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Sharma AD, Grewal RK, Gorle S, Cuspoca AF, Kaushik V, Rajjak Shaikh A, Cavallo L, Chawla M. T cell epitope based vaccine design while targeting outer capsid proteins of rotavirus strains infecting neonates: an immunoinformatics approach. J Biomol Struct Dyn 2024; 42:4937-4955. [PMID: 37382214 DOI: 10.1080/07391102.2023.2226721] [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: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
Gastrointestinal diarrhea is majorly caused by the rotavirus (RV) in the children who generally are under the age group of 5 years. WHO estimates that ∼95% of the children contract RV infection, by this age. The disease is highly contagious; notably in many cases, it is proven fatal with high mortality rates especially in the developing countries. In India alone, an estimated 145,000 yearly deaths occurs due to RV related gastrointestinal diarrhea. WHO pre-qualified vaccines that are available for RV are all live attenuated vaccines with modest efficacy range between 40 and 60%. Further, the risk of intussusceptions has been reported in some children on RV vaccination. Thus, in a quest to develop alternative candidate to overcome challenges associated with these oral vaccines, we chose immunoinformatics approach to design a multi-epitope vaccine (MEV) while targeting the outer capsid viral proteinsVP4 and VP7 of the neonatal strains of rotavirus. Interestingly, ten epitopes, that is, six CD8+T-cells and four CD4+T-cell epitopes were identified which were predicted to be antigenic, non-allergic, non-toxic and stable. These epitopes were then linked to adjuvants, linkers, and PADRE sequences to create a multi-epitope vaccine for RV. The in silico designed RV-MEV and human TLR5 complex displayed stable interactions during molecular dynamics simulations. Further, the immune simulation studies of RV-MEV corroborated that the vaccine candidate emerges as a promising immunogen. Future investigations while performing in vitro and in vivo analyses with designed RV-MEV construct are highly desirable to warrant the potential of this vaccine candidate in protective immunity against different strains of RVs infecting neonates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arijit Das Sharma
- School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Suresh Gorle
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Andrés Felipe Cuspoca
- Grupo de Investigación Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
- Centro de Atención e Investigación Médica - CAIMED, Chía, Colombia
| | - Vikas Kaushik
- School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Babar V, Sharma S, Shaikh AR, Oliva R, Chawla M, Cavallo L. Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS 2 and Janus MoSSe Monolayers. ACS Appl Mater Interfaces 2024; 16:21427-21437. [PMID: 38634539 PMCID: PMC11071042 DOI: 10.1021/acsami.3c18400] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS2 and MoSSe monolayers. Through a comprehensive conformational search, we pinpoint the most favorable adsorption sites, quantifying their adsorption energies and charge transfer properties. The analysis of electronic band structure unveils the emergence of flat bands in close proximity to the Fermi level post-adsorption, a departure from the pristine MoS2 and MoSSe monolayers. Furthermore, leveraging the nonequilibrium Green's function approach, we compute the current-voltage characteristics, providing valuable insights into the electronic transport properties of the system. All hachimoji bases exhibit physisorption with a horizontal orientation on both monolayers. Notably, base G demonstrates high sensitivity on both substrates. The obtained current-voltage (I-V) characteristics, both without and with base adsorption on MoS2 and the Se side of MoSSe, affirm excellent sensing performance. This research significantly advances our understanding of potential DNA sensing platforms and their electronic characteristics, thereby propelling the endeavor for personalized medicine through enhanced DNA sequencing technologies.
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Affiliation(s)
- Vasudeo Babar
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sitansh Sharma
- Department
of Research and Innovation, STEMskills Research
and Education Lab Private Limited, Faridabad, Haryana 121002, India
| | - Abdul Rajjak Shaikh
- Department
of Research and Innovation, STEMskills Research
and Education Lab Private Limited, Faridabad, Haryana 121002, India
| | - Romina Oliva
- Department
of Sciences and Technologies, University
Parthenope of Naples, Centro Direzionale Isola C4, 80143 Naples, Italy
| | - Mohit Chawla
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
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Meng YJ, Mankuzhy NP, Chawla M, Lee RP, Yorke ED, Zhang Z, Gelb E, Lim SB, Cuaron JJ, Wu AJ, Simone CB, Gelblum DY, Lovelock DM, Harris W, Rimner A. A Prospective Study on Deep Inspiration Breath Hold Thoracic Radiation Therapy Guided by Bronchoscopically Implanted Electromagnetic Transponders. Cancers (Basel) 2024; 16:1534. [PMID: 38672616 PMCID: PMC11048337 DOI: 10.3390/cancers16081534] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/03/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Electromagnetic transponders bronchoscopically implanted near the tumor can be used to monitor deep inspiration breath hold (DIBH) for thoracic radiation therapy (RT). The feasibility and safety of this approach require further study. METHODS We enrolled patients with primary lung cancer or lung metastases. Three transponders were implanted near the tumor, followed by simulation with DIBH, free breathing, and 4D-CT as backup. The initial gating window for treatment was ±5 mm; in a second cohort, the window was incrementally reduced to determine the smallest feasible gating window. The primary endpoint was feasibility, defined as completion of RT using transponder-guided DIBH. Patients were followed for assessment of transponder- and RT-related toxicity. RESULTS We enrolled 48 patients (35 with primary lung cancer and 13 with lung metastases). The median distance of transponders to tumor was 1.6 cm (IQR 0.6-2.8 cm). RT delivery ranged from 3 to 35 fractions. Transponder-guided DIBH was feasible in all but two patients (96% feasible), where it failed because the distance between the transponders and the antenna was >19 cm. Among the remaining 46 patients, 6 were treated prone to keep the transponders within 19 cm of the antenna, and 40 were treated supine. The smallest feasible gating window was identified as ±3 mm. Thirty-nine (85%) patients completed one year of follow-up. Toxicities at least possibly related to transponders or the implantation procedure were grade 2 in six patients (six incidences, cough and hemoptysis), grade 3 in three patients (five incidences, cough, dyspnea, pneumonia, and supraventricular tachycardia), and grade 4 pneumonia in one patient (occurring a few days after implantation but recovered fully and completed RT). Toxicities at least possibly related to RT were grade 2 in 18 patients (41 incidences, most commonly cough, fatigue, and pneumonitis) and grade 3 in four patients (seven incidences, most commonly pneumonia), and no patients had grade 4 or higher toxicity. CONCLUSIONS Bronchoscopically implanted electromagnetic transponder-guided DIBH lung RT is feasible and safe, allowing for precise tumor targeting and reduced normal tissue exposure. Transponder-antenna distance was the most common challenge due to a limited antenna range, which could sometimes be circumvented by prone positioning.
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Affiliation(s)
- Yuzhong Jeff Meng
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
| | - Nikhil P. Mankuzhy
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
| | - Mohit Chawla
- Department of Medicine, Pulmonary Service, Section of Interventional Pulmonology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (M.C.); (R.P.L.)
| | - Robert P. Lee
- Department of Medicine, Pulmonary Service, Section of Interventional Pulmonology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (M.C.); (R.P.L.)
| | - Ellen D. Yorke
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (E.D.Y.); (S.B.L.); (D.M.L.)
| | - Zhigang Zhang
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA;
| | - Emily Gelb
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
| | - Seng Boh Lim
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (E.D.Y.); (S.B.L.); (D.M.L.)
| | - John J. Cuaron
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
| | - Abraham J. Wu
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
| | - Charles B. Simone
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
- New York Proton Center, New York, NY 10035, USA
| | - Daphna Y. Gelblum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
| | - Dale Michael Lovelock
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (E.D.Y.); (S.B.L.); (D.M.L.)
| | - Wendy Harris
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (E.D.Y.); (S.B.L.); (D.M.L.)
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; (Y.J.M.); (N.P.M.); (E.G.); (J.J.C.); (A.J.W.); (C.B.S.II)
- Department of Radiation Oncology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK), Partner Site DKTK-Freiburg, Robert-Koch-Strasse 3, 79106 Freiburg, Germany
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Makkar P, Schwartz J, Shayani K, Imran S, Flynn J, Chu J, Chawla M, Lee R. Indwelling tunneled pleural catheter infections and host related factors. Respir Med 2024; 224:107579. [PMID: 38408706 PMCID: PMC11036657 DOI: 10.1016/j.rmed.2024.107579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/11/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Affiliation(s)
- Priyanka Makkar
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacob Schwartz
- Department of Pulmonary and Critical Care Medicine, Lenox Hill Hospital, New York, NY, USA
| | - Kevin Shayani
- Department of Pulmonary and Critical Care Medicine, Lenox Hill Hospital, New York, NY, USA.
| | - Saira Imran
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Flynn
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joanne Chu
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohit Chawla
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert Lee
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Chawla M, Cuspoca AF, Akthar N, Magdaleno JSL, Rattanabunyong S, Suwattanasophon C, Jongkon N, Choowongkomon K, Shaikh AR, Malik T, Cavallo L. Immunoinformatics-aided rational design of a multi-epitope vaccine targeting feline infectious peritonitis virus. Front Vet Sci 2023; 10:1280273. [PMID: 38192725 PMCID: PMC10773687 DOI: 10.3389/fvets.2023.1280273] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Feline infectious peritonitis (FIP) is a grave and frequently lethal ailment instigated by feline coronavirus (FCoV) in wild and domestic feline species. The spike (S) protein of FCoV assumes a critical function in viral ingress and infection, thereby presenting a promising avenue for the development of a vaccine. In this investigation, an immunoinformatics approach was employed to ascertain immunogenic epitopes within the S-protein of FIP and formulate an innovative vaccine candidate. By subjecting the amino acid sequence of the FIP S-protein to computational scrutiny, MHC-I binding T-cell epitopes were predicted, which were subsequently evaluated for their antigenicity, toxicity, and allergenicity through in silico tools. Our analyses yielded the identification of 11 potential epitopes capable of provoking a robust immune response against FIPV. Additionally, molecular docking analysis demonstrated the ability of these epitopes to bind with feline MHC class I molecules. Through the utilization of suitable linkers, these epitopes, along with adjuvants, were integrated to design a multi-epitope vaccine candidate. Furthermore, the stability of the interaction between the vaccine candidate and feline Toll-like receptor 4 (TLR4) was established via molecular docking and molecular dynamics simulation analyses. This suggests good prospects for future experimental validation to ascertain the efficacy of our vaccine candidate in inducing a protective immune response against FIP.
