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Sanchon L, Bardaji M, Labro M, Curto J, Soto C, Puig A, Pastor JC, Gómez C, Osorio A, Guariglia C, Pardo S, Vidal C, Collera P. Oncological monitoring after transanal total mesorectal excision (TaTME) for rectal neoplasia. Tech Coloproctol 2023; 27:739-746. [PMID: 36648600 DOI: 10.1007/s10151-023-02755-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND The surgical treatment of choice for rectal neoplasia is total mesorectal excision (TME). The transanal approach enables a better approach in male and obese patients and/or those with a narrow pelvis and in patients with small tumors. Short-term results are comparable with those for laparoscopy or the open approach, but the medium- and long-term oncological data are sparse. The aim of the present study was to evaluate our early experience with transanal TME (TaTME). METHODS This was a retrospective study conducted on patients who underwent TaTME at our center between August 2013 and April 2017 with a follow-up ≥ 3 years. Histopathology, complications, mortality, neoplastic recurrence and disease-free survival were analyzed. RESULTS One hundred patients (68 men and 32 women,, median age 66.8 years [range 29.6-91.2 years]) were included. There were 67 T3 cases (67%) with 74 N0 cases (74%), the mesorectal quality was graded optimal for 87.6% and only 2 cases of radial margin involvement were detected (2%). The median follow-up period was 47.6 months (range 11.8-78.9 months). Eighteen cases of recurrence were diagnosed, of which 3 (3%) recurred locally with an average disease-free period of 43.1 months. Overall survival was 80% and mortality due to progression of disease was 13%. CONCLUSIONS TaTME is a safe surgical procedure with surgical, anatomopathological and oncological results at 3 years (medium-term) comparable with those for the laparoscopic and open approaches. Better monitoring is required with studies of the long-term functional and quality of life outcomes, i.e., at 5 or 10 years.
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Affiliation(s)
- L Sanchon
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain.
| | - M Bardaji
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - M Labro
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - J Curto
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - C Soto
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - A Puig
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - J C Pastor
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - C Gómez
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - A Osorio
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - C Guariglia
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - S Pardo
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - C Vidal
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
| | - P Collera
- General Surgery and Digestive System Department, Althaia Foundation, Xarxa Assistencial Universitaria de Manresa, Barcelona, Spain
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Loras C, Ruiz-Ramirez P, Romero J, Andújar X, Bargallo J, Bernardos E, Boscá-Watts MM, Brugiotti C, Brunet E, Busquets D, Cerrillo E, Cortina FJ, Díaz-Milanés JA, Dueñas C, Farrés R, Golda T, González-Huix F, Gornals JB, Guardiola J, Julià D, Lira A, Llaó J, Mañosa M, Marin I, Millán M, Monfort D, Moro D, Mullerat J, Navarro M, Pérez Roldán F, Pijoan E, Pons V, Reyes J, Rufas M, Sainz E, Sanchiz V, Serracant A, Sese E, Soto C, Troya J, Zaragoza N, Tebé C, Paraira M, Sudrià-Lopez E, Mayor V, Fernández-Bañares F, Esteve M. Endoscopic treatment (endoscopic balloon dilation/self-expandable metal stent) vs surgical resection for the treatment of de novo stenosis in Crohn's disease (ENDOCIR study): an open-label, multicentre, randomized trial. Trials 2023; 24:432. [PMID: 37365665 DOI: 10.1186/s13063-023-07447-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Stenosis is one of the most common complications in patients with Crohn's disease (CD). Endoscopic balloon dilation (EBD) is the treatment of choice for a short stenosis adjacent to the anastomosis from previous surgery. Self-expandable metal stents (SEMS) may be a suitable treatment option for longer stenoses. To date, however, there is no scientific evidence as to whether endoscopic (EBD/SEMS) or surgical treatment is the best approach for de novo or primary stenoses that are less than 10 cm in length. METHODS/DESIGN Exploratory study as "proof-of-concept", multicentre, open-label, randomized trial of the treatment of de novo stenosis in the CD; endoscopic treatment (EBD/SEMS) vs surgical resection (SR). The type of endoscopic treatment will initially be with EDB; if a therapeutic failure occurs, then a SEMS will be placed. We estimate 2 years of recruitment and 1 year of follow-up for the assessment of quality of life, costs, complications, and clinical recurrence. After the end of the study, patients will be followed up for 3 years to re-evaluate the variables over the long term. Forty patients with de novo stenosis in CD will be recruited from 15 hospitals in Spain and will be randomly assigned to the endoscopic or surgical treatment groups. The primary aim will be the evaluation of the patient quality of life at 1 year follow-up (% of patients with an increase of 30 points in the 32-item Inflammatory Bowel Disease Questionnaire (IBDQ-32). The secondary aim will be evaluation of the clinical recurrence rate, complications, and costs of both treatments at 1-year follow-up. DISCUSSION The ENDOCIR trial has been designed to determine whether an endoscopic or surgical approach is therapeutically superior in the treatment of de novo stenosis in CD. TRIAL REGISTRATION ClinicalTrials.gov NCT04330846. Registered on 1 April 1 2020. https://clinicaltrials.gov/ct2/home.
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Affiliation(s)
- Carme Loras
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain.
