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Trapp LP, Sukumar N, Cristel RT, Yu J. Head and Neck Injuries among Powered Scooter Users between 2010 and 2019. Facial Plast Surg 2024. [PMID: 38052417 DOI: 10.1055/a-2222-8961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
Powered scooters, including electric scooters (e-scooters), have become an increasingly available and popular mode of personal transportation, but the health risks of these devices are poorly explored. We aim to quantify the increase in frequency of powered scooter-associated head and neck region injuries occurring yearly from 2010 to 2019, and to compare the frequency and severity of injury with those involving unpowered scooters. Here we present a retrospective cross-sectional study of all patients with head and neck injuries associated with powered and unpowered scooters seen in emergency departments reporting to the National Electronic Injury Surveillance System (NEISS) database from January 1, 2010 to December 31, 2019. During this time frame, a total of 1,620 injuries associated with powered scooters and a total of 5,675 injuries associated with unpowered scooters were reported to the NEISS. The database estimates these to reflect a nationwide total of 54,036 powered scooter-related injuries and 168,265 unpowered scooter-related injuries. Powered scooter injuries have increased for both children and adults since 2014, and estimated powered scooter injuries (16,243) surpassed estimated unpowered scooter injuries (14,124) when including all age groups for the first time in 2019. In 2019, adults are estimated to have nearly twice as many powered scooter-related head and neck injuries as children (10,884 vs. 5,359, respectively). In 2019, a higher proportion of powered scooter-related injuries involving adults were severe injuries when compared with those involving children (13.3 vs. 5.2%, respectively). Interestingly, unpowered scooters still cause many more estimated injuries in children than powered scooters did during 2019 (11,953 vs. 5,083). We find that powered scooters are now associated with a greater number and severity of head and neck injuries among the adult population than the pediatric population. But unpowered scooters still cause more head and neck injuries than powered scooters in the pediatric population.
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Affiliation(s)
- Luke P Trapp
- Department of Otolaryngology, University of Illinois at Chicago, Chicago, Illinois
| | - Nitin Sukumar
- Washington University School of Medicine in St. Louis, Mallinckrodt Institute of Radiology, St. Louis, Missouri
| | - Robert T Cristel
- Department of Facial Plastic & Reconstructive Surgery, Synergi Facial Surgery, Chesterfield, Missouri
| | - Jeffrey Yu
- Department of Otolaryngology, Kaiser Permanente, Seattle, Washington
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Ahmad A, Siddiqui SA, Mittal G, Sukumar N, Dubey KD, Kapat A. Design and Synthesis of Co-initiators via Base-Catalysed Sequential Conjugate Addition: Application in Photoinduced Radical Polymerisation Reaction. Chemistry 2023; 29:e202301844. [PMID: 37503865 DOI: 10.1002/chem.202301844] [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: 06/10/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 07/29/2023]
Abstract
Applications of photochemistry are becoming very popular in modern-day life due to its operational simplicity, environmentally friendly and economically sustainable nature in comparison to thermochemistry. In particular photoinduced radical polymerisation (PRP) reactions are finding more biological applications and especially in the areas of dental restoration processes, tissue engineering and artificial bone generation. A type-II photoinitiator and co-initiator-promoted PRP turned out to be a cost-effective protocol, and herein we report the design and synthesis of a new efficient co-initiator for a PRP reaction via a barrierless sequential conjugate addition reaction. Experimental mechanistic observations have been further complemented by computational data. Time for newly synthesised 1,2-benzenedithiol (DTH) based co-initiator promoted polymerisation of urethane dimethacrylate (UDMA, 70 %) and triethylene glycol dimethacrylate (TEGDMA, 30 %) in presence of 450 nm LED (15 W) under the aerobic conditions is 38 seconds. Polymeric material has high glass transition temperature, improved mechanical strength (860 BHN) and longer in-depth polymerisation (3 cm).
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Affiliation(s)
- Asrar Ahmad
- Department of Chemistry, School of Natural Science, Shiv Nadar (Institution of Eminence Deemed to be University), Delhi-NCR, Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Shakir Ali Siddiqui
- Department of Chemistry, School of Natural Science, Shiv Nadar (Institution of Eminence Deemed to be University), Delhi-NCR, Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Garvisha Mittal
- Department of Chemistry, School of Natural Science, Shiv Nadar (Institution of Eminence Deemed to be University), Delhi-NCR, Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - N Sukumar
- Department of Chemistry, School of Natural Science, Shiv Nadar (Institution of Eminence Deemed to be University), Delhi-NCR, Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
- Current affiliation: Centre for Computational Engineering & Networking, School of Artificial Intelligence, Amrita Vishwa Vidyapeetham, Coimbatore, 641105, Tamil Nadu, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar (Institution of Eminence Deemed to be University), Delhi-NCR, Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Ajoy Kapat
- Department of Chemistry, School of Natural Science, Shiv Nadar (Institution of Eminence Deemed to be University), Delhi-NCR, Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
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Berrone S, Canuto C, Pintore M, Sukumar N. Enforcing Dirichlet boundary conditions in physics-informed neural networks and variational physics-informed neural networks. Heliyon 2023; 9:e18820. [PMID: 37600384 PMCID: PMC10432987 DOI: 10.1016/j.heliyon.2023.e18820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/29/2023] [Accepted: 07/29/2023] [Indexed: 08/22/2023] Open
Abstract
In this paper, we present and compare four methods to enforce Dirichlet boundary conditions in Physics-Informed Neural Networks (PINNs) and Variational Physics-Informed Neural Networks (VPINNs). Such conditions are usually imposed by adding penalization terms in the loss function and properly choosing the corresponding scaling coefficients; however, in practice, this requires an expensive tuning phase. We show through several numerical tests that modifying the output of the neural network to exactly match the prescribed values leads to more efficient and accurate solvers. The best results are achieved by exactly enforcing the Dirichlet boundary conditions by means of an approximate distance function. We also show that variationally imposing the Dirichlet boundary conditions via Nitsche's method leads to suboptimal solvers.
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Affiliation(s)
- S. Berrone
- Dipartimento di Scienze Matematiche, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - C. Canuto
- Dipartimento di Scienze Matematiche, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - M. Pintore
- Dipartimento di Scienze Matematiche, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - N. Sukumar
- Department of Civil and Environmental Engineering, University of California, Davis, CA 95616, USA
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Milano SK, Huang Q, Nguyen TTT, Ramachandran S, Finke A, Kriksunov I, Schuller D, Szebenyi M, Arenholz E, McDermott LA, Sukumar N, Cerione RA, Katt WP. New insights into the molecular mechanisms of glutaminase C inhibitors in cancer cells using serial room temperature crystallography. J Biol Chem 2021; 298:101535. [PMID: 34954143 PMCID: PMC8784640 DOI: 10.1016/j.jbc.2021.101535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer cells frequently exhibit uncoupling of the glycolytic pathway from the TCA cycle (i.e. the "Warburg effect"), and as a result, often become dependent on their ability to increase glutamine catabolism. The mitochondrial enzyme Glutaminase C (GAC) helps to satisfy this 'glutamine addiction' of cancer cells by catalyzing the hydrolysis of glutamine to glutamate, which is then converted to the TCA-cycle intermediate α-ketoglutarate. This makes GAC an intriguing drug target, and spurred the molecules derived from bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (the so-called BPTES-class of allosteric GAC inhibitors), including CB-839, which is currently in clinal trials. However, none of the drugs targeting GAC are yet approved for cancer treatment and their mechanism of action is not well understood. Here, we shed new light on the underlying basis for the differential potencies exhibited by members of the BPTES/CB-839 family of compounds, which could not previously be explained with standard cryo-cooled X-ray crystal structures of GAC bound to CB-839 or its analogs. Using an emerging technique known as serial room temperature crystallography, we were able to observe clear differences between the binding conformations of inhibitors with significantly different potencies. We also developed a computational model to further elucidate the molecular basis of differential inhibitor potency. We then corroborated the results from our modeling efforts using recently established fluorescence assays that directly read out inhibitor binding to GAC. Together, these findings should aid in future design of more potent GAC inhibitors with better clinical outlook.