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Affiliation(s)
- Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrés Felipe Cuspoca
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica yTecnológica de Colombia, Tunja, Colombia
- Centro de Atención e Investigación Médica–CAIMED, Chía, Colombia
| | - Nahid Akthar
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Jorge Samuel Leon Magdaleno
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Nathjanan Jongkon
- Department of Social and Applied Science, College of Industrial Technology, King Mongkut’s University of Technology North Bangkok, Bangkok, Thailand
| | | | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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6
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Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez‐Lumbreras LA, Fernandez‐Recio J, Harmalkar A, Chu L, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang S, Roel‐Touris J, Jimenez‐Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas‐Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman‐Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota‐Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda‐Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins 2023; 91:1658-1683. [PMID: 37905971 PMCID: PMC10841881 DOI: 10.1002/prot.26609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023]
Abstract
We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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Affiliation(s)
- Marc F. Lensink
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et FonctionnelleLilleFrance
| | - Guillaume Brysbaert
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et FonctionnelleLilleFrance
| | - Nessim Raouraoua
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et FonctionnelleLilleFrance
| | - Paul A. Bates
- Biomolecular Modeling LaboratoryThe Francis Crick InstituteLondonUK
| | - Marco Giulini
- Bijvoet Center for Biomolecular Research, Faculty of Science – ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Rodrigo V. Honorato
- Bijvoet Center for Biomolecular Research, Faculty of Science – ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Charlotte van Noort
- Bijvoet Center for Biomolecular Research, Faculty of Science – ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Joao M. C. Teixeira
- Bijvoet Center for Biomolecular Research, Faculty of Science – ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Alexandre M. J. J. Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science – ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information EngineeringJiangsu University of TechnologyChangzhouChina
| | - Hang Shi
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information EngineeringJiangsu University of TechnologyChangzhouChina
| | - Xufeng Lu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information EngineeringJiangsu University of TechnologyChangzhouChina
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information EngineeringJiangsu University of TechnologyChangzhouChina
| | - Jian Liu
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Zhiye Guo
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Xiao Chen
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Alex Morehead
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Raj S. Roy
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Tianqi Wu
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Nabin Giri
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Farhan Quadir
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Chen Chen
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Jianlin Cheng
- Dept. of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | | | - Eichiro Ichiishi
- International University of Health and Welfare (IUHV Hospital)Nasushiobara‐CityJapan
| | - Luis A. Rodriguez‐Lumbreras
- Instituto de Ciencias de la Vida y del Vino (ICVV)CSIC ‐ Universidad de La Rioja ‐ Gobierno de La RiojaLogronoSpain
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
| | - Juan Fernandez‐Recio
- Instituto de Ciencias de la Vida y del Vino (ICVV)CSIC ‐ Universidad de La Rioja ‐ Gobierno de La RiojaLogronoSpain
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
| | - Ameya Harmalkar
- Dept. of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Lee‐Shin Chu
- Dept. of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Sam Canner
- Dept. of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Rituparna Smanta
- Dept. of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Jeffrey J. Gray
- Dept. of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Hao Li
- School of PhysicsHuazhong University of Science and TechnologyWuhanChina
| | - Peicong Lin
- School of PhysicsHuazhong University of Science and TechnologyWuhanChina
| | - Jiahua He
- School of PhysicsHuazhong University of Science and TechnologyWuhanChina
| | - Huanyu Tao
- School of PhysicsHuazhong University of Science and TechnologyWuhanChina
| | - Sheng‐You Huang
- School of PhysicsHuazhong University of Science and TechnologyWuhanChina
| | - Jorge Roel‐Touris
- Protein Design and Modeling Lab, Dept. of Structural BiologyMolecular Biology Institute of Barcelona (IBMB‐CSIC)BarcelonaSpain
| | | | | | - Anika J. Jain
- Dept. of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Yuki Kagaya
- Dept. of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Harini Kannan
- Dept. of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
- Dept. of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiIndia
| | - Tsukasa Nakamura
- Dept. of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Genki Terashi
- Dept. of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Jacob C. Verburgt
- Dept. of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Yuanyuan Zhang
- Dept. of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | - Zicong Zhang
- Dept. of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | - Hayato Fujuta
- Dept. of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiIndia
| | | | - Daisuke Kihara
- Dept. of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
- Dept. of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | | | | | | | | | | | | | | | - Surendra S. Negi
- Sealy Center for Structural Biology and Molecular BiophysicsUniversity of Texas Medical BranchGalvestonTexasUSA
| | | | | | - Zhen Cao
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
- Department of Chemistry and BiologyUniversity of SalernoFiscianoItaly
| | | | - Rui Yin
- University of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMarylandUSA
- Dept. of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMarylandUSA
| | - Melyssa Cheung
- University of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMarylandUSA
- Dept. of Chemistry and BiochemistryUniversity of MarylandCollege ParkMarylandUSA
| | - Johnathan D. Guest
- University of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMarylandUSA
- Dept. of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMarylandUSA
| | - Jessica Lee
- University of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMarylandUSA
- Dept. of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMarylandUSA
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMarylandUSA
- Dept. of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMarylandUSA
| | - Ben Shor
- School of Computer Science and EngineeringThe Hebrew University of JerusalemJerusalemIsrael
| | - Tomer Cohen
- School of Computer Science and EngineeringThe Hebrew University of JerusalemJerusalemIsrael
| | - Matan Halfon
- School of Computer Science and EngineeringThe Hebrew University of JerusalemJerusalemIsrael
| | | | - Shaowen Zhu
- Department of Electrical and Computer EngineeringTexas A&M UniversityCollege StationTexasUSA
| | - Rujie Yin
- Department of Electrical and Computer EngineeringTexas A&M UniversityCollege StationTexasUSA
| | - Yuanfei Sun
- Department of Electrical and Computer EngineeringTexas A&M UniversityCollege StationTexasUSA
| | - Yang Shen
- Department of Electrical and Computer EngineeringTexas A&M UniversityCollege StationTexasUSA
- Department of Computer Science and EngineeringTexas A&M UniversityCollege StationTexasUSA
- Institute of Biosciences and Technology and Department of Translational Medical SciencesTexas A&M UniversityHoustonTexasUSA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yuta Miyakawa
- School of PharmacyKitasato UniversityMinato‐kuTokyoJapan
| | - Yasuomi Kiyota
- School of PharmacyKitasato UniversityMinato‐kuTokyoJapan
| | | | - Kliment Olechnovic
- Institute of Biotechnology, Life Sciences CenterVilnius UniversityVilniusLithuania
| | - Lukas Valancauskas
- Institute of Biotechnology, Life Sciences CenterVilnius UniversityVilniusLithuania
| | - Justas Dapkunas
- Institute of Biotechnology, Life Sciences CenterVilnius UniversityVilniusLithuania
| | - Ceslovas Venclovas
- Institute of Biotechnology, Life Sciences CenterVilnius UniversityVilniusLithuania
| | - Bjorn Wallner
- Bioinformatics Division, Department of Physics, Chemistry, and BiologyLinkoping UniversityLinköpingSweden
| | - Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and StructuresHarbin Institute of TechnologyHarbinChina
- School of Aerospace, Mechanical and Mechatronic EngineeringThe University of SydneyNew South WalesAustralia
| | - Chengyu Hou
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbinChina
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and StructuresHarbin Institute of TechnologyHarbinChina
- Shenzhen STRONG Advanced Materials Research Institute Col, LtdShenzhenPeople's Republic of China
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and StructuresHarbin Institute of TechnologyHarbinChina
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and StructuresHarbin Institute of TechnologyHarbinChina
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and StructuresHarbin Institute of TechnologyHarbinChina
| | - Rui Duan
- Dalton Cardiovascular Research CenterUniversity of MissouriColumbiaMissouriUSA
| | - Liming Qui
- Dalton Cardiovascular Research CenterUniversity of MissouriColumbiaMissouriUSA
| | - Xianjin Xu
- Dalton Cardiovascular Research CenterUniversity of MissouriColumbiaMissouriUSA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research CenterUniversity of MissouriColumbiaMissouriUSA
- Dept. of Physics and AstronomyUniversity of MissouriColumbiaMissouriUSA
- Dept. of BiochemistryUniversity of MissouriColumbiaMissouriUSA
- Institute for Data Science and InformaticsUniversity of MissouriColumbiaMissouriUSA
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)HinxtonCambridgeUK
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Kumari S, Leon Magdaleno JS, Grewal RK, Narsing Rao MP, Rajjak Shaikh A, Cavallo L, Chawla M, Kumar M. High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics. J Biomol Struct Dyn 2023:1-12. [PMID: 37768075 DOI: 10.1080/07391102.2023.2262600] [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: 05/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Kumari
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
| | - Jorge S Leon Magdaleno
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manoj Kumar
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
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8
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Rimner A, Moore ZR, Lobaugh S, Geyer A, Gelblum DY, Abdulnour REE, Shepherd AF, Shaverdian N, Wu AJ, Cuaron J, Chaft JE, Zauderer MG, Eng J, Riely GJ, Rudin CM, Vander Els N, Chawla M, McCune M, Li H, Jones DR, Sopka DM, Simone CB, Mak R, Weinhouse GL, Liao Z, Gomez DR, Zhang Z, Paik PK. Randomized Phase 2 Placebo-Controlled Trial of Nintedanib for the Treatment of Radiation Pneumonitis. Int J Radiat Oncol Biol Phys 2023; 116:1091-1099. [PMID: 36889516 PMCID: PMC10751877 DOI: 10.1016/j.ijrobp.2023.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/08/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
PURPOSE Radiation pneumonitis (RP) is the most common dose-limiting toxicity for thoracic radiation therapy. Nintedanib is used for the treatment of idiopathic pulmonary fibrosis, which shares pathophysiological pathways with the subacute phase of RP. Our goal was to investigate the efficacy and safety of nintedanib added to a prednisone taper compared with a prednisone taper alone in reducing pulmonary exacerbations in patients with grade 2 or higher (G2+) RP. METHODS AND MATERIALS In this phase 2, randomized, double-blinded, placebo-controlled trial, patients with newly diagnosed G2+ RP were randomized 1:1 to nintedanib or placebo in addition to a standard 8-week prednisone taper. The primary endpoint was freedom from pulmonary exacerbations at 1 year. Secondary endpoints included patient-reported outcomes and pulmonary function tests. Kaplan-Meier analysis was used to estimate the probability of freedom from pulmonary exacerbations. The study was closed early due to slow accrual. RESULTS Thirty-four patients were enrolled between October 2015 and February 2020. Of 30 evaluable patients, 18 were randomized to the experimental Arm A (nintedanib + prednisone taper) and 12 to the control Arm B (placebo + prednisone taper). Freedom from exacerbation at 1 year was 72% (confidence interval, 54%-96%) in Arm A and 40% (confidence interval, 20%-82%) in Arm B (1-sided, P = .037). In Arm A, there were 16 G2+ adverse events possibly or probably related to treatment compared with 5 in the placebo arm. There were 3 deaths during the study period in Arm A due to cardiac failure, progressive respiratory failure, and pulmonary embolism. CONCLUSIONS There was an improvement in pulmonary exacerbations by the addition of nintedanib to a prednisone taper. Further investigation is warranted for the use of nintedanib for the treatment of RP.
