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Rajendran P, Saini S, Kumar N, Vashistha H, Thiruvengadam K, Ramamoorthy T, Gopalaswamy R, Kayesth J, Alavadi U, Moore M, Joshi RP, Ramachandran R, Anand S, Shanmugam S, Padmapriyadarsini C. Establishing proof of concept for utility of Trueprep ®-extracted DNA in line-probe assay testing. Int J Tuberc Lung Dis 2023; 27:742-747. [PMID: 37749831 PMCID: PMC10519390 DOI: 10.5588/ijtld.23.0003] [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: 01/01/2023] [Accepted: 04/01/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND AND OBJECTIVES: With an increased demand for rapid, diagnostic tools for TB and drug resistance detection, Truenat® MTB-RIF assay has proven to be a rapid point of care molecular test. The present study aimed to establish a proof of concept of using Trueprep-extracted DNA for line-probe assay (LPA) testing.METHODS: A total of 150 sputum samples (MTB-positive at Truenat sites) were divided into two aliquots. One aliquot was used for DNA extraction using the Trueprep device and MTB testing. The second aliquot of the sample was subjected to GenoLyse® DNA extraction. DNA from both the Trueprep and GenoLyse methods was subjected to first-line (FL) and second-line (SL) LPA testing.RESULTS: Of 139 Trueprep-extracted DNA, respectively 135 (97%) and 105 (75%) had interpretable results by FL and SL-LPA testing. Of 128 GenoLyse-extracted DNA, all 128 (100%) had interpretable FL-LPA results and 114 (89%) had interpretable SL-LPA results.CONCLUSION: The results obtained in this study indicate that Trueprep-extracted DNA can be used in obtaining valid LPA results. However, the study needs to be conducted on a larger sample size before our recommendations can be used for policy-making decisions.
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Affiliation(s)
- P Rajendran
- National Institute for Research in Tuberculosis, Indian Council of Medical Research, New Delhi
| | - S Saini
- Infectious Disease Detection and Surveillance Project, United States Agency for International Development (USAID), ICF Incorporated, Reston, VA, USA
| | - N Kumar
- Central TB Division, Ministry of Health and Family Welfare, New Delhi
| | - H Vashistha
- Infectious Disease Detection and Surveillance Project, United States Agency for International Development (USAID), ICF Incorporated, Reston, VA, USA
| | - K Thiruvengadam
- National Institute for Research in Tuberculosis, Indian Council of Medical Research, New Delhi
| | - T Ramamoorthy
- National Institute for Research in Tuberculosis, Indian Council of Medical Research, New Delhi
| | - R Gopalaswamy
- National Institute for Research in Tuberculosis, Indian Council of Medical Research, New Delhi
| | - J Kayesth
- Infectious Disease Detection and Surveillance Project, United States Agency for International Development (USAID), ICF Incorporated, Reston, VA, USA
| | | | - M Moore
- Infectious Disease Detection and Surveillance Project, United States Agency for International Development (USAID), ICF Incorporated, Reston, VA, USA
| | - R P Joshi
- Central TB Division, Ministry of Health and Family Welfare, New Delhi
| | - R Ramachandran
- World Health Organization India Office, New Delhi, India
| | - S Anand
- World Health Organization India Office, New Delhi, India
| | - S Shanmugam
- National Institute for Research in Tuberculosis, Indian Council of Medical Research, New Delhi
| | - C Padmapriyadarsini
- National Institute for Research in Tuberculosis, Indian Council of Medical Research, New Delhi
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2
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Raju R, Prasad BM, Alavadi U, Saini S, Sabharwal M, Duhan A, Anand S, Lal M, Kaur H, Arora N, Jaju J, Moore M, Ramachandran R, Kumar N, Joshi RP. Experience of "One Stop TB Diagnostic Solution" Model in Engaging a Private Laboratory for End-to-End Diagnostic Services in the National TB Elimination Program in Hisar, India. Diagnostics (Basel) 2023; 13:2823. [PMID: 37685361 PMCID: PMC10486804 DOI: 10.3390/diagnostics13172823] [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: 07/17/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The complete diagnostic evaluation of tuberculosis based on its drug-resistance profile is critical for appropriate treatment decisions. The TB diagnostic landscape in India has been transformed with the scaling-up of WHO-recommended diagnostics, but challenges remain with specimen transportation, completing diagnostic assessment, turnaround time (TAT), and maintaining laboratories. Private laboratories have demonstrated efficiencies for specimen collection, transportation, and the timely testing and issue of results. A one-stop TB diagnostic model was designed to assess the feasibility of providing end-to-end diagnostic services in the Hisar district of Haryana state, India. A NTEP-certified private laboratory was engaged to provide the services, complementing the existing public sector diagnostic services. A total of 10,164 specimens were collected between May 2022 and January 2023 and these were followed for the complete diagnostic assessment of Drug-Susceptible TB (DS-TB) and Drug-Resistant TB (DR-TB) and the time taken for issuing results. A total of 2152 (21%) patients were detected with TB, 1996 (93%) Rifampicin-Sensitive and 134 (6%) with Rifampicin-Resistant TB. Nearly 99% of the patients completed the evaluation of DS-TB and DR-TB within the recommended TAT. The One-Stop TB/DR-TB Diagnostic Solution model has demonstrated that diagnostic efficiencies could be enhanced through the strategic purchase of private laboratory services.
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Affiliation(s)
- Rajesh Raju
- Directorate of Health Services, Government of Haryana, Swasthya Bhavan, Sector 6, Panchkula 134109, India (M.S.); (A.D.)
| | | | - Umesh Alavadi
- United States Agency for International Development, New Delhi 110021, India;
| | - Sanjeev Saini
- Infectious Disease Detection and Surveillance (IDDS), New Delhi 110058, India
| | - Mukesh Sabharwal
- Directorate of Health Services, Government of Haryana, Swasthya Bhavan, Sector 6, Panchkula 134109, India (M.S.); (A.D.)
| | - Akshay Duhan
- Directorate of Health Services, Government of Haryana, Swasthya Bhavan, Sector 6, Panchkula 134109, India (M.S.); (A.D.)
| | - Sridhar Anand
- TB Support Network, Office of the World Health Organization (WHO) Representative to India, WHO Country Office, New Delhi 110021, India
| | - Manohar Lal
- Infectious Disease Detection and Surveillance (IDDS), New Delhi 110058, India
| | - Harpreet Kaur
- Infectious Disease Detection and Surveillance (IDDS), New Delhi 110058, India
| | | | - Jyoti Jaju
- iDEFEAT Project, The International Union against Tuberculosis and Lung Disease (The Union), New Delhi 110016, India
| | - Moe Moore
- Infectious Disease Detection and Surveillance (IDDS), New Delhi 110058, India
| | - Ranjani Ramachandran
- Office of the World Health Organization (WHO) Representative to India, WHO Country Office, New Delhi 110021, India
| | - Nishant Kumar
- Central TB Division, Ministry of Health and Family Welfare Government of India, New Delhi 110001, India
| | - Rajendra P. Joshi
- Central TB Division, Ministry of Health and Family Welfare Government of India, New Delhi 110001, India
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3
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Baker C, Milestone W, Garner AL, Joshi RP. Selective Electroporation of Tumor Cells Under AC Radiofrequency Stimulation - A Numerical Study. IEEE Trans Biomed Eng 2023; PP:1-9. [PMID: 37418405 DOI: 10.1109/tbme.2023.3293278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Self-consistent evaluations of membrane electroporation along with local heating in single spherical cells arising from external AC radiofrequency electrical stimulation have been carried out. The present numerical study seeks to determine whether healthy and malignant cells exhibit separate electroporative responses with regards to operating frequency. It is shown that cells of Burkitt's lymphoma would respond to frequencies >4.5 MHz, while normal B-cells would have negligible porative effects in that higher frequency range. Similarly, a frequency separation between the response of healthy T-cells and malignant species is predicted with a threshold of about 4 MHz for cancer cells. The present simulation technique is general and so would be able to ascertain the beneficial frequency range for different cell types. The demonstration of higher frequencies to induce poration in malignant cells, while having minimal affecting healthy ones, suggests the possibility of selective electrical targeting for tumor treatments and protocols. It also opens the doorway for tabulating selectivity enhancement regimes as a guide for parameter selection towards more effective treatments while minimizing deleterious effects on healthy cells and tissues.
