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Marvasti TB, Philip R, Parikh H, Hazan E, Liu PJ, Saeed O, Billick MJ. Reviewing Your ABCs - Acute Kidney Injury, Bartonella Endocarditis, and C-ANCA Vasculitis. Am J Med 2024; 137:e22-e25. [PMID: 37918779 DOI: 10.1016/j.amjmed.2023.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/20/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Affiliation(s)
- Tina B Marvasti
- Temerty Faculty of Medicine, University of Toronto, Ontario, Canada
| | - Rohan Philip
- Temerty Faculty of Medicine, University of Toronto, Ontario, Canada
| | - Harsh Parikh
- Temerty Faculty of Medicine, University of Toronto, Ontario, Canada
| | - Elias Hazan
- Temerty Faculty of Medicine, University of Toronto, Ontario, Canada
| | | | - Omar Saeed
- Temerty Faculty of Medicine, University of Toronto, Ontario, Canada; Division of General Internal Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Maxime J Billick
- Temerty Faculty of Medicine, University of Toronto, Ontario, Canada; Division of Infectious Diseases, University of Toronto, Ontario, Canada.
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Parikh H, Sun H, Amerineni R, Rosenthal ES, Volfovsky A, Rudin C, Westover MB, Zafar SF. How Many Patients Do You Need? Investigating Trial Designs for Anti-Seizure Treatment in Acute Brain Injury Patients. medRxiv 2023:2023.08.21.23294339. [PMID: 37662339 PMCID: PMC10473786 DOI: 10.1101/2023.08.21.23294339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Objectives Epileptiform activity (EA) worsens outcomes in patients with acute brain injuries (e.g., aneurysmal subarachnoid hemorrhage [aSAH]). Randomized trials (RCTs) assessing anti-seizure interventions are needed. Due to scant drug efficacy data and ethical reservations with placebo utilization, RCTs are lacking or hindered by design constraints. We used a pharmacological model-guided simulator to design and determine feasibility of RCTs evaluating EA treatment. Methods In a single-center cohort of adults (age >18) with aSAH and EA, we employed a mechanistic pharmacokinetic-pharmacodynamic framework to model treatment response using observational data. We subsequently simulated RCTs for levetiracetam and propofol, each with three treatment arms mirroring clinical practice and an additional placebo arm. Using our framework we simulated EA trajectories across treatment arms. We predicted discharge modified Rankin Scale as a function of baseline covariates, EA burden, and drug doses using a double machine learning model learned from observational data. Differences in outcomes across arms were used to estimate the required sample size. Results Sample sizes ranged from 500 for levetiracetam 7 mg/kg vs placebo, to >4000 for levetiracetam 15 vs. 7 mg/kg to achieve 80% power (5% type I error). For propofol 1mg/kg/hr vs. placebo 1200 participants were needed. Simulations comparing propofol at varying doses did not reach 80% power even at samples >1200. Interpretation Our simulations using drug efficacy show sample sizes are infeasible, even for potentially unethical placebo-control trials. We highlight the strength of simulations with observational data to inform the null hypotheses and assess feasibility of future trials of EA treatment.
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Affiliation(s)
| | - Haoqi Sun
- Beth Israel Deaconess Medical Center, Department of Neurology
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Parikh H, Hoffman K, Sun H, Zafar SF, Ge W, Jing J, Liu L, Sun J, Struck A, Volfovsky A, Rudin C, Westover MB. Effects of epileptiform activity on discharge outcome in critically ill patients in the USA: a retrospective cross-sectional study. Lancet Digit Health 2023; 5:e495-e502. [PMID: 37295971 PMCID: PMC10528143 DOI: 10.1016/s2589-7500(23)00088-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/13/2023] [Accepted: 04/19/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Epileptiform activity is associated with worse patient outcomes, including increased risk of disability and death. However, the effect of epileptiform activity on neurological outcome is confounded by the feedback between treatment with antiseizure medications and epileptiform activity burden. We aimed to quantify the heterogeneous effects of epileptiform activity with an interpretability-centred approach. METHODS We did a retrospective, cross-sectional study of patients in the intensive care unit who were admitted to Massachusetts General Hospital (Boston, MA, USA). Participants were aged 18 years or older and had electrographic epileptiform activity identified by a clinical neurophysiologist or epileptologist. The outcome was the dichotomised modified Rankin Scale (mRS) at discharge and the exposure was epileptiform activity burden defined as mean or maximum proportion of time spent with epileptiform activity in 6 h windows in the first 24 h of electroencephalography. We estimated the change in discharge mRS if everyone in the dataset had experienced a specific epileptiform activity burden and were untreated. We combined pharmacological modelling with an interpretable matching method to account for confounding and epileptiform activity-antiseizure medication feedback. The quality of the matched groups was validated by the neurologists. FINDINGS Between Dec 1, 2011, and Oct 14, 2017, 1514 patients were admitted to Massachusetts General Hospital intensive care unit, 995 (66%) of whom were included in the analysis. Compared with patients with a maximum epileptiform activity of 0 to less than 25%, patients with a maximum epileptiform activity burden of 75% or more when untreated had a mean 22·27% (SD 0·92) increased chance of a poor outcome (severe disability or death). Moderate but long-lasting epileptiform activity (mean epileptiform activity burden 2% to <10%) increased the risk of a poor outcome by mean 13·52% (SD 1·93). The effect sizes were heterogeneous depending on preadmission profile-eg, patients with hypoxic-ischaemic encephalopathy or acquired brain injury were more adversely affected compared with patients without these conditions. INTERPRETATION Our results suggest that interventions should put a higher priority on patients with an average epileptiform activity burden 10% or greater, and treatment should be more conservative when maximum epileptiform activity burden is low. Treatment should also be tailored to individual preadmission profiles because the potential for epileptiform activity to cause harm depends on age, medical history, and reason for admission. FUNDING National Institutes of Health and National Science Foundation.