| | - Pablo Ruiz-Ramirez
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Juan Romero
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
| | - Xavier Andújar
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | | | - Esther Bernardos
- Hospital General La Mancha Centro, Alcázar de San Juan, Ciudad Real, Spain
| | | | | | - Eduard Brunet
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Corporació Sanitària Universitària Parc Taulí, Sabadell, Spain
| | - David Busquets
- Hospital Universitari de Girona Dr. Josep Trueta, Girona, Spain
| | - Elena Cerrillo
- Hospital Universitari i Politècnic la Fe, Valencia, Spain
| | | | | | | | | | - Thomas Golda
- Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | | | - Joan B Gornals
- Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Jordi Guardiola
- Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - David Julià
- Hospital Universitari de Girona Dr. Josep Trueta, Girona, Spain
| | - Alba Lira
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Corporació Sanitària Universitària Parc Taulí, Sabadell, Spain
| | - Jordina Llaó
- Althaia, Xarxa Assistencial Universitaria de Manresa, Manresa, Spain
| | - Miriam Mañosa
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Ingrid Marin
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Mónica Millán
- Hospital Universitari i Politècnic la Fe, Valencia, Spain
| | | | - David Moro
- Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Josep Mullerat
- Hospital de Sant Joan Despí Moisès Broggi, Sant Joan Despí, Spain
| | - Mercè Navarro
- Hospital de Sant Joan Despí Moisès Broggi, Sant Joan Despí, Spain
| | | | | | - Vicente Pons
- Hospital Universitari i Politècnic la Fe, Valencia, Spain
| | - José Reyes
- Hospital Comarcal d'Inca, Inca, Mallorca, Spain
- IdISBa- Institut de Investigació Sanitaria de les Illes Balears, Palma, Spain
| | - María Rufas
- Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Empar Sainz
- Althaia, Xarxa Assistencial Universitaria de Manresa, Manresa, Spain
| | | | - Anna Serracant
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Corporació Sanitària Universitària Parc Taulí, Sabadell, Spain
| | - Eva Sese
- Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Cristina Soto
- Althaia, Xarxa Assistencial Universitaria de Manresa, Manresa, Spain
| | - Jose Troya
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | - Cristian Tebé
- Unitat de Bioestadística, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Marta Paraira
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
| | - Emma Sudrià-Lopez
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Vicenç Mayor
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
| | - Fernando Fernández-Bañares
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Maria Esteve
- Endoscopy Unit, Department of Digestive Diseases, Hospital Universitari Mútua Terrassa, Plaça Dr Robert n° 5, Terrassa, Barcelona, 08221, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
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Joshi Y, Scheuer S, Soto C, Chew H, Hwang B, Iyer A, Connellan M, Watson A, Granger E, Jansz P, MacDonald P. Pushing The Boundaries of Donation After Circulatory Death Heart Transplantation - The Australian Experience. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Ponce DM, Alousi AM, Nakamura R, Slingerland J, Calafiore M, Sandhu KS, Barker JN, Devlin S, Shia J, Giralt S, Perales MA, Moore G, Fatmi S, Soto C, Gomes A, Giardina P, Marcello L, Yan X, Tang T, Dreyer K, Chen J, Daley WL, Peled JU, van den Brink MRM, Hanash AM. A phase 2 study of interleukin-22 and systemic corticosteroids as initial treatment for acute GVHD of the lower GI tract. Blood 2023; 141:1389-1401. [PMID: 36399701 PMCID: PMC10163318 DOI: 10.1182/blood.2021015111] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 10/12/2022] [Accepted: 10/29/2022] [Indexed: 11/19/2022] Open
Abstract
Graft-versus-host disease (GVHD) is a major cause of morbidity and mortality following allogeneic hematopoietic transplantation. In experimental models, interleukin-22 promotes epithelial regeneration and induces innate antimicrobial molecules. We conducted a multicenter single-arm phase 2 study evaluating the safety and efficacy of a novel recombinant human interleukin-22 dimer, F-652, used in combination with systemic corticosteroids for treatment of newly diagnosed lower gastrointestinal acute GVHD. The most common adverse events were cytopenias and electrolyte abnormalities, and there were no dose-limiting toxicities. Out of 27 patients, 19 (70%; 80% confidence interval, 56%-79%) achieved a day-28 treatment response, meeting the prespecified primary endpoint. Responders exhibited a distinct fecal microbiota composition characterized by expansion of commensal anaerobes, which correlated with increased overall microbial α-diversity, suggesting improvement of GVHD-associated dysbiosis. This work demonstrates a potential approach for combining immunosuppression with tissue-supportive strategies to enhance recovery of damaged mucosa and promote microbial health in patients with gastrointestinal GVHD. This trial was registered at www.clinicaltrials.gov as NCT02406651.
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Affiliation(s)
- Doris M. Ponce
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College; New York, NY
| | - Amin M. Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryotaro Nakamura
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA
| | - John Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marco Calafiore
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karamjeet S. Sandhu
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA
| | - Juliet N. Barker
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College; New York, NY
| | - Sean Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio Giralt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College; New York, NY
| | - Miguel-Angel Perales
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College; New York, NY
| | - Gillian Moore
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samira Fatmi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Cristina Soto
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonio Gomes
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul Giardina
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - LeeAnn Marcello
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaoqiang Yan
- Evive Biotechnology (Shanghai) Ltd (formerly Generon [Shanghai] Corporation Ltd), Shanghai, China
| | - Tom Tang
- Evive Biotechnology (Shanghai) Ltd (formerly Generon [Shanghai] Corporation Ltd), Shanghai, China
| | - Kevin Dreyer
- Evive Biotechnology (Shanghai) Ltd (formerly Generon [Shanghai] Corporation Ltd), Shanghai, China
| | - Jianmin Chen
- Evive Biotechnology (Shanghai) Ltd (formerly Generon [Shanghai] Corporation Ltd), Shanghai, China
| | - William L. Daley
- Evive Biotechnology (Shanghai) Ltd (formerly Generon [Shanghai] Corporation Ltd), Shanghai, China
| | - Jonathan U. Peled
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College; New York, NY
| | - Marcel R. M. van den Brink
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College; New York, NY
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alan M. Hanash
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College; New York, NY
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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Soto C, Gázquez JMM, Llorente M. Hand preferences in coordinated bimanual tasks in non-human primates: A systematic review and meta-analysis. Neurosci Biobehav Rev 2022; 141:104822. [PMID: 35961384 DOI: 10.1016/j.neubiorev.2022.104822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/02/2022] [Accepted: 08/07/2022] [Indexed: 11/17/2022]
Abstract
The evolutionary significance of hand preferences among non-human primates and humans has been studied for decades with the aim of determining the origins of the population-level tendency. In this study, a meta-analysis was conducted to statistically integrate data on hand preferences in non-human primates performing the tube task and other bimanual tasks to determine the presence and direction of manual laterality. Significant individual-level lateralization was obtained for these bimanual tasks. In nonhuman primates, 82% of the animals analysed showed right or left-hand preference performing the tube task, this figure being 90% for other bimanual tasks. In contrast with humans, no asymmetry was found at the population level. Additionally, population-level preferences were not found in either of the tasks, although a strong manual preference was found when performing the tube task and other bimanual tasks. Species was studied as a variable moderator throughout the meta-analysis. These results highlight the importance of standardized testing methodologies across species and institutions to obtain comparable data and fill the gaps in the taxonomy.
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Affiliation(s)
- Cristina Soto
- Fundació UdG: Innovació i Formació, Universitat de Girona, Carrer Pic de Peguera 11, 17003 Girona, Spain
| | - José M M Gázquez
- Fundació UdG: Innovació i Formació, Universitat de Girona, Carrer Pic de Peguera 11, 17003 Girona, Spain
| | - Miquel Llorente
- Fundació UdG: Innovació i Formació, Universitat de Girona, Carrer Pic de Peguera 11, 17003 Girona, Spain; Grup de Recerca "Llenguatge i Cognició", Departament de Psicologia, Facultat d'Educació i Psicologia, Universitat de Girona, Plaça Sant Domènec 9, 17004 Girona, Spain.