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4
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Diaz L, Karkash A, Alsharari S, Joshi RP, Schamiloglu E, Sanati M. Author Correction: Importance of surface morphology on secondary electron emission: a case study of Cu covered with carbon, carbon pairs, or graphitic-like layers. Sci Rep 2023; 13:10749. [PMID: 37400484 DOI: 10.1038/s41598-023-37839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Affiliation(s)
- L Diaz
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - A Karkash
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - S Alsharari
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - R P Joshi
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - E Schamiloglu
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - M Sanati
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA.
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5
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Diaz L, Karkash A, Alsharari S, Joshi RP, Schamiloglu E, Sanati M. Importance of surface morphology on secondary electron emission: a case study of Cu covered with carbon, carbon pairs, or graphitic-like layers. Sci Rep 2023; 13:8260. [PMID: 37217573 DOI: 10.1038/s41598-023-34721-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023] Open
Abstract
Understanding the relationship between surface adsorbates and secondary electronic emission is critical for a variety of technologies, since the secondary electrons can have deleterious effects on the operation of devices. The mitigation of such phenomena is desirable. Here, using the collective efforts of first-principles, molecular dynamics, and Monte Carlo simulations, we studied the effects of a variety of carbon adsorbates on the secondary electron emission of Cu (110). It was demonstrated that the adsorption of atomic C and C[Formula: see text] pair layers can both reduce and increase the number of secondary electrons depending on the adsorbate coverage. It was shown that under electron irradiation, the C-Cu bonds can be dissociated and reformed into C[Formula: see text] pairs and graphitic-like layers, in agreement with experimental observation. It was verified that the lowest secondary electron emission was due to the formation of the graphitic-like layer. To understand the physical reason for changes in number of secondary electrons for different systems from an electronic structure perspective, two-dimensional potential energy surfaces and charge density contour plots were calculated and analyzed. It was shown that the changes are strongly influenced by the Cu surface morphology and depends highly on the nature of the interactions between the surface Cu and C atoms.
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Affiliation(s)
- L Diaz
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - A Karkash
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - S Alsharari
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - R P Joshi
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - E Schamiloglu
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - M Sanati
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA.
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6
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McNaughton AD, Joshi RP, Knutson CR, Fnu A, Luebke KJ, Malerich JP, Madrid PB, Kumar N. Machine Learning Models for Predicting Molecular UV-Vis Spectra with Quantum Mechanical Properties. J Chem Inf Model 2023; 63:1462-1471. [PMID: 36847578 DOI: 10.1021/acs.jcim.2c01662] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Accurate understanding of ultraviolet-visible (UV-vis) spectra is critical for the high-throughput synthesis of compounds for drug discovery. Experimentally determining UV-vis spectra can become expensive when dealing with a large quantity of novel compounds. This provides us an opportunity to drive computational advances in molecular property predictions using quantum mechanics and machine learning methods. In this work, we use both quantum mechanically (QM) predicted and experimentally measured UV-vis spectra as input to devise four different machine learning architectures, UVvis-SchNet, UVvis-DTNN, UVvis-Transformer, and UVvis-MPNN, and assess the performance of each method. We find that the UVvis-MPNN model outperforms the other models when using optimized 3D coordinates and QM predicted spectra as input features. This model has the highest performance for predicting UV-vis spectra with a training RMSE of 0.06 and validation RMSE of 0.08. Most importantly, our model can be used for the challenging task of predicting differences in the UV-vis spectral signatures of regioisomers.
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Affiliation(s)
- Andrew D McNaughton
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carter R Knutson
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Anubhav Fnu
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kevin J Luebke
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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7
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Joshi RP, Schultz KJ, Wilson JW, Kruel A, Varikoti RA, Kombala CJ, Kneller DW, Galanie S, Phillips G, Zhang Q, Coates L, Parvathareddy J, Surendranathan S, Kong Y, Clyde A, Ramanathan A, Jonsson CB, Brandvold KR, Zhou M, Head MS, Kovalevsky A, Kumar N. AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. J Chem Inf Model 2023; 63:1438-1453. [PMID: 36808989 PMCID: PMC9969887 DOI: 10.1021/acs.jcim.2c01377] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/23/2023]
Abstract
Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic's evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (Mpro), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. This work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic "warhead" to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of Mpro with micromolar affinities (KI of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.
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Affiliation(s)
- Rajendra P. Joshi
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Katherine J. Schultz
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Jesse William Wilson
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Agustin Kruel
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Rohith Anand Varikoti
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Chathuri J. Kombala
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Process Research and Development,
Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New
Jersey 07065, United States
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Leighton Coates
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Second Target Station, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Ying Kong
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Austin Clyde
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Colleen B. Jonsson
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
- Institute for the Study of Host-Pathogen Systems,
University of Tennessee Health Science Center, Memphis,
Tennessee 38103, United States
- Department of Microbiology, Immunology and
Biochemistry, University of Tennessee Health Science Center,
Memphis, Tennessee 38103, United States
| | - Kristoffer R. Brandvold
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Mowei Zhou
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Martha S. Head
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- Center for Research Acceleration by Digital
Innovation, Amgen Research, Thousand Oaks, California 91320,
United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
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8
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Kalra A, ThekkePurakkal AS, Rao R, Parija D, Ghule V, Lone A, Showket T, Joshi RP, Sarin S, Chadha SS. Implementation of a tuberculosis elimination project, India 2018-2019. Bull World Health Organ 2023; 101:179-190. [PMID: 36865603 PMCID: PMC9948499 DOI: 10.2471/blt.22.288277] [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: 03/15/2022] [Revised: 11/19/2022] [Accepted: 11/30/2022] [Indexed: 03/04/2023] Open
Abstract
Objective To describe the changes in tuberculosis case notifications by the private sector after implementation of the Joint Effort for Elimination of Tuberculosis project in India in 2018. Methods We retrieved data from the project recorded in India's national tuberculosis surveillance system. We analysed data on 95 project districts in six states (Andhra Pradesh, Himachal Pradesh, Karnataka, Punjab including Chandigarh, Telangana and West Bengal) to assess changes in the number of tuberculosis notifications, private provider notifiers and microbiological confirmations of cases from 2017 (baseline) to 2019. We compared case notification rates in districts where the project was implemented with the rates in districts where it was not. Findings From 2017 to 2019, tuberculosis notifications increased by 138.1% (from 44 695 to 106 404), and case notification rates more than doubled from 20 to 44 per 100 000 population. The number of private notifiers increased by over threefold, from 2912 to 9525, during this period. The number of microbiologically confirmed pulmonary and extra-pulmonary tuberculosis cases notified increased by more than two times (from 10 780 to 25 384) and nearly three times (from 1477 to 4096), respectively. The districts where the project was implemented showed a 150.3% increase in case notification rates per 100 000 population from 2017 to 2019 (from 16.8 to 41.9) while in non-project districts, this increase was only 89.8% (from 6.1 to 11.6). Conclusion The substantial increase in tuberculosis notifications demonstrate the value of the project in engaging the private sector. Scaling up these interventions is important to consolidate and extend these gains towards tuberculosis elimination.
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Affiliation(s)
- Aakshi Kalra
- FIND, Flat No. 8, 9th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110001, India
| | - Akhil S ThekkePurakkal
- FIND, Flat No. 8, 9th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110001, India
| | - Raghuram Rao
- Central TB Division, Ministry of Health and Family Welfare, New Delhi, India
| | - Debadutta Parija
- FIND, Flat No. 8, 9th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110001, India
| | - Vaibhav Ghule
- FIND, Flat No. 8, 9th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110001, India
| | - Ajaz Lone
- FIND, Flat No. 8, 9th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110001, India
| | - Tajamul Showket
- FIND, Flat No. 8, 9th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110001, India
| | - Rajendra P Joshi
- Central TB Division, Ministry of Health and Family Welfare, New Delhi, India
| | | | - Sarabjit S Chadha
- FIND, Flat No. 8, 9th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110001, India
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9
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Arinaminpathy N, Rade K, Kumar R, Joshi RP, Rao R. The potential impact of vaccination on tuberculosis burden in India: A modelling analysis. Indian J Med Res 2023; 157:119-126. [PMID: 37202930 PMCID: PMC10319376 DOI: 10.4103/ijmr.ijmr_328_23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Indexed: 05/20/2023] Open
Abstract
Background & objectives Vaccination will play an important role in meeting the end tuberculosis (TB) goals. While certain vaccine candidates in advanced stages of clinical trials raise hope for the future availability of new tools, in the immediate term, there is also increasing interest in Bacille Calmette-Guérin revaccination among adults and adolescents as a potential strategy. Here, we sought to estimate the potential epidemiological impact of TB vaccination in India. Methods We developed a deterministic, age-structured, compartmental model of TB in India. Data from the recent national prevalence survey was used to inform epidemiological burden while also incorporating a vulnerable population who may be prioritized for vaccination, the latter consistent with the burden of undernutrition. Using this framework, the potential impact on incidence and mortality of a vaccine with 50 per cent efficacy was estimated, if rolled out in 2023 to cover 50 per cent of the unvaccinated each year. Simulated impacts were compared for disease- vs. infection-preventing vaccines, as well as when prioritizing vulnerable groups (those with undernutrition) rather than the general population. A sensitivity analyses were also conducted with respect to the duration, and efficacy, of vaccine immunity. Results When rolled out in the general population, an infection-preventing vaccine would avert 12 per cent (95% Bayesian credible intervals (Crl): 4.3-28%) of cumulative TB incidence between 2023 and 2030, while a disease-preventing vaccine would avert 29 per cent (95% Crl: 24-34%). Although the vulnerable population accounts for only around 16 per cent of India's population, prioritizing this group for vaccination would achieve almost half the impact of rollout in the general population, in the example of an infection-preventing vaccine. Sensitivity analysis also highlights the importance of the duration and efficacy of vaccine-induced immunity. Interpretation & conclusions These results highlight how even a vaccine with moderate effectiveness (50%) could achieve substantial reductions in TB burden in India, especially when prioritized for the most vulnerable.
