & Francis | Studies in Conservation
Cordelia Ziraldo, Alexey Solovyev, Ana Allegretti, Shilpa Krishnan, M. Kristi Henzel, Gwendolyn Sowa, David M. Brienza, Gary An, Qi Mi, Yoram Vodovotz,
People with spinal cord injury (SCI) are predisposed to pressure ulcers (PU). PU remain a significant burden in cost of care and quality of life despite improved mechanistic understanding and advanced interventions. An agent-based model (ABM) of ischemia/reperfusion-induced inflammation and PU (the PUABM) was created, calibrated to serial images of post-SCI PU, and used to investigate potential treatments in silico. Tissue-level features of the PUABM recapitulated visual patterns of ulcer formation ...
Tópico(s): Diabetic Foot Ulcer Assessment and Management
2015 - Public Library of Science | PLoS Computational Biology
Cordelia Ziraldo, Qi Mi, Gary An, Yoram Vodovotz,
Inflammation is both central to proper wound healing and a key driver of chronic tissue injury via a positive-feedback loop incited by incidental cell damage. We seek to derive actionable insights into the role of inflammation in wound healing in order to improve outcomes for individual patients.To date, dynamic computational models have been used to study the time evolution of inflammation in wound healing. Emerging clinical data on histo-pathological and macroscopic images of evolving wounds, ...
Tópico(s): Wound Healing and Treatments
2013 - Mary Ann Liebert, Inc. | Advances in Wound Care
Cordelia Ziraldo, Yoram Vodovotz, Rami A. Namas, Khalid Almahmoud, Vı́ctor Tapias, Qi Mi, Derek Barclay, Bahiyyah Jefferson, Guoqiang Chen, Timothy R. Billiar, Rubén Zamora,
The translation of in vitro findings to clinical outcomes is often elusive. Trauma/hemorrhagic shock (T/HS) results in hepatic hypoxia that drives inflammation. We hypothesize that in silico methods would help bridge in vitro hepatocyte data and clinical T/HS, in which the liver is a primary site of inflammation. Primary mouse hepatocytes were cultured under hypoxia (1% O2) or normoxia (21% O2) for 1–72 h, and both the cell supernatants and protein lysates were assayed for 18 inflammatory mediators ...
Tópico(s): Sepsis Diagnosis and Treatment
2013 - Public Library of Science | PLoS ONE
Nabil Azhar, Cordelia Ziraldo, Derek Barclay, David A. Rudnick, Robert H. Squires, Yoram Vodovotz,
Background Tools to predict death or spontaneous survival are necessary to inform liver transplantation (LTx) decisions in pediatric acute liver failure (PALF), but such tools are not available. Recent data suggest that immune/inflammatory dysregulation occurs in the setting of acute liver failure. We hypothesized that specific, dynamic, and measurable patterns of immune/inflammatory dysregulation will correlate with outcomes in PALF. Methods We assayed 26 inflammatory mediators on stored serum samples ...
Tópico(s): Sepsis Diagnosis and Treatment
2013 - Public Library of Science | PLoS ONE
Simone Ziraldo, Alessandro Silva, Giuseppe E. Santoro,
We study the unitary relaxation dynamics of disordered spin chains following a sudden quench of the Hamiltonian. We give analytical arguments, corroborated by specific numerical examples, to show that the existence of a stationary state depends crucially on the spectral and localization properties of the final Hamiltonian, and not on the initial state. We test these ideas on integrable one-dimensional models of the Ising or XY class, but argue more generally on their validity for more complex (nonintegrable) ...
Tópico(s): Quantum Chromodynamics and Particle Interactions
2012 - American Physical Society | Physical Review Letters
Gary F. Nieman, David Brown, Joydeep Sarkar, Brian D. Kubiak, Cordelia Ziraldo, Joyeeta Dutta‐Moscato, Christopher J. Vieau, Derek Barclay, Louis A. Gatto, Kristopher G. Maier, Gregory Constantine, Timothy R. Billiar, Rubén Zamora, Qi Mi, Steve W. C. Chang, Yoram Vodovotz,
Objective: To gain insights into individual variations in acute inflammation and physiology. Design: Large-animal study combined with mathematical modeling. Setting: Academic large-animal and computational laboratories. Subjects: Outbred juvenile swine. Interventions: Four swine were instrumented and subjected to endotoxemia (100 µg/kg), followed by serial plasma sampling. Measurements and Main Results: Swine exhibited various degrees of inflammation and acute lung injury, including one death with ...