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Affiliation(s)
- Shawn K Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Thuy-Tien T Nguyen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sekar Ramachandran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Aaron Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Irina Kriksunov
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - David Schuller
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Marian Szebenyi
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Elke Arenholz
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Lee A McDermott
- Department of Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15261, United States; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - N Sukumar
- Department of Chemistry and Center for Informatics, Shiv Nadar University, India
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States; Department of Molecular Medicine, Cornell University, Ithaca, New York 14853, United States.
| | - William P Katt
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14853, United States
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Becher RD, Sukumar N, DeWane MP, Stolar MJ, Gill TM, Schuster KM, Maung AA, Zogg CK, Davis KA. Hospital Variation in Geriatric Surgical Safety for Emergency Operation. J Am Coll Surg 2020; 230:966-973.e10. [PMID: 32032720 PMCID: PMC7409563 DOI: 10.1016/j.jamcollsurg.2019.10.018] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND The American College of Surgeons maintains that surgical care in the US has not reached optimal safety and quality. This can be driven partially by higher-risk, emergency operations in geriatric patients. We therefore sought to answer 2 questions: First, to what degree does standardized postoperative mortality vary in hospitals performing nonelective operations in geriatric patients? Second, can the differences in hospital-based mortality be explained by patient-, operative-, and hospital-level characteristics among outlier institutions? STUDY DESIGN Patients 65 years and older who underwent 1 of 8 common emergency general surgery operations were identified using the California State Inpatient Database (2010 to 2011). Expected mortality was obtained from hierarchical, Bayesian mixed-effects logistic regression models. A risk-adjusted hospital-level standardized mortality ratio (SMR) was calculated from observed-to-expected in-hospital deaths. "Outlier" hospitals had an SMR 80% CI that did not cross the mean SMR of 1.0. High-mortality (SMR >1.0) and low-mortality (SMR <1.0) outliers were compared. RESULTS We included 24,207 patients from 107 hospitals. SMRs varied widely, from 2.3 (highest) to 0.3 (lowest). Eleven hospitals (10.3%) were poor-performing high-SMR outliers, and 10 hospitals (9.3%) were exceptional-performing low-SMR outliers. SMR was 3 times worse in the high-SMR compared with the low-SMR group (1.7 vs 0.6; p < 0.001). Patient-, operation-, and hospital-level characteristics were equivalent among outlier-hospitals. CONCLUSIONS Significant hospital variation exists in standardized mortality after common general surgery operations done emergently in older patients. More than 10% of institutions have substantial excess mortality. These findings confirm that the safety of emergency operation in geriatric patients can be significantly improved by decreasing the wide variability in mortality outcomes.
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Affiliation(s)
- Robert D Becher
- Division of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, New Haven, CT.
| | - Nitin Sukumar
- Yale Center for Analytical Sciences Yale School of Public Health, New Haven, CT
| | - Michael P DeWane
- Division of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, New Haven, CT
| | - Marilyn J Stolar
- Yale Center for Analytical Sciences Yale School of Public Health, New Haven, CT
| | - Thomas M Gill
- Section of Geriatrics, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Kevin M Schuster
- Division of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, New Haven, CT
| | - Adrian A Maung
- Division of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, New Haven, CT
| | - Cheryl K Zogg
- Division of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, New Haven, CT
| | - Kimberly A Davis
- Division of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, New Haven, CT
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Becher RD, Sukumar N, DeWane MP, Gill TM, Maung AA, Schuster KM, Stolar MJ, Davis KA. Regionalization of emergency general surgery operations: A simulation study. J Trauma Acute Care Surg 2020; 88:366-371. [PMID: 31804419 PMCID: PMC7472889 DOI: 10.1097/ta.0000000000002543] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 11/25/2022]
Abstract
BACKGROUND It has been theorized that a tiered, regionalized system of care for emergency general surgery (EGS) patients-akin to regional trauma systems-would translate into significant survival benefits. Yet data to support this supposition are lacking. The aim of this study was to determine the potential number of lives that could be saved by regionalizing EGS care to higher-volume, lower-mortality EGS institutions. METHODS Adult patients who underwent one of 10 common EGS operations were identified in the California Inpatient Database (2010-2011). An algorithm was constructed that "closed" lower-volume, higher-mortality hospitals and referred those patients to higher-volume, lower-mortality institutions ("closure" based on hospital EGS volume-threshold that optimized to 95% probability of survival). Primary outcome was the number of lives saved. Fifty thousand regionalization simulations were completed (5,000 for each operation) employing a bootstrap resampling method to proportionally redistribute patients. Estimates of expected deaths at the higher-volume hospitals were recalculated for every bootstrapped sample. RESULTS Of the 165,123 patients who underwent EGS operations over the 2-year period, 17,655 (10.7%) were regionalized to a higher-volume hospital. On average, 128 (48.8%) of lower-volume hospitals were "closed," ranging from 68 (22.0%) hospital closures for appendectomy to 205 (73.2%) for small bowel resection. The simulations demonstrated that EGS regionalization would prevent 9.7% of risk-adjusted EGS deaths, significantly saving lives for every EGS operation: from 30.8 (6.5%) deaths prevented for appendectomy to 122.8 (7.9%) for colectomy. Regionalization prevented 4.6 deaths per 100 EGS patient-transfers, ranging from 1.3 for appendectomy to 8.0 for umbilical hernia repair. CONCLUSION This simulation study provides important new insight into the concept of EGS regionalization, suggesting that 1 in 10 risk-adjusted deaths could be prevented by a structured system of EGS care. Future work should expand upon these findings using more complex discrete-event simulation models. LEVEL OF EVIDENCE Therapeutic/Care Management, level IV.
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Affiliation(s)
- Robert D Becher
- From the Section of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery (R.D.B., M.P.D., A.A.M., K.M.S., K.A.D.), Yale School of Medicine; Yale Center for Analytical Sciences (N.S., M.J.S.), Yale School of Public Health; and Section of Geriatrics, Department of Internal Medicine (T.M.G.), Yale School of Medicine, New Haven, Connecticut
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Owusu KA, Dhakar MB, Bautista C, McKimmy D, Cotugno S, Sukumar N, Deng Y, Farooque P, Hirsch LJ, Maciel CB. Comparison of intranasal midazolam versus intravenous lorazepam for seizure termination and prevention of seizure clusters in the adult epilepsy monitoring unit. Epilepsy Behav 2019; 98:161-167. [PMID: 31374472 DOI: 10.1016/j.yebeh.2019.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The objective of the study was to compare the performance of intravenous (IV) lorazepam (IVL) and intranasal midazolam (INM) for seizure termination and prevention of seizure clusters in adults admitted to the epilepsy monitoring unit (EMU) in whom seizures were captured on continuous video-electroencephalogram. METHODS Retrospective cohort of consecutive adults (≥18 years) with epilepsy admitted to the EMU at a single tertiary academic center, who experienced epileptic seizures (confirmed electroencephalographically) and required rescue therapy. The study spanned from January 2015 until December 2016, which included one year before and one year after transitioning from IVL to INM as the standard rescue therapy at our institution. RESULTS A total of 50 subjects received rescue therapy and were included in the analysis. In the first year, out of 216 patients with epilepsy admitted to the EMU, 27 (13%) received IVL; in the second year, 23/217 (11%) received INM. There were no differences in baseline characteristics and markers of epilepsy severity, the median duration of index seizure (1.7 min [interquartile range (IQR): 1.1-2.7] in IVL vs. 2.0 min [IQR: 1.5-2.6] in INM group, p = 0.20), or in the number of subjects requiring repeat benzodiazepine administrations (IVL 8/27 [29.6%] vs. INM 7/23 [30.4%], p = 0.95). There were no differences in the median number of recurrent seizures in 24 h (1 [IQR: 1-3] in IVL vs. 2 [IQR: 1-4] in INM, p = 0.27), occurrence of status epilepticus (IVL 4/27 [14.8%] subjects vs. INM 1/23 [4.3%] subjects, p = 0.36), incidence of seizure clusters (IVL 8/27 [29.6%] subjects vs. INM 7/23 [30.4%] subjects, p = 0.95), need for transfer to an intensive care unit (ICU), or other adverse events. SIGNIFICANCE In our retrospective study, INM was comparable with IVL for seizure termination and prevention of seizure clusters in the adult EMU. Intranasal midazolam circumvents the need for IV access to be maintained throughout hospitalization and is an attractive alternative to IVL as a rescue therapy in this setting. Ideally, future large, prospective, randomized, and double blind studies are needed to confirm these findings.
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Affiliation(s)
- Kent A Owusu
- Yale New Haven Health, Department of Pharmacy, 20 York Street, New Haven, CT 6510, United States of America; Yale New Haven Health, Office of Strategy Management, 200 Orchard Street, New Haven, CT 06511, United States of America.