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Affiliation(s)
- Nimalan Arinaminpathy
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Kirankumar Rade
- WHO India Country Office, Ministry of Health & Family Welfare, New Delhi, India
| | - Ravinder Kumar
- Central TB Division, Ministry of Health & Family Welfare, New Delhi, India
| | - Rajendra P. Joshi
- Central TB Division, Ministry of Health & Family Welfare, New Delhi, India
| | - Raghuram Rao
- Central TB Division, Ministry of Health & Family Welfare, New Delhi, India
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10
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Dahal KR, Pokhrel NR, Gaire S, Mahatara S, Joshi RP, Gupta A, Banjade HR, Joshi J. A comparative study on effect of news sentiment on stock price prediction with deep learning architecture. PLoS One 2023; 18:e0284695. [PMID: 37098089 PMCID: PMC10128930 DOI: 10.1371/journal.pone.0284695] [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: 01/19/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
The accelerated progress in artificial intelligence encourages sophisticated deep learning methods in predicting stock prices. In the meantime, easy accessibility of the stock market in the palm of one's hand has made its behavior more fuzzy, volatile, and complex than ever. The world is looking at an accurate and reliable model that uses text and numerical data which better represents the market's highly volatile and non-linear behavior in a broader spectrum. A research gap exists in accurately predicting a target stock's closing price utilizing the combined numerical and text data. This study uses long short-term memory (LSTM) and gated recurrent unit (GRU) to predict the stock price using stock features alone and incorporating financial news data in conjunction with stock features. The comparative study carried out under identical conditions dispassionately evaluates the importance of incorporating financial news in stock price prediction. Our experiment concludes that incorporating financial news data produces better prediction accuracy than using the stock fundamental features alone. The performances of the model architecture are compared using the standard assessment metrics -Root Mean Square Error (RMSE), Mean Absolute Percentage Error (MAPE), and Correlation Coefficient (R). Furthermore, statistical tests are conducted to further verify the models' robustness and reliability.
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Affiliation(s)
- Keshab Raj Dahal
- Department of Statistics, Truman State University, Kirksville, MO, United States of America
| | - Nawa Raj Pokhrel
- Department of Physics and Computer Science, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Santosh Gaire
- Department of Physics, The Catholic University of America, Washington, DC, United States of America
| | - Sharad Mahatara
- Department of Physics, New Mexico State University, Las Cruces, NM, United States of America
| | | | - Ankrit Gupta
- Department of Computer Science, Central Michigan University, Mount Pleasant, MI, United States of America
| | - Huta R Banjade
- Department of Physics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Jeorge Joshi
- Kathmandu Engineering College, Tribhuvan University, Kathmandu, Nepal
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11
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Brown M, Diaz L, Aslan A, Sanati M, Portillo S, Schamiloglu E, Joshi RP. Carbon-oxygen surface formation enhances secondary electron yield in Cu, Ag and Au. Sci Rep 2022; 12:15808. [PMID: 36138077 PMCID: PMC9499956 DOI: 10.1038/s41598-022-19924-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
First-principles calculations coupled with Monte Carlo simulations are used to probe the role of a surface CO monolayer formation on secondary electron emission (SEE) from Cu, Ag, and Au (110) materials. It is shown that formation of such a layer increases the secondary electron emission in all systems. Analysis of calculated total density of states (TDOS) in Cu, Ag, and Au, and partial density of states (PDOS) of C and O confirm the formation of a covalent type bonding between C and O atoms. It is shown that such a bond modifies the TDOS and extended it to lower energies, which is then responsible for an increase in the probability density of secondary electron generation. Furthermore, a reduction in inelastic mean free path is predicted for all systems. Our predicted results for the secondary electron yield (SEY) compare very favorably with experimental data in all three materials, and exhibit increases in SEY. This is seen to occur despite increases in the work function for Cu, Ag, and Au. The present analysis can be extended to other absorbates and gas atoms at the surface, and such analyses will be present elsewhere.
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Affiliation(s)
- M Brown
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - L Diaz
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - A Aslan
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - M Sanati
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, 79409, USA
| | - S Portillo
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - E Schamiloglu
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - R P Joshi
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA.
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12
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Kumari J, Harish, Akash, Pandey A, Kumar P, Singh MK, Singh A, Shishodia MS, Joshi RP, Mukhopadhyay AK. Thickness Controlled Physical Properties of Chemically Synthesized Nanostructured Calcite Thin Films. ChemistrySelect 2022. [DOI: 10.1002/slct.202200416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jyoti Kumari
- Department of Physics Manipal University Jaipur Jaipur 303007 Rajasthan India
| | - Harish
- Department of Physics Manipal University Jaipur Jaipur 303007 Rajasthan India
| | - Akash
- Department of Physics Manipal University Jaipur Jaipur 303007 Rajasthan India
| | - Arushi Pandey
- Centre of Material Sciences University of Allahabad Prayagraj 211002 India
| | - Pushpendra Kumar
- Department of Physics Manipal University Jaipur Jaipur 303007 Rajasthan India
| | - Manoj K Singh
- Centre of Material Sciences University of Allahabad Prayagraj 211002 India
| | - Alok Singh
- Department of Applied Physics Gautam Buddha University Greater Noida 201312 India
| | | | | | - Anoop Kumar Mukhopadhyay
- Department of Physics Manipal University Jaipur Jaipur 303007 Rajasthan India
- Department of Physics Biyani Group of Colleges, Vidhyadhar Nagar Jaipur 302039 Rajasthan India
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13
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Louis SY, Siriwardane EMD, Joshi RP, Omee SS, Kumar N, Hu J. Accurate Prediction of Voltage of Battery Electrode Materials Using Attention-Based Graph Neural Networks. ACS Appl Mater Interfaces 2022; 14:26587-26594. [PMID: 35666275 DOI: 10.1021/acsami.2c00029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Performing first-principles calculations to discover electrodes' properties in the large chemical space is a challenging task. While machine learning (ML) has been applied to effectively accelerate those discoveries, most of the applied methods ignore the materials' spatial information and only use predefined features: based only on chemical compositions. We propose two attention-based graph convolutional neural network techniques to learn the average voltage of electrodes. Our proposed methods, which combine both atomic composition and atomic coordinates in 3D-space, improve the accuracy in voltage prediction significantly when compared to composition-based ML models. The first model directly learns the chemical reaction of electrodes and metal ions to predict their average voltage, whereas the second model combines electrodes' ML predicted formation energy (Eform) to compute their average voltage. Our Eform-based model demonstrates improved accuracy in transferability from our subset of learned Li ions to Na ions. Moreover, we predicted the theoretical voltage of 10 NaxMPO4F (M = Ti, Cr, Fe, Cu, Mn, Co, and Ni) fluorophosphate battery frameworks, which are unavailable in the Material Project database. It could be shown that we can expect average voltages higher than 3.1 V from those Na battery frameworks except from the NaTiPO4F and TiPO4F pair of electrodes, which offer an average voltage of 1.32 V.