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Joshi Y, Scheuer S, Soto C, Hwang B, Zhao C, Chew H, Iyer A, Watson A, Connellan M, Granger E, Jansz P, Macdonald P. Heart Transplantation from Donation After Circulatory Death Donors: An Update on the Australian Experience. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Soto C, Algee-Hewitt B, Morante G, Slice D, Steadman D. Age-at-Death Estimation for Modern Populations in Mexico and Puerto Rico through the Use of 3D Laser Scans of the Pubic Symphysis. Hum Biol 2022. [DOI: 10.1353/hub.2017.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Anthony AK, Niu CY, Wang RS, Wieske J, Brown KW, Chajecki Z, Lynch WG, Ayyad Y, Barney J, Baumann T, Bazin D, Beceiro-Novo S, Boza J, Chen J, Cook KJ, Cortesi M, Ginter T, Mittig W, Pype A, Smith MK, Soto C, Sumithrarachchi C, Swaim J, Sweany S, Teh FCE, Tsang CY, Tsang MB, Watwood N, Wuosmaa AH. Beam particle identification and tagging of incompletely stripped heavy beams with HEIST. Rev Sci Instrum 2022; 93:013306. [PMID: 35104937 DOI: 10.1063/5.0068180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
A challenge preventing successful inverse kinematics measurements with heavy nuclei that are not fully stripped is identifying and tagging the beam particles. For this purpose, the HEavy ISotope Tagger (HEIST) has been developed. HEIST utilizes two micro-channel plate timing detectors to measure the time-of-flight, a multi-sampling ion chamber to measure energy loss, and a high-purity germanium detector to identify isomer decays and calibrate the isotope identification system. HEIST has successfully identified 198Pb and other nearby nuclei at energies of about 75 MeV/A. In the experiment discussed, a typical cut containing 89% of all 198Pb80+ in the beam had a purity of 86%. We examine the issues of charge state contamination. The observed charge state populations of these ions are presented and, using an adjusted beam energy, are well described by the charge state model GLOBAL.
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Affiliation(s)
- A K Anthony
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - C Y Niu
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - R S Wang
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - J Wieske
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - K W Brown
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Z Chajecki
- Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - W G Lynch
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Y Ayyad
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - J Barney
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - T Baumann
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - D Bazin
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - S Beceiro-Novo
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - J Boza
- Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - J Chen
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - K J Cook
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - M Cortesi
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - T Ginter
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - W Mittig
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - A Pype
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - M K Smith
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - C Soto
- Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - C Sumithrarachchi
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - J Swaim
- Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - S Sweany
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - F C E Teh
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - C Y Tsang
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - M B Tsang
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - N Watwood
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - A H Wuosmaa
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
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9
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Ramos GG, West AE, Begay C, Telles VM, D'Isabella J, Antony V, Soto C. Substance use disorder and homelessness among American Indians and Alaska Natives in California. J Ethn Subst Abuse 2021; 22:350-371. [PMID: 34339341 DOI: 10.1080/15332640.2021.1952125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
American Indian and Alaska Native (AIAN) communities have higher rates of substance use than other racial and ethnic groups. Substance use disorder (SUD) is tied to the increased risk of experiencing homelessness. National policies have also led to the disproportionate rates of homelessness among AIAN communities. However, specific experiences related to the occurrence of SUD and homelessness among AIAN in California, as well as seeking and accessing SUD treatment, are not well understood. This study explored potential SUD risk and resilience factors for AIANs experiencing homelessness and their experiences when seeking services for SUD. Nineteen interviews were conducted in northern, central, and southern California. Thematic analysis was used for these data. The five primary codes were: (1) risk factors for SUD, (2) resilience related to SUD service seeking, (3) services available, (4) barriers accessing services, and (5) services needed. Based on the results, themes for risk were trauma, mental health, and community conditions. Themes for resilience were identified at individual and community levels and included personal motivation and community support and inclusiveness. Themes for services available were limited knowledge about service types and services' location. The themes for barriers accessing services were identified at internal and external levels, and included lack of readiness and transportation challenges, respectively. Themes for services needed included continuum of care, integrated care, and culturally sensitive services. Findings highlight the importance of addressing the potential risk factors and service needs of AIANs experiencing homelessness to provide comprehensive and culturally sensitive services to reduce substance use.
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Affiliation(s)
- G G Ramos
- University of Southern California, Los Angeles, CA, USA
| | - A E West
- University of Southern California, Los Angeles, CA, USA
| | - C Begay
- University of Southern California, Los Angeles, CA, USA
| | - V M Telles
- University of Southern California, Los Angeles, CA, USA
| | - J D'Isabella
- University of Southern California, Los Angeles, CA, USA
| | - V Antony
- University of Southern California, Los Angeles, CA, USA
| | - C Soto
- University of Southern California, Los Angeles, CA, USA
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10
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Rodriguez N, Lee J, Flynn L, Murray F, Devlin SM, Soto C, Cho C, Dahi P, Giralt S, Perales MA, Sauter C, Ponce DM. Oral Proteasome Inhibitor Ixazomib for Switch-Maintenance Prophylaxis of Recurrent or Late Acute and Chronic Graft-versus-Host Disease after Day 100 in Allogeneic Stem Cell Transplantation. Transplant Cell Ther 2021; 27:920.e1-920.e9. [PMID: 34029766 DOI: 10.1016/j.jtct.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/03/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
Graft-versus-host disease (GVHD) is a frequent complication in the first year after allogeneic stem cell transplantation (allo-HCT). Recipients of reduced-intensity (RI) or nonmyeloablative (NMA) conditioning combined with calcineurin inhibitor (CNI)-based GVHD prophylaxis frequently develop GVHD in the context of immunosuppression taper. Ixazomib is an oral proteasome inhibitor with a wide safety profile that has demonstrated immunomodulatory properties, inhibition of pro-inflammatory cytokines, and anti-tumor activity. We hypothesized that switch-maintenance GVHD prophylaxis using ixazomib would facilitate CNI taper without increased GVHD frequency and severity while maintaining graft-versus-tumor (GVT) effect and an acceptable safety profile. We conducted an open-label, prospective, single-center pilot study in patients with hematologic malignancies who received an RI or NMA conditioning and CNI-based GVHD prophylaxis that were within day 100 to 150 after HCT (n = 18). Patients were treated with ixazomib once weekly on a 28-day cycle (3 weeks on, 1 week off). Treatment was safe; most adverse events were grade 1 or 2, with cytopenia and elevation in transaminases the most common. Five patients were removed from the study because of toxicity or side effects. Only 5 of 18 patients developed GVHD during the study, and its severity was driven by acute manifestations while chronic involvement was mild. The cumulative incidence of grade II-IV acute and chronic GVHD at 1-year after HCT was 33% (95% confidence interval [CI], 13-55). No patients died during the study, and only 1 had malignant relapse. An additional patient relapsed after completion of the study but within 1 year after HCT. The probability of progression-free survival and GVHD-free/relapse-free survival (composite endpoint) at 1 year were 89% (95% CI, 75-100) and 78% (95% CI, 61-100), respectively. Immune reconstitution analysis showed a rapid and sustained recovery in T-cell subpopulations and B cell reconstitution, and vaccine response in a subset of patients demonstrated continuing or de novo positive protective antibody titers. This study demonstrated low incidence of recurrent and late acute and chronic GVHD within 1 year after HCT possible associated with switch-maintenance GVHD prophylaxis using ixazomib. This approach allowed for CNI taper while preserving GVT effect, without aggravating GVHD. Our findings support further development of this approach and provide a proof-of-concept for switch-maintenance GVHD prophylaxis.