| | - Monica B Dhakar
- Division of Epilepsy, Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, United States of America; Department of Neurology, Yale School of Medicine, New Haven, CT 06510, United States of America
| | - Cynthia Bautista
- Department of Emergency & Psychiatric Services, Yale-New Haven Hospital, New Haven, CT 06510, United States of America
| | - Dani McKimmy
- Department of Pharmacy, University of Florida Health, Gainesville, FL 32610, United States of America
| | - Stephanie Cotugno
- Emergency Department, Department of Pharmacy, University of Pittsburgh Medical Center, Shadyside Hospital, Pittsburgh, PA 15232, United States of America
| | - Nitin Sukumar
- Yale Center for Analytical Sciences, Yale University School of Public Health, New Haven, CT 06510, United States of America
| | - Yanhong Deng
- Yale Center for Analytical Sciences, Yale University School of Public Health, New Haven, CT 06510, United States of America
| | - Pue Farooque
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, United States of America; Yale Comprehensive Epilepsy Center, Yale School of Medicine, New Haven, CT 06510, United States of America
| | - Lawrence J Hirsch
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, United States of America; Yale Comprehensive Epilepsy Center, Yale School of Medicine, New Haven, CT 06510, United States of America
| | - Carolina B Maciel
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, United States of America; Division of Neurocritical Care, Department of Neurology, University of Florida College of Medicine, Gainesville, FL 32610, United States of America
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DeWane MP, Sukumar N, Stolar MJ, Gill TM, Maung AA, Schuster KM, Davis KA, Becher RD. High-performance acute care hospitals: Excelling across multiple emergency general surgery operations in the geriatric patient. J Trauma Acute Care Surg 2019; 87:140-146. [PMID: 31259872 PMCID: PMC7656193 DOI: 10.1097/ta.0000000000002273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Indexed: 11/27/2022]
Abstract
BACKGROUND As the geriatric population grows, the need for hospitals performing high quality emergency general surgery (EGS) on older patients will increase. Identifying clusters of high-performing geriatric emergency general surgery hospitals would substantiate the need for in-depth analyses of hospital-specific structures and practices that benefit older EGS patients. The objectives of this study were therefore to identify clusters of hospitals based on mortality performance for geriatric patients undergoing common EGS operations and to determine if hospital performance was similar for all operation types. METHODS Hospitals in the California State Inpatient Database were included if they performed a range of eight common EGS operations in patients 65 years or older, with a minimum requirement of three of each operation performed over 2 years. Multivariable beta regression models were created to define hospital-level risk-adjusted mortality. Centroid cluster analysis was used to identify groups of hospitals based on mortality and to determine if mortality-performance differed by operation. RESULTS One hundred seven hospitals were included, performing a total of 24,279 operations in older patients. Hospitals separated into three distinct clusters: high, average, and low performers. The high-performing hospitals had survival rates 1 to 2 standard deviations better than the low-performers (p < 0.001). For each cluster, high performance in any one EGS operation consistently translated into high performance across all EGS operations. CONCLUSION Hospitals conducting EGS operations in the geriatric patient population cluster into three distinct groups based on their survival performance. High-performing hospitals significantly outperform the average and low performers across every operation. The high-performers achieve reliable, high-quality results regardless of operation type. Further qualitative research is needed to investigate the perioperative drivers of hospital performance in the geriatric EGS population. LEVEL OF EVIDENCE Study Type Prognostic, level III.
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Affiliation(s)
- Michael P DeWane
- From the Section of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery (M.P.D., A.A.M., K.M.S., K.A.D., R.D.B.), Yale School of Medicine; Yale Center for Analytical Sciences (N.S., M.J.S.), Yale School of Public Health; and Section of Geriatrics, Department of Internal Medicine (T.M.G.), Yale School of Medicine, New Haven, Connecticut
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9
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Becher RD, DeWane MP, Sukumar N, Stolar MJ, Gill TM, Becher RM, Maung AA, Schuster KM, Davis KA. Hospital Operative Volume as a Quality Indicator for General Surgery Operations Performed Emergently in Geriatric Patients. J Am Coll Surg 2019; 228:910-923. [PMID: 31005629 DOI: 10.1016/j.jamcollsurg.2019.02.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Within the growing geriatric population, there is an increasing need for emergency operations. Optimizing outcomes can require a structured system of surgical care based on key quality indicators. To investigate this, the current study sought to answer 2 questions. First, to what degree does hospital emergency operative volume impact mortality for geriatric patients undergoing emergency general surgery (EGS) operations? Second, at what procedure-specific hospital volume will geriatric patients undergoing an emergency operation achieve at or better than average mortality risk? STUDY DESIGN Retrospective cohort study of geriatric patients (aged 65 years and older) who underwent 1 of 10 EGS operations identified from the California State Inpatient Database (2010 to 2011). β-Logistic generalized linear regression was used, with the hospital as the unit of analysis, to investigate the relationship between hospital operative volume and in-hospital riskv-adjusted mortality. Hospital operative volume thresholds to optimize probability of survival were defined. RESULTS There were 41,860 operations evaluated at 299 hospitals. For each operation, mortality decreased as hospital emergency operative volume increased (p < 0.001 for each operation); for every standardized increase in volume (meaning +1 natural logarithm of volume), the reduction in mortality ranged from 14% for colectomy to 61% for appendectomy. Hospital volume thresholds, which optimize to 95% probability of survival, varied by procedure, with a mean of 14 operations over 2 years. More than 50% of hospitals did not meet the threshold benchmarks, representing 22% of patients. CONCLUSIONS Survival rates for geriatric patients were improved substantially when emergency operations were performed at hospitals with higher operative volumes. Consistent with all active Quality Programs of the American College of Surgeons, hospital operative volume appears to be an important metric of surgical quality for older patients undergoing emergency operations.
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Affiliation(s)
- Robert D Becher
- Section of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, Yale School of Medicine, New Haven, CT.
| | - Michael P DeWane
- Section of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Nitin Sukumar
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT
| | - Marilyn J Stolar
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT
| | - Thomas M Gill
- Section of Geriatrics, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | | | - Adrian A Maung
- Section of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Kevin M Schuster
- Section of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Kimberly A Davis
- Section of General Surgery, Trauma, and Surgical Critical Care, Department of Surgery, Yale School of Medicine, New Haven, CT
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Antaya RJ, del Carmen M, Alonso F, Sukumar N, Yong F, Dvoretzky I. An Open Label Study of an Occlusive Heat Patch in the Treatment of Warts. J Drugs Dermatol 2019; 18:368-373. [PMID: 31012566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Background: Local hyperthermia has been demonstrated to be a safe and efficacious treatment for warts. Objective: We aimed to evaluate the safety and efficacy of an epicutaneous heat patch to induce local hyperthermia for the treatment of warts. Methods: We performed an uncontrolled, proof of concept study by applying a novel, reproducible, epicutaneous heat patch to a target wart for 2 hours per day for 12 weeks. There were 15 evaluable participants. An untreated wart was also observed and measured. Wart measurements included the diameter in two dimensions, an investigator global assessment (IGA) score, wart clearance, and monitoring for adverse events as endpoints at week 12 (end of treatment) and week 24 (end of study). Results: No major adverse events were observed. 6.7% of participants reported minor cutaneous events. At week 24, 46.7% of participants achieved complete clearance of both warts. Limitations: The small sample size and lack of independent control in each participant were the main limiting factors. Conclusion: Local hyperthermia delivered by epicutaneous heat patches was well-tolerated, safe, and achieved complete clearance in both treated as well untreated warts in 46.7% of participants at week 24 after 12 weeks of daily use. Clinicaltrials.gov: NCT01746056 J Drugs Dermatol. 2019;18(4):368-373.
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11
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Sukumar N, Liu S, Li W, Mathews FS, Mitra B, Kandavelu P. Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2 Å resolution. Biochimie 2018; 154:45-54. [PMID: 30071260 DOI: 10.1016/j.biochi.2018.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
Abstract
The x-ray structure of the monotopic membrane protein (S)-mandelate dehydrogenase (MDH) from Pseudomonas putida reveals an inherent flexibility of its membrane binding segment that might be important for its biological activity. The surface of MDH exhibits a concentration of the positive charges on one side and the negative charges on the other side. The putative membrane binding surface of MDH has a concentric circular ridge, formed by positively charged residues, which projects away from the protein surface by ∼4 Å; this is an unique structural feature and not observed in other monotopic membrane proteins to our knowledge. There are three α-helixes in the membrane binding region. Based on the structure of MDH, it is possible to propose that the interaction of MDH with the membrane is stabilized by coplanar electrostatic interactions, between the positively charged concentric circular ridge and the negatively charged head-groups of the phospholipid bilayer, along with three α-helixes that provide additional stability by inserting into the membrane. The structure reveals the possible orientation of these helixes along with possible roles for the individual residues which form those helixes. These α-helixes may play a role in the enzyme's mobility. A detergent molecule, N-Dodecyl-β-maltoside, is inserted between the membrane binding region and rest of the molecule and may provide structural stability to intra-protein regions by forming hydrogen bonds and close contacts. From the average B-factor of the MDH structure, it is likely that MDH is highly mobile, which might be essential for its interaction in membrane and non-membrane environments, as its substrate (S)-mandelate, is from the cytoplasm, while its electron acceptor is a component of the membrane electron transport chain.