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Affiliation(s)
- Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Zachary R. Moore
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Stephanie Lobaugh
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Alexander Geyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
| | - Daphna Y. Gelblum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Raja-Elie E. Abdulnour
- Department of Pulmonary and Critical Care, Brigham and Women’s Hospital/Dana-Farber Cancer Institute Boston, MA, USA
| | - Annemarie F. Shepherd
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Narek Shaverdian
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Abraham J. Wu
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - John Cuaron
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Jamie E. Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
| | - Marjorie G. Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
| | - Juliana Eng
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Gregory J. Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
| | - Nicholas Vander Els
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
| | - Mohit Chawla
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
| | - Megan McCune
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Henry Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - David R. Jones
- Department of Surgery Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Dennis M. Sopka
- Department of Radiation Oncology Lehigh Valley Health Network, MSK Alliance Allentown, PA, USA
| | - Charles B. Simone
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Raymond Mak
- Department of Radiation Oncology Brigham and Women’s Hospital/Dana-Farber Cancer Institute Boston, MA, USA
| | - Gerald L. Weinhouse
- Department of Pulmonary and Critical Care, Brigham and Women’s Hospital/Dana-Farber Cancer Institute Boston, MA, USA
| | - Zhongxing Liao
- Department of Radiation Oncology MD Anderson Cancer Center Houston, TX, USA
| | - Daniel R. Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Zhigang Zhang
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Paul K. Paik
- Department of Medicine, Memorial Sloan Kettering Cancer Center New York, NY, USA
- Department of Medicine, Weill Cornell Medical Center New York, NY, USA
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9
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Magdaleno JSL, Grewal RK, Medina-Franco JL, Oliva R, Shaikh AR, Cavallo L, Chawla M. Toward α-1,3/4 fucosyltransferases targeted drug discovery: In silico uncovering of promising natural inhibitors of fucosyltransferase 6. J Cell Biochem 2023; 124:1173-1185. [PMID: 37357420 DOI: 10.1002/jcb.30440] [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: 03/13/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
Sialyl Lewis X (sLex ) antigen is a fucosylated cell-surface glycan that is normally involved in cell-cell interactions. The enhanced expression of sLex on cell surface glycans, which is attributed to the upregulation of fucosyltransferase 6 (FUT6), has been implicated in facilitating metastasis in human colorectal, lung, prostate, and oral cancers. The role that the upregulated FUT6 plays in the progression of tumor to malignancy, with reduced survival rates, makes it a potential target for anticancer drugs. Unfortunately, the lack of experimental structures for FUT6 has hampered the design and development of its inhibitors. In this study, we used in silico techniques to identify potential FUT6 inhibitors. We first modeled the three-dimensional structure of human FUT6 using AlphaFold. Then, we screened the natural compound libraries from the COCONUT database to sort out potential natural products (NPs) with best affinity toward the FUT6 model. As a result of these simulations, we identified three NPs for which we predicted binding affinities and interaction patterns quite similar to those we calculated for two experimentally tested FUT6 inhibitors, that is, fucose mimetic-1 and a GDP-triazole derived compound. We also performed molecular dynamics (MD) simulations for the FUT6 complexes with identified NPs, to investigate their stability. Analysis of the MD simulations showed that the identified NPs establish stable contacts with FUT6 under dynamics conditions. On these grounds, the three screened compounds appear as promising natural alternatives to experimentally tested FUT6 synthetic inhibitors, with expected comparable binding affinity. This envisages good prospects for future experimental validation toward FUT6 inhibition.
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Affiliation(s)
- Jorge Samuel Leon Magdaleno
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Ravneet K Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - José L Medina-Franco
- Department of Pharmacy, DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Naples, Italy
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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10
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Ho ATN, Gorthi R, Lee R, Chawla M, Patolia S. Solitary Lung Nodule: CT-Guided Transthoracic Biopsy vs Transbronchial Biopsy With Endobronchial Ultrasound and Flexible Bronchoscope, a Meta-Analysis of Randomized Controlled Trials. Lung 2023; 201:85-93. [PMID: 36695890 DOI: 10.1007/s00408-023-00596-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
BACKGROUND Transbronchial lung biopsy with radial endobronchial ultrasound (rEBUS-TBB) and Computed tomography (CT) scan-guided transthoracic biopsy (CT-TTB) are commonly used to investigate peripheral lung nodules but high-quality data are still not clear about the diagnostic and safety profile comparison of these two modalities. METHOD We included all randomized controlled trials (RCT) comparing rEBUS-TBB with a flexible bronchoscope and CT-TTB for solitary lung nodules. Two reviewers extracted data independently on diagnostic performance and complication rates. RESULTS 170 studies were screened, 4 RCT with a total of 325 patients were included. CT-TTB had a higher diagnostic yield than rEBUS-TBB (83.45% vs 68.82%, risk difference - 0.15, 95% CI, [- 0.24, - 0.05]), especially for lesion size 1-2 cm (83% vs 50%, risk difference - 0.33, 95% CI, [- 0.51, - 0.14]). For malignant diseases, rEBUS-TBB had a diagnostic yield of 75.75% vs 87.7% of CT-TTB. rEBUS-TBB had a significant better safety profile with lower risks of pneumothorax (2.87% vs 21.43%, OR = 0.12, 95% CI [0.05-0.32]) and combined outcomes of hospital admission, hemorrhage, and pneumothorax (8.62% vs 31.81%, OR 0.21, 95% CI, [0.11-0.40]). Factors increasing diagnostic yield of rEBUS were lesion size and localization of the probe but not the distance to the chest wall and hilum. CONCLUSION CT-TTB had a higher diagnostic yield than rEBUS-TBB in diagnosing peripheral lung nodules, particularly for lesions from 1 to 2 cm. However, rEBUS-TBB was significantly safer with five to eight times less risk of pneumothorax and composite complications of hospital admission, hemorrhage, and pneumothorax. The results of this study only apply to flexible bronchoscopy with radial ebus without navigational technologies. More data are needed for a comparison between CT-TTB with rEBUS-TBB combined with advanced navigational modalities.
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Affiliation(s)
- An Thi Nhat Ho
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 425 E 67th St, New York, NY, 10065, USA.
| | - Ramya Gorthi
- Department of Pulmonary and Critical Care, St Louis University Hospital, St. Louis, MO, USA
| | - Robert Lee
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 425 E 67th St, New York, NY, 10065, USA
| | - Mohit Chawla
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 425 E 67th St, New York, NY, 10065, USA
| | - Setu Patolia
- Department of Pulmonary and Critical Care, St Louis University Hospital, St. Louis, MO, USA
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11
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Shaikh AR, Posada-Pérez S, Brotons-Rufes A, Pajski JJ, Vajiha, Kumar G, Mateen A, Poater A, Solà M, Chawla M, Cavallo L. Selective absorption of H2S and CO2 by azole based protic ionic liquids: A combined density functional theory and molecular dynamics study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120558] [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: 11/07/2022]
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12
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Connolly JG, Kalchiem-Dekel O, Tan KS, Dycoco J, Chawla M, Rocco G, Park BJ, Lee RP, Beattie JA, Solomon SB, Ziv E, Adusumilli PS, Buonocore DJ, Husta BC, Jones DR, Baine MK, Bott MJ. Feasibility of shape-sensing robotic-assisted bronchoscopy for biomarker identification in patients with thoracic malignancies. J Thorac Cardiovasc Surg 2022:S0022-5223(22)01258-2. [PMID: 36621452 DOI: 10.1016/j.jtcvs.2022.10.059] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/11/2022] [Accepted: 10/29/2022] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Molecular diagnostic assays require samples with high nucleic acid content to generate reliable data. Similarly, programmed death-ligand 1 (PD-L1) immunohistochemistry (IHC) requires samples with adequate tumor content. We investigated whether shape-sensing robotic-assisted bronchoscopy (ssRAB) provides adequate samples for molecular and predictive testing. METHODS We retrospectively identified diagnostic samples from a prospectively collected database. Pathologic reports were reviewed to assess adequacy of samples for molecular testing and feasibility of PD-L1 IHC. Tumor cellularity was quantified by an independent pathologist using paraffin-embedded sections. Univariable and multivariable linear regression models were constructed to assess associations between lesion- and procedure-related variables and tumor cellularity. RESULTS In total, 128 samples were analyzed: 104 primary lung cancers and 24 metastatic lesions. On initial pathologic assessment, ssRAB samples were deemed to be adequate for molecular testing in 84% of cases; on independent review of cellular blocks, median tumor cellularity was 60% (interquartile range, 25%-80%). Hybrid capture-based next-generation sequencing was successful for 25 of 26 samples (96%), polymerase chain reaction-based molecular testing (Idylla; Biocartis) was successful for 49 of 52 samples (94%), and PD-L1 IHC was successful for 61 of 67 samples (91%). Carcinoid and small cell carcinoma histologic subtype and adequacy on rapid on-site evaluation were associated with higher tumor cellularity. CONCLUSIONS The ssRAB platform provided adequate tissue for next-generation sequencing, polymerase chain reaction-based molecular testing, and PD-L1 IHC in >80% of cases. Tumor histology and adequacy on intraoperative cytologic assessment might be associated with sample quality and suitability for downstream assays.
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Affiliation(s)
- James G Connolly
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Or Kalchiem-Dekel
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kay See Tan
- Biostatistics Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joe Dycoco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mohit Chawla
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bernard J Park
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert P Lee
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jason A Beattie
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stephen B Solomon
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Etay Ziv
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darren J Buonocore
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bryan C Husta
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marina K Baine
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Matthew J Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY.
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13
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Chawla M, Kalra K, Cao Z, Cavallo L, Oliva R. Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules. Nucleic Acids Res 2022; 50:11455-11469. [PMID: 36416268 PMCID: PMC9723503 DOI: 10.1093/nar/gkac1081] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.