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Affiliation(s)
- Harsh Parikh
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Kentaro Hoffman
- Deptartment of Statistics and Operation Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Haoqi Sun
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Sahar F Zafar
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Wendong Ge
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Jin Jing
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Lin Liu
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA; Institute of Natural Sciences, MOELSC, School of Mathematical Sciences and SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Jimeng Sun
- The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Aaron Struck
- Department of Neurology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Cynthia Rudin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - M Brandon Westover
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
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McAlister FA, Parikh H, Lee DS, Wijeysundera HC. Health Care Implications of the COVID-19 Pandemic for the Cardiovascular Practitioner. Can J Cardiol 2022:S0828-282X(22)01051-0. [PMID: 36481398 PMCID: PMC9721374 DOI: 10.1016/j.cjca.2022.11.014] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
There has been substantial excess morbidity and mortality during the COVID-19 pandemic, not all of which was directly attributable to SARS-CoV-2 infection, and many non-COVID-19 deaths were cardiovascular. The indirect effects of the pandemic have been profound, resulting in a substantial increase in the burden of cardiovascular disease and cardiovascular risk factors, both in individuals who survived SARS-CoV-2 infection and in people never infected. In this report, we review the direct effect of SARS-CoV-2 infection on cardiovascular and cardiometabolic disease burden in COVID-19 survivors as well as the indirect effects of the COVID-19 pandemic on the cardiovascular health of people who were never infected with SARS-CoV-2. We also examine the pandemic effects on health care systems and particularly the care deficits caused (or exacerbated) by health care delayed or foregone during the COVID-19 pandemic. We review the consequences of: (1) deferred/delayed acute care for urgent conditions; (2) the shift to virtual provision of outpatient care; (3) shortages of drugs and devices, and reduced access to: (4) diagnostic testing, (5) cardiac rehabilitation, and (6) homecare services. We discuss the broader implications of the COVID-19 pandemic for cardiovascular health and cardiovascular practitioners as we move forward into the next phase of the pandemic.
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Affiliation(s)
- Finlay A. McAlister
- The Division of General Internal Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada,The Alberta Strategy for Patient Oriented Research Support Unit, Edmonton, Alberta, Canada,Corresponding author: Dr Finlay A. McAlister, 5-134C Clinical Sciences Building, University of Alberta, 11350 83 Avenue, Edmonton, Alberta T6G 2G3, Canada. Tel.: +1-780-492-9824; fax: +1-780-492-7277
| | - Harsh Parikh
- Peter Munk Cardiac Center, Ted Rogers Centre for Heart Research, University of Toronto, Toronto, Ontario, Canada
| | - Douglas S. Lee
- Peter Munk Cardiac Center, Ted Rogers Centre for Heart Research, University of Toronto, Toronto, Ontario, Canada,ICES (formerly Institute for Clinical Evaluative Sciences), Toronto, Ontario, Canada
| | - Harindra C. Wijeysundera
- ICES (formerly Institute for Clinical Evaluative Sciences), Toronto, Ontario, Canada,Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada,Schulich Heart Program, Sunnybrook Health Sciences Center, University of Toronto, Toronto, Ontario, Canada
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Frost A, Tomou G, Parikh H, Kaur J, Zivcevska M, Niemeier M. Correction to: Working memory in action: inspecting the systematic and unsystematic errors of spatial memory across saccades. Exp Brain Res 2022; 240:2219-2220. [PMID: 35727367 DOI: 10.1007/s00221-022-06396-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Adam Frost
- University of Toronto Scarborough, Toronto, Canada.
| | - George Tomou
- University of Toronto Scarborough, Toronto, Canada.,York University, Toronto, Canada.,Centre for Vision Research, Toronto, Canada
| | - Harsh Parikh
- University of Toronto Scarborough, Toronto, Canada
| | - Jagjot Kaur
- University of Toronto Scarborough, Toronto, Canada
| | | | - Matthias Niemeier
- University of Toronto Scarborough, Toronto, Canada. .,Centre for Vision Research, Toronto, Canada.