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Affiliation(s)
- Natasia Rodriguez
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jasme Lee
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lisa Flynn
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fiona Murray
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sean M Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cristina Soto
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina Cho
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Parastoo Dahi
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Sergio Giralt
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Miguel-Angel Perales
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Craig Sauter
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Doris M Ponce
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York.
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Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Chen S, Coates L, Cooper C, Demerdash O, Daidone I, Eblen J, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller D, Kovalevsky A, Larkin J, Lawrence T, LeGrand S, Liu SH, Mitchell J, Park G, Parks J, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen Y, Smith J, Smith M, Soto C, Tsaris A, Thavappiragasam M, Tillack A, Vermaas J, Vuong V, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J Chem Inf Model 2020; 60:5832-5852. [PMID: 33326239 PMCID: PMC7754786 DOI: 10.1021/acs.jcim.0c01010] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.
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Affiliation(s)
- A. Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - R. Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M. Baker
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - J. Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - D. Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - S. Boehm
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - K. G. Byler
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - S.Y. Chen
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - L. Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C.J. Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - O. Demerdash
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - I. Daidone
- Department of Physical and Chemical Sciences, University of L’Aquila, I-67010 L’Aquila, Italy
| | - J.D. Eblen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - S. Ellingson
- University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington KY, 40536, USA
| | - S. Forli
- Scripps Research, La Jolla, CA, 92037, USA
| | - J. Glaser
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - J. C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - J. Gunnels
- HPC Engineering, Amazon Web Services, Seattle, WA 98121, USA
| | - O. Hernandez
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - D.W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - A. Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J. Larkin
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - T.J. Lawrence
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. LeGrand
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - S.-H. Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - J.C. Mitchell
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - G. Park
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - J.M. Parks
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - A. Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - L. Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - D. Poole
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - L. Pouchard
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Ramanathan
- Data Science and Learning Division, Argonne National Lab, Lemont, IL 60439, USA
| | - D. Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - A. Sedova
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - Y. Shen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - J.C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - M.D. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - C. Soto
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Tsaris
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - J.V. Vermaas
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - V.Q. Vuong
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - J. Yin
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - S. Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - M. Zahran
- Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, NY 11201, USA
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12
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Soto C, Aguilar Lugo C, Rodríguez S, Palacio L, Lozano Á, Prádanos P, Hernandez A. Enhancement of CO2/CH4 permselectivity via thermal rearrangement of mixed matrix membranes made from an o-hydroxy polyamide with an optimal load of a porous polymer network. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.116895] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Larkin J, Lawrence TJ, LeGrand S, Liu SH, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen S, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasam M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. ChemRxiv 2020:12725465. [PMID: 33200117 PMCID: PMC7668744 DOI: 10.26434/chemrxiv.12725465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/29/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.
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Affiliation(s)
- A Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - R Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - M Baker
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - J Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899
| | - D Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - S Boehm
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - K G Byler
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899
| | - L Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - S Y Chen
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - C J Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - O Demerdash
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - I Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - J D Eblen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - S Ellingson
- University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington KY, 40536
| | - S Forli
- Scripps Research, La Jolla, CA, 92037
| | - J Glaser
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - J C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - J Gunnels
- HPC Engineering, Amazon Web Services, Seattle, WA 98121
| | - O Hernandez
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996
| | - J Larkin
- NVIDIA Corporation, Santa Clara, CA 95051
| | - T J Lawrence
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S LeGrand
- NVIDIA Corporation, Santa Clara, CA 95051
| | - S-H Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - J C Mitchell
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - G Park
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - J M Parks
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - A Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - L Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - D Poole
- NVIDIA Corporation, Santa Clara, CA 95051
| | - L Pouchard
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - A Ramanathan
- Data Science and Learning Division, Argonne National Lab, Lemont, IL 60439
| | - D Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | | | | | - A Sedova
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S Shen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - J C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - M D Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - C Soto
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - A Tsaris
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | | | | | - J V Vermaas
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - V Q Vuong
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996
| | - J Yin
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - S Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - M Zahran
- Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, NY 11201
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Scheuer S, Chew H, Soto C, Hicks M, Gao L, Villanueva J, Kawanishi Y, Watson A, Connellan M, Granger E, Jansz P, Macdonald P. Getting the Time Right: What Matters, What Doesn't, and How Should We Really Be Defining Ischemic Times in DCD Withdrawals? J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.1042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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15
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Ponce DM, Alousi AM, Nakamura R, Sandhu KS, Barker JN, Shia J, Yan X, Daley WL, Moore G, Fatmi S, Soto C, Gomes A, Slingerland J, Giardina P, Peled JU, van den Brink MR, Hanash AM. A Phase 2 Study of F-652, a Novel Tissue-Targeted Recombinant Human Interleukin-22 (IL-22) Dimer, for Treatment of Newly Diagnosed Acute Gvhd of the Lower GI Tract. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Soto C, Smolentsev S, García-Rosales C. Mitigation of MHD phenomena in DCLL blankets by Flow Channel Inserts based on a SiC-sandwich material concept. Fusion Engineering and Design 2020. [DOI: 10.1016/j.fusengdes.2019.111381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Soto C, García-Rosales C, Echeberria J. Production of porous SiC by liquid phase sintering using graphite as sacrificial phase: Influence of SiO2 and graphite on the sintering mechanisms. Ann Ital Chir 2019. [DOI: 10.1016/j.jeurceramsoc.2019.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Soto C, García-Rosales C, Echeberria J, Platacis E, Shisko A, Muktepavela F, Malo M, Hernández T. Characterization and thermomechanical assessment of a SiC-sandwich material for Flow Channel Inserts in DCLL blankets. Fusion Engineering and Design 2019. [DOI: 10.1016/j.fusengdes.2019.03.082] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Chew H, Jabbour A, Keogh A, Kotlyar E, Hayward C, Macdonald P, Dhital K, Scheuer S, Iyer A, Connellan M, Soto C, Nair P, Watson A. Extracorporeal Membrane Oxygenation Post-Dead After Circulatory Death Heart Transplantation: A Retrospective Study. Heart Lung Circ 2019. [DOI: 10.1016/j.hlc.2019.02.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Soto C, Deemer ED. Communal Goals, Campus Racial Climate Perceptions, and Cultural Differences in Perceived Academic Satisfaction. The Career Development Quarterly 2018. [DOI: 10.1002/cdq.12120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cristina Soto
- Department of Educational Studies; Purdue University
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Rodríguez-Muñoz MDLF, Vallejo Slocker L, Olivares Crespo ME, Izquierdo Méndez N, Soto C, Le HN. [Psychometric properties of postpartum depression predictors inventory- revised- prenatal version in a sample of spanish pregnant women.]. Rev Esp Salud Publica 2017; 91:e201712047. [PMID: 29231186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/10/2017] [Indexed: 06/07/2023] Open
Abstract
OBJECTIVE Prenatal depression is a major public health problem, therefore predicting and preventing it is a relevant objective for public health agendas. Consequently, it is important to have adequate screening tools to detect risk factors associated with prenatal depression. The aim of this study was to evaluate the psychometric properties reliability and factor structure of the Spanish version of the Postpartum Depression Predictors Inventory- Revised- Prenatal Version (PDI-R) in pregnant women who attend prenatal care in an urban hospital in Spain. METHODS The sample was formed of 445 women receiving prenatal care in an obstetrics clinic in an urban public hospital in Madrid, Spain. The internal consistency of PDPI-R was assessed by measuring Cronbach's Alfa index, calculating the COR curve and percentiles for this sample. RESULTS The PDPI-R showed good internal consistency in this sample (Cronbach's Alfa = 0,855). The area under the COR curve is 0,84 p≤0,001. Sensibility and specificity values were 62,3% and 69,5% respectively, and the cut-off point with greatest sensibility and specificity was 4. CONCLUSIONS The PDPI-R is reliable and can be used to screen for risk factor for depression during pregnancy.