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Affiliation(s)
- Mohit Chawla
- Correspondence may also be addressed to Mohit Chawla. ;
| | - Kanav Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Zhen Cao
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Correspondence may also be addressed to Luigi Cavallo. Tel: +966 02 8027566; Fax: +966 02 8021347;
| | - Romina Oliva
- To whom correspondence should be addressed. Tel: +39 081 5476541; Fax: +39 081 5476514;
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14
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Moore Z, Huang X, Lobaugh S, Geyer A, Gelblum D, Shepherd A, Shaverdian N, Wu A, Chaft J, Zauderer M, Rudin C, Chawla M, Jones D, Sopka D, Mak R, Liao Z, Gomez D, Zhang Z, Paik P, Rimner A. Biomarkers Associated with Pulmonary Exacerbations in a Prospective, Placebo-Controlled, Randomized Trial of Nintedanib for the Treatment of Radiation Pneumonitis. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.2128] [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: 10/31/2022]
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Chawla M, Chawla P, Saboo B, Chawla R, Gangopadhyay KK, Kalra S, Aravind S, Sinha B, Shah T, Kesavadev J, Rajput R. Scientific advisory on nocturnal hypoglycemia in insulin-treated patients with diabetes: Recommendations from Indian experts. Diabetes Metab Syndr 2022; 16:102587. [PMID: 36055167 DOI: 10.1016/j.dsx.2022.102587] [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: 02/07/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Insulin is one of the commonly prescribed glucose lowering agents in diabetes. Hypoglycemia is the most common complication, and severe hypoglycemia is the most serious complication of insulin therapy. Almost half of all severe hypoglycemia episodes (HEs) occur at night. However, patients are often unaware of their nocturnal hypoglycaemia (NH) risk. Additionally, both healthcare professionals and patients find it difficult to manage NH. The purpose of this expert group meeting is to improve NH awareness and provide guidance for the physicians to recognize and manage NH. METHOD The panel of experts in an e-board deliberated extensively upon the available literature and guidelines on hypoglycemia and NH discussed the consensus on definition, detection, reporting, monitoring, treatment, and optimization of therapy in NH. RESULT & Conclusion: Though there are many guidelines on the management of HEs in patients with diabetes, very few touch the topic of NH. This scientific advisory on management of NH in insulin treated patients with diabetes is formulated to address this gap in understanding regarding management of NH. The experts provide recommendations for the nocturnal window, defining NH based on blood glucose values, recognition, prevention and management of NH.
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Affiliation(s)
- M Chawla
- Lina Diabetes Care Centre, Mumbai, India.
| | - P Chawla
- Consultant Diabetologist and Director of Clinical Research, Lina Diabetes Care and Mumbai Diabetes Research Centre, Mumbai, India
| | - B Saboo
- Dept of Endocrinology, Dia Care, Ahmedabad, Gujrat, India
| | - R Chawla
- North Delhi Diabetes Centre, Rohini, New Delhi, India
| | - K K Gangopadhyay
- Consultant in Endocrinology, CK Birla Hospitals, Peerless Hospital, India
| | - S Kalra
- Department of Endocrinology, Bharti Hospital, Karnal, India
| | | | - B Sinha
- AMRI and Fortis Hospitals, Kolkata, India
| | - T Shah
- Director and Diabetologist Iva Diabetes Care Centre Mumbai, Sl Raheja Fortis Hospital, Mumbai, India
| | - J Kesavadev
- Jothydev's Diabetes and Research Center, Kerala, India
| | - R Rajput
- Department of Endocrinology, PGIMS, Rohtak, Haryana, India
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Kaushik V, Jain P, Akhtar N, Joshi A, Gupta LR, Grewal RK, Oliva R, Shaikh AR, Cavallo L, Chawla M. Immunoinformatics-Aided Design and In Vivo Validation of a Peptide-Based Multiepitope Vaccine Targeting Canine Circovirus. ACS Pharmacol Transl Sci 2022. [DOI: 10.1021/acsptsci.2c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Pankaj Jain
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Nahid Akhtar
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Amit Joshi
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Lovi Raj Gupta
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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Kaushik V, G SK, Gupta LR, Kalra U, Shaikh AR, Cavallo L, Chawla M. Immunoinformatics Aided Design and In-Vivo Validation of a Cross-Reactive Peptide Based Multi-Epitope Vaccine Targeting Multiple Serotypes of Dengue Virus. Front Immunol 2022; 13:865180. [PMID: 35799781 PMCID: PMC9254734 DOI: 10.3389/fimmu.2022.865180] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 01/29/2022] [Accepted: 05/05/2022] [Indexed: 02/03/2023] Open
Abstract
Dengue virus (DENV) is an arboviral disease affecting more than 400 million people annually. Only a single vaccine formulation is available commercially and many others are still under clinical trials. Despite all the efforts in vaccine designing, the improvement in vaccine formulation against DENV is very much needed. In this study, we used a roboust immunoinformatics approach, targeting all the four serotypes of DENV to design a multi-epitope vaccine. A total of 13501 MHC II binding CD4+ epitope peptides were predicted from polyprotein sequences of four dengue virus serotypes. Among them, ten conserved epitope peptides that were interferon-inducing were selected and found to be conserved among all the four dengue serotypes. The vaccine was formulated using antigenic, non-toxic and conserved multi epitopes discovered in the in-silico study. Further, the molecular docking and molecular dynamics predicted stable interactions between predicted vaccine and immune receptor, TLR-5. Finally, one of the mapped epitope peptides was synthesized for the validation of antigenicity and antibody production ability where the in-vivo tests on rabbit model was conducted. Our in-vivo analysis clearly indicate that the imunogen designed in this study could stimulate the production of antibodies which further suggest that the vaccine designed possesses good immunogenicity.
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Affiliation(s)
- Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Sunil Krishnan G
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Lovi Raj Gupta
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Utkarsh Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, India
- Department of Data Science, Innopolis University, Innopolis, Russia
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, India
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
| | - Luigi Cavallo
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
| | - Mohit Chawla
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
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18
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Willmann J, Sidiqi B, Wang C, Czmielewski C, Li HJ, Dick-Godfrey R, Chawla M, Lee RP, Gelb E, Wu AJ, Lovelock M, Zhang Z, Yorke ED, Rimner A. Four-Dimensional Computed Tomography-Based Correlation of Respiratory Motion of Lung Tumors With Implanted Fiducials and an External Surrogate. Adv Radiat Oncol 2022; 7:100885. [PMID: 35198837 PMCID: PMC8792087 DOI: 10.1016/j.adro.2021.100885] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
Purpose Our purpose was to assess the suitability of airway-implanted internal fiducial markers and an external surrogate of respiratory motion for motion management during radiation therapy of lung tumors. Methods and Materials We analyzed 4-dimensional computed tomography scans acquired during radiation therapy simulation for 28 patients with lung tumors who had anchored fiducial markers bronchoscopically implanted inside small airways in or near the tumor in a prospective trial. We used a linear mixed model to build population-based correlative models of tumor and surrogate motion. The first 24 of the 28 patients were used to build correlative models, and 4 of the 28 consecutive patients were excluded and used as an internal validation cohort. Of the 24 patients from the model building cohort, all were used for the models based on the internal fiducial. The external surrogate was completely visualized in 11 patients from the model building cohort, so only those were used for the models based on the external surrogate. Furthermore, we determined the predicted residual error sum of squares for our correlative models, which may serve as benchmarks for future research. Results The motion of the internal fiducials was significantly associated with the tumor motion in the anterior-posterior (P < .0001) and superior-inferior (SI) directions (P < .0001). We also observed a strong correlation of the external surrogate anterior-posterior motion to the tumor dominant SI motion (P < .0001). In the validation cohort, the internal fiducial SI motion was the only reliable predictor of lung tumor motion. Conclusions The internal fiducials appear to be more reliable predictors of lung tumor motion than the external surrogate. The suitability of such airway-implanted internal fiducial markers for advanced motion management techniques should be further investigated. Although the external surrogate seems to be less reliable, its wide availability and noninvasive application support its clinical utility, albeit the greater uncertainty will need to be compensated for.
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Harris W, Yorke E, Li H, Czmielewski C, Chawla M, Lee RP, Hotca-Cho A, McKnight D, Rimner A, Lovelock DM. Can bronchoscopically implanted anchored electromagnetic transponders be used to monitor tumor position and lung inflation during deep inspiration breath-hold lung radiotherapy? Med Phys 2022; 49:2621-2630. [PMID: 35192211 PMCID: PMC9007909 DOI: 10.1002/mp.15565] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/22/2022] [Accepted: 02/05/2022] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To evaluate the efficacy of using bronchoscopically implanted anchored electromagnetic transponders (EMTs) as surrogates for 1) tumor position and 2) repeatability of lung inflation during deep-inspiration breath-hold (DIBH) lung radiotherapy. METHODS 41 patients treated with either hypofractionated (HF) or conventional (CF) lung radiotherapy on an IRB approved prospective protocol using coached DIBH were evaluated for this study. Three anchored EMTs were bronchoscopically implanted into small airways near or within the tumor. DIBH treatment was gated by tracking the EMT positions. Breath-hold cone-beam-CTs (CBCTs) were acquired prior to every HF treatment or weekly for CF patients. Retrospectively, rigid registrations between each CBCT and the breath-hold planning CT were performed to match to 1) spine 2) EMTs and 3) tumor. Absolute differences in registration between EMTs and spine were analyzed to determine surrogacy of EMTs for lung inflation. Differences in registration between EMTs and tumor were analyzed to determine surrogacy of EMTs for tumor position. The stability of the EMTs was evaluated by analyzing the difference between inter-EMT displacements recorded at treatment from that of the plan for the CF patients, as well as the geometric residual (GR) recorded at the time of treatment. RESULTS 219 CBCTs were analyzed. The average differences between EMT centroid and spine registration among all CBCTs were 0.45±0.42cm, 0.29±0.28cm, and 0.18±0.15cm in superior-inferior (SI), anterior-posterior (AP) and lateral directions, respectively. Only 59% of CBCTs had differences in registration <0.5cm for EMT centroid compared to spine, indicating that lung inflation is not reproducible from simulation to treatment. The average differences between EMT centroid and tumor registration among all CBCTs were 0.13±0.13cm, 0.14±0.13cm and 0.12±0.12cm in SI, AP and lateral directions, respectively. 95% of CBCTs resulted in <0.5cm change between EMT centroid and tumor registration, indicating that EMT positions correspond well with tumor position during treatments. Six out of the 7 recorded CF patients had average differences in inter-EMT displacements to be ≤0.26cm and average GR ≤0.22cm, indicating that the EMTs are stable throughout treatment. CONCLUSIONS Bronchoscopically implanted anchored EMTs are good surrogates for tumor position and are reliable for maintaining tumor position when tracked during DIBH treatment, as long as the tumor size and shape are stable. Large differences in registration between EMTs and spine for many treatments suggest that lung inflation achieved at simulation is often not reproduced. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wendy Harris
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Ellen Yorke
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Henry Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Christian Czmielewski
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Mohit Chawla
- Department of Medicine, Pulmonary Service, Section of Interventional Pulmonology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Robert P Lee
- Department of Medicine, Pulmonary Service, Section of Interventional Pulmonology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Alexandra Hotca-Cho
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Dominique McKnight
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - D Michael Lovelock
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
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20
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Chawla M, Said Noor M. 988 A Quality Improvement Project; Improving the Quality and Safety of Handover During COVID-19. Br J Surg 2021. [PMCID: PMC8524555 DOI: 10.1093/bjs/znab259.114] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Aim The World Health Organisation (WHO) positions effective handover, in its top five patient safety solutions. During our District Hospital Trust’s COVID-19 response, an unprecedented reorganisation of all teams occurred. All surgical and medical speciality junior doctors were re-deployed and split into 4 zones to cover the hospital. In this quality improvement project (QIP), we sought to understand our trainees’ thoughts on this new multi-zonal handover process and aimed to identify risk-reduction measures to aid better patient care. Method The opinions of trainees on the new handover system were obtained using an online Likert scale survey. Following the responses, a new morning and night handover proforma was developed. This was used trust-wide and a post-intervention repeat survey was conducted to assess the new changes. Results The primary survey received 31 responses with feedback illustrating mixed effectiveness of the existing handover process. Free text comments highlighted issues surrounding “safety”, “poor organisation”, “poor continuity of care” with one serious incident reported. Post-intervention of a new handover proforma, a repeat online survey received 25 responses. Results were significantly more positive with >84% of responses being in the “strongly agree to agree” category, including for “continuity of care”, “organisation”, and “safety”. Conclusions This QIP illustrates a good example of a low-cost intervention to create a better handover system and aid hospitals during time of crises. For us, it managed to reform the handover process and ultimately improved our patient care. Forthcoming, we would like to create a national best practice guide for effective handover.