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Affiliation(s)
- Steph-Yves Louis
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina 29201, United States
| | - Edirisuriya M Dilanga Siriwardane
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina 29201, United States
- Department of Physics, University of Colombo, PO Box 1490, Colombo 0300, Sri Lanka
| | - Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- TQuT Inc., 10205 Edgerton Avenue NE, Rockford, Michigan 49341, United States
| | - Sadman Sadeed Omee
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina 29201, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jianjun Hu
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina 29201, United States
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14
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Moses IA, Joshi RP, Ozdemir B, Kumar N, Eickholt J, Barone V. Machine Learning Screening of Metal-Ion Battery Electrode Materials. ACS Appl Mater Interfaces 2021; 13:53355-53362. [PMID: 34160211 DOI: 10.1021/acsami.1c04627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rechargeable batteries provide crucial energy storage systems for renewable energy sources, as well as consumer electronics and electrical vehicles. There are a number of important parameters that determine the suitability of electrode materials for battery applications, such as the average voltage and the maximum specific capacity which contribute to the overall energy density. Another important performance criterion for battery electrode materials is their volume change upon charging and discharging, which contributes to determine the cyclability, Coulombic efficiency, and safety of a battery. In this work, we present deep neural network regression machine learning models (ML), trained on data obtained from the Materials Project database, for predicting average voltages and volume change upon charging and discharging of electrode materials for metal-ion batteries. Our models exhibit good performance as measured by the average mean absolute error obtained from a 10-fold cross-validation, as well as on independent test sets. We further assess the robustness of our ML models by investigating their screening potential beyond the training database. We produce Na-ion electrodes by systematically replacing Li-ions in the original database by Na-ions and, then, selecting a set of 22 electrodes that exhibit a good performance in energy density, as well as small volume variations upon charging and discharging, as predicted by the machine learning model. The ML predictions for these materials are then compared to quantum-mechanics based calculations. Our results reaffirm the significant role of machine learning techniques in the exploration of materials for battery applications.
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Affiliation(s)
- Isaiah A Moses
- Science of Advanced Materials Program, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Burak Ozdemir
- Department of Physics, Faculty of Science, University of Ostrava, 30 dubna 22, 70103 Ostrava, Czech Republic
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jesse Eickholt
- Department of Computer Science, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Veronica Barone
- Science of Advanced Materials Program, Central Michigan University, Mount Pleasant, Michigan 48859, United States
- Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859, United States
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15
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Joshi RP, Gebauer NWA, Bontha M, Khazaieli M, James RM, Brown JB, Kumar N. 3D-Scaffold: A Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds. J Phys Chem B 2021; 125:12166-12176. [PMID: 34662142 DOI: 10.1021/acs.jpcb.1c06437] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The prerequisite of therapeutic drug design and discovery is to identify novel molecules and developing lead candidates with desired biophysical and biochemical properties. Deep generative models have demonstrated their ability to find such molecules by exploring a huge chemical space efficiently. An effective way to generate new molecules with desired target properties is by constraining the critical fucntional groups or the core scaffolds in the generation process. To this end, we developed a domain aware generative framework called 3D-Scaffold that takes 3D coordinates of the desired scaffold as an input and generates 3D coordinates of novel therapeutic candidates as an output while always preserving the desired scaffolds in generated structures. We demonstrated that our framework generates predominantly valid, unique, novel, and experimentally synthesizable molecules that have drug-like properties similar to the molecules in the training set. Using domain specific data sets, we generate covalent and noncovalent antiviral inhibitors targeting viral proteins. To measure the success of our framework in generating therapeutic candidates, generated structures were subjected to high throughput virtual screening via docking simulations, which shows favorable interaction against SARS-CoV-2 main protease (Mpro) and nonstructural protein endoribonuclease (NSP15) targets. Most importantly, our deep learning model performs well with relatively small 3D structural training data and quickly learns to generalize to new scaffolds, highlighting its potential application to other domains for generating target specific candidates.
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Affiliation(s)
- Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Niklas W A Gebauer
- Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany.,BASLEARN - TU Berlin/BASF Joint Lab for Machine Learning, Technische Universität Berlin, 10587 Berlin, Germany.,Berlin Institute for the Foundations of Learning and Data, 10587 Berlin, Germany
| | - Mridula Bontha
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mercedeh Khazaieli
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Rhema M James
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - James B Brown
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkley, California 94710, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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16
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Joshi RP, Kumar N. Artificial Intelligence for Autonomous Molecular Design: A Perspective. Molecules 2021; 26:molecules26226761. [PMID: 34833853 PMCID: PMC8619999 DOI: 10.3390/molecules26226761] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/23/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022] Open
Abstract
Domain-aware artificial intelligence has been increasingly adopted in recent years to expedite molecular design in various applications, including drug design and discovery. Recent advances in areas such as physics-informed machine learning and reasoning, software engineering, high-end hardware development, and computing infrastructures are providing opportunities to build scalable and explainable AI molecular discovery systems. This could improve a design hypothesis through feedback analysis, data integration that can provide a basis for the introduction of end-to-end automation for compound discovery and optimization, and enable more intelligent searches of chemical space. Several state-of-the-art ML architectures are predominantly and independently used for predicting the properties of small molecules, their high throughput synthesis, and screening, iteratively identifying and optimizing lead therapeutic candidates. However, such deep learning and ML approaches also raise considerable conceptual, technical, scalability, and end-to-end error quantification challenges, as well as skepticism about the current AI hype to build automated tools. To this end, synergistically and intelligently using these individual components along with robust quantum physics-based molecular representation and data generation tools in a closed-loop holds enormous promise for accelerated therapeutic design to critically analyze the opportunities and challenges for their more widespread application. This article aims to identify the most recent technology and breakthrough achieved by each of the components and discusses how such autonomous AI and ML workflows can be integrated to radically accelerate the protein target or disease model-based probe design that can be iteratively validated experimentally. Taken together, this could significantly reduce the timeline for end-to-end therapeutic discovery and optimization upon the arrival of any novel zoonotic transmission event. Our article serves as a guide for medicinal, computational chemistry and biology, analytical chemistry, and the ML community to practice autonomous molecular design in precision medicine and drug discovery.
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17
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Hu Q, Joshi RP. Continuum analysis to assess field enhancements for tailoring electroporation driven by monopolar or bipolar pulsing based on nonuniformly distributed nanoparticles. Phys Rev E 2021; 103:022402. [PMID: 33736030 DOI: 10.1103/physreve.103.022402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/15/2021] [Indexed: 11/07/2022]
Abstract
Recent reports indicate that nanoparticle (NP) clusters near cell membranes could enhance local electric fields, leading to heightened electroporation. This aspect is quantitatively analyzed through numerical simulations whereby time dependent transmembrane potentials are first obtained on the basis of a distributed circuit mode, and the results then used to calculate pore distributions from continuum Smoluchowski theory. For completeness, both monopolar and bipolar nanosecond-range pulse responses are presented and discussed. Our results show strong increases in TMP with the presence of multiple NP clusters and demonstrate that enhanced poration could be possible even over sites far away from the poles at the short pulsing regime. Furthermore, our results demonstrate that nonuniform distributions would work to enable poration at regions far away from the poles. The NP clusters could thus act as distributed electrodes. Our results were roughly in line with recent experimental observations.
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Affiliation(s)
- Q Hu
- School of Engineering, Eastern Michigan University, Ypsilanti, Michigan 48197, USA
| | - R P Joshi
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, USA
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18
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Siriwardane EMD, Joshi RP, Kumar N, Çakır D. Revealing the Formation Energy-Exfoliation Energy-Structure Correlation of MAB Phases Using Machine Learning and DFT. ACS Appl Mater Interfaces 2020; 12:29424-29431. [PMID: 32495630 DOI: 10.1021/acsami.0c03536] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
MAB phases became popular as ultrahigh-temperature materials with high damage tolerance and excellent electrical conductivity. MAB is used to exfoliate two-dimensional (2D) transition-metal borides (MBenes), which are promising materials for developing next-generation nanodevices. In this report, we explore the correlation between the formation energy, exfoliation energy, and structural factors of MAB phases with orthorhombic and hexagonal crystal symmetries using density functional theory (DFT) and machine learning. For this, we developed three different machine learning models based on the support vector machine, deep neural network, and random forest regressor to study the stability of the MAB phases by calculating their formation energies. Our support vector machine and deep neural network models are capable of predicting the formation energies with mean absolute errors less than 0.1 eV/atom. MAB phases with the chemical formulas, MAB, M2AB2, and M3AB4, where M = Nb, Mn, Ti, W, V, Sc, Cr, Hf, Mo, Zr, Ta, and Fe, and A = group III-A elements (Al, Ga, In and Tl), were investigated to find out the formation energy and their structure correlation. We demonstrated that the stability of a MAB phase for a given transition-metal decreases when the A element changes from Al to Tl. DFT revealed that M-A and B-A bond strength strongly correlates with the stability of MAB phases. In addition, the exfoliation possibility of 2D MBenes becomes higher when the A element changes from Al to Tl because of weakening of M-A and B-A bonds.