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Affiliation(s)
- María de la Fe Rodríguez-Muñoz
- Departamento de Personalidad, Evaluación y Tratamiento Psicológico. Facultad de Psicología. Universidad Nacional de Educación a Distancia. Madrid. España
| | - Laura Vallejo Slocker
- Departamento de Personalidad, Evaluación y Tratamiento Psicológico. Facultad de Psicología. Universidad Nacional de Educación a Distancia. Madrid. España
| | - María Eugenia Olivares Crespo
- Departamento de Ginecología y Obstetricia. Instituto de la Mujer José Botella Llusiá. Hospital Clínico San Carlos. Facultad de Medicina. Universidad Complutense. Madrid. España
| | - Nuria Izquierdo Méndez
- Departamento de Ginecología y Obstetricia. Instituto de la Mujer José Botella Llusiá. Hospital Clínico San Carlos. Facultad de Medicina. Universidad Complutense. Madrid. España
| | - Cristina Soto
- Departamento de Ginecología y Obstetricia. Hospital Universitario Central de Asturias. Oviedo. España
| | - Huynh-Nhu Le
- Departamento de Psicología. George Washington University. Washington DC. EEUU
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Soto C, Concha-Marambio L, Pritzkow S. Protein amplification from peripheral tissues. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Chew H, Cheong C, Fulton M, Shah M, Doyle A, Gao L, Villanueva J, Soto C, Hicks M, Connellan M, Granger E, Jansz P, Spratt P, Hayward C, Keogh A, Kotlyar E, Jabbour A, Dhital K, Macdonald P. Outcome After Warm Machine Perfusion (WMP) Recovery of Marginal Brain Dead (MBD) and Donation After Circulatory Death (DCD) Heart Transplantation. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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24
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Dhital K, Connellan M, Chew H, Iyer A, Soto C, Dinale A, Granger E, Jansz P, Hayward C, Jabbour A, Keogh A, Kotlyar E, Spratt P, Macdonald P. Rapid Retrieval and Ex Situ Portable Machine Perfusion Allows Successful Cardiac Transplantation with Donor Hearts from Controlled Donation After Circulatory Death. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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25
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Connellan M, Chew H, Iyer A, Soto C, Macdonald P, Dhital K. Warm Ischaemic Time for Donation After Circulatory Death Heart Donors - How Long Is Too Long? J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.1102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Abstract
Threatening stereotypes have been theorized as having negative consequences for domain identification among members of the stigmatized groups. The present research tested this disidentification hypothesis among college women ( N = 650) in academic majors that should be vulnerable (i.e., science and engineering) and immune (e.g., humanities and education) to these theorized effects. Results of structural equation modeling analyses were consistent with theoretical expectations, as stereotype threat was negatively and indirectly associated with the adoption of self- and task-approach achievement goals through its relationship with science identity for science and engineering majors but not women in nonstereotyped majors. For the latter group, stereotype threat bypassed science identity and was instead both directly and indirectly related to approach motivation. Implications for academic/career motivation, science identity, and career counseling intervention are discussed.
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Affiliation(s)
- Eric D. Deemer
- Department of Educational Studies, Purdue University, West Lafayette, IN, USA
| | - Chaihua Lin
- Department of Educational Studies, Purdue University, West Lafayette, IN, USA
| | - Cristina Soto
- Department of Educational Studies, Purdue University, West Lafayette, IN, USA
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Connellan M, Chew H, Iyer A, Watson A, Soto C, Dinale A, Nair P, Granger E, Jansz P, Jabbour A, Kotlyar E, Keogh A, Hayward C, Spratt P, MacDonald P, Dhital K. Early Results of Heart Transplantation Using Donation after Circulatory Death Donors. J Heart Lung Transplant 2016. [DOI: 10.1016/j.healun.2016.01.233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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28
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Soto C, Tarrant C, Dixon-Woods M. What is the right approach to infection prevention and control for children living at home with invasive devices? J Hosp Infect 2016; 93:89-91. [PMID: 26944898 DOI: 10.1016/j.jhin.2015.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/23/2015] [Indexed: 11/16/2022]
Affiliation(s)
- C Soto
- Social Science Applied to Healthcare Improvement Research (SAPPHIRE) Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - C Tarrant
- Social Science Applied to Healthcare Improvement Research (SAPPHIRE) Group, Department of Health Sciences, University of Leicester, Leicester, UK.