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Affiliation(s)
- N Sukumar
- NE-CAT, Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, Argonne, IL 60439, USA.
| | - S Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - W Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - F S Mathews
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - B Mitra
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - P Kandavelu
- SER-CAT and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Tantawy H, Li A, Dai F, Elgammal M, Sukumar N, Elefteriades J, Akhtar S. Association of red blood cell transfusion and short- and longer-term mortality after coronary artery bypass graft surgery. J Cardiothorac Vasc Anesth 2018; 32:1225-1232. [DOI: 10.1053/j.jvca.2017.12.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Indexed: 11/11/2022]
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13
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Qiu R, Perrino AC, Zurich H, Sukumar N, Dai F, Popescu W. Effect of preoperative gabapentin and acetaminophen on opioid consumption in video-assisted thoracoscopic surgery: a retrospective study. Rom J Anaesth Intensive Care 2018; 25:43-48. [PMID: 29756062 DOI: 10.21454/rjaic.7518.251.gab] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background Patients undergoing video-assisted thoracoscopic surgery (VATS) are particularly vulnerable to opioid-induced sedation and hypoventilation. Accordingly, reducing opioid consumption in these patients is a primary goal of multimodal analgesic regimens. Although administration of preoperative gabapentin and acetaminophen has been shown to decrease postoperative opioid consumption in other surgeries, this approach has not been studied in VATS lobectomy. Our objective was to examine the impact of the addition of preoperative gabapentin and acetaminophen to a VATS lobectomy multimodal analgesic plan on postoperative opioid consumption, nausea/vomiting, and sedation. Methods With IRB approval, we performed a retrospective chart review of patients who underwent VATS lobectomy at a single center between 2015 and 2016 to identify those that received preoperative gabapentin and acetaminophen and those that received neither. Opioid consumption in the first 24 hours postoperatively was converted to oral morphine equivalents (OMEQs). Postoperative sedation was evaluated using Aldrete scores and the percentage of patients requiring antiemetics in the first 24 hours was also examined. Results There were 133 patients who were opioid naive: 31 received preoperative gabapentin and acetaminophen and 102 received neither. Median 24 hour postoperative opioid consumption was lower but not statistically significant in the gabapentin and acetaminophen group vs. neither (36 mg vs. 45 mg, p = 0.08). Notably, there was a change in the distribution of opioid consumption, with no patients in the gabapentin and acetaminophen group requiring more than 200 mg OMEQ in the first 24 hours postoperatively. No significant difference in postoperative nausea/vomiting or sedation was observed. Conclusions The addition of preoperative gabapentin and acetaminophen to a VATS lobectomy multimodal analgesic regimen reduces the incidence of high dose postoperative opioid consumption without observed negative side effects.
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Affiliation(s)
- Robert Qiu
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Albert C Perrino
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA.,Veterans Administration Connecticut Healthcare System, West Haven, CT, USA
| | - Holly Zurich
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Nitin Sukumar
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Feng Dai
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Wanda Popescu
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA.,Veterans Administration Connecticut Healthcare System, West Haven, CT, USA
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14
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Acevedo-Alvarez M, Yeh J, Alvarez-Lugo L, Lu M, Sukumar N, Hill WG, Chai TC. Mouse urothelial genes associated with voiding behavior changes after ovariectomy and bladder lipopolysaccharide exposure. Neurourol Urodyn 2018; 37:2398-2405. [PMID: 29682797 DOI: 10.1002/nau.23592] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 03/23/2018] [Indexed: 12/15/2022]
Abstract
AIMS Symptoms from overactive bladder (OAB) and cystitis secondary to urinary tract infection (UTI) can be similar in post-menopausal women. Effects of ovariectomy (OVX) on voiding behavior after lipopolysaccharide (LPS) intravesical exposure (surrogate for cystitis) in mice were measured. Urothelial genes associated with micturition changes were identified. METHODS Female C57BL6/J mice underwent OVX or sham surgeries (n = 10 for each). Voiding spot assays (VSA) were performed prior to surgery, 4 weeks post-surgery, and each time after 3 consecutive days of transurethral instillation of LPS. In another experiment, mice underwent either sham (n = 9) or OVX (n = 9) surgeries. Urothelial RNAs were collected 4 weeks post-surgery, day 1 and day 3 after LPS instillation. Mouse Gene 2.0 ST Arrays (entire 34 K transcripts) were used for microarray hybridization. A set of criteria was utilized to identify gene expression changes that mimicked voiding behavior changes. RESULTS Three days after LPS exposure, OVX mice persisted with overactive whereas sham mice normalized voiding behavior. Nine urothelial paralleling voiding behavior changes were identified: IL6 (interleukin 6), IL6rα (Interleukin 6 receptor α), Ptgs2 (Prostaglandin-endoperoxide synthase 2 or COX-2), Ereg (epiregulin), Dusp6 (dual specificity phosphatase 6), Zfp948 (zinc finger protein 948), Zfp52 (Zinc finger protein 52), Gch1 (GTP cyclohydrolase 1), and Amd (S-adenosylmethionine decarboxylase). Three other genes, coding unknown proteins, were also identified: GM12840, GM23134, and GM26809. CONCLUSIONS OVX mice persisted with increased voiding frequency after LPS. Urothelial genes that could mediate this voiding behavior include IL6, COX-2, and S-adenosylmethionine decarboxylase.
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Affiliation(s)
- Marian Acevedo-Alvarez
- Departments of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut
| | - Judy Yeh
- Departments of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut
| | - Lery Alvarez-Lugo
- Department of Urology, Yale School of Medicine, New Haven, Connecticut
| | - Ming Lu
- Department of Urology, Yale School of Medicine, New Haven, Connecticut
| | - Nitin Sukumar
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Warren G Hill
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Toby C Chai
- Departments of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut.,Department of Urology, Yale School of Medicine, New Haven, Connecticut
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15
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Goldberg SB, Narayan A, Kole AJ, Decker RH, Teysir J, Carriero NJ, Lee A, Nemati R, Nath SK, Mane SM, Deng Y, Sukumar N, Zelterman D, Boffa DJ, Politi K, Gettinger SN, Wilson LD, Herbst RS, Patel AA. Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA. Clin Cancer Res 2018; 24:1872-1880. [PMID: 29330207 DOI: 10.1158/1078-0432.ccr-17-1341] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/05/2017] [Accepted: 01/08/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Decisions to continue or suspend therapy with immune checkpoint inhibitors are commonly guided by tumor dynamics seen on serial imaging. However, immunotherapy responses are uniquely challenging to interpret because tumors often shrink slowly or can appear transiently enlarged due to inflammation. We hypothesized that monitoring tumor cell death in real time by quantifying changes in circulating tumor DNA (ctDNA) levels could enable early assessment of immunotherapy efficacy.Experimental Design: We compared longitudinal changes in ctDNA levels with changes in radiographic tumor size and with survival outcomes in 28 patients with metastatic non-small cell lung cancer (NSCLC) receiving immune checkpoint inhibitor therapy. CtDNA was quantified by determining the allele fraction of cancer-associated somatic mutations in plasma using a multigene next-generation sequencing assay. We defined a ctDNA response as a >50% decrease in mutant allele fraction from baseline, with a second confirmatory measurement.Results: Strong agreement was observed between ctDNA response and radiographic response (Cohen's kappa, 0.753). Median time to initial response among patients who achieved responses in both categories was 24.5 days by ctDNA versus 72.5 days by imaging. Time on treatment was significantly longer for ctDNA responders versus nonresponders (median, 205.5 vs. 69 days; P < 0.001). A ctDNA response was associated with superior progression-free survival [hazard ratio (HR), 0.29; 95% CI, 0.09-0.89; P = 0.03], and superior overall survival (HR, 0.17; 95% CI, 0.05-0.62; P = 0.007).Conclusions: A drop in ctDNA level is an early marker of therapeutic efficacy and predicts prolonged survival in patients treated with immune checkpoint inhibitors for NSCLC. Clin Cancer Res; 24(8); 1872-80. ©2018 AACR.
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Affiliation(s)
- Sarah B Goldberg
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Azeet Narayan
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Adam J Kole
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roy H Decker
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Jimmitti Teysir
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | | | - Angela Lee
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roxanne Nemati
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Sameer K Nath
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Shrikant M Mane
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Yanhong Deng
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Nitin Sukumar
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Daniel Zelterman
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Daniel J Boffa
- Department of Thoracic Surgery, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Scott N Gettinger
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Lynn D Wilson
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roy S Herbst
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut.
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16
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Donroe JH, Holt SR, O'Connor PG, Sukumar N, Tetrault JM. Interpreting quantitative urine buprenorphine and norbuprenorphine levels in office-based clinical practice. Drug Alcohol Depend 2017; 180:46-51. [PMID: 28866369 DOI: 10.1016/j.drugalcdep.2017.07.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 07/25/2017] [Accepted: 07/29/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND Quantitative urine buprenorphine testing is used to monitor patients receiving buprenorphine for the treatment of opioid use disorder (OUD), however the interpretation of urine buprenorphine testing is complex. Currently, interpretation of quantitative buprenorphine testing is guided by data from drug assay development studies and forensic labs rather than clinical treatment cohorts. METHODS In this retrospective study, we describe the patterns of urine buprenorphine and norbuprenorphine levels in patients prescribed sublingual buprenorphine for OUD in an office-based addiction treatment clinic. Urine buprenorphine and norbuprenorphine levels were analyzed in patients who reported having adulterated their urine, patients clinically suspected of adulterating their urine, and patients without concern for urine adulteration. Finally, we tested the accuracy of urine buprenorphine, norbuprenorphine, and norbuprenorphine: buprenorphine ratio (Norbup:Bup) to identify adulterated urine samples. RESULTS Patients without suspicion for urine adulteration rarely provided specimens with buprenorphine >=1000ng/ml (4.4%), while the proportion provided by those who endorsed or were suspected of urine adulteration was higher (42.9%, 40.6%, respectively). Compared to patients without reported urine adulteration, specimens from patients who reported or were suspected of urine adulteration had significantly higher buprenorphine (p=0.0001) and lower norbuprenorphine (<0.0001) levels, and significantly lower Norbup:Bup ratios (p=0.04). Buprenorphine >=700ng/ml offered the best accuracy for discriminating between adulterated and non-adulterated specimens. CONCLUSION This study describes the patterns of urine buprenorphine and norbuprenorphine levels from patients with OUD receiving buprenorphine treatment in an office-based addiction treatment clinic. Parameters for identifying urine adulterated by submerging buprenorphine medication in the urine specimen are discussed.