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Freking W, Okelana B, Only A, McMillan L, Kibble K, Parikh H, Williams B, Shearer D, Cunningham B. Can Reducing Implant Costs Increase Revenue for Surgically Treated Ankle Fractures: Time-Driven Activity-Based Costing for 1-Year Episode of Care. Foot Ankle Spec 2021:19386400211062456. [PMID: 34872365 DOI: 10.1177/19386400211062456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The purpose of this study was to investigate whether decision-making regarding implant selection affects the reimbursement margins for the surgical fixation of ankle fractures. METHODS All ankle fractures treated between 2010 and 2017 within a single-insurer database were identified via Current Procedural Terminology codes by review of electronic medical record. Implant cost was determined via the implant record cross-referenced with the single contract institutional charge master database. The Time-Driven Activity-Based Costing (TDABC) technique was used to determine the costs of care during all activities throughout the 1-year episode of care. Statistical analysis consisted of multiple linear regression and goodness-of-fit analyses. RESULTS In all, 249 patients met inclusion criteria. Implant costs ranged from $173 to $3944, averaging $1342 ± $751. The TDABC-estimated cost of care ranged from $1416 to $9185, averaging $3869 ± $1384. Finally, the total reimbursed cost of care ranged between $1335 and $65 645, averaging $13 954 ± $9445. The implant costs occupied an estimated 34.7% of the TDABC-estimated cost of care per surgical encounter. Implant cost, as a percentage of the overall TDABC, was estimated as 36.2% in the inpatient setting and 33% in the outpatient setting, which was the second highest percentage behind surgical costs in both settings. We found a significant increase in net revenue of $1.93 for each dollar saved on implants in the outpatient setting, whereas the increase in net revenue per dollar saved of $1.03 approached significance in the inpatient setting. CONCLUSION There is a direct relationship between intraoperative decision-making, as evidenced by implant choices, and the revenue generated by surgical fixation of ankle fractures. Intraoperative decision-making that is cognitive of implant cost can facilitate adoption of institutional cost containment measures and prompt increased healthcare value. LEVEL OF EVIDENCE Level III: Retrospective cohort study.
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Affiliation(s)
- Will Freking
- Department of Orthopaedic Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Bandele Okelana
- Department of Orthopaedic Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Arthur Only
- Department of Orthopaedic Surgery, TRIA Orthopedic Center, Bloomington, Minnesota
| | - Logan McMillan
- Department of Orthopaedic Surgery, Regions Hospital, St. Paul, Minnesota
| | - Kendra Kibble
- Department of Orthopaedic Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Harsh Parikh
- Department of Orthopaedic Surgery, Regions Hospital, St. Paul, Minnesota
| | - Benjamin Williams
- Department of Orthopaedic Surgery, Park Nicollet Methodist Hospital, St. Louis Park, Minnesota
| | - David Shearer
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, California
| | - Brian Cunningham
- Department of Orthopaedic Surgery, Park Nicollet Methodist Hospital, St. Louis Park, Minnesota
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Parikh H, Lui E, Faughnan ME, Al-Hesayen A, Segovia S, Gupta S. Supine vs upright exercise in patients with hepatopulmonary syndrome and orthodeoxia: study protocol for a randomized controlled crossover trial. Trials 2021; 22:683. [PMID: 34625098 PMCID: PMC8500814 DOI: 10.1186/s13063-021-05633-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The hepatopulmonary syndrome (HPS) is a pulmonary complication of liver disease found in 10 to 32% of patients with cirrhosis and is characterized by intrapulmonary vascular dilatations and abnormal oxygenation. Liver transplantation is the only effective therapy for this disease. Patients with HPS have significant exercise limitations, impacting their quality of life and associated with poor liver transplant outcomes. Many patients with HPS exhibit orthodeoxia-an improvement in oxygenation in the supine compared to the upright position. We hypothesize that exercise capacity will be superior in the supine compared to the upright position in such patients. METHODS We propose a randomized controlled crossover trial in patients with moderate HPS (PaO2 < 80 mmHg) and orthodeoxia (supine to upright PaO2 decrease > 4 mmHg) comparing the effect of supine vs upright position on exercise. Patients with pulmonary hypertension, FEV1/FVC ratio < 0.65, significant coronary artery disease, disorders preventing or contraindicating use of a cycle ergometer, and/or moderate or severe ascites will be excluded. Participants will be randomized to cycle ergometry in either the supine or upright position. After a short washout period (a minimum of 1 day to a maximum of 4 weeks), participants will crossover and perform an exercise in the alternate position. Exercise will be performed at a constant work rate of 70-85% of the predicted peak work rate until the "stopping time" is reached, defined by exhaustion, profound desaturation, or safety concerns (drop in systolic blood pressure or life-threatening arrhythmia). The primary outcome will be the difference in the stopping time between exercise positions, compared with a repeated measures analysis of variance method with a mixed effects model approach. The model will be adjusted for period effects. P < 0.05 will be considered statistically significant. DISCUSSION HPS patients have hypoxemia leading to significant exercise limitations. If our study is positive, a supine exercise regimen could become a routine prescription for patients with HPS and orthodeoxia, enabling them to exercise more effectively. Future studies could explore the corresponding effects of a supine exercise training regimen on physiologic variables such as long-term exercise capacity, quality of life, dyspnea, and liver transplantation outcomes. TRIAL REGISTRATION ClinicalTrials.gov Protocol Registration and Results System (PRS) NCT04004104 . Registered on 1 July 2019.