| | - M Dixon-Woods
- Social Science Applied to Healthcare Improvement Research (SAPPHIRE) Group, Department of Health Sciences, University of Leicester, Leicester, UK
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Soto C, Bugueño I, Hoare A, Gonzalez S, Venegas D, Salinas D, Melgar-Rodríguez S, Vernal R, Gamonal J, Quest AFG, Pérez-Donoso JM, Bravo D. The Porphyromonas gingivalis O antigen is required for inhibition of apoptosis in gingival epithelial cells following bacterial infection. J Periodontal Res 2015; 51:518-28. [PMID: 26530544 DOI: 10.1111/jre.12331] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2015] [Indexed: 01/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Porphyromonas gingivalis infection induces apoptosis inhibition in gingival epithelial cells; however, it is not fully understood which bacterial effectors are involved in this process. The aim of this study is to evaluate whether the P. gingivalis lipopolysaccharide (LPS), specifically the O-antigen region, affects adherence, invasion, viability and apoptosis of gingival epithelial cells. MATERIAL AND METHODS Gingival epithelial cells (OKF6/TERT2 line) were infected by different freshly prepared P. gingivalis clinical isolates, obtained from subjects with chronic periodontitis (CP3 and CP4) and healthy individuals (H1 and H3). Periodontitis and healthy isolates show differences in O-antigen production, as healthy isolates lack the O-antigen region. In addition, cells were infected by a site-specific mutant lacking the O-antigen portion. After 24 h postinfection, cell proliferation, viability and apoptosis were evaluated by Trypan blue, MTS and annexin V assays, respectively. Bacterial invasion, adhesion and proliferation were measured by gentamicin/metronidazole protection assays. Finally, toll-like receptor (TLR)2 and TLR4 mRNA expression was evaluated by quantitative reverse transcription-polymerase chain reaction. Statistical analysis was performed using ANOVA, Tukey's or Dunnett's tests (p < 0.05). RESULTS At 24 h postinfection, strains lacking the O-antigen region (healthy isolates and O-antigen ligase-deficient strain) were unable to increase proliferation and viability, or decrease apoptosis as compared with strains producing intact LPS (periodontitis isolates and reference strain). However, the presence of the O-antigen neither contributed to changes in the ability of the bacteria to adhere to or invade cells, nor to intracellular survival. The presence of O-antigen also increased the expression of TLR4 (nearly sixfold), which correlated with inhibition of apoptosis. CONCLUSION The O-antigen region of P. gingivalis LPS is required to increase gingival epithelial cell viability upon infection by bacteria and this increase is attributable to a reduction in apoptosis. Moreover, although bacterial internalization is required, the effects observed are not due to alterations in P. gingivalis adherence, invasion or intracellular survival. Interestingly, inhibition of apoptosis correlates with increased TLR4 expression, suggesting a role for TLR4 in this process.
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Affiliation(s)
- C Soto
- Oral Microbiology Laboratory, Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - I Bugueño
- Oral Microbiology Laboratory, Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - A Hoare
- Oral Microbiology Laboratory, Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - S Gonzalez
- Oral Microbiology Laboratory, Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - D Venegas
- Oral Microbiology Laboratory, Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - D Salinas
- Oral Microbiology Laboratory, Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - S Melgar-Rodríguez
- Laboratory of Periodontal Biology, Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - R Vernal
- Laboratory of Periodontal Biology, Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - J Gamonal
- Laboratory of Periodontal Biology, Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - A F G Quest
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago, Chile.,Laboratory of Cell Communication, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - J M Pérez-Donoso
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, Santiago, Chile
| | - D Bravo
- Oral Microbiology Laboratory, Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
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Iyer A, Gao L, Doyle A, Rao P, Cropper JR, Soto C, Dinale A, Kumarasinghe G, Jabbour A, Hicks M, Jansz PC, Feneley MP, Harvey RP, Graham RM, Dhital KK, MacDonald PS. Normothermic ex vivo perfusion provides superior organ preservation and enables viability assessment of hearts from DCD donors. Am J Transplant 2015; 15:371-80. [PMID: 25612491 DOI: 10.1111/ajt.12994] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/11/2014] [Accepted: 08/25/2014] [Indexed: 01/25/2023]
Abstract
The shortage of donors in cardiac transplantation may be alleviated by the use of allografts from donation after circulatory death (DCD) donors. We have previously shown that hearts exposed to 30 min warm ischemic time and then flushed with Celsior supplemented with agents that activate ischemic postconditioning pathways, show complete recovery on a blood-perfused ex vivo working heart apparatus. In this study, these findings were assessed in a porcine orthotopic heart transplant model. DCD hearts were preserved with either normothermic ex vivo perfusion (NEVP) using a clinically approved device, or with standard cold storage (CS) for 4 h. Orthotopic transplantation into recipient animals was subsequently undertaken. Five of six hearts preserved with NEVP demonstrated favorable lactate profiles during NEVP and all five could be weaned off cardiopulmonary bypass posttransplant, compared with 0 of 3 hearts preserved with CS (p < 0.05, Fisher's exact test). In conclusion, DCD hearts flushed with supplemented Celsior solution and preserved with NEVP display viability before and after transplantation. Viability studies of human DCD hearts using NEVP are warranted.
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Affiliation(s)
- A Iyer
- The Victor Chang Cardiac Research Institute, Sydney, Australia; Heart & Lung Transplant Unit, St Vincent's Hospital, Darlinghurst, Australia; Department of Cardiothoracic Surgery, St Vincent's Hospital, Darlinghurst, Australia
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Abstract
Despite increasing evidence that negative stereotypes adversely affect the career development of women in science, technology, engineering, and mathematics, measuring their effects has been a challenge. This study focuses specifically on the sciences, since some, particularly physics, are notably imbalanced in terms of gender diversity. Our aim was to develop and begin to validate a measure of gender stereotypes in science, referred to as the Stereotype Threat in Science Scale-Gender (STSS-G). Participants consisted of 629 undergraduate women enrolled in biology, chemistry, and physics courses. Results of exploratory and factor mixture analyses yielded support for a 7-item scale consisting of two factors, social identity and identity threat, and five latent classes underlying a heterogeneous population. Results of structural equation modeling indicated that the two latent variables were significantly associated with scores on existing measures of science identity and stereotype threat. The construct, differential, and concurrent validity of the STSS-G are discussed.
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Affiliation(s)
- Eric D. Deemer
- Department of Educational Studies, Purdue University, West Lafayette, IN, USA
| | - Chaihua Lin
- Department of Educational Studies, Purdue University, West Lafayette, IN, USA
| | - Ryan Graham
- Department of Educational Studies, Purdue University, West Lafayette, IN, USA
| | - Cristina Soto
- Department of Educational Studies, Purdue University, West Lafayette, IN, USA
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Soto C, Raya L, Juárez J, Pérez J, González I. Effect of Silymarin in Pdx-1 expression and the proliferation of pancreatic β-cells in a pancreatectomy model. Phytomedicine 2014; 21:233-9. [PMID: 24176839 DOI: 10.1016/j.phymed.2013.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/27/2013] [Accepted: 09/19/2013] [Indexed: 06/02/2023]
Abstract
In type 1 Diabetes Mellitus (DM) there is a destruction of pancreatic β-cells (80-90%) at the time of detection, in DM type 2 these cells are decreased significantly. The Pdx1 transcription factor plays a central role in pancreatic development and in insulin gene expression. Previously, we have demonstrated that Silymarin recovers the normal morphology and endocrine function of damaged pancreatic tissue in alloxan induced diabetic rats. The aim of this study was to analyze the effect of Silymarin in Pdx1 gene expression and its repercussion on insulin gene expression and β-cell proliferation. 72 Wistar rats were partially pancreatectomized (60%) and divided into 12 groups. Six groups were treated daily with Silymarin (200mg/kg p.o.) for 3, 7, 14, 21, 42 and 63 day periods. Also, an unpancreatectomized control group was performed. At each time interval three animals from each group were administered BrdU 18 h before the sacrifice. Insulin and Pdx-1 gene expression were assessed by RT-PCR assay in total pancreatic RNA. β-Cell proliferation was determined by immunoperoxidase assay. In contrast to the animals that were only pancreatectomized, the Silymarin treatment induced an increase in both Pdx1 and insulin gene expression as well as β-cell proliferation in pancreatic tissue (control=2.6±0.28%; untreated=14.25±0.56%; treated=39.08±4.62%). Consequently, serum insulin levels rose (control=1.01±0.02 ng/ml; untreated=1.18±0.42 ng/ml; treated=4.58±0.58 ng/ml) and serum glucose levels decreased in these animals (control=6.2±0.01 mM; untreated=9.02±0.41 mM; treated=6.41±0.32 mM). These results suggest that Silymarin may induce the proliferation of insulin-producing cells.