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Affiliation(s)
- M Chawla
- University College London, London, United Kingdom
| | - M Said Noor
- University College London, London, United Kingdom
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21
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Said Noor M, Chawla M. 1613 A Case Study Implementing A Strength Training Programme with The Aim to Reduce the Risk of Osteosarcopenia And Bone Fractures. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.396] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Aim
Strength training induces a mechanical load, both increasing muscle mass and enhancing osteoblast activity. This results in increased muscle and bone strength, reducing the risk of osteosarcopenia. Osteosarcopenia can start after the age of 30, putting patients at increased risk of bone fractures, with an untrained individual losing 0.23kg of muscle mass per year. In this case study, we illustrate a training programme, implemented over a period of 4 weeks on an untrained individual. The aim is to set an exemplar strengthening regimen for patients to reduce their risk of developing osteosarcopenia and bone fractures.
Method
One untrained novice subject was recruited. Two physical profile measurements were taken, prior to the start of the programme and at its conclusion. These included height, weight, BMI, lean body mass, muscle circumference and 1 repetition max (1RM) for upper body strength (bench press) and lower body strength (deadlift and squat).
Results
The subject had increased strength performance with increased 1RM, or equivalent, in the deadlift (+2.9kg), squat (+3kg) and bench press (+2.5kg) He also had a small increase in lean body mass of 0.1kg and increased body circumference in all muscle groups.
Conclusions
Our study shows that a simple strength training programme performed independently can lead to improved muscle strength and increased lean body mass. We illustrated that the programme can be performed inexpensively. Forthcoming, we would like to perform a prospective cohort study with the aim to implement a standardised programme within national guidelines for fracture risk-reduction.
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Affiliation(s)
- M Said Noor
- University College London, London, United Kingdom
| | - M Chawla
- University College London, London, United Kingdom
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22
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Kalchiem-Dekel O, Hossain S, Gauran C, Beattie JA, Husta BC, Lee RP, Chawla M. An evolving role for endobronchial ultrasonography in the intensive care unit. J Thorac Dis 2021; 13:5183-5194. [PMID: 34527358 PMCID: PMC8411164 DOI: 10.21037/jtd-2019-ipicu-09] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 11/06/2022]
Abstract
Endobronchial ultrasound (EBUS) bronchoscopy is an established minimally-invasive modality for visualization, characterization, and guidance of sampling of paratracheal and parabronchial structures and tissues. In the intensive care unit (ICU), rapidly obtaining an accurate diagnosis is paramount to the management of critically ill patients. In some instances, diagnosing and confirming terminal illness in a critically ill patient provides needed closure for patients and their loved ones. Currently available data on feasibility, safety, and yield of EBUS bronchoscopy in critically ill patients is based on single center experiences. These data suggest that in select ICU patients convex and radial probe-EBUS bronchoscopy can serve as useful tools in the evaluation of mediastinal lymphadenopathy, central airway obstruction, pulmonary embolism, and peripheral lung lesions. Barriers to the use of EBUS bronchoscopy in the ICU include: (I) requirement for dedicated equipment, prolonged procedure time, and bronchoscopy team expertise that may not be available; (II) applicability to a limited number of patients and conditions in the ICU; and (III) technical difficulty related to the relatively large outer diameter of the convex probe-EBUS bronchoscope and an increased risk for adverse cardiopulmonary consequences due to intermittent obstruction of the artificial airway. While the prospects for EBUS bronchoscopy in critically ill patients appear promising, judicious patient selection in combination with bronchoscopy team expertise are of utmost importance when considering performance of EBUS bronchoscopy in the ICU setting.
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Affiliation(s)
- Or Kalchiem-Dekel
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saamia Hossain
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cosmin Gauran
- Department of Anesthesia and Critical Care Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason A Beattie
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bryan C Husta
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert P Lee
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohit Chawla
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Shaikh AR, Chawla M, Hassan AA, Abdulazeez I, Salawu OA, Siddiqui MN, Pervez S, Cavallo L. Adsorption of industrial dyes on functionalized and nonfunctionalized asphaltene: A combined molecular dynamics and quantum mechanics study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116433] [Citation(s) in RCA: 10] [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] [Indexed: 11/28/2022]
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Robson PC, O’Connor D, Pardini P, Akard TF, Dietrich MS, Kotin A, Solomon A, Chawla M, Kennedy M, Solomon SB. Hemoptysis associated with percutaneous transthoracic needle biopsy: Development of critical events checklist and procedure outcomes. J Radiol Nurs 2021; 40:221-226. [PMID: 34483778 PMCID: PMC8409504 DOI: 10.1016/j.jradnu.2021.04.002] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND A percutaneous transthoracic needle biopsy (PTNB) is performed to obtain tissue for a pathologic diagnosis. A PTNB is necessary prior to the initiation of many cancer treatments. There is a risk of hemoptysis, the expectoration of blood, with the possibility for adverse, life-threatening outcomes. A critical event checklist is a cognitive aid used in an emergency to ensure critical steps are followed. To date, there are no known checklists published for management of PTNB-related, life-threatening hemoptysis. The purpose of this report is to describe the development and implementation of a critical event checklist and the adoption of the checklist into hemoptysis management. METHODS In March 2017, a process improvement team convened to evaluate the hemoptysis response using the Plan-Do-Study-Act (PDSA) methodology. The checklist was evaluated and updated through September 2019. The team educated Interventional Radiology (IR) clinicians on the new checklist and conducted simulations on its use. A retrospective chart review was performed on hemoptysis events between the ten-year period of October 1, 2008 and September 30, 2018 to evaluate the adoption of the checklist into practice. RESULTS There were 231 hemoptysis events occurring in 229 patients (2 with repeat biopsies). Prior to implementing the protocol and checklist, there were 166 (71.9%) hemoptysis events. After implementation there were 65 (28.1%) events. The median amount of documented blood expectorated with hemoptysis was 100 mL (IQR 20.0-300.0). Twenty-six patients were admitted after PTNB for reasons related to the hemoptysis event (11.3%). During the procedure, four (1.7%) patients with hemoptysis suffered a cardiac arrest. Prior to implementation of the protocol and critical events checklist, nurses positioned patients in the lateral decubitus (LD) position in 40 out of 162 (24.7%) cases. After implementation of the critical events checklist, nurses positioned patients in the LD position 42 out of 65 cases (64.6%) (OR=5.57(95% CI 2.99-10.367), p<0.001). DISCUSSION Interventional Radiology nurses successfully adopted the checklist into management of hemoptysis events. The reported incidence of hemoptysis suggests a need for IR teams to prepare for and simulate hemoptysis events. Future research is needed to evaluate the change in patient outcomes before and after critical events checklist implementation.