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Affiliation(s)
- Harsh Parikh
- Li Ka Shing Knowledge Institute, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Eric Lui
- Li Ka Shing Knowledge Institute, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Marie E Faughnan
- Li Ka Shing Knowledge Institute, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada.,Division of Respirology, St. Michael's Hospital, Toronto, Canada
| | - Abdul Al-Hesayen
- Department of Medicine, University of Toronto, Toronto, Canada.,Division of Cardiology, St Michael's Hospital, Toronto, Canada
| | | | - Samir Gupta
- Li Ka Shing Knowledge Institute, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada. .,Department of Medicine, University of Toronto, Toronto, Canada. .,Division of Respirology, St. Michael's Hospital, Toronto, Canada.
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Dileep P, Shah K, Dhebar C, Thakkar K, Parikh H, Patel A, Dileep A. Complicated Chikungunya Infection in Tertiary ICU in Western India - A Prospective Study Over 3 Years. J Assoc Physicians India 2021; 69:11-12. [PMID: 34781654] [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: 06/13/2023]
Abstract
BACKGROUND Chikungunya is a globally spreading infectious arboviral disease transmitted from a diurnal bite of the Aedes aegypti and Aedes albopictus Mosquitoes. It is a disease with sporadic outbreaks. It is now resurfacing in South East Asia especially in India, where it is found to have high mortality and morbidity and presenting with atypical presentation, especially with the neurotropic presentation. OBJECTIVE To review clinical profile of patients who required admission in the Intensive care unit with atypical presentation of Chikungunya and to study their clinical spectrum and outcome over a course of three years in India. METHOD AND FINDINGS Using Established guidelines, we conducted a prospective study in a Tertiary care center where we identified patients who required intensive care admissions and were admitted with complicated chikungunya infection and then evaluated their clinical progression of the disease. CONCLUSION CHIKV infection is rapidly emerging in more than 100 countries and more and more atypical serious neurological manifestations are seen in elderly populations. Many of these patients have high morbidity and mortality.
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Affiliation(s)
- Pratibha Dileep
- HOD, Department of Critical Care Medicine, Zydus Hospital, Ahmedabad, Gujarat
| | - Kushal Shah
- Associate Consultant, Department of Critical Care Medicine, Zydus Hospital, Ahmedabad, Gujarat
| | - Chintan Dhebar
- Associate Consultant, Department of Critical Care Medicine, Zydus Hospital, Ahmedabad, Gujarat
| | - Kapildev Thakkar
- Associate Consultant, Department of Critical Care Medicine, Zydus Hospital, Ahmedabad, Gujarat
| | - Harsh Parikh
- Associate Consultant, Department of Critical Care Medicine, Zydus Hospital, Ahmedabad, Gujarat
| | - Aneet Patel
- Registar, Department of Critical Care Medicine, Zydus Hospital, Ahmedabad, Gujarat
| | - Arundhati Dileep
- PGY-3, Resident Internal Medicine Department, BronxCare Health System, Bronx, NY, USA
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Malik S, Parikh H, Shah N, Anand S, Gupta S. Non-invasive platform to estimate fasting blood glucose levels from salivary electrochemical parameters. Healthc Technol Lett 2019; 6:87-91. [PMID: 31531221 PMCID: PMC6718070 DOI: 10.1049/htl.2018.5081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/03/2019] [Indexed: 01/23/2023] Open
Abstract
Diabetes is a metabolic disorder that affects more than 400 million people worldwide. Most existing approaches for measuring fasting blood glucose levels (FBGLs) are invasive. This work presents a proof-of-concept study in which saliva is used as a proxy biofluid to estimate FBGL. Saliva collected from 175 volunteers was analysed using portable, handheld sensors to measure its electrochemical properties such as conductivity, redox potential, pH and K+, Na+ and Ca2+ ionic concentrations. These data, along with the person's gender and age, were trained and tested after casewise annotation with their true FBGL values using a set of mathematical algorithms. An accuracy of 87.4 ± 1.7% and a mean relative deviation of 14.1% (R2 = 0.76) was achieved using a mathematical algorithm. All parameters except the gender were found to play a key role in the FBGL determination process. Finally, the individual electrochemical sensors were integrated into a single platform and interfaced with the authors’ algorithm through a simple graphical user interface. The system was revalidated on 60 new saliva samples and gave an accuracy of 81.67 ± 2.53% (R2 = 0.71). This study paves the way for rapid, efficient and painless FBGL estimation from saliva.