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MESH Headings
- Animals
- Blood Glucose/metabolism
- Cell Differentiation
- Cell Proliferation
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 1/drug therapy
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/pathology
- Diabetes Mellitus, Type 2/drug therapy
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Disease Models, Animal
- Gene Expression/drug effects
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Insulin/blood
- Insulin/genetics
- Insulin/metabolism
- Insulin-Secreting Cells/cytology
- Insulin-Secreting Cells/drug effects
- Insulin-Secreting Cells/metabolism
- Male
- Silybum marianum/chemistry
- Pancreatectomy
- Phytotherapy
- Plant Extracts/pharmacology
- Plant Extracts/therapeutic use
- RNA/metabolism
- Rats
- Rats, Wistar
- Silymarin/pharmacology
- Silymarin/therapeutic use
- Trans-Activators/genetics
- Trans-Activators/metabolism
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Affiliation(s)
- C Soto
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Mexico.
| | - L Raya
- Facultad de Medicina, Universidad Nacional Autónoma de México, México, D.F., Mexico
| | - J Juárez
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Mexico
| | - J Pérez
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Mexico
| | - I González
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Mexico
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Soto C, Avila E, Arce J, Rosas F, McIntyre D. Evaluation of different strategies for broiler feed formulation using near infrared reflectance spectroscopy as a source of information for determination of amino acids and metabolizable energy. J APPL POULTRY RES 2013. [DOI: 10.3382/japr.2013-00655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Arriagada C, Soto C, Peña V, Villegas J. Compromiso intestinal por quemadura eléctrica de alto voltaje: caso clínico. Cir plást iberolatinoam 2013. [DOI: 10.4321/s0376-78922013000400013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Pardo J, García C, Martinez A, Sabater M, Soto C, Marí G. Radiotherapy nursing clinic. A survey of its impact on department care. Rep Pract Oncol Radiother 2013. [DOI: 10.1016/j.rpor.2013.03.361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Vaquero Sosa E, Bodas Pinedo A, Llanos D, Soto C, Rivilla F, Maluenda Carrillo C. Quiste de colédoco como causa de dolor epigástrico. An Pediatr (Barc) 2013; 78:191-2. [DOI: 10.1016/j.anpedi.2012.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 03/17/2012] [Indexed: 10/28/2022] Open
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Abstract
Alzheimer's disease (AD), the most common type of senile dementia, is associated to the build-up of misfolded amyloid-β (Aβ) in the brain. Although compelling evidences indicate that the misfolding and oligomerization of Aβ is the triggering event in AD, the mechanisms responsible for the initiation of Aβ accumulation are unknown. In this study, we show that Aβ deposition can be induced by injection of AD brain extracts into animals, which, without exposure to this material, will never develop these alterations. The accumulation of Aβ deposits increased progressively with the time after inoculation, and the Aβ lesions were observed in brain areas far from the injection site. Our results suggest that some of the typical brain abnormalities associated with AD can be induced by a prion-like mechanism of disease transmission through propagation of protein misfolding. These findings may have broad implications for understanding the molecular mechanisms responsible for the initiation of AD, and may contribute to the development of new strategies for disease prevention and intervention.
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Affiliation(s)
- R Morales
- Mitchell Center for Alzheimer's Disease and Related Brain Disorders, Department of Neurology, University of Texas Houston Medical School, Houston, TX 77030, USA
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Font P, Loscertales J, Benavente C, Bermejo A, Callejas M, Garcia-Alonso L, Garcia-Marcilla A, Gil S, Lopez-Rubio M, Martin E, Muñoz C, Ricard P, Soto C, Balsalobre P, Villegas A. Inter-observer variance with the diagnosis of myelodysplastic syndromes (MDS) following the 2008 WHO classification. Ann Hematol 2012; 92:19-24. [DOI: 10.1007/s00277-012-1565-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/21/2012] [Indexed: 10/27/2022]
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40
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Avila E, Arce J, Soto C, Rosas F, Ceccantini M, McIntyre D. Evaluation of an enzyme complex containing nonstarch polysaccharide enzymes and phytase on the performance of broilers fed a sorghum and soybean meal diet. J APPL POULTRY RES 2012. [DOI: 10.3382/japr.2011-00382] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Alonso Villán E, Pérez Rodríguez J, Rodríguez J, Ruiz J, del Cerro M, Hierro L, García Pose A, Aroca A, Asensio A, García-Miguel P, Soto C, del Diego J, Díaz C, Iglesias A, Lahoz A, Rodríguez I. Mortalidad infantil en un hospital de nivel terciario. Limitación de esfuerzo terapéutico, correspondencia clínico–patológica y precisión diagnóstica. An Pediatr (Barc) 2012; 76:343-9. [DOI: 10.1016/j.anpedi.2011.09.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 09/08/2011] [Accepted: 09/19/2011] [Indexed: 10/15/2022] Open
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Slimani E, Soto C, Pye R, Granger E, Robson D, Macdonald P, Keogh A, Kotlyar E, Dhital K, Spratt P, Hayward C, Jansz P. 582 Veno-Pulmonary Arterial ECMO as Temporary Right Ventricular Support in Patients Undergoing Left Ventricular Assist Device Implantation. J Heart Lung Transplant 2012. [DOI: 10.1016/j.healun.2012.01.595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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44