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Affiliation(s)
- Piera C. Robson
- Memorial Sloan Kettering Cancer Center Department of Nursing and, Vanderbilt University School of Nursing, 1275 York Avenue, S121, New York, NY 10065
| | - David O’Connor
- Memorial Sloan Kettering Cancer Center Department of Anesthesiology and Critical Care Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, C-613D, New York, NY 10065
| | - Perri Pardini
- Memorial Sloan Kettering Cancer Center Department of Nursing, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, M2 D-desk, New York, NY 10065
| | - Terrah F. Akard
- Vanderbilt University School of Nursing, 461 21 Ave South, 514 Godchaux Hall, Nashville, TN 37240
| | - Mary S. Dietrich
- Vanderbilt University School of Nursing and School of Medicine (Biostatistics, VICC, Psychiatry), 461 21 Ave South, 410 Godchaux Hall, Nashville, TN 37240
| | - Alan Kotin
- Memorial Sloan Kettering Cancer Center, Department of Anesthesiology and Critical Care Medicine, 1275 York Avenue, C330A, New York, NY
| | - Alexandra Solomon
- Memorial Sloan Kettering Cancer Center, Department of Nursing, 1275 York Avenue, New York, NY
| | - Mohit Chawla
- Memorial Sloan Kettering Cancer Center, Department of Medicine, 1275 York Avenue, New York, NY
| | - Matthew Kennedy
- Memorial Sloan Kettering Cancer Center, Department of Nursing, 1275 York Avenue, New York, NY
| | - Stephen B. Solomon
- Memorial Sloan Kettering Cancer Center, Department of Radiology, Memorial Sloan Kettering Cancer Center, H118, 1275 York Avenue, New York, NY 10065
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Chawla M, Gorle S, Shaikh AR, Oliva R, Cavallo L. Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study. Comput Struct Biotechnol J 2021; 19:1312-1324. [PMID: 33738080 PMCID: PMC7940798 DOI: 10.1016/j.csbj.2021.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 01/14/2023] Open
Abstract
The non-natural ethynylmethylpyridone C-nucleoside (W), a thymidine (T) analogue that can be incorporated in oligonucleotides by automated synthesis, has recently been reported to form a high fidelity base pair with adenosine (A) and to be well accommodated in B-DNA duplexes. The enhanced binding affinity for A of W, as compared to T, makes it an ideal modification for biotechnological applications, such as efficient probe hybridization for the parallel detection of multiple DNA strands. In order to complement the experimental study and rationalize the impact of the non-natural W nucleoside on the structure, stability and dynamics of DNA structures, we performed quantum mechanics (QM) calculations along with molecular dynamics (MD) simulations. Consistently with the experimental study, our QM calculations show that the A:W base pair has an increased stability as compared to the natural A:T pair, due to an additional CH-π interaction. Furthermore, we show that mispairing between W and guanine (G) causes a distortion in the planarity of the base pair, thus explaining the destabilization of DNA duplexes featuring a G:W pair. MD simulations show that incorporation of single or multiple consecutive A:W pairs in DNA duplexes causes minor changes to the intra- and inter-base geometrical parameters, while a moderate widening/shrinking of the major/minor groove of the duplexes is observed. QM calculations applied to selected stacks from the MD simulations also show an increased stacking energy for W, over T, with the neighboring bases.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abdul Rajjak Shaikh
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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Beattie J, Rizvi H, Fuentes P, Luo J, Schoenfeld A, Lin IH, Postow M, Callahan M, Voss MH, Shah NJ, Betof Warner A, Chawla M, Hellmann MD. Success and failure of additional immune modulators in steroid-refractory/resistant pneumonitis related to immune checkpoint blockade. J Immunother Cancer 2021; 9:jitc-2020-001884. [PMID: 33568350 PMCID: PMC7878154 DOI: 10.1136/jitc-2020-001884] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Pneumonitis related to immune checkpoint blockade is uncommon but can be severe, fatal or chronic. Steroids are first-line treatment, however, some patients are refractory or become resistant to steroids. Like many immune-related adverse events, little is known regarding the outcomes and optimal management of patients in whom steroids are ineffective. METHODS We performed a single-center retrospective cohort study at a high-volume tertiary cancer center to evaluate the clinical course, management strategies and outcomes of patients treated for immune checkpoint pneumonitis with immune modulatory medications in addition to systemic steroids. Pharmacy records were queried for patients treated with both immune checkpoint blockade and receipt of additional immune modulators. Records were then manually reviewed to identify patients who received the additional immune modulators for immune checkpoint pneumonitis. RESULTS From 2013 to 2020, we identified 26 patients treated for immune checkpoint pneumonitis with additional immune modulators in addition to steroids. Twelve patients (46%) were steroid-refractory and 14 (54%) were steroid-resistant. Pneumonitis severity included grade 2 (42%) or grade 3-4 (58%). Additional immune modulation consisted of tumor necrosis factor-alpha inhibitor (77%) and/or mycophenolate (23%). Durable improvement in pneumonitis following initiation of additional immune modulators occurred in 10 patients (38%), including three patients (12%) in whom pneumonitis resolved and all immunosuppressants ceased. The rate of 90-day all-cause mortality/hospice referral was 50%. At last follow-up, mortality attributable to pneumonitis was 23%. In addition to mortality from pneumonitis and cancer, 3 patients (12%) died due to infections possibly associated with immunosuppression. CONCLUSIONS Steroid-refractory or -resistant immune checkpoint pneumonitis is uncommon but associated with significant morbidity and mortality. Additional immunomodulators can yield durable improvement, attained in over one third of patients. An improved understanding of the underlying biology of immune-related pneumonitis will be crucial to guide more precise and effective treatment strategies in the future.
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Affiliation(s)
- Jason Beattie
- Pulmonary Division, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Paige Fuentes
- Pulmonary Division, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jia Luo
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Adam Schoenfeld
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - I-Hsin Lin
- Department of Epidemiology and Biostatistics, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael Postow
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Melanoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Margaret Callahan
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Melanoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Martin H Voss
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Genitourinary Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Neil J Shah
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Genitourinary Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Allison Betof Warner
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Melanoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mohit Chawla
- Pulmonary Division, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Matthew D Hellmann
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA .,Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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27
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Flamme M, Röthlisberger P, Levi-Acobas F, Chawla M, Oliva R, Cavallo L, Gasser G, Marlière P, Herdewijn P, Hollenstein M. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate. ACS Chem Biol 2020; 15:2872-2884. [PMID: 33090769 DOI: 10.1021/acschembio.0c00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l’École de Médecine, 75006 Paris, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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28
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Kalchiem-Dekel O, Fuentes P, Bott MJ, Beattie JA, Lee RP, Chawla M, Husta BC. Multiplanar 3D fluoroscopy redefines tool-lesion relationship during robotic-assisted bronchoscopy. Respirology 2020; 26:120-123. [PMID: 33140495 DOI: 10.1111/resp.13966] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/22/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Or Kalchiem-Dekel
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paige Fuentes
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew J Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason A Beattie
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert P Lee
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohit Chawla
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bryan C Husta
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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29
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Kalra K, Gorle S, Cavallo L, Oliva R, Chawla M. Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs. Nucleic Acids Res 2020; 48:5825-5838. [PMID: 32392301 PMCID: PMC7293021 DOI: 10.1093/nar/gkaa345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 01/15/2023] Open
Abstract
We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.
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Affiliation(s)
- Kanav Kalra
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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30
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Kalra S, Ghosh S, Das AK, Nair T, Bajaj S, Priya G, Mehrotra RN, Das S, Shah P, Deshmukh V, Chawla M, Sanyal D, Chandrasekaran S, Khandelwal D, Joshi A, Eliana F, Permana H, Fariduddin MD, Shrestha PK, Shrestha D, Kahandawa S, Sumanathilaka M, Shaheed A, Rahim AA, Orabi A, Al-Ani A, Hussein W, Kumar D, Shaikh K. Unravelling the utility of modern sulfonylureas from cardiovascular outcome trials and landmark trials: expert opinion from an international panel. Indian Heart J 2020; 72:7-13. [PMID: 32423565 PMCID: PMC7231843 DOI: 10.1016/j.ihj.2020.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/25/2019] [Accepted: 01/05/2020] [Indexed: 12/13/2022] Open
Abstract
AIM The primary objective of this review is to develop practice-based expert group opinions on the cardiovascular (CV) safety and utility of modern sulfonylureas (SUs) in cardiovascular outcome trials (CVOTs). BACKGROUND The United States Food and Drug Administration issued new guidance to the pharmaceutical industry in 2008 regarding the development of new antihyperglycemic drugs. The guidance expanded the scope for the approval of novel antihyperglycemic drugs by mandating CVOTs for safety. A few long-term CVOTs on dipeptidyl peptidase 4 inhibitors, glucagon-like peptide 1 receptor agonists, and sodium-glucose cotransporter 2 inhibitors have been completed, while others are ongoing. SUs, which constitute one of the key antihyperglycemic agents used for the management of type 2 diabetes mellitus (T2DM), have been used as comparator agents in several CVOTs. However, the need for CVOTs on modern SUs remains debatable. In this context, a multinational group of endocrinologists convened for a meeting and discussed the need for CVOTs of modern SUs to evaluate their utility in the management of patients with T2DM. At the meeting, CVOTs of modern SUs conducted to date and the hypotheses derived from the results of these trials were discussed. REVIEW RESULTS The expert group analyzed the key trials emphasizing the CV safety of modern SUs and also reviewed the results of various CVOTs in which modern SUs were used as comparators. Based on literature evidence and individual clinical insights, the expert group opined that modern SUs are cardiosafe and that since they have been used as comparators in other CVOTs, CVOTs of SUs are not required. CONCLUSION Modern SUs can be considered a cardiosafe option for the management of patients with diabetes mellitus and CV disease; thus CVOTs among individuals with T2DM are not required.
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Affiliation(s)
- S Kalra
- Department of Endocrinology, Bharti Hospital and BRIDE, Karnal, Haryana, India.
| | - S Ghosh
- Department of Endocrinology and Metabolism, IPGMER, Kolkata, West Bengal, India
| | - A K Das
- Department of Endocrinology & Medicine, Pondicherry Institute of Medical Sciences, Puducherry, India
| | - T Nair
- Dept. of Cardiology, PRS Hospital, Trivandrum, Kerala, India
| | - S Bajaj
- Department of Endocrinology, MLN Medical College, Allahabad, Uttar Pradesh, India
| | - G Priya
- Department of Endocrinology, Fortis Hospital, Chandigarh, Punjab, India
| | - R N Mehrotra
- Department of Endocrinology, Apollo Hospitals, Jubilee Hills, Hyderabad, India
| | - S Das
- Department of Endocrinology, Apollo Hospitals in Bhubaneswar, India
| | - P Shah
- Department of Endocrinology and Diabetes Gujarat Endocrine Centre, Ahmedabad, India
| | - V Deshmukh
- Department of Endocrinology, Deshmukh Clinic and Research Centre, Pune, Maharashtra
| | - M Chawla
- Department of Diabetology, Lina Diabetes Care and Mumbai Diabetes Research Centre, Mumbai, India
| | - D Sanyal
- Department of Endocrinology, KPC Medical College, Kolkata, West Bengal
| | - S Chandrasekaran
- Department of Endocrinology & Diabetes, Dr. Rela Institute of Medical Science (RIMC), Chennai, Tamil Nadu, India
| | - D Khandelwal
- Department of Endocrinology & Diabetes, Maharaja Agrasen Hospital, New Delhi, India
| | - A Joshi
- Department of Endocrinology & Diabetes, Bhaktivedanta Hospital and Research Institute, Mumbai, India
| | - F Eliana
- Department of Internal Medicine, Faculty of Medicine, YARSI University, Jakarta, Indonesia
| | - H Permana
- Department of Internal Medicine, Faculty of Medicine, Padjadjaran University, Bandung, Indonesia
| | - M D Fariduddin
- Department of Endocrinology of Bangabandhu Sheikh, Mujib Medical University, Dhaka, Bangladesh
| | - P K Shrestha
- Department of Internal Medicine, Tribhuwan University Teaching Hospital, Kathmandu, Nepal
| | - D Shrestha
- Department of Endocrinologist, Norvic International Hospital Kathmandu, Nepal
| | - S Kahandawa
- Department of Endocrinology, Teaching Hospital Karapitiya, Sri Lanka
| | - M Sumanathilaka
- Department of Endocrinology, National Hospital of Sri Lanka, Colombo, Sri Lanka
| | - A Shaheed
- Department of Internal Medicine, Indira Gandhi Memorial Hospital, Malé, Maldives
| | - A A Rahim
- Department of Diabetes and Metabolism, Alexandria University, Alexandria, Egypt
| | - A Orabi
- Department of Internal Medicine, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - A Al-Ani
- Department of Internal Medicine, Hamad General Hospital, Doha, Qatar
| | - W Hussein
- Department of Endocrinology & Diabetes, Royal Hospital, Bahrain
| | - D Kumar
- Department of Endocrinology, NMC Specialty Hospital, Abu Dhabi
| | - K Shaikh
- Department of Diabetes, Faculty of Internal Medicine, Royal Oman Police Hospital, Muscat, Oman
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31
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Beattie J, Fuentes P, Rizvi H, Luo J, Schoenfeld AJ, Postow MA, Callahan MK, Warner AB, Chawla M, Hellmann MD. Success and failure of additional immunosuppressants in steroid-refractory pneumonitis related to immune checkpoint blockade. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3078 Background: Severe immune related adverse events (irAEs) with immune checkpoint blockade are uncommon but can be fatal. Steroids are the most common initial treatment for most non-endocrine irAEs, but some patients are or become refractory to steroids. When steroids are not effective, there is limited data to guide management strategies, particularly in the context of pneumonitis. Methods: All patients at MSK treated with immune checkpoint blockade from 2013-2020 were queried for receipt of an immunosuppressant (e.g. TNF antagonists, mycophenolate mofetil, cyclophosphamide) beyond steroids. Patient records were then manually reviewed to identify patients who received such therapy for management of immunotherapy-related pneumonitis. Results: Among 5363 patients treated with immune checkpoint blockade, 364 (6.8%) received an additional immunosuppressant for an irAE, including 28 (0.5% of all patients treated) patients treated for pneumonitis. Most of these pneumonitis events (19/28, 68%) were grade 3 or higher. Agents used included mycophenolate mofetil (7/28; 25%), TNF antagonists (23/28; 82%), and cyclophosphamide (1/28; 3.5%); more than one medication was used in 3 patients (11%). The indications were primary non-response to steroids (n = 16, 57%) and recrudescence after initial response to steroids (n = 12, 43%). At 90 days from initiation of the additional immunosuppressant, 13/28 (46%) patients were alive with improvement or resolution of pneumonitis while 15/28 (54%) had died. Survival with resolution/improvement was more common in patients treated for recrudescence vs primary non-response (67% vs 25%, p = 0.05). Conclusions: Outcomes with additional immunosuppressants in the setting of steroid-refractory immune-related pneumonitis are poor, but resolution can occur in some cases. A deeper understanding of the mechanistic underpinnings of irAEs is needed to more effectively tailor immunosuppressant therapies, particularly in severe pneumonitis events.