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Affiliation(s)
- Sarul Malik
- Center for Biomedical Engineering, Indian Institute of Technology Delhi, India
| | - Harsh Parikh
- Department of Computer Science, Indian Institute of Technology Delhi, India
| | - Neil Shah
- Department of Computer Science, Indian Institute of Technology Delhi, India
| | - Sneh Anand
- Center for Biomedical Engineering, Indian Institute of Technology Delhi, India.,Department of Biomedical Engineering, All India Institute of Medical Science, New Delhi 110016, India
| | - Shalini Gupta
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas 110016, India
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Mehta M, Puntambekar S, Chitale M, Puntambekar S, Parikh H. Reconstruction of the Distal Ureter Following an Extensive Resection of Ureter for Stage IV Endometriosis. J Minim Invasive Gynecol 2017. [DOI: 10.1016/j.jmig.2017.08.242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
BACKGROUND The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interactions, however, they are highly time and resource intensive. Here, we present a novel algorithm designed for high throughput prediction of optimal zinc finger protein for 9 bp DNA sequences of choice. In accordance with the principles of information theory, a subset identified by using K-means clustering was used as a representative for the space of all possible 9 bp DNA sequences. The modeling and simulation results assuming synergistic mode of binding obtained from this subset were used to train an ensemble micro neural network. Synergistic mode of binding is the closest to the DNA-protein binding seen in nature, and gives much higher quality predictions, while the time and resources increase exponentially in the trade off. Our algorithm is inspired from an ensemble machine learning approach, and incorporates the predictions made by 100 parallel neural networks, each with a different hidden layer architecture designed to pick up different features from the training dataset to predict optimal zinc finger proteins for any 9 bp target DNA. RESULTS The model gave an accuracy of an average 83% sequence identity for the testing dataset. The BLAST e-value are well within the statistical confidence interval of E-05 for 100% of the testing samples. The geometric mean and median value for the BLAST e-values were found to be 1.70E-12 and 7.00E-12 respectively. For final validation of approach, we compared our predictions against optimal ZFPs reported in literature for a set of experimentally studied DNA sequences. The accuracy, as measured by the average string identity between our predictions and the optimal zinc finger protein reported in literature for a 9 bp DNA target was found to be as high as 81% for DNA targets with a consensus sequence GCNGNNGCN reported in literature. Moreover, the average string identity of our predictions for a catalogue of over 100 9 bp DNA for which the optimal zinc finger protein has been reported in literature was found to be 71%. CONCLUSIONS Validation with experimental data shows that our tool is capable of domain adaptation and thus scales well to datasets other than the training set with high accuracy. As synergistic binding comes the closest to the ideal mode of binding, our algorithm predicts biologically relevant results in sync with the experimental data present in the literature. While there have been disjointed attempts to approach this problem synergistically reported in literature, there is no work covering the whole sample space. Our algorithm allows designing zinc finger proteins for DNA targets of the user's choice, opening up new frontiers in the field of targeted genome editing. This algorithm is also available as an easy to use web server, ZifNN, at http://web.iitd.ac.in/~sundar/ZifNN/ .