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Connellan M, Orr Y, Pye R, Granger E, Dhital K, Soto C, Malouf M, Spratt P, Glanville A, Jansz P. 706 100% 3-Year Survival after Extracorporeal Membrane Oxygenation (ECMO) Bridge to Lung Transplantation (N=10). J Heart Lung Transplant 2012. [DOI: 10.1016/j.healun.2012.01.721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Andvik S, Soto C, Jackson A, Pye R, Nichols M, Fulde G, Granger E. CPR-ECMO for In-Hospital Cardiac Arrest: What are the Predictive Factors for Survival and are We Missing Anyone? Heart Lung Circ 2012. [DOI: 10.1016/j.hlc.2012.05.582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Soto C, Canedo A. Intracellular recordings of subnucleus reticularis dorsalis neurones revealed novel electrophysiological properties and windup mechanisms. J Physiol 2011; 589:4383-401. [PMID: 21746779 DOI: 10.1113/jphysiol.2011.212464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Aδ- and/or C-fibre nociceptive inputs drive subnucleus reticularis dorsalis (SRD) neurones projecting to a variety of regions including the spinal cord and the nucleus reticularis gigantocellularis (NRGc), but their electrophysiological properties are largely unknown. Here we intracellularly recorded the SRD neuronal responses to injection of polarising current pulses as well as to electrical stimulation of the cervical spinal posterior quadrant (PQ) and the NRGc. Three different classes of neurones with distinct electrophysiological properties were found: type I were characterised by the absence of a fast postspike hyperpolarisation, type II by the presence of a postspike hyperpolarisation followed by a depolarisation resembling low threshold calcium spikes (LTSs), and type III (lacking LTSs) had a fast postspike hyperpolarisation deinactivating A-like potassium channels leading to enlarged interspike intervals. All three classes generated depolarising sags to hyperpolarising current pulses and showed 3-4.5 Hz subthreshold oscillatory activity leading to windup when intracellularly injecting low-frequency repetitive depolarising pulses as well as in response to 0.5-2 Hz NRGc and PQ electrical stimulation. About half of the 132 sampled neurones responded antidromically to NRGc stimulation with more than 65% of the NRGc-antidromic cells, pertaining to all three types, also responding antidromically to PQ stimulation. NRGc stimulation induced exclusively excitatory first-synaptic-responses whilst PQ stimulation induced first-response excitation in most cases, but inhibitory postsynaptic potentials in a few type II and type III neurones not projecting to the spinal cord that also displayed cumulative inhibitory effects (inverse windup). The results show that SRD cells (i) can actively regulate different temporal firing patterns due to their intrinsic electrophysiological properties, (ii) generate windup upon gradual membrane depolarisation produced by low-frequency intracellular current injection and by C-fibre tonic input, both processes leading subthreshold oscillations to threshold, and (iii) collateralise to the NRGc and the spinal cord, potentially providing simultaneous regulation of ascending noxious information and motor reactions to pain.
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Affiliation(s)
- Cristina Soto
- A. Canedo: Health Research Institute (IDIS), Department of Physiology, Faculty of Medicine, 15704 Santiago de Compostela, Spain.
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Soto C, Reinoso V. Modelo de formulación de raciones al mínimo costo para ganado de carne basado en el sistema nrc 2000. ARCH ZOOTEC 2011. [DOI: 10.21071/az.v61i234.2799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Los requerimientos nutricionales del ganado de carne descrito por el NRC (2000) se establecen mediante ecuaciones, siendo algunas de ellas no lineales o no aditivas lo cual dificulta su incorporación a modelos de programación lineal para formular raciones al mínimo costo. El presente trabajo describe un modelo de programación lineal entero mixto para formular dietas de mínimo costo que incorpora las recomendaciones del Modelo Nivel Uno del NRC (2000). La falta de aditividad o linealidad de algunas funciones fueron superadas empleando restricciones alternativas modeladas con variables binarias. El modelo considera factores ambientales que modifican los requerimientos de los animales y los efectos de la dieta que afectan la eficiencia de síntesis de proteína microbiana a nivel ruminal y el consumo potencial voluntario de alimentos. Se consideran los requerimientos de energía, proteína metabolizable, calcio, fósforo y fibra efectiva. Se acota el consumo de pastura al consumo voluntario de la misma y el consumo de suplemento al máximo nivel de suplementación permitido. Se presenta un ejemplo de aplicación del modelo y se describen posibles ampliaciones.
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Granger E, Soto C, Jackson A, Pye R, Jansz P, Dhital K, Hayward C, Macdonald P, Spratt P. Venous Arterial Ecmo: “Good for Some, Not for All”. Heart Lung Circ 2011. [DOI: 10.1016/j.hlc.2010.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Soto C, Pérez J, García V, Uría E, Vadillo M, Raya L. Effect of silymarin on kidneys of rats suffering from alloxan-induced diabetes mellitus. Phytomedicine 2010; 17:1090-4. [PMID: 20579862 DOI: 10.1016/j.phymed.2010.04.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 03/27/2010] [Accepted: 04/29/2010] [Indexed: 05/29/2023]
Abstract
Oxidative stress contributes to the pathogenesis of diabetes mellitus and its sequelae nephropathy. The kidneys are especially prone to damage by free radicals. We therefore tested the effect of the flavonoid mixture silymarin, a free radical scavenger, on the activity and gene expression of superoxide dismutase, glutathione peroxidase and catalase, as well as on renal tissue morphology in rats with alloxan-induced diabetes mellitus. Alloxan-intoxicated rats were treated with silymarin 20 days after alloxan administration for 9 weeks. Alloxan-induced tissue damage and decreased the activity of the three enzymes, SOD (U/mg prot.): 14.4±1.75 vs 112±6.45 control, p<0.05, n=6; GSHPx (μM NADPH/min/mg prot.): 0.02±0.002 vs 0.121±0.01 control, p<0.05, n=6; CAT (k/seg/mg prot.): 0.022±0.003 vs 0.044±0.002 control, p<0.05, n=6. Silymarin treatment prevented tissue damage and restored the activity (SOD: 110.7±12.9U/mg prot.; GSHPx: 0.329±0.031 μM NADPH/min/mg prot.; CAT: 0.054±0.002 k/seg/mg prot., n=6) and gene expression of the three antioxidant enzymes after 20 days of alloxan administration (SOD: 12.00±0.57 control, 9.00±0.1 diabetic p<0.05, 11.00±0.20 silymarin treated; GSHPx: 6.01±0.78 control, 9.03±0.3 diabetic p<0.05, 7.02±0.07 silymarin treated; CAT: 9.03±1.07 control, 12.02±0.60 diabetic p<0.05, 8.06±0.31 silymarin treated, n=6). It is suggested in this study that recuperative effect of silymarin on the renal tissue damage induced by alloxan may be related to an increase in the activity and recovery of gene expression of antioxidant enzymes which in addition to the glutathione system constitute some of the most important defense mechanisms against free radicals damage. As these results show, silymarin may be considered potentially in the treatment of diabetic nephropathy.
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Affiliation(s)
- C Soto
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Mexico.
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Soto C, Zuñiga M. Polyunsaturated fatty acid enrichment using a Candida cylindracea lipase. J Biotechnol 2010. [DOI: 10.1016/j.jbiotec.2010.09.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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