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Affiliation(s)
- Edirisuriya M D Siriwardane
- Department of Physics and Astrophysics, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Deniz Çakır
- Department of Physics and Astrophysics, University of North Dakota, Grand Forks, North Dakota 58202, United States
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19
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Joshi RP, Phillips JJ, Mitchell KJ, Christou G, Jackson KA, Peralta JE. Accuracy of density functional theory methods for the calculation of magnetic exchange couplings in binuclear iron(III) complexes. Polyhedron 2020. [DOI: 10.1016/j.poly.2019.114194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Singh AP, Joshi RP, Abboud KA, Peralta JE, Christou G. Molecular spin frustration in mixed-chelate Fe5 and Fe6 oxo clusters with high ground state spin values. Polyhedron 2020. [DOI: 10.1016/j.poly.2019.114182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Joshi RP, Eickholt J, Li L, Fornari M, Barone V, Peralta JE. Machine Learning the Voltage of Electrode Materials in Metal-Ion Batteries. ACS Appl Mater Interfaces 2019; 11:18494-18503. [PMID: 31034195 DOI: 10.1021/acsami.9b04933] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Machine-learning (ML) techniques have rapidly found applications in many domains of materials chemistry and physics where large data sets are available. Aiming to accelerate the discovery of materials for battery applications, in this work, we develop a tool ( http://se.cmich.edu/batteries ) based on ML models to predict voltages of electrode materials for metal-ion batteries. To this end, we use deep neural network, support vector machine, and kernel ridge regression as ML algorithms in combination with data taken from the Materials Project database, as well as feature vectors from properties of chemical compounds and elemental properties of their constituents. We show that our ML models have predictive capabilities for different reference test sets and, as an example, we utilize them to generate a voltage profile diagram and compare it to density functional theory calculations. In addition, using our models, we propose nearly 5000 candidate electrode materials for Na- and K-ion batteries. We also make available a web-accessible tool that, within a minute, can be used to estimate the voltage of any bulk electrode material for a number of metal ions. These results show that ML is a promising alternative for computationally demanding calculations as a first screening tool of novel materials for battery applications.
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22
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Sharkas K, Li L, Trepte K, Withanage KPK, Joshi RP, Zope RR, Baruah T, Johnson JK, Jackson KA, Peralta JE. Shrinking Self-Interaction Errors with the Fermi-Löwdin Orbital Self-Interaction-Corrected Density Functional Approximation. J Phys Chem A 2018; 122:9307-9315. [PMID: 30412407 DOI: 10.1021/acs.jpca.8b09940] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The self-interaction error (SIE) is one of the major drawbacks of practical exchange-correlation functionals for Kohn-Sham density functional theory. Despite this, the use of methods that explicitly remove SIE from approximate density functionals is scarce in the literature due to their relatively high computational cost and lack of consistent improvement over standard modern functionals. In this article we assess the performance of a novel approach recently proposed by Pederson, Ruzsinszky, and Perdew [ J. Chem. Phys. 2014, 140, 121103] for performing self-interaction free calculations in density functional theory based on Fermi orbitals. To this end, we employ test sets consisting of reaction energies that are considered particularly sensitive to SIE. We found that the parameter-free Fermi-Löwdin orbital self-interaction correction method combined with the standard local spin density approximation (LSDA) and Perdew-Burke-Ernzerhof (PBE) functionals gives a much better estimate of reaction energies compared to their parent LSDA and PBE functionals for most of the reactions in these two sets. They also perform on par with the global PBE0 and range-separated LC-ωPBE hybrids, which partially eliminate the SIE by including Hartree-Fock exchange. This shows the potential of the Fermi-Löwdin orbital self-interaction correction (FLOSIC) method for practical density functional calculations without SIE.
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Affiliation(s)
| | - Lin Li
- Department of Chemical and Petroleum Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | | | | | | | - Rajendra R Zope
- Department of Physics , University of Texas El Paso , El Paso , Texas 79968 , United States
| | - Tunna Baruah
- Department of Physics , University of Texas El Paso , El Paso , Texas 79968 , United States
| | - J Karl Johnson
- Department of Chemical and Petroleum Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
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23
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Joshi RP, Trepte K, Withanage KPK, Sharkas K, Yamamoto Y, Basurto L, Zope RR, Baruah T, Jackson KA, Peralta JE. Fermi-Löwdin orbital self-interaction correction to magnetic exchange couplings. J Chem Phys 2018; 149:164101. [PMID: 30384709 DOI: 10.1063/1.5050809] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We analyze the effect of removing self-interaction error on magnetic exchange couplings using the Fermi-Löwdin orbital self-interaction correction (FLOSIC) method in the framework of density functional theory (DFT). We compare magnetic exchange couplings obtained from self-interaction-free FLOSIC calculations with the local spin density approximation (LSDA) with several widely used DFT realizations and wave function based methods. To this end, we employ the linear H-He-H model system, six organic radical molecules, and [Cu2Cl6]2- as representatives of different types of magnetic interactions. We show that the simple self-interaction-free version of LSDA improves calculated couplings with respect to LSDA in all cases, even though the nature of the exchange interaction varies across the test set, and in most cases, it yields results comparable to modern hybrids and range-separated approximate functionals.
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Affiliation(s)
- Rajendra P Joshi
- Department of Physics, Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Kai Trepte
- Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Kushantha P K Withanage
- Department of Physics, Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Kamal Sharkas
- Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Yoh Yamamoto
- Department of Physics, University of Texas El Paso, El Paso, Texas 79968, USA
| | - Luis Basurto
- Department of Physics, University of Texas El Paso, El Paso, Texas 79968, USA
| | - Rajendra R Zope
- Department of Physics, University of Texas El Paso, El Paso, Texas 79968, USA
| | - Tunna Baruah
- Department of Physics, University of Texas El Paso, El Paso, Texas 79968, USA
| | - Koblar A Jackson
- Department of Physics, Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Juan E Peralta
- Department of Physics, Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, USA
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24
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Affiliation(s)
- Bayileyegn A. Abate
- Science of Advanced Materials and ‡Department of Physics, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Rajendra P. Joshi
- Science of Advanced Materials and ‡Department of Physics, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Juan E. Peralta
- Science of Advanced Materials and ‡Department of Physics, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
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25
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Joshi RP, Phillips JJ, Peralta JE. Magnetic Exchange Couplings in Heterodinuclear Complexes Based on Differential Local Spin Rotations. J Chem Theory Comput 2016; 12:1728-34. [DOI: 10.1021/acs.jctc.6b00112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajendra P. Joshi
- Department of Physics
and
Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Jordan J. Phillips
- Department of Physics
and
Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Juan E. Peralta
- Department of Physics
and
Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, United States
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Abstract
We have investigated the stability, maximum intercalation capacity, and voltage profile of alkali metal intercalated hexagonal BC3 (MxBC3), for 0 < x ≤ 2 and M = Li, Na, and K. Our calculations, based on dispersion-corrected density functional theory, show that these intercalation compounds are stable with respect to BC3 and their bulk metal counterparts. Moreover, we found that among all MxBC3 considered, the maximum stable capacity corresponds to an x value of 1.5, 1, and 1.5 for Li, Na, and K, respectively. These values are associated with large gravimetric capacities of 572 mA h/g for Na and 858 mA h/g for Li and K. Importantly, we show that metal intercalated hexagonal BC3 has the advantage of a small open-circuit voltage variation of approximately 0.49, 0.12, and 0.16 V for Li, Na, and K, respectively. Our results suggest that BC3 can become a robust alternative to graphitic electrodes in metal ion batteries, thus encouraging further experimental work.