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Affiliation(s)
- Shayoni Dutta
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Spandan Madan
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Harsh Parikh
- Department of Computer Science and Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016 India
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Parikh H, Bajaj P, Tripathy R, Pande A. Improving Properties of Recombinant SsoPox by Site-Specific Pegylation. Protein Pept Lett 2015; 22:1098-103. [DOI: 10.2174/0929866522666151002122751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 11/22/2022]
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Puntambekar SP, Sugoor D, Joshi G, Puntambekar SP, kumbhare S, Sharma V, Parikh H. Single Institutional Experience of 410 Cases of Type B & Type C (Querleu Morrow Classification) Laparoscopic Radical Hysterectomy. J Minim Invasive Gynecol 2015; 22:S91-S92. [DOI: 10.1016/j.jmig.2015.08.247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ekman C, Elgzyri T, Ström K, Almgren P, Parikh H, Dekker Nitert M, Rönn T, Manderson Koivula F, Ling C, Tornberg ÅB, Wollmer P, Eriksson KF, Groop L, Hansson O. Less pronounced response to exercise in healthy relatives to type 2 diabetic subjects compared with controls. J Appl Physiol (1985) 2015; 119:953-60. [PMID: 26338460 DOI: 10.1152/japplphysiol.01067.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 12/02/2014] [Accepted: 08/27/2015] [Indexed: 01/03/2023] Open
Abstract
Healthy first-degree relatives with heredity of type 2 diabetes (FH+) are known to have metabolic inflexibility compared with subjects without heredity for diabetes (FH-). In this study, we aimed to test the hypothesis that FH+ individuals have an impaired response to exercise compared with FH-. Sixteen FH+ and 19 FH- insulin-sensitive men similar in age, peak oxygen consumption (V̇o2 peak), and body mass index completed an exercise intervention with heart rate monitored during exercise for 7 mo. Before and after the exercise intervention, the participants underwent a physical examination and tests for glucose tolerance and exercise capacity, and muscle biopsies were taken for expression analysis. The participants attended, on average, 39 training sessions during the intervention and spent 18.8 MJ on exercise. V̇o2 peak/kg increased by 14%, and the participants lost 1.2 kg of weight and 3 cm waist circumference. Given that the FH+ group expended 61% more energy during the intervention, we used regression analysis to analyze the response in the FH+ and FH- groups separately. Exercise volume had a significant effect on V̇o2 peak, weight, and waist circumference in the FH- group, but not in the FH+ group. After exercise, expression of genes involved in metabolism, oxidative phosphorylation, and cellular respiration increased more in the FH- compared with the FH+ group. This suggests that healthy, insulin-sensitive FH+ and FH- participants with similar age, V̇o2 peak, and body mass index may respond differently to an exercise intervention. The FH+ background might limit muscle adaptation to exercise, which may contribute to the increased susceptibility to type 2 diabetes in FH+ individuals.
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Affiliation(s)
- C Ekman
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - T Elgzyri
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - K Ström
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden; Swedish Winter Sports Research Centre, Department of Health Sciences, Mid Sweden University, Östersund, Sweden
| | - P Almgren
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - H Parikh
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden; Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Marloes Dekker Nitert
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - T Rönn
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | | | - C Ling
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - Å B Tornberg
- Department of Health Sciences, Division of Physiotherapy, Lund University, Lund, Sweden; Genetic Molecular Epidemiology Unit, Lund University Diabetes Center, Clinical Research Centre, Malmö, Sweden; and
| | - P Wollmer
- Department of Health Sciences, Division of Physiotherapy, Lund University, Lund, Sweden; Department of Clinical Sciences, Clinical Physiology and Nuclear Medicine Unit, Lund University, Malmö, Sweden
| | - K F Eriksson
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - L Groop
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - O Hansson
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden;
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Parikh H, Singh A, Krishnamachari A, Shah K. Computational prediction of origin of replication in bacterial genomes using correlated entropy measure (CEM). Biosystems 2015; 128:19-25. [DOI: 10.1016/j.biosystems.2015.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 12/31/2014] [Accepted: 01/01/2015] [Indexed: 01/28/2023]
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Elgzyri T, Parikh H, Zhou Y, Dekker Nitert M, Rönn T, Segerström ÅB, Ling C, Franks PW, Wollmer P, Eriksson KF, Groop L, Hansson O. First-degree relatives of type 2 diabetic patients have reduced expression of genes involved in fatty acid metabolism in skeletal muscle. J Clin Endocrinol Metab 2012; 97:E1332-7. [PMID: 22547424 DOI: 10.1210/jc.2011-3037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
CONTEXT First-degree relatives of patients with type 2 diabetes (FH+) have been shown to have decreased energy expenditure and decreased expression of mitochondrial genes in skeletal muscle. In previous studies, it has been difficult to distinguish whether mitochondrial dysfunction and differential regulation of genes are primary (genetic) or due to reduced physical activity, obesity, or other correlated factors. OBJECTIVE The aim of this study was to investigate whether mitochondrial dysfunction is a primary defect or results from an altered metabolic state. DESIGN We compared gene expression in skeletal muscle from 24 male subjects with FH and 26 without FH matched for age, glucose tolerance, VO(2peak) (peak oxygen uptake), and body mass index using microarrays. Additionally, type fiber composition, mitochondrial DNA content, and citrate synthase activity were measured. The results were followed up in an additional cohort with measurements of in vivo metabolism. RESULTS FH+ vs. FH- subjects showed reduced expression of mitochondrial genes (P = 2.75 × 10(-6)), particularly genes involved in fatty acid metabolism (P = 4.08 × 10(-7)), despite similar mitochondrial DNA content. Strikingly, a 70% reduced expression of the monoamine oxidase A (MAOA) gene was found in FH+ vs. FH- individuals (P = 0.0009). Down-regulation of the genes involved in fat metabolism was associated with decreased in vivo fat oxidation and increased glucose oxidation examined in an additional cohort of elderly men. CONCLUSIONS These results suggest that genetically altered fatty acid metabolism predisposes to type 2 diabetes and propose a role for catecholamine-metabolizing enzymes like MAOA in the regulation of energy metabolism.