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Affiliation(s)
- Jason Beattie
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paige Fuentes
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hira Rizvi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jia Luo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Mohit Chawla
- Memorial Sloan Kettering Cancer Center, New York, NY
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32
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Shaikh AR, Ashraf M, AlMayef T, Chawla M, Poater A, Cavallo L. Amino acid ionic liquids as potential candidates for CO2 capture: Combined density functional theory and molecular dynamics simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137239] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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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33
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Salat H, Modi A, Lee R, Chawla M. ENDOBRONCHIAL LIPOMA: THERE IS OFTEN MORE THAN MEETS THE EYE. Chest 2019. [DOI: 10.1016/j.chest.2019.08.1366] [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: 10/25/2022] Open
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34
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Chawla M, Minenkov Y, Vu KB, Oliva R, Cavallo L. Structural and Energetic Impact of Non-natural 7-Deaza-8-azaguanine, 7-Deaza-8-azaisoguanine, and Their 7-Substituted Derivatives on Hydrogen-Bond Pairing with Cytosine and Isocytosine. Chembiochem 2019; 20:2262-2270. [PMID: 30983115 DOI: 10.1002/cbic.201900245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/13/2019] [Indexed: 12/12/2022]
Abstract
The impact of 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications on the geometry and stability of the G:C Watson-Crick (cWW) base pair and the G:iC and iG:C reverse Watson-Crick (tWW) base pairs has been characterized theoretically. In addition, the effect on the same base pairs of seven C7-substituted DAG and DAiG derivatives, some of which have been previously experimentally characterized, has been investigated. Calculations indicate that all of these modifications have a negligible impact on the geometry of the above base pairs, and that modification of the heterocycle skeleton has a small impact on the base-pair interaction energies. Instead, base-pair interaction energies are dependent on the nature of the C7 substituent. For the 7-substituted DAG-C cWW systems, a linear correlation between the base-pair interaction energy and the Hammett constant of the 7-substituent is found, with higher interaction energies corresponding to more electron-withdrawing substituents. Therefore, the explored modifications are expected to be accommodated in both parallel and antiparallel nucleic acid duplexes without perturbing their geometry, while the strength of a base pair (and duplex) featuring a DAG modification can, in principle, be tuned by incorporating different substituents at the C7 position.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Khanh B Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ho Chi Minh City, Vietnam
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
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35
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Willmann J, Sidiqi B, Wang C, Wu A, Lovelock D, Czmielewski C, Li H, Dick-Godfrey R, Chawla M, Lee R, Yorke E, Rimner A. 4DCT-Based Correlation of Respiratory Motion of Lung Tumors with Implanted Fiducials and an External Surrogate. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1555] [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: 10/28/2022]
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36
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Chawla M, Kumari A, Siril PF. Exceptional Catalytic Activities and Sensing Performance of Palladium Decorated Anisotropic Gold Nanoparticles. ChemistrySelect 2018. [DOI: 10.1002/slct.201801426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mohit Chawla
- Advanced Materials Research Centre and School of Basic Science; Indian Institute of Technology Mandi; Mandi-175005, Himachal Pradesh India
| | - Anu Kumari
- Advanced Materials Research Centre and School of Basic Science; Indian Institute of Technology Mandi; Mandi-175005, Himachal Pradesh India
| | - Prem Felix Siril
- Advanced Materials Research Centre and School of Basic Science; Indian Institute of Technology Mandi; Mandi-175005, Himachal Pradesh India
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37
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Lee YJ, Bacchus M, Schmidt E, Chawla M, Barker JN, Papanicolaou GA. Paradoxical immune reconstitution inflammatory syndrome associated with disseminated tuberculosis infection in an unrelated donor cord blood transplant recipient. Transpl Infect Dis 2018; 20:e12889. [PMID: 29569815 DOI: 10.1111/tid.12889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 11/28/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 01/09/2023]
Abstract
Tuberculosis (TB) is an infrequent infection after hematopoietic cell transplant (HCT), with associated mortality up to 30%. The utility of universal screening for latent TB in HCT candidates is controversial due to the lack of sensitive screening tests. We describe a case of disseminated TB infection complicated by immune reconstitution inflammatory syndrome in an adult double unit umbilical cord blood transplant recipient who originated from the United Arab Emirates.
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Affiliation(s)
- Yeon Joo Lee
- Department of Medicine, Infectious Diseases Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Melissa Bacchus
- Department of Medicine, Infectious Diseases Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth Schmidt
- Department of Medicine, Infectious Diseases Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohit Chawla
- Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Pulmonary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliet N Barker
- Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Adult Bone Marrow Transplantation Services, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Genovefa A Papanicolaou
- Department of Medicine, Infectious Diseases Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
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Chawla M, Poater A, Besalú-Sala P, Kalra K, Oliva R, Cavallo L. Theoretical characterization of sulfur-to-selenium substitution in an emissive RNA alphabet: impact on H-bonding potential and photophysical properties. Phys Chem Chem Phys 2018; 20:7676-7685. [PMID: 29497733 DOI: 10.1039/c7cp07656h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We employ density functional theory (DFT) and time-dependent DFT (TDDFT) calculations to investigate the structural, energetic and optical properties of a new computationally designed RNA alphabet, where the nucleobases, tsA, tsG, tsC, and tsU (ts-bases), have been derived by replacing sulfur with selenium in the previously reported tz-bases, based on the isothiazolo[4,3-d]pyrimidine heterocycle core. We find out that the modeled non-natural bases have minimal impact on the geometry and energetics of the classical Watson-Crick base pairs, thus potentially mimicking the natural bases in a RNA duplex in terms of H-bonding. In contrast, our calculations indicate that H-bonded base pairs involving the Hoogsteen edge of purines are destabilized as compared to their natural counterparts. We also focus on the photophysical properties of the non-natural bases and correlate their absorption/emission peaks to the strong impact of the modification on the energy of the lowest unoccupied molecular orbital. It is indeed stabilized by roughly 1.1-1.6 eV as compared to the natural analogues, resulting in a reduction of the gap between the highest occupied and the lowest unoccupied molecular orbital from 5.3-5.5 eV in the natural bases to 3.9-4.2 eV in the modified ones, with a consequent bathochromic shift in the absorption and emission spectra. Overall, our analysis clearly indicates that the newly modelled ts-bases are expected to exhibit better fluorescent properties as compared to the previously reported tz-bases, while retaining similar H-bonding properties. In addition, we show that a new RNA alphabet based on size-extended benzo-homologated ts-bases can also form stable Watson-Crick base pairs with the natural complementary nucleobases.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
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Tollinche LE, Chawla M, Lee EW, Rolando Peralta A. Collaborating with interventional pulmonology in managing a massive tracheoesophageal fistula that extends from cricoid to carina: a case report. JA Clin Rep 2018; 3:62. [PMID: 29457105 PMCID: PMC5804658 DOI: 10.1186/s40981-017-0133-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
Tracheoesophageal fistulas (TEF) present a perioperative management challenge. A 62 year-old man with esophageal carcinoma presented with a large tracheoesophageal fistula extending most of the trachea. Previously, the patient had two overlapping esophageal and one tracheal stent placed, but he developed progressive tracheal disruption due to esophageal stent perforation near the level of the cricoid. This case describes the anesthetic management of tracheal stent placement for an expanding TEF. Management included a spontaneous breathing inhalation induction followed by ventilation through a supraglottic device—laryngeal mask airway (LMA). Finally, during rigid bronchoscopy, a combination of bag ventilation and jet ventilation was utilized.