Tópico(s): Immune cells in cancer
2012 - Lippincott Williams & Wilkins | Critical Care Medicine
Qi Mi, Gregory Constantine, Cordelia Ziraldo, Alexey Solovyev, Andrés Torres, Rajaie Namas, Timothy Bentley, Timothy R. Billiar, Rubén Zamora, Juan Carlos Puyana, Yoram Vodovotz,
Background Complex biological processes such as acute inflammation induced by trauma/hemorrhagic shock/ (T/HS) are dynamic and multi-dimensional. We utilized multiplexing cytokine analysis coupled with data-driven modeling to gain a systems perspective into T/HS. Methodology/Principal Findings Mice were subjected to surgical cannulation trauma (ST) ± hemorrhagic shock (HS; 25 mmHg), and followed for 1, 2, 3, or 4 h in each case. Serum was assayed for 20 cytokines and NO2−/NO3−. These data were analyzed ...
Tópico(s): Influenza Virus Research Studies
2011 - Public Library of Science | PLoS ONE
Qi Mi, Nicole Y. K. Li‐Jessen, Cordelia Ziraldo, Ali Ghuma, Maxim Mikheev, Robert H. Squires, David O. Okonkwo, Katherine Verdolini-Abbott, Gregory Constantine, Gary An, Yoram Vodovotz,
A central goal of industrialized nations is to provide personalized, pre-emptive and predictive medicine, while maintaining healthcare costs at a minimum. To do so, we must confront and gain an understanding of inflammation, a complex, nonlinear process central to many diseases that affect both industrialized and developing nations. Herein, we describe the work aimed at creating a rational, engineering-oriented and evidence-based synthesis of inflammation geared towards rapid clinical application. ...
Tópico(s): Immune cells in cancer
2010 - Future Medicine | Personalized Medicine
Alexey Solovyev, Maxim Mikheev, Leming Zhou, Joyeeta Dutta‐Moscato, Cordelia Ziraldo, Gary An, Yoram Vodovotz, Qi Mi,
Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform ...
Tópico(s): Gene Regulatory Network Analysis
2010 - IGI Global | International Journal of Agent Technologies and Systems
Jeffrey W. Stewart, Linda Bramble, Donald Ziraldo,
Abstract Purpose – The purpose of this paper is to present recommendations for future growth and continued success of wine and culinary tourism in the Niagara region. Design/methodology/approach – Through industry interviews with practitioners, researchers and stakeholders the recommendations of this paper were formed. Secondary research examined the issues and advances made in other area of the globe specific to wine and culinary tourism. The research is intended to cover the issues associated with ...
Tópico(s): Sport and Mega-Event Impacts
2008 - Emerald Publishing Limited | International Journal of Contemporary Hospitality Management
Maire E. Percy, Sharon Moalem, Ángeles García, Martin J. Somerville, Mark Hicks, David Andrews, Azar Azad, Peter Schwarz, Reza Beheshti Zavareh, Rivka Birkan, Clara M. Choo, Vinca Chow, Sandeep Dhaliwal, Victoria Duda, Anthony L. Kupferschmidt, K.W. Lam, Deborah Lightman, Karolina Machalek, Wanna Mar, Frank Nguyen, Piotr J. Rytwinski, Erin Svara, Maithy Tran, Lisa Yeung, Katherine Zanibbi, Rebecca Zener, Melissa Ziraldo, Morris Freedman,
Dysregulation of iron homeostasis is implicated in Alzheimer's disease (AD). In this pilot study, common variants of the apolipoprotein E (APOE) and HFE genes resulting in the iron overload disorder of hereditary hemochromatosis (C282Y, H63D and S65C
Tópico(s): Hemoglobinopathies and Related Disorders
2008 - IOS Press | Journal of Alzheimer s Disease