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Affiliation(s)
- T Elgzyri
- Department of Clinical Sciences, Clinical Research Center, Malmö University Hospital, Lund University, 20502 Malmö, Sweden
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Yazdan-Shahmorad A, Lehmkuhle MJ, Gage GJ, Marzullo TC, Parikh H, Miriani RM, Kipke DR. Estimation of electrode location in a rat motor cortex by laminar analysis of electrophysiology and intracortical electrical stimulation. J Neural Eng 2011; 8:046018. [PMID: 21690656 DOI: 10.1088/1741-2560/8/4/046018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
While the development of microelectrode arrays has enabled access to disparate regions of a cortex for neurorehabilitation, neuroprosthetic and basic neuroscience research, accurate interpretation of the signals and manipulation of the cortical neurons depend upon the anatomical placement of the electrode arrays in a layered cortex. Toward this end, this report compares two in vivo methods for identifying the placement of electrodes in a linear array spaced 100 µm apart based on in situ laminar analysis of (1) ketamine-xylazine-induced field potential oscillations in a rat motor cortex and (2) an intracortical electrical stimulation-induced movement threshold. The first method is based on finding the polarity reversal in laminar oscillations which is reported to appear at the transition between layers IV and V in laminar 'high voltage spindles' of the rat cortical column. Analysis of histological images in our dataset indicates that polarity reversal is detected 150.1 ± 104.2 µm below the start of layer V. The second method compares the intracortical microstimulation currents that elicit a physical movement for anodic versus cathodic stimulation. It is based on the hypothesis that neural elements perpendicular to the electrode surface are preferentially excited by anodic stimulation while cathodic stimulation excites those with a direction component parallel to its surface. With this method, we expect to see a change in the stimulation currents that elicits a movement at the beginning of layer V when comparing anodic versus cathodic stimulation as the upper cortical layers contain neuronal structures that are primarily parallel to the cortical surface and lower layers contain structures that are primarily perpendicular. Using this method, there was a 78.7 ± 68 µm offset in the estimate of the depth of the start of layer V. The polarity reversal method estimates the beginning of layer V within ±90 µm with 95% confidence and the intracortical stimulation method estimates it within ±69.3 µm. We propose that these methods can be used to estimate the in situ location of laminar electrodes implanted in the rat motor cortex.
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Affiliation(s)
- A Yazdan-Shahmorad
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, USA.
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Fassett DR, Rammos SK, Patel P, Parikh H, Couldwell WT. Intracranial subarachnoid hemorrhage resulting from cervical spine dural arteriovenous fistulas: literature review and case presentation. Neurosurg Focus 2009; 26:E4. [DOI: 10.3171/foc.2009.26.1.e4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cervical dural arteriovenous fistulas (dAVFs) are a rare cause of intracranial subarachnoid hemorrhage (SAH) but should be considered when other sources are not found. Subarachnoid hemorrhage caused by dAVF is thought to occur as a result of venous hypertension in most cases. The clinical presentation, acute onset of severe headache, is similar to that in patients with other causes of SAH; however, severe neurological deficits (Hunt and Hess Grade IV and V SAH) have not been reported in SAH caused by cervical dAVFs. Patients with this type of SAH commonly report suboccipital headache, neck pain, and nausea, and thus these hemorrhages can be easily dismissed as perimesencephalic SAH. Vigilant evaluation with 4-vessel cerebral angiography, including selective catherization of both proximal vertebral arteries, should be performed. The practice of unilateral vertebral artery injection with reflux into the contralateral vertebral and posterior inferior cerebellar arteries has the potential to overlook cervical dAVF. Magnetic resonance imaging may be useful to evaluate for other causes of SAH but is probably not sensitive for the identification of a cervical dAVF. Surgical treatment of this lesion has an excellent outcome.