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Affiliation(s)
- Rajendra P Joshi
- Department of Physics and Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Burak Ozdemir
- Department of Physics and Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Veronica Barone
- Department of Physics and Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Juan E Peralta
- Department of Physics and Science of Advanced Materials, Central Michigan University, Mount Pleasant, Michigan 48859, United States
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Agrawal AR, Joshi RP, Shah V. Mandating audio-video recording of informed consent: are we right in enforcing this? Int J Clin Pract 2014; 68:794-5. [PMID: 24942306 DOI: 10.1111/ijcp.12441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Medicines are the result of experimentation carried out in animals and humans. However, there are numerous instances in the history of medicine where humans were subjected to undue risks and abuses, requiring regulations for their safety. Idea of informed consent has found its presence in medical literature from the times of Hippocratic Oath propagating principles of '...never do harm to anyone' and physician directed care of patients. This was revived in post-world war II era in the form of Nuremberg code and the declaration of Helsinki in response to various debilitating experimentations done on prisoners in concentration camps and elsewhere. Complete information and voluntary participation forms the ethical tenets of these acts and the same has been reflected in various guidelines enacted worldwide, which are sufficient to make sure that patient consent is obtained in fair and just manner. Despite this, there have been undesirable lapses in the conduct of clinical trials. This situation worsens, when intentional lapses in conduct of trial hamper the ability of socially and economically disadvantaged communities in developing countries to make free and informed decision.
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Abstract
Models for electric field interactions with biological cells predict that pulses with durations shorter than the charging time of the outer membrane can affect intracellular structures. Experimental studies in which human cells were exposed to pulsed electric fields of up to 300 kV/cm amplitude, with durations as short as 10 ns, have confirmed this hypothesis. The observed effects include the breaching of intracellular granule membranes without permanent damage to the cell membrane, abrupt rises in intracellular free calcium levels, enhanced expression of genes, cytochrome c release, and electroporation for gene transfer and drug delivery. At increased electric fields, the application of nanosecond pulses induces apoptosis (programmed cell death) in biological cells, an effect that has been shown to reduce the growth of tumors. Possible applications of the intracellular electroeffects are enhancing gene delivery to the nucleus, controlling cell functions that depend on calcium release (causing cell immobilization), and treating tumors. Such nanosecond electrical pulses have been shown to successfully treat melanoma tumors by using needle arrays as pulse delivery systems. Reducing the pulse duration of intense electric field pulses even further into the subnanosecond range will allow for the use of wideband antennas to deliver the electromagnetic fields into tissue with a spatial resolution in the centimeter range. This review carefully examines the above concepts, provides a theoretical basis, and modeling results based on both continuum approaches and atomistic molecular dynamics methods. Relevant experimental data are also presented, and some of the many potential bioengineering applications discussed.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, and Frank Reidy Research Center for Bioelectrics, Old Domonion University, Norfolk, VA 23529-0246, USA.
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29
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Rood JE, Migueles SA, Berkley AM, Compton AA, Joshi RP, Duerr A, McElrath J, Connors M. 0A07-01. HIV-specific CD8+ T-cells of vaccinees exhibit proliferative and cytotoxic capacities comparable to those of progressors. Retrovirology 2009. [PMCID: PMC2767572 DOI: 10.1186/1742-4690-6-s3-o49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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30
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Hu Q, Joshi RP. Transmembrane voltage analyses in spheroidal cells in response to an intense ultrashort electrical pulse. Phys Rev E Stat Nonlin Soft Matter Phys 2009; 79:011901. [PMID: 19257063 DOI: 10.1103/physreve.79.011901] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 10/09/2008] [Indexed: 05/27/2023]
Abstract
Self-consistent evaluations of both the transmembrane potential (TMP) and possible electroporation density across membrane of spheroidal cells in response to ultrashort, high-intensity pulses are reported and discussed. Most treatments in the literature have been based on spherical cells, and this represents a step towards more realistic analyses. The present study couples the Laplace equation with Smoluchowski theory of pore formation, to yield dynamic membrane conductivities that influence the TMP. It is shown that the TMP induced by pulsed external voltages can be substantial higher in oblate spheroids as compared to spherical or prolate spheroidal cells. Flattening of the surface area in oblate spheroids leads to both higher electric fields seen by the membrane, and allows a great fraction of the surface area to be porated. This suggests that biomedical applications such as drug delivery and electrochemotherapy could work best for flatter-shaped cells, and secondary field-enabled orienting would be beneficial. Results for arbitrary field orientations and different cell sizes have also been presented.
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Affiliation(s)
- Q Hu
- Department of Engineering and Technology, Central Michigan University, Mt Pleasant, Michigan 48859, USA
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31
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Joshi RP, Mishra A, Hu Q, Schoenbach KH, Pakhomov A. Self-consistent analyses for potential conduction block in nerves by an ultrashort high-intensity electric pulse. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 75:061906. [PMID: 17677299 DOI: 10.1103/physreve.75.061906] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Indexed: 05/16/2023]
Abstract
Simulation studies are presented that probe the possibility of using high-field (> 100 kV/cm) , short-duration ( approximately 50 ns) electrical pulses for nonthermal and reversible cessation of biological electrical signaling pathways. This would have obvious applications in neurophysiology, clinical research, neuromuscular stimulation therapies, and even nonlethal bioweapons development. The concept is based on the creation of a sufficiently high density of pores on the nerve membrane by an electric pulse. This modulates membrane conductance and presents an effective "electrical short" to an incident voltage wave traveling across a nerve. Net blocking of action potential propagation can then result. A continuum approach based on the Smoluchowski equation is used to treat electroporation. This is self-consistently coupled with a distributed circuit representation of the nerve dynamics. Our results indicate that poration at a single neural segment would be sufficient to produce an observable, yet reversible, effect.
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Affiliation(s)
- R P Joshi
- Department of Electrical & Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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32
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Pliquett U, Joshi RP, Sridhara V, Schoenbach KH. High electrical field effects on cell membranes. Bioelectrochemistry 2007; 70:275-82. [PMID: 17123870 DOI: 10.1016/j.bioelechem.2006.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 10/07/2006] [Accepted: 10/09/2006] [Indexed: 10/24/2022]
Abstract
Electrical charging of lipid membranes causes electroporation with sharp membrane conductance increases. Several recent observations, especially at very high field strength, are not compatible with the simple electroporation picture. Here we present several relevant experiments on cell electrical responses to very high external voltages. We hypothesize that, not only are aqueous pores created within the lipid membranes, but that nanoscale membrane fragmentation occurs, possibly with micelle formation. This effect would produce conductivity increases beyond simple electroporation and display a relatively fast turn-off with external voltage. In addition, material loss can be expected at the anode side of cells, in agreement with published experimental reports at high fields. Our hypothesis is qualitatively supported by molecular dynamics simulations. Finally, such cellular responses might temporarily inactivate voltage-gated and ion-pump activity, while not necessarily causing cell death. This hypothesis also supports observations on electrofusion.
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Affiliation(s)
- U Pliquett
- Frank Reidy Research Center for Bioelectrics 830 Southampton Ave., Suite 5100, Norfolk, VA 23510, United States
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33
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Joshi RP, Nguyen A, Sridhara V, Hu Q, Nuccitelli R, Beebe SJ, Kolb J, Schoenbach KH. Simulations of intracellular calcium release dynamics in response to a high-intensity, ultrashort electric pulse. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 75:041920. [PMID: 17500934 DOI: 10.1103/physreve.75.041920] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 03/06/2007] [Indexed: 05/15/2023]
Abstract
Numerical simulations for electrically induced, intracellular calcium release from the endoplasmic reticulum are reported. A two-step model is used for self-consistency. Distributed electrical circuit representation coupled with the Smoluchowski equation yields the ER membrane nanoporation for calcium outflow based on a numerical simulation. This is combined with the continuum Li-Rinzel model and drift diffusion for calcium dynamics. Our results are shown to be in agreement with reported calcium release data. A modest increase (rough doubling) of the cellular calcium is predicted in the absence of extra-cellular calcium. In particular, the applied field of 15 kV/cm with 60 ns pulse duration makes for a strong comparison. No oscillations are predicted and the net recovery period of about 5 min are both in agreement with published experimental results. A quantitative explanation for the lack of such oscillatory behavior, based on the density dependent calcium fluxes, is also provided.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, VA 23529-0246, USA
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34
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Joshi RP, Sridhara V, Schoenbach KH. Microscopic calculations of local lipid membrane permittivities and diffusion coefficients for application to electroporation analyses. Biochem Biophys Res Commun 2006; 348:643-8. [PMID: 16890913 DOI: 10.1016/j.bbrc.2006.07.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 07/20/2006] [Indexed: 11/17/2022]
Abstract
Interaction of electric fields with biological systems has begun to receive considerable attention for applications that include field-assisted drug delivery, medical interventions, and genetic engineering. External fields induce the strongest effects at membranes with electroporation being a common feature. Membrane transport in this context of poration is often based on continuum approaches utilizing macroscopic parameters such as the permittivity, diffusion coefficients, and mobilities. In such modeling, field dependences, local inhomogeneities, and microscopic details are usually ignored. Here, a molecular dynamics (MD) scheme is used for a more rigorous and physically realistic evaluation of such parameters for potential application to electroporative transport model development. A suitable membrane structure containing a nanopore derived from MD analysis is used as the initial geometric configuration. Both static and frequency dependent diffusion coefficients have been evaluated. Permittivities are also calculated and shown to be dramatically non-uniform in the vicinity of membranes under high external fields. A positive feedback mechanism leading to enhanced membrane fields is discussed.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, VA 23529-0246, USA.