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Affiliation(s)
- Luis E Tollinche
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, C330F, New York, NY 10065 USA
| | - Mohit Chawla
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, C330F, New York, NY 10065 USA
| | - Eunice W Lee
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, C330F, New York, NY 10065 USA
| | - A Rolando Peralta
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, C330F, New York, NY 10065 USA
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40
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Kumar V, Chawla M, Cavallo L, Wani AB, Manhas A, Kaur S, Poater A, Chadar H, Upadhyay N. Complexation of trichlorosalicylic acid with alkaline and first row transition metals as a switch for their antibacterial activity. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.08.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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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41
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Abstract
Quantum mechanics and molecular dynamics methods are used to compare the non-natural 4AP–DAP base pair to natural base pairs.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
| | - Ida Autiero
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies
- University Parthenope of Naples
- Centro Direzionale Isola C4
- Naples
- Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
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42
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Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L. Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs. Nucleic Acids Res 2017; 45:11019-11032. [PMID: 28977572 PMCID: PMC5737201 DOI: 10.1093/nar/gkx757] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 08/17/2017] [Indexed: 12/13/2022] Open
Abstract
The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Qingyun Zhang
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy.,King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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Dong Y, Manley BJ, Becerra MF, Redzematovic A, Casuscelli J, Tennenbaum DM, Reznik E, Han S, Benfante N, Chen YB, Arcila ME, Aras O, Voss MH, Feldman DR, Motzer RJ, Fabbri N, Healey JH, Boland PJ, Chawla M, Durack JC, Lee CH, Coleman JA, Russo P, Hakimi AA, Cheng EH, Hsieh JJ. Tumor Xenografts of Human Clear Cell Renal Cell Carcinoma But Not Corresponding Cell Lines Recapitulate Clinical Response to Sunitinib: Feasibility of Using Biopsy Samples. Eur Urol Focus 2017; 3:590-598. [PMID: 28753786 PMCID: PMC5608640 DOI: 10.1016/j.euf.2016.08.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 07/07/2016] [Accepted: 08/10/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Parallel development of preclinical models that recapitulate treatment response observed in patients is central to the advancement of personalized medicine. OBJECTIVE To evaluate the use of biopsy specimens to develop patient-derived xenografts and the use of corresponding cell lines from renal cell carcinoma (RCC) tumors for the assessment of histopathology, genomics, and treatment response. DESIGN, SETTING, AND PARTICIPANTS A total of 74 tumor specimens from 66 patients with RCC were implanted into immunocompromised NOD-SCID IL2Rg-/- mice. Four cell lines generated from patients' specimens with clear cell pathology were used for comparative studies. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Preclinical models were established and assessed. Engraftment rates were analyzed using chi-square testing. Analysis of variance (two-way analysis of variance) was conducted to assess tumor growth. RESULTS AND LIMITATIONS Overall, 33 RCC mouse xenograft models were generated with an overall engraftment rate of 45% (33 of 74). Tumor biopsies engrafted comparably with surgically resected tumors (58% vs 41%; p=0.3). Xenograft tumors and their original tumors showed high fidelity in regard to histology, mutation status, copy number change, and targeted therapy response. Engraftment rates from metastatic tumors were higher but not more significant than primary tumors (54% vs 34%; p=0.091). Our engraftment rate using metastases or biopsies was comparable with recent reports using resected primary tumors. In stark contrast to corresponding cell lines, all tested xenografts recapitulated patients' clinical response to sunitinib. CONCLUSIONS Patient-derived xenograft models can be effectively established from tumor biopsies. Preclinical xenograft models but not matched cell lines reflected clinical responses to sunitinib. PATIENT SUMMARY Matched patient-derived clear cell renal cell carcinoma xenografts and cell lines from responsive and refractory patients treated with sunitinib were established and evaluated for pharmacologic response to anti-vascular endothelial growth factor treatment. Both models accurately reflected the genetic characteristics of original tumors, but only xenografts recapitulated drug responses observed in patients. These models could serve as a powerful platform for precision medicine.
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Affiliation(s)
- Yiyu Dong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brandon J Manley
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria F Becerra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Almedina Redzematovic
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jozefina Casuscelli
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel M Tennenbaum
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Song Han
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Benfante
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omer Aras
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin H Voss
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darren R Feldman
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert J Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicola Fabbri
- Orthopedics Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John H Healey
- Orthopedics Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Patrick J Boland
- Orthopedics Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohit Chawla
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy C Durack
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chung-Han Lee
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan A Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily H Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James J Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Lovelock D, Yorke E, Pham H, Hotca-Cho A, Lim S, Chawla M, Lee R, Gelblum D, Gelb E, Cuaron J, Gewanter R, Rimner A. Can Bronchoscopically Implanted Anchored Transponders be Used As a Surrogate to Accurately Track Lung Tumors During Deep Inspiration Breath Hold Radiation Therapy? Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1742] [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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45
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Hotca A, Lovelock D, Yorke E, Gelb E, Gelblum D, Wu A, Cuaron J, Gewanter R, Lim S, Chawla M, Lee R, Rimner A. Variability in Anatomic Position of Implanted Electromagnetic Lung Transponders During Deep Inspiration Breath Hold. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1708] [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: 11/29/2022]
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46
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Yorke E, Lovelock D, Hotca A, Gelb E, Gelblum D, Wu A, Cuaron J, Gewanter R, Lim S, Chawla M, Lee R, Rimner A. Can Lung Volume at DIBH Treatment be Estimated Using Implanted Electromagnetic Transponders? Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1816] [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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Kaur S, Kumar V, Chawla M, Cavallo L, Poater A, Upadhyay N. Pesticides Curbing Soil Fertility: Effect of Complexation of Free Metal Ions. Front Chem 2017; 5:43. [PMID: 28725644 PMCID: PMC5495828 DOI: 10.3389/fchem.2017.00043] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/12/2017] [Indexed: 12/19/2022] Open
Abstract
Researchers have suggested that the reason behind infertility is pernicious effect of broad spectrum pesticides on non target, beneficial microorganism of soil. Here, studying the chelating effect of selective organophosphate and carbamate pesticides with essential metal ions, at all possible combinations of three different pH (4 ± 0.05, 7 ± 0.05 and 9 ± 0.05) and three different temperatures (15 ± 0.5°C, 30 ± 0.5°C and 45 ± 0.5°C), shows very fast rate of reaction which further increases with increase of pH and temperature. Carbonyl oxygen of carbamate and phosphate oxygen of organophosphate were found to be common ligating sites among all the complexes. Formed metal complexes were found to be highly stable and water insoluble on interaction with essential metal ions in solvent medium as well as over silica. Density functional theory (DFT) calculations not only reinforced the experimental observations, but, after a wide computational conformational analysis, unraveled the nature of the high stable undesired species that consist of pesticides complexed by metal ions from the soil. All in all, apart from the direct toxicity of pesticides, the indirect effect by means of complexation of free metal ions impoverishes the soil.
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Affiliation(s)
- Sukhmanpreet Kaur
- Department of Chemistry, Lovely Professional UniversityJalandhar, India
| | - Vijay Kumar
- Department of Chemistry, Lovely Professional UniversityJalandhar, India.,Regional Ayurveda Research Institute for Drug DevelopmentGwalior, India
| | - Mohit Chawla
- Kaust Catalysis Center, Physical Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Luigi Cavallo
- Kaust Catalysis Center, Physical Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Albert Poater
- Kaust Catalysis Center, Physical Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia.,Departament de Química, Facultat de Ciències, Institut de Química Computacional i Catàlisi, Universitat de GironaGirona, Spain
| | - Niraj Upadhyay
- Department of Chemistry, Lovely Professional UniversityJalandhar, India.,Department of Chemistry, Dr. Harisingh Gour VishwavidyalayaSagar, India
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Orpana H, Chawla M, Gallagher E, Escaravage E. Developing indicators for evaluation of age-friendly communities in Canada: process and results. Health Promot Chronic Dis Prev Can 2017; 36:214-223. [PMID: 27768558 DOI: 10.24095/hpcdp.36.10.02] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
INTRODUCTION In 2006, the World Health Organization launched the Global Age-Friendly Cities Project to support active aging. Canada has a large number of age-friendly initiatives; however, little is known about the effectiveness and outcomes of age-friendly community (AFC) initiatives. In addition, stakeholders report that they lack the capacity and tools to develop and conduct evaluations of their AFC initiatives. In order to address these gaps, the Public Health Agency of Canada developed indicators to support the evaluation of AFC initiatives relevant to a wide range of Canadian communities. These indicators meet the varied needs of communities, but are not designed to evaluate collective impact or enable crosscommunity comparisons. METHODS An evidence-based, iterative consultation approach was used to develop indicators for AFCs. This involved a literature review and an environmental scan. Two rounds of key expert and stakeholder consultations were conducted to rate potential indicators according to their importance, actionability and feasibility. A final list of indicators and potential measures were developed based on results from these consultations, as well as key policy considerations. RESULTS Thirty-nine indicators emerged across eight AFC domains plus four indicators related to long-term health and social outcomes. All meet the intended purpose of evaluating AFC initiatives at the community level. A user-friendly guide is available to support and share this work. CONCLUSION The AFC indicators can help communities evaluate age-friendly initiatives, which is the final step in completing a cycle of the Pan-Canadian AFC milestones. Communities are encouraged to use the evaluation results to improve their AFC initiatives, thereby benefiting a broad range of Canadians.
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Affiliation(s)
- H Orpana
- Science Integration Division, Social Determinants of Health and Science Integration Directorate, Public Health Agency of Canada, Ottawa, Ontario, Canada.,School of Psychology, University of Ottawa, Ottawa, Ontario, Canada
| | - M Chawla
- Population Health Promotion and Innovation Division, Centre for Health Promotion, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - E Gallagher
- School of Nursing (Emeritus), Faculty of Human and Social Development, University of Victoria, Victoria, British Columbia, Canada
| | - E Escaravage
- Population Health Promotion and Innovation Division, Centre for Health Promotion, Public Health Agency of Canada, Ottawa, Ontario, Canada
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Chawla M, Randhawa JK, Siril PF. Calcination temperature as a probe to tune the non-enzymatic glucose sensing activity of Cu–Ni bimetallic nanocomposites. NEW J CHEM 2017. [DOI: 10.1039/c6nj03920k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A seven-fold increase in the glucose sensing activity of CuO–NiO bimetallic nanocomposites was induced via calcination.
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Affiliation(s)
- Mohit Chawla
- Advanced Materials Research Centre
- School of Basic Sciences
- Indian Institute of Technology Mandi
- Mandi
- India
| | | | - Prem Felix Siril
- Advanced Materials Research Centre
- School of Basic Sciences
- Indian Institute of Technology Mandi
- Mandi
- India
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50
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Panikar V, Sosale A, Agarwal S, Unnikrishnan A, Kalra S, Bhattacharya A, Chawla M, Anjana RM, Bhatt A, Jaggi S, Sosale B, Hasnani D, Vadgama J. RSSDI clinical practice recommendations for management of In-hospital hyperglycaemia—2016. Int J Diabetes Dev Ctries 2016. [DOI: 10.1007/s13410-016-0528-z] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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