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Affiliation(s)
| | | | - Pankti Patel
- 2University of Illinois College of Medicine atPeoria, Peoria, Illinois; and
| | - Harsh Parikh
- 2University of Illinois College of Medicine atPeoria, Peoria, Illinois; and
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Hirte HW, Raghunadharao D, Baetz T, Hotte S, Rajappa S, Iacobucci A, Sharma S, Parikh H, Kulkarni S, Patil S, Gaston S. A phase 1 study of the selective cyclin dependent kinase inhibitor P276–00 in patients with advanced refractory neoplasms. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.14117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
14117 Background: In human cancers, genetic and epigenetic events result in over-expression of cyclins or absence or diminished levels of Cdk inhibitors, providing tumor cells with selective growth advantage. This has prompted the development of pharmacological Cdk inhibitors that could potentially produce anti-tumor effect. P276–00 is a selective Cdk4-D1 and Cdk1-B inhibitor. This study was designed to determine the maximum tolerated dose (MTD), toxicity profile, pharmacokinetics, and antitumour activity of P276–00 given intravenously to patients with advanced refractory solid tumours. Methods: P276–00 was administered in escalating doses to cohorts of eligible patients (pts), starting with a dose of 9 mg/m2 as a 30 minute iv infusion day 1 to 5, and day 8 to 12, q 3 weekly. To date 22 pts have been entered on the study (cohort 1 - 4 pts at 9 mg/m2, cohort 2 - 4 pts at 12.6 mg/m2, cohort 3 - 6 pts at 17.6 mg/m2, cohort 4 - 8 pts at 24.6 mg/m2) with PS 0–2, and mean age of 56 years. Pharmacokinetic profiles were obtained on cycle 1 days 1 and 5. Skin biopsies were obtained immediately prior to starting study treatment and on day 21 of cycle 2 and will be analyzed for Ki67, cleaved caspase 3, phospho-Rb, cyclin D1 and cdk4, and microarray. Results: To date dose limiting toxicity has occurred in one pt. Grade 3 fatigue occurred in 1 pt at 17.6 mg/m2. The most common drug-related adverse events, which were all grade 1 or 2, were fatigue, nausea, hypotension, sweating, and dry mouth. No Grade 3 biochemical toxicities have been reported so far. There have been no responses noted to date. 4 pts have stable disease after 2 cycles. Pharmacokinetic results: The Cmax, t1/2, and AUC0–8 on day 1 were as follows: 9 mg/m2- 315 ng/mL, 6.6 hr, 883 ng.h/mL; 12.6 mg/m2- 402 ng/mL, 5.5 hr, 848 ng.h/mL; 17.6 mg/m2- 589 ng/mL, 5.3 hr, 1289 ng.h/mL; 24.6 mg/m2- 621 ng/mL, 5.6 hr, 1286 ng.h/mL. Conclusions: P276–00 is well tolerated, but grade 3 fatigue has been noted in 1 pt at 17.6 mg/m2 dose level. We have observed confirmed stable disease in one patient. PK results indicate that at 9 mg/m2,12.6 mg/m2, 17.6 mg/m2 and 24.6 mg/m2 we are able to cross the cdk4 enzyme IC50 approximately 10, 13, 19 and 20 times and cross the anti-proliferative IC50 1.1, 1.4, 2.1 and 2.2 times respectively. Accrual continues at the 34.4 mg/m2 dose level. No significant financial relationships to disclose.
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Affiliation(s)
- H. W. Hirte
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - D. Raghunadharao
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - T. Baetz
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Hotte
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Rajappa
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - A. Iacobucci
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Sharma
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - H. Parikh
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Kulkarni
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Patil
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Gaston
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
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Shaat N, Lernmark A, Karlsson E, Ivarsson S, Parikh H, Berntorp K, Groop L. A variant in the transcription factor 7-like 2 (TCF7L2) gene is associated with an increased risk of gestational diabetes mellitus. Diabetologia 2007; 50:972-9. [PMID: 17342473 DOI: 10.1007/s00125-007-0623-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [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] [Received: 10/24/2006] [Accepted: 01/21/2007] [Indexed: 12/18/2022]
Abstract
AIMS/HYPOTHESIS Genetic and epidemiological studies suggest an association between gestational diabetes mellitus and type 2 diabetes. Both are polygenic multifactorial disorders characterised by beta cell dysfunction and insulin resistance. Our aim was to investigate whether common genetic variants that have previously been associated with type 2