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35
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Frey W, White JA, Price RO, Blackmore PF, Joshi RP, Nuccitelli R, Beebe SJ, Schoenbach KH, Kolb JF. Plasma membrane voltage changes during nanosecond pulsed electric field exposure. Biophys J 2006; 90:3608-15. [PMID: 16513782 PMCID: PMC1440741 DOI: 10.1529/biophysj.105.072777] [Citation(s) in RCA: 195] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The change in the membrane potential of Jurkat cells in response to nanosecond pulsed electric fields was studied for pulses with a duration of 60 ns and maximum field strengths of approximately 100 kV/cm (100 V/cell diameter). Membranes of Jurkat cells were stained with a fast voltage-sensitive dye, ANNINE-6, which has a subnanosecond voltage response time. A temporal resolution of 5 ns was achieved by the excitation of this dye with a tunable laser pulse. The laser pulse was synchronized with the applied electric field to record images at times before, during, and after exposure. When exposing the Jurkat cells to a pulse, the voltage across the membrane at the anodic pole of the cell reached values of 1.6 V after 15 ns, almost twice the voltage level generally required for electroporation. Voltages across the membrane on the side facing the cathode reached values of only 0.6 V in the same time period, indicating a strong asymmetry in conduction mechanisms in the membranes of the two opposite cell hemispheres. This small voltage drop of 0.6-1.6 V across the plasma membrane demonstrates that nearly the entire imposed electric field of 10 V/mum penetrates into the interior of the cell and every organelle.
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Affiliation(s)
- W Frey
- Forschungszentrum Karlsruhe, IHM, D-76344, Eggenstein-Leopoldshafen, Germany
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36
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Hu Q, Joshi RP, Schoenbach KH. Simulations of nanopore formation and phosphatidylserine externalization in lipid membranes subjected to a high-intensity, ultrashort electric pulse. Phys Rev E Stat Nonlin Soft Matter Phys 2005; 72:031902. [PMID: 16241477 DOI: 10.1103/physreve.72.031902] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Indexed: 05/05/2023]
Abstract
A combined MD simulator and time dependent Laplace solver are used to analyze the electrically driven phosphatidylserine externalization process in cells. Time dependent details of nanopore formation at cell membranes in response to a high-intensity (100 kV/cm), ultrashort (10 ns) electric pulse are also probed. Our results show that nanosized pores could typically be formed within about 5 ns. These predictions are in very good agreement with recent experimental data. It is also demonstrated that defect formation and PS externalization in membranes should begin on the anode side. Finally, the simulations confirm that PS externalization is a nanopore facilitated event, rather than the result of molecular translocation across the trans-membrane energy barrier.
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Affiliation(s)
- Q Hu
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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37
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Hu Q, Viswanadham S, Joshi RP, Schoenbach KH, Beebe SJ, Blackmore PF. Simulations of transient membrane behavior in cells subjected to a high-intensity ultrashort electric pulse. Phys Rev E Stat Nonlin Soft Matter Phys 2005; 71:031914. [PMID: 15903466 DOI: 10.1103/physreve.71.031914] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Indexed: 05/02/2023]
Abstract
A molecular dynamics (MD) scheme is combined with a distributed circuit model for a self-consistent analysis of the transient membrane response for cells subjected to an ultrashort (nanosecond) high-intensity (approximately 0.01-V/nm spatially averaged field) voltage pulse. The dynamical, stochastic, many-body aspects are treated at the molecular level by resorting to a course-grained representation of the membrane lipid molecules. Coupling the Smoluchowski equation to the distributed electrical model for current flow provides the time-dependent transmembrane fields for the MD simulations. A good match between the simulation results and available experimental data is obtained. Predictions include pore formation times of about 5-6 ns. It is also shown that the pore formation process would tend to begin from the anodic side of an electrically stressed membrane. Furthermore, the present simulations demonstrate that ions could facilitate pore formation. This could be of practical importance and have direct relevance to the recent observations of calcium release from the endoplasmic reticulum in cells subjected to such ultrashort, high-intensity pulses.
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Affiliation(s)
- Q Hu
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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38
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Joshi RP, Hu Q, Schoenbach KH, Beebe SJ. Energy-landscape-model analysis for irreversibility and its pulse-width dependence in cells subjected to a high-intensity ultrashort electric pulse. Phys Rev E Stat Nonlin Soft Matter Phys 2004; 69:051901. [PMID: 15244841 DOI: 10.1103/physreve.69.051901] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Revised: 12/15/2003] [Indexed: 05/24/2023]
Abstract
We provide a simple, but physical analysis for cell irreversibility and apoptosis in response to an ultrashort (nanosecond), high-intensity electric pulse. Our approach is based on an energy landscape model for determining the temporal evolution of the configurational probability function p(q). The primary focus is on obtaining qualitative predictions of a pulse width dependence to apoptotic cell irreversibility that has been observed experimentally. The analysis couples a distributed electrical model for current flow with the Smoluchowski equation to provide self-consistent, time-dependent transmembrane voltages. The model captures the essence of the experimentally observed pulse-width dependence, and provides a possible physical picture that depends only on the electrical trigger. A number of interesting features are predicted.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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Joshi RP, Schoenbach KH. Mechanism for membrane electroporation irreversibility under high-intensity, ultrashort electrical pulse conditions. Phys Rev E Stat Nonlin Soft Matter Phys 2002; 66:052901. [PMID: 12513540 DOI: 10.1103/physreve.66.052901] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Indexed: 05/24/2023]
Abstract
An improved electroporation model is used to address membrane irreversibility under ultrashort electric pulse conditions. It is shown that membranes can survive a strong electric pulse and recover provided the pore distribution has a relatively large spread. If, however, the population consists predominantly of larger radii pores, then irreversibility can result. Physically, such a distribution could arise if pores at adjacent sites coalesce. The requirement of close proximity among the pore sites is more easily satisfied in smaller organelles than in outer cell membranes. Model predictions are in keeping with recent observations of cell damage to intracellular organelles (e.g., mitochondria), without irreversible shock at the outer membranes, by a nanosecond, high-intensity electric pulse. This mechanism also explains the greater damage from multiple electric shocks.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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40
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Joshi RP, Hu Q, Schoenbach KH, Hjalmarson HP. Improved energy model for membrane electroporation in biological cells subjected to electrical pulses. Phys Rev E Stat Nonlin Soft Matter Phys 2002; 65:041920. [PMID: 12005886 DOI: 10.1103/physreve.65.041920] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2001] [Revised: 02/01/2002] [Indexed: 05/23/2023]
Abstract
A self-consistent model analysis of electroporation in biological cells has been carried out based on an improved energy model. The simple energy model used in the literature is somewhat incorrect and unphysical for a variety of reasons. Our model for the pore formation energy E(r) includes a dependence on pore population and density. It also allows for variable surface tension, incorporates the effects of finite conductivity on the electrostatic correction term, and is dynamic in nature. Self-consistent calculations, based on a coupled scheme involving the Smoluchowski equation and the improved energy model, are presented. It is shown that E(r) becomes self-adjusting with variations in its magnitude and profile, in response to pore population, and inhibits uncontrolled pore growth and expansion. This theory can be augmented to include pore-pore interactions to move beyond the independent pore picture.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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41
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Joshi RP, Hu Q, Schoenbach KH, Hjalmarson HP. Theoretical predictions of electromechanical deformation of cells subjected to high voltages for membrane electroporation. Phys Rev E Stat Nonlin Soft Matter Phys 2002; 65:021913. [PMID: 11863569 DOI: 10.1103/physreve.65.021913] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2001] [Indexed: 11/07/2022]
Abstract
An electromechanical analysis based on thin-shell theory is presented to analyze cell shape changes in response to external electric fields. This approach can be extended to include osmotic-pressure changes. Our calculations demonstrate that at large fields, the spherical cell geometry can be significantly modified, and even ellipsoidal forms would be inappropriate to account for the deformation. Values of the surface forces obtained from our calculations are in very good agreement with the 1--10 mN/m range for membrane rupture reported in the literature. The results, in keeping with reports in the literature, demonstrate that the final shape depends on membrane thickness. This has direct implications for tissues in which significant molecular restructuring can occur. It is also shown that, at least for the smaller electric fields, both the cellular surface area and volume change roughly in a quadratic manner with the electric field. Finally, it is shown that the bending moments are generally quite small and can be neglected for a simpler analysis.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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Joshi RP, Hu Q, Aly R, Schoenbach KH, Hjalmarson HP. Self-consistent simulations of electroporation dynamics in biological cells subjected to ultrashort electrical pulses. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 64:011913. [PMID: 11461294 DOI: 10.1103/physreve.64.011913] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2001] [Revised: 04/04/2001] [Indexed: 05/23/2023]