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Affiliation(s)
- Joseph H Donroe
- Yale University School of Medicine, Department of Internal Medicine,1450 Chapel Street, Office M330, New Haven, CT 06511, USA.
| | - Stephen R Holt
- Yale University School of Medicine, Department of Internal Medicine, 1450 Chapel Street, Office P312, New Haven, CT 06511, USA.
| | - Patrick G O'Connor
- Yale University School of Medicine, Department of General Internal Medicine, 367 Cedar Street, Suite 402, New Haven, CT 06510, USA.
| | - Nitin Sukumar
- Yale University School of Public Health, Yale Center for Analytical Sciences, 300 George Street, Suite 511, New Haven, CT 06510, USA.
| | - Jeanette M Tetrault
- Yale University School of Medicine, Department of Internal Medicine, 367 Cedar Street, Suite 305, New Haven, CT 06510, USA.
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17
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Goldberg S, Narayan A, Kole A, Decker R, Teysir J, Carriero N, Lee A, Nemati R, Nath S, Mane S, Deng Y, Sukumar N, Zelterman D, Boffa D, Politi K, Gettinger S, Wilson L, Herbst R, Patel A. Assessing response to immunotherapy in patients with non-small cell lung cancer using circulating tumor DNA. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx380.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Mandal SK, Saha P, Munshi P, Sukumar N. Exploring potent ligand for proteins: insights from knowledge-based scoring functions and molecular interaction energies. Struct Chem 2017. [DOI: 10.1007/s11224-017-1007-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Chen EY, Sukumar N, Dai F, Akhtar S, Schonberger RB. A Pilot Analysis of the Association Between Types of Monitored Anesthesia Care Drugs and Outcomes in Transfemoral Aortic Valve Replacement Performed Without General Anesthesia. J Cardiothorac Vasc Anesth 2017; 32:666-671. [PMID: 29277298 DOI: 10.1053/j.jvca.2017.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The types of agents used for monitored anesthesia care (MAC) and their possible differential effects on outcomes have received less study despite increased use over general anesthesia (GA) in transfemoral aortic valve replacements (TAVRs). In this pilot analysis of patients undergoing TAVR using MAC, the authors described the anesthetic agents used and sought to investigate the possible association of anesthetic agent choice with outcomes and the extent to which total weight and time-adjusted doses of anesthetics declined with increasing 10-year age increments. DESIGN Retrospective observational study. SETTING Tertiary teaching hospital. PARTICIPANTS Ninety-three participants scheduled to undergo TAVR, with a primary plan of conscious sedation between November 2014 and June 2016, were included. INTERVENTION None. MEASUREMENTS AND MAIN RESULTS Types of MAC were divided into 4 primary groups, but 2 groups were focused: propofol (n = 39) and dexmedetomidine plus propofol (n = 34). Conversion to GA occurred in 6 participants (6.45%) and was not associated with the type of sedation received. The authors also compared patients who received dexmedetomidine with those who did not in accordance with their a priori analytic plan. There were no associations between the use of dexmedetomidine and postoperative delirium or intensive care unit/hospital length of stay. No significant trends in medication dose adjustments were seen across increasing 10-year age increments. CONCLUSIONS A wide breadth of MAC medications is in use among TAVR patients and does not support differences in outcomes. Despite recommendations to reduce anesthetic drug dosing in the elderly, no significant trends in dose reduction with increasing age were noted.
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Affiliation(s)
- Eric Y Chen
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT.
| | - Nitin Sukumar
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT
| | - Feng Dai
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT
| | - Shamsuddin Akhtar
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT
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20
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Wu K, Sukumar N, Lanzillo NA, Wang C, “Rampi” Ramprasad R, Ma R, Baldwin AF, Sotzing G, Breneman C. Prediction of polymer properties using infinite chain descriptors (ICD) and machine learning: Toward optimized dielectric polymeric materials. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/polb.24117] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- K. Wu
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; 110 8th Street Troy New York 12180
| | - N. Sukumar
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; 110 8th Street Troy New York 12180
- Department of Chemistry and Center for Informatics; School of Natural Sciences, Shiv Nadar University; NH-91, Tehsil Dadri, Gautam Budh Nagar 201314 Uttar Pradesh India
| | - N. A. Lanzillo
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; 110 8th Street Troy New York 12180
| | - C. Wang
- Department of Materials Science and Engineering; University of Connecticut; Storrs Connecticut 06269
| | | | - R. Ma
- Polymer Program, Institute of Materials Science, University of Connecticut; Storrs Connecticut 06269
| | - A. F. Baldwin
- Polymer Program, Institute of Materials Science, University of Connecticut; Storrs Connecticut 06269
| | - G. Sotzing
- Polymer Program, Institute of Materials Science, University of Connecticut; Storrs Connecticut 06269
- Deparment of Chemistry; University of Connecticut, Storrs; Connecticut 06269
| | - C. Breneman
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; 110 8th Street Troy New York 12180
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21
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Tchaparian E, Sambol NC, Arinaitwe E, McCormack SA, Bigira V, Wanzira H, Muhindo M, Creek DJ, Sukumar N, Blessborn D, Tappero JW, Kakuru A, Bergqvist Y, Aweeka FT, Parikh S. Population Pharmacokinetics and Pharmacodynamics of Lumefantrine in Young Ugandan Children Treated With Artemether-Lumefantrine for Uncomplicated Malaria. J Infect Dis 2016; 214:1243-51. [PMID: 27471317 PMCID: PMC5034953 DOI: 10.1093/infdis/jiw338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/23/2016] [Indexed: 12/21/2022] Open
Abstract
Background. The pharmacokinetics and pharmacodynamics of lumefantrine, a component of the most widely used treatment for malaria, artemether-lumefantrine, has not been adequately characterized in young children. Methods. Capillary whole-blood lumefantrine concentration and treatment outcomes were determined in 105 Ugandan children, ages 6 months to 2 years, who were treated for 249 episodes of Plasmodium falciparum malaria with artemether-lumefantrine. Results. Population pharmacokinetics for lumefantrine used a 2-compartment open model with first-order absorption. Age had a significant positive correlation with bioavailability in a model that included allometric scaling. Children not receiving trimethoprim-sulfamethoxazole with capillary whole blood concentrations <200 ng/mL had a 3-fold higher hazard of 28-day recurrent parasitemia, compared with those with concentrations >200 ng/mL (P = .0007). However, for children receiving trimethoprim-sulfamethoxazole, the risk of recurrent parasitemia did not differ significantly on the basis of this threshold. Day 3 concentrations were a stronger predictor of 28-day recurrence than day 7 concentrations. Conclusions. We demonstrate that age, in addition to weight, is a determinant of lumefantrine exposure, and in the absence of trimethoprim-sulfamethoxazole, lumefantrine exposure is a determinant of recurrent parasitemia. Exposure levels in children aged 6 months to 2 years was generally lower than levels published for older children and adults. Further refinement of artemether-lumefantrine dosing to improve exposure in infants and very young children may be warranted.
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Affiliation(s)
- Eskouhie Tchaparian
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco
| | - Nancy C Sambol
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco
| | | | - Shelley A McCormack
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco
| | - Victor Bigira
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Mary Muhindo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Darren J Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Nitin Sukumar
- Yale School of Public Health, New Haven, Connecticut
| | | | - Jordan W Tappero
- Centers for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Abel Kakuru
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Sunil Parikh
- Yale School of Public Health, New Haven, Connecticut
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22
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Pilania G, Wang CC, Wu K, Sukumar N, Breneman C, Sotzing G, Ramprasad R. New Group IV chemical motifs for improved dielectric permittivity of polyethylene. J Chem Inf Model 2013; 53:879-86. [PMID: 23521565 DOI: 10.1021/ci400033h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An enhanced dielectric permittivity of polyethylene and related polymers, while not overly sacrificing their excellent insulating properties, is highly desirable for various electrical energy storage applications. In this computational study, we use density functional theory (DFT) in combination with modified group additivity based high throughput techniques to identify promising chemical motifs that can increase the dielectric permittivity of polyethylene. We consider isolated polyethylene chains and allow the CH2 units in the backbone to be replaced by a number of Group IV halides (viz., SiF2, SiCl2, GeF2, GeCl2, SnF2, or SnCl2 units) in a systematic, progressive, and exhaustive manner. The dielectric permittivity of the chemically modified polyethylene chains is determined by employing DFT computations in combination with the effective medium theory for a limited set of compositions and configurations. The underlying chemical trends in the DFT data are first rationalized in terms of various tabulated atomic properties of the constituent atoms. Next, by parametrizing a modified group contribution expansion using the DFT data set, we are able to predict the dielectric permittivity and bandgap of nearly 30,000 systems spanning a much larger part of the configurational and compositional space. Promising motifs which lead to simultaneously large dielectric constant and band gap in the modified polyethylene chains have been identified. Our theoretical work is expected to serve as a possible motivation for future experimental efforts.
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Affiliation(s)
- G Pilania
- Chemical, Materials, and Biomolecular Engineering, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, USA
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Register KB, Sukumar N, Palavecino EL, Rubin BK, Deora R. Bordetella bronchiseptica in a paediatric cystic fibrosis patient: possible transmission from a household cat. Zoonoses Public Health 2012; 59:246-50. [PMID: 22212633 DOI: 10.1111/j.1863-2378.2011.01446.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bordetella bronchiseptica is a zoonotic respiratory pathogen commonly found in domesticated farm and companion animals, including dogs and cats. Here, we report isolation of B. bronchiseptica from a sputum sample of a cystic fibrosis patient recently exposed to a kitten with an acute respiratory illness. Genetic characterization of the isolate and comparison with other isolates of human or feline origin strongly suggest that the kitten was the source of infection.
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Affiliation(s)
- K B Register
- USDA/Agricultural Research Service/National Animal Disease Center, Ames, IA, USA.
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Sukumar N, Krein MP, Embrechts MJ. Predictive cheminformatics in drug discovery: statistical modeling for analysis of micro-array and gene expression data. Methods Mol Biol 2012; 910:165-94. [PMID: 22821597 DOI: 10.1007/978-1-61779-965-5_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The vast amounts of chemical and biological data available through robotic high-throughput assays and micro-array technologies require computational techniques for visualization, analysis, and predictive -modeling. Predictive cheminformatics and bioinformatics employ statistical methods to mine this data for hidden correlations and to retrieve molecules or genes with desirable biological activity from large databases, for the purpose of drug development. While many statistical methods are commonly employed and widely accessible, their proper use involves due consideration to data representation and preprocessing, model validation and domain of applicability estimation, similarity assessment, the nature of the structure-activity landscape, and model interpretation. This chapter seeks to review these considerations in light of the current state of the art in statistical modeling and to summarize the best practices in predictive cheminformatics.
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Affiliation(s)
- N Sukumar
- Rensselaer Exploratory Center for Cheminformatics Research and Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA.
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Affiliation(s)
- Michael P. Krein
- Rensselaer Exploratory Center for Cheminformatics Research, and Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - N. Sukumar
- Rensselaer Exploratory Center for Cheminformatics Research, and Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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Kourinov I, Ealick SE, Capel M, Banerjee S, Murphy F, Neau D, Perry K, Rajashankar K, Schuermann J, Sukumar N. NE-CAT crystallography beamlines for challenging structural biology research. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311087770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Thong KY, Jose B, Sukumar N, Cull ML, Mills AP, Sathyapalan T, Shafiq W, Rigby AS, Walton C, Ryder REJ. Safety, efficacy and tolerability of exenatide in combination with insulin in the Association of British Clinical Diabetologists nationwide exenatide audit*. Diabetes Obes Metab 2011; 13:703-10. [PMID: 21410858 DOI: 10.1111/j.1463-1326.2011.01393.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [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: 01/22/2023]
Abstract
AIM To assess the extent, safety, efficacy and tolerability of reported off-licence exenatide use through a nationwide audit. METHODS The Association of British Clinical Diabetologists hosted a password-protected, online collection of anonymized data of exenatide use in real clinical practice. Three hundred and fifteen contributors from 126 centres across UK provided data on 6717 patients. HbA1c and weight changes, exenatide discontinuation, adverse events and treatment satisfaction were compared between non-insulin and insulin-treated patients. RESULTS Four thousand eight hundred and fifty-seven patients had baseline and follow-up treatment status with mean (±s.d.) baseline HbA1c 9.45 ± 1.69% and BMI 40.0 ± 8.2 kg/m(2) . Of the 4857 patients, 1921 (39.6%) used exenatide with insulin. Comparing patients who continued insulin with exenatide with non-insulin-treated patients, mean (±s.e.) latest HbA1c and weight reduction (median 26 weeks) were 0.51 ± 0.06 versus 0.94 ± 0.04% (p < 0.001) and 5.8 ± 0.2 versus 5.5 ± 0.1 kg (p = 0.278). Insulin-treated patients had higher rates of exenatide discontinuation (31.0 vs. 13.9%, p < 0.001), hypoglycaemia (8.9 vs. 6.1%, p < 0.001), gastrointestinal side effects (28.4 vs. 25.0%, p = 0.008) and treatment dissatisfaction (20.8 vs. 5.7%, p < 0.001). However, 34.2% of the patients continuing insulin still achieved HbA1c reduction ≥1%. There was significant insulin discontinuation, dose reduction and greater sulphonylurea discontinuation among insulin-treated patients. CONCLUSIONS Addition of exenatide to obese, insulin-treated patients can improve glycaemia and weight. Adverse events were statistically but probably not clinically significantly higher, but combination treatment was less well tolerated. Overall, exenatide was less effective in lowering HbA1c among insulin-treated patients, although significant number of insulin-treated patients still achieved significant HbA1c, weight and insulin reductions. Further research into identifying obese, insulin-treated patients who will tolerate and benefit from exenatide treatment is urgently needed.
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Affiliation(s)
- K Y Thong
- Department of Diabetes, City Hospital, Birmingham, UK.
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Sukumar N, Mathews FS, Langan P, Davidson VL. A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer. Proc Natl Acad Sci U S A 2010; 107:6817-22. [PMID: 20351252 PMCID: PMC2872398 DOI: 10.1073/pnas.0912672107] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [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] [Indexed: 12/20/2022] Open
Abstract
The joint x-ray/neutron diffraction model of the Type I copper protein, amicyanin from Paracoccus denitrificans was determined at 1.8 A resolution. The protein was crystallized using reagents prepared in D(2)O. About 86% of the amide hydrogen atoms are either partially or fully exchanged, which correlates well with the atomic depth of the amide nitrogen atom and the secondary structure type, but with notable exceptions. Each of the four residues that provide copper ligands is partially deuterated. The model reveals the dynamic nature of the protein, especially around the copper-binding site. A detailed analysis of the presence of deuterated water molecules near the exchange sites indicates that amide hydrogen exchange is primarily due to the flexibility of the protein. Analysis of the electron transfer path through the protein shows that residues in that region are highly dynamic, as judged by hydrogen/deuterium exchange. This could increase the rate of electron transfer by transiently shortening through-space jumps in pathways or by increasing the atomic packing density. Analysis of C-HX bonding reveals previously undefined roles of these relatively weak H bonds, which, when present in sufficient number can collectively influence the structure, redox, and electron transfer properties of amicyanin.
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Affiliation(s)
- N Sukumar
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, Argonne, IL 60439, USA.
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Kulshrestha P, Sukumar N, Murray JS, Giese RF, Wood TD. Computational Prediction of Antibody Binding Sites on Tetracycline Antibiotics: Electrostatic Potentials and Average Local Ionization Energies on Molecular Surfaces. J Phys Chem A 2009; 113:756-66. [DOI: 10.1021/jp8089165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [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)
- Pankaj Kulshrestha
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115, and Department of Geology, University at Buffalo, The State University of New York, Buffalo, New York 14260
| | - N. Sukumar
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115, and Department of Geology, University at Buffalo, The State University of New York, Buffalo, New York 14260
| | - Jane S. Murray
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115, and Department of Geology, University at Buffalo, The State University of New York, Buffalo, New York 14260
| | - Rossman F. Giese
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115, and Department of Geology, University at Buffalo, The State University of New York, Buffalo, New York 14260
| | - Troy D. Wood
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115, and Department of Geology, University at Buffalo, The State University of New York, Buffalo, New York 14260
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Sukumar N, Mathews FS, Gordon MM, Ealick SE, Alpers DH. Postcrystallization Analysis of the Irreproducibility of the Human Intrinsic Factor-Cobalamin Complex Crystals. Cryst Growth Des 2009; 9:348-351. [PMID: 19884970 PMCID: PMC2631276 DOI: 10.1021/cg800509f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Approximately 15% (w/w) of human intrinsic factor (IF) is comprised of carbohydrate side chains, making crystallization problematic. In addition, IF is sensitive to proteolysis. To understand the role of these factors in crystallization, we carried out dynamic light scattering studies and assessed their correlation with crystallization. The packing of the IF-cobalamin complex and the known properties of the protein in solution were also analyzed to explore the irreproducibility of the IF-cobalamin complex crystals and the difficulty in obtaining apo-IF crystals suitable for crystallographic analysis. The results indicate that although glycosylation may in general be inhibitory for crystallization, time-dependent proteolysis appears to play a much more important role in the process of crystallization of IF. Thus, the presence of cobalamin and of domain fragments that can form incomplete dimers lacking one of two β-domains appears to promote the crystallization of IF.
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Kourinov I, Ealick E, Capel M, Lynch E, Murphy F, Rajashankar K, Sukumar N, Unik P, Withrow J. NorthEastern Collaborative Access Team (NE-CAT) beam lines at the Advanced Photon Source. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308094300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sukumar N, Krein M, Breneman CM. Bioinformatics and cheminformatics: where do the twain meet? Curr Opin Drug Discov Devel 2008; 11:311-319. [PMID: 18428084] [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] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bridging the domains of cheminformatics and bioinformatics in the post-genomic era requires the convergence of goals, tools, techniques and annotations. This article reviews recent research at the interface of the domains that shows evidence of this convergence. While graph theoretical representations have long been used to develop simple topological descriptions of molecules, graph theory-based network concepts are also widely employed in systems biology. Shape and conformation are important for understanding intermolecular interactions, and several structure-based cheminformatic descriptors have been developed and applied to drug-like molecules and biomolecules. Data fusion methods and shared ontologies can also help integrate data from multiple sources in order to generate a holistic picture of the shared molecular informatics domain.
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Affiliation(s)
- N Sukumar
- Department of Chemistry and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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Lukman MR, Sangar P, Sukumar N. Obstructed paraesophageal hernia in a nonagenerian treated by laparoscopic anterior gastropexy. Med J Malaysia 2007; 62:83-4. [PMID: 17682583] [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] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Paraesophageal hernias have been historically associated with risk of substantial morbidity and mortality. We report a case of a 92 year old lady with acute gastric outlet obstruction due to a chronic paraesophageal hernia that was successfully treated by minimal invasive surgery. Anterior gastropexy was performed after the stomach was reduced. The hiatal opening was enlarged to reduce the risk of obstruction in the future. She was discharged well on the third day.
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Affiliation(s)
- M R Lukman
- Department of Surgery, Faculty of Medicine, Hospital Universiti Kebangsaan Malaysia, Kuala Lumpur
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Razman J, Shaharin S, Lukman MR, Sukumar N, Jasmi AY. Initial experience of laparoscopic incisional hernia repair. Med J Malaysia 2006; 61:142-6. [PMID: 16898302] [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] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Laparoscopic repair of ventral and incisional hernia has become increasingly popular as compared to open repair. The procedure has the advantages of minimal access surgery, reduction of post operative pain and the recurrence rate. A prospective study of laparoscopic incisional hernia repair was performed in our center from August 2002 to April 2004. Eighteen cases (n: 18) were performed during the study period. Fifteen cases (n: 15) had open hernia repair previously. Sixteen patients (n: 16) had successful repair of the hernia with the laparoscopic approach and two cases were converted to open repair. The mean hernia defect size was 156cm2. There was no intraoperative or immediate postoperative complication. The mean operating time was 100 +/- 34 minutes (75 - 180 minutes). The postoperative pain was graded as mild to moderate according to visual analogue score. The mean day of discharge after surgery was two days (1 - 3 days). During follow up, three patients (16.7%) developed seroma at the hernia sac which was resolved with conservative management after three weeks. One (5.6%) patient developed recurrence six months after surgery. In conclusion, laparoscopic repair of incisional hernia particularly recurrent hernia has been shown to be safe and effective in our centre. However, careful patient selection and acquiring the necessary advanced laparoscopic surgical skills coupled with the proper use of equipment are mandatory before embarking on this procedure.
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Affiliation(s)
- J Razman
- Department of Surgery, Faculty of Medicine, Hospital Universiti Kebangsaan Malaysia, Jalan Yaakob Latiff, Cheras, Kuala Lumpur
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Malathy Sony SM, Saraboji K, Sukumar N, Ponnuswamy MN. Role of amino acid properties to determine backbone τ(N–Cα–C′) stretching angle in peptides and proteins. Biophys Chem 2006; 120:24-31. [PMID: 16269209 DOI: 10.1016/j.bpc.2005.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [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: 06/08/2005] [Revised: 07/27/2005] [Accepted: 07/28/2005] [Indexed: 11/22/2022]
Abstract
The analysis of the basic geometry of amino acid residues of protein structures has demonstrated the invariability of all the bond lengths and bond angles except for tau, the backbone N-Calpha-C' angle. This angle can be widened or contracted significantly from the tetrahedral geometry to accommodate various other strains in the structure. In order to accurately determine the cause for this deviation, a survey is made for the tau angles using the peptide structures and the ultrahigh resolution protein structures. The average deviation of N-Calpha-C' angles from tetrahedral geometry for each amino acid in all the categories were calculated and then correlated with forty-eight physiochemical, energetic and conformational properties of amino acids. Linear and multiple regression analysis were carried out between the amino acid deviation and the 48 properties. This study confirms the deviation of tau angles in both the peptide and protein structures but similar forces do not influence them. The peptide structures are influenced by physical properties whereas as expected the conformational properties influence the protein structures. And it is not any single property that dominates the deviation but the combination of different factors contributes to the tau angle deviation.
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Affiliation(s)
- S M Malathy Sony
- Department of Crystallography and Biophysics, University of Madras, Guindy campus, Chennai--600025, India
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Hamidon BB, Abdullah SA, Zawawi MF, Sukumar N, Aminuddin A, Raymond AA. A prospective comparison of percutaneous endoscopic gastrostomy and nasogastric tube feeding in patients with acute dysphagic stroke. Med J Malaysia 2006; 61:59-66. [PMID: 16708735] [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] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Dysphagia following stroke is common problem and is of particular concern because of its potental for malnutrition. Nasogastric (NG) and percutaneous endoscopic gastrostomy (PEG) tube feeding are recognized methods for nutritional support for patients with persistent neurologic dysphagia. However, the former is associated with tube dislodgement and blockage that might compromise the patients' nutritional status. There have been few randomized prospective studies to date comparing the efficacy and safety of these 2 modes of dysphagia management in stroke patients. The objective of this study was to compare PEG with NG tube feeding after acute dysphagic stroke in terms of nutritional status and treatment failure. This was a randomized prospective clinical trial. A total of 23 consecutive patients who fulfilled the criteria were recruited from the medical wards in Hospital Universiti Kebangsaan Malaysia. The diagnosis of stroke (acute cerebral infarct) was based on clinical and brain computed tomographic (CT scan) findings; and the diagnosis of dysphagia was done clinically by using the 'swallowing test'. At recruitment, upper-arm skin fold thickness (triceps and biceps) and mid-arm circumference were measured; and blood was drawn for serum albumin level. They were then followed up at 4 weeks where the above tests were repeated. A total of 22 patients completed the study (12 patients in the NG group and 10 patients in the PEG group). Serum albumin levels (p = 0.045) were significantly higher in the PEG as compared to the NG group at 4 weeks post-intervention. There were statistically significant improvements in serum albumin level (p = 0.024) in the PEG group; and statistically significant reductions in serum albumin level (p = 0.047) in the NG group 4 weeks after the intervention. However, there were no significant differences in anthropometric parameters between the two groups and no significant changes in these parameters for each group 4 weeks after the intervention. Treatment failure occurred in 5 out of 10 patients (50.0%) in the NG group, but none in PEG group (p = 0.036). PEG tube feeding is more effective than NG tube feeding in improving the nutritional status (in terms of the serum albumin level) of patients with dysphagic stroke. NG tube feeding, in fact, reduced the nutritional status (in terms of the serum albumin level) of the patients.
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Affiliation(s)
- B B Hamidon
- Department of Medicine, Department of Surgery, Faculty of Medicine UKM, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras Kuala Lumpur, Malaysia
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Teoh CM, Gunasegaram T, Chan KY, Sukumar N, Sagap I. Review of risk factors associated with the anastomosis leakage in anterior resection in Hospital Universiti Kebangsaan Malaysia. Med J Malaysia 2005; 60:275-80. [PMID: 16379179] [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] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This is a retrospective study evaluating the risk factors for clinical anastomotic leakage after anterior resection in 64 patients with rectal cancer operated from November 2001 till August 2003. The percentage of anastomosis leakage was higher in those patients with diabetic, low albumin level, neoadjuvant radiotherapy, higher staging, and poorly differentiated tumour. However, these differences were statistically not significant. There was a significant difference (p=0.03) of anastomosis leakage in those patients with very distal tumour of < 4cm from anal verge (42%), when compare to those patients with proximal tumor of > 15cm from anal verge (4.3%). The mortality associated with this complication was 30%. Hence, a surgeon may consider a covering stoma or be more vigilant in operating patients with multiple risk factors.
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Affiliation(s)
- C M Teoh
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur
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Kalyani A, Teoh CM, Sukumar N. I jejunal patch repair of a duodenal perforation. Med J Malaysia 2005; 60:237-8. [PMID: 16114169] [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] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A patient with duodenal ulcer who developed iatrogenic perforation post endoscopy is presente. We present t is case that was treated successfully treated by jejunal serosal patch.
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Affiliation(s)
- A Kalyani
- Department of Surgery, University Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur
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Sukumar N, Langan P, Mathews FS, Jones LH, Thiyagarajan P, Schoenborn BP, Davidson VL. A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans. Acta Crystallogr D Biol Crystallogr 2005; 61:640-2. [PMID: 15858277 DOI: 10.1107/s090744490500541x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Accepted: 02/17/2005] [Indexed: 11/10/2022]
Abstract
Crystals of the blue copper protein amicyanin suitable for neutron diffraction were grown by the sitting-drop method, followed by repeated macroseeding using solutions prepared with D(2)O. Although the crystal sizes were the same, crystals grown using solutions made up in H(2)O in the initial stages of macroseeding and solutions with D(2)O in later stages did not diffract neutrons well. However, when the protein was initially exchanged with buffered D(2)O and then crystallized and also macroseeded using solutions made up in D(2)O throughout, the crystals diffracted neutrons to high resolution. One of those crystals was used to collect a data set to a resolution of 1.9 A.
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Affiliation(s)
- N Sukumar
- NE-CAT, Building 436, Argonne National Laboratory, Argonne, IL 60439, USA.
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Chan KY, Teoh CM, Sukumar N. Case report of a difficult venous access: retroperitoneal approach of inserting an improved non-heparinised port for long-term use. Med J Malaysia 2005; 60:94-6. [PMID: 16250289] [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] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This is a case report of a patient with difficult venous access following thrombosis of major superficial and deep veins of the limbs as documented by ultrasound doppler and venography. The insertion of a few central ports were infected and the vein thrombosed. Venography revealed that central venous access was no longer feasible. The previous laparotomies had resulted in dense intra-peritoneal adhesions, and rendered further laparotomy virtually impossible. The patient had occasional adhesion colics, vomiting and hypoglycemic episodes. A rarely performed retro-peritoneal approach of inserting an improved non-heparinised port proved to be effective for long-term management of this patient. The surgical approach and the selected port are discussed.
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Affiliation(s)
- K Y Chan
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, 56000, Kuala Lumpur
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Marjmin O, Badrulhisham B, Teoh CM, Sukumar N, Ahmad Zakuan K. Metastatic cervical carcinoma in the caecum. Med J Malaysia 2005; 60:97-8. [PMID: 16250290] [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] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A patient who presented with acute intestinal obstruction had a right hemicolectomy for a caecal tumour. The histopathology report confirmed metastatic carcinoma in the caecum from the cervical carcinoma. Caecum is a very rare site of metastasis from cervical carcinoma. From our literature review, there have been no such cases reported.
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Affiliation(s)
- O Marjmin
- Department of Surgery, Hospital Universiti Kebangsaan Malaysia, Jalan Yaakob Latif, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur
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Song M, Breneman CM, Sukumar N. Three-dimensional quantitative structure-activity relationship analyses of piperidine-based CCR5 receptor antagonists. Bioorg Med Chem 2004; 12:489-99. [PMID: 14723967 DOI: 10.1016/j.bmc.2003.10.019] [Citation(s) in RCA: 19] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CCR5 chemokine receptor has recently been found to play a crucial role in the viral entry stage of HIV infection and has therefore become an attractive potential target for anti-HIV therapeutics. On the other hand, the lack of CCR5 crystal structure data has impeded the development of structure-based CCR5 antagonist design. In this paper, we compare two three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) methods: Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) on a series of piperidine-based CCR5 antagonists as an alternative approach to investigate the interaction between CCR5 antagonists and their receptor. Superimposition of antagonist structures was performed using two alignment rules: atomic/centroid rms fit and rigid body field fit techniques. The 3D QSAR models were derived from a training set of 72 compounds, and were found to have predictive capability for a set of 19 holdout test compounds. The resulting contour maps produced by the best CoMFA and CoMSIA models were used to identify the structural features relevant to biological activity in this series of compounds. Further analyses of these interaction-field contour maps also showed a high level of internal consistency.
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Affiliation(s)
- Minghu Song
- Department of Chemistry, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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Sukumar N, Teoh CM. Heterotopic pancreas in the stomach. Med J Malaysia 2004; 59:541-3. [PMID: 15779591] [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] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A patient diagnosed with gastrointestinal stromal tumour of the stomach underwent gastrectomy. Post-operatively, histopathology was reported as heterotopic pancreas of the stomach. Heterotopic pancreas is very rare and though most of them appear asymptomatic, surgical resection is advisable.
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Affiliation(s)
- N Sukumar
- Department of Surgery, Hospital University Kebangsaan Malaysia, Jalan Yacob Latif, Bandar Tun Razak, 56000 Kuala Lumpur
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Sukumar N, Shaharin S, Razman J, Jasmi AY. Bogota bag in the treatment of abdominal wound dehiscence. Med J Malaysia 2004; 59:281-3. [PMID: 15559181] [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] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
A patient who underwent emergency laparotomy for rectal prolapse developed repeated abdominal wound dehiscence and subsequently an enteric fistula. The management of abdominal wound dehiscence is discussed, specifically with regards to the Bogota bag. Use of Bogota bag has been reported worldwide but this may be the first report here.
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Affiliation(s)
- N Sukumar
- Department of Surgery, Hospital University Kebangsaan Malaysia, Jalan Yacob Latif, Bandar Tun Razak, 56000 Kuala Lumpur
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Abstract
Recent investigations have shown that the inclusion of hybrid shape/property descriptors together with 2D topological descriptors increases the predictive capability of QSAR and QSPR models. Property-Encoded Surface Translator (PEST) descriptors may be computed using ab initio or semi-empirical electron density surfaces and/or electronic properties, as well as atomic fragment-based TAE/RECON property-encoded surface reconstructions. The RECON and PEST algorithms also include rapid fragment-based wavelet coefficient descriptor (WCD) computation. These descriptors enable a compact encoding of chemical information. We also briefly discuss the use of the RECON/PEST methodology in a virtual high-throughput mode, as well as the use of TAE properties for molecular surface autocorrelation analysis.
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Affiliation(s)
- Curt M Breneman
- Department of Chemistry, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Malathy Sony SM, Sukumar N, Ponnuswamy MN, Jayakumar R. Presence of pseudo-peptide bond in the crystal structure of n-(t-butoxycarbonyl)-ɛ-n′-benzyloxycarbony-l-lysyl-l-isoleucine (boc-lys(obzl)-ile). Cryst Res Technol 2004. [DOI: 10.1002/crat.200310197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Tugcu N, Song M, Breneman CM, Sukumar N, Bennett KP, Cramer SM. Prediction of the Effect of Mobile-Phase Salt Type on Protein Retention and Selectivity in Anion Exchange Systems. Anal Chem 2003; 75:3563-72. [PMID: 14570211 DOI: 10.1021/ac0263519] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [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: 11/28/2022]
Abstract
This study examines the effect of different salt types on protein retention and selectivity in anion exchange systems. Particularly, linear retention data for various proteins were obtained on two structurally different anion exchange stationary-phase materials in the presence of three salts with different counterions. The data indicated that the effects are, for the most part, nonspecific, although various specific effects could also be observed. Quantitative structure retention relationship (QSRR) models based on support vector machine feature selection and regression models were developed using the experimental chromatographic data in conjunction with various molecular descriptors computed from protein crystal structure geometries. Star plots for each descriptor used in the final model were generated to aid in interpretation. The resulting QSRR models were predictive, with cross-validated r2 values of 0.9445, 0.9676, and 0.8897 for Source 15Q and 0.9561, 0.9876, and 0.9760 for Q Sepharose resins in the presence of three different salts. The predictive power of these models was validated using a set of test proteins that were not used in the generation of these models. Interpretation of the models revealed that particular trends for proteins and salts could be captured using QSRR techniques.
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Affiliation(s)
- Nihal Tugcu
- Department of Chemical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Abstract
The transferability of atomic and functional group properties is an implicit concept in chemistry. The work presented here describes the use of Transferable Atom Equivalents (TAE) to represent molecular electrostatic potential fields through the use of integrated atomic multipole moments that are associated with each TAE atom type used in the reconstruction. TAE molecular surface distributions of electrostatic potentials are compared with analytical ab initio and empirical (Gasteiger) partial charge reference models for several conformations of test peptides. Surface electrostatic potential distributions computed using TAE multipole representations were found to converge at the octopole level, with incremental improvement observed when hexadecapoles were included. Molecular electrostatic potential fields that were produced using the TAE method were observed to be responsive to conformational changes and to compare well with ab initio reference distributions. Generation of TAE atom types and their associated multipoles does not involve fitting to sample electrostatic potential fields, but rather utilizes integrated AIM atomic electron density distributions within representative chemical environments. The RECON program was used for TAE reconstruction. RECON is capable of processing 5,000 drug-sized molecules or 25 proteins per minute per 1.7 GHz P4 Linux processor.
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Affiliation(s)
- C E Whitehead
- Department of Chemistry, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY 12180, USA.
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