Abstract
The temporal dynamics of electroporation of cells subjected to ultrashort voltage pulses are studied based on a coupled scheme involving the Laplace, Nernst-Plank, and Smoluchowski equations. A pore radius dependent energy barrier for ionic transport, accounts for cellular variations. It is shown that a finite time delay exists in pore formation, and leads to a transient overshoot of the transmembrane potential V(mem) beyond 1.0 V. Pore resealing is shown to consist of an initial fast process, a 10(-4) s delay, followed by a much slower closing at a time constant of about 10(-1) s. This establishes a time-window during which the pores are mostly open, and hence, the system is most vulnerable to destruction by a second electric pulse. The existence of such a time window for effective killing by a second pulse is amply supported by our experimental data for E. coli cells. The time constant for the longer process also matches experiments. The study suggests that controlled manipulation of the pore "open times" can be achieved through multiple, ultrashort pulses.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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Joshi RP, Schoenbach KH. Electroporation dynamics in biological cells subjected to ultrafast electrical pulses: a numerical simulation study. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 62:1025-1033. [PMID: 11088559 DOI: 10.1103/physreve.62.1025] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/1999] [Indexed: 05/23/2023]
Abstract
A model analysis of electroporation dynamics in biological cells has been carried out based on the Smoluchowski equation. Results of the cellular response to short, electric pulses are presented, taking account of the growth and resealing dynamics of transient aqueous pores. It is shown that the application of large voltages alone may not be sufficient to cause irreversible breakdown, if the time duration is too short. Failure to cause irreversible damage at small pulse widths could be attributed to the time inadequacy for pores to grow and expand beyond a critical threshold radius. In agreement with earlier studies, it is shown that irreversible breakdown would lead to the formation of a few large pores, while a large number of smaller pores would appear in the case of reversible breakdown. Finally, a pulse width dependence of the applied voltage for irreversible breakdown has been obtained. It is shown that in the absence of dissipation, the associated energy input necessary reduces with decreasing pulse width to a limiting value. However, with circuit effects taken into account, a local minima in the pulse dependent energy function is predicted, in keeping with previously published experimental reports.
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Affiliation(s)
- R P Joshi
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529-0246, USA
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Abstract
This study evaluated an instrument for measuring patellar mobility in the coronal plane in normal subjects, established baseline quantitative data and compared with methods of measurement described in the literature. This data can be used as a baseline for clinical assessment of patellar mobility. The findings suggest that 8-20 mm displacement is normal patellar mobility in the coronal plane. Displacement less than 8 mm may be considered as retinacular tightness and displacement greater than 20 mm considered as abnormal retinacular laxity.
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Affiliation(s)
- R P Joshi
- Orthopaedic Academic Unit, Rayne Institute, St. Thomas' Hospital, London SE1 7EH, UK
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Abstract
Fifty-nine consecutive primary total elbow replacements were performed with the modified posterior approach. The approach differs from other described approaches. The fascia and periosteum over the subcutaneous border of the ulna are preserved, and dissection is carried out on either side of the ulna. This enables a more secure repair of the posteromedial and posterolateral muscle compartments. The ulnar nerve is mobilized to prevent any injury. The distal humerus and proximal ulna can be fully exposed by this approach, giving wide access so necessary for accurate positioning of the prosthesis. The overall complication rate in 59 total elbow replacements was 33.9% including 4 (6.7%) ulnar nerve palsy, 4 (6.7%) wound infections, 2 (3.3%) delayed healing, 4 (11.8%) diminished range of motion in the affected elbow, 2 (3.3%) instability (1 had dislocated elbow and 1 had subluxation), and 1 (1.7%) triceps dehiscence requiring exploration and repair. All the patients could perform active resisted extension of the elbow, indicating continuity of the triceps. The senior author (SCG) has been using this approach for the Roper-Tuke unconstrained total elbow replacement for the last 15 years, and it has been associated with a lower incidence of complications. This approach has not been described before and is recommended for total elbow replacement.
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Affiliation(s)
- R P Joshi
- Orthopaedic Academic Unit, Rayne Institute, St. Thomas' Hospital, London, UK
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Joshi RP, Eftekhar NS, McMahon DJ, Nercessian OA. Osteolysis after Charnley primary low-friction arthroplasty. A comparison of two matched paired groups. J Bone Joint Surg Br 1998; 80:585-90. [PMID: 9699816 DOI: 10.1302/0301-620x.80b4.7361] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We reviewed 249 consecutive Charnley primary low-friction arthroplasties in 191 patients performed by one surgeon using a transtrochanteric approach at a minimum follow-up of ten years. Of these, 37 hips in 32 patients showed osteolysis and were compared with 41 hips in 37 matched patients with no osteolysis. We assessed in each case the wear rate, stability of the prosthesis, acetabular angle, socket angle, thickness of the acetabular and femoral cement mantle, canal flare index, femoral score, stem alignment, implant:canal ratio and stem:canal ratio. We found that a high rate of wear, component instability and osteolysis were associated. Osteolysis was three times more common in men than in women. Factors which reduced osteolysis were cement mantles of 6 mm at the acetabulum and of 3 mm in all zones of the femur, a stem:canal ratio of 60% to 70% and an implant:canal ratio of over 99%. The overall incidence of osteolysis was 14.9% but when these technical criteria were met, the incidence was 5.2%. This suggests that careful technique can dramatically reduce the risk of this complication.
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Affiliation(s)
- R P Joshi
- Department of Orthopaedic Surgery, Columbia Presbyterian Medical Center and New York Orthopaedic Hospital, NY 10032, USA
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Affiliation(s)
- R P Joshi
- Orthopaedic Department, Conquest Hospital, Sussex, UK
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Abstract
A study was done of 70 patients who had internal fixation of an olecranon fracture with an Attenborough spring and Rush nail at the Royal East Sussex Hospital (now called Conquest Hospital), Hastings. This method has been in use since 1970. The age-sex distribution showed more men in the younger age group and more women in the older one. A subjective evaluation was done of all patients. The results were recorded for pain, activities, range of movement, further operations and re-referral after discharge. In the series more than 90 per cent of the patients were satisfied in terms of pain relief, daily activities and range of movements. There were four dissatisfied patients and seven complications. This method provides a quick, safe and effective method of fixing olecranon fractures and appears to give a high level of patient satisfaction.
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Affiliation(s)
- R P Joshi
- Orthopaedic Department, Conquest Hospital, St. Leonard on Sea, East Sussex, UK
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Abstract
Ten- to 20-year (average, 14 years) results of primary Charnley low friction arthroplasties performed in patients 50 years of age or younger (55 sockets and 53 femoral prostheses) were compared with those in patients older than 50 years (273 sockets and 273 femoral prostheses). The incidence of radiologic loosening of the socket, including revision cases, was higher in the younger (29.1%) than in the older patients (14.3%). The revision rate for aseptic loosening of the socket was higher in the younger (20%) than in the older group (4%). This poor performance of the socket may be attributable to the higher incidences of rheumatoid diseases and accelerated polyethylene wear in the younger patients. In contrast, only 3.8% of the femoral prostheses were radiologically loose, and none of them were revised in the younger patients. These figures were comparable with those in the older patients. Quality of structure of bone available for implant fixation may be important for the durability of the arthroplasty. It was considered inferior on the acetabular side and better on the femoral side in the younger patients than in the older. Continued use of the cemented Charnley femoral prostheses can be justified in young patients, although further research is required for the socket problem.
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Affiliation(s)
- S Kobayashi
- New York Orthopaedic Hospital, College of Physicians and Surgeons of Columbia University, New York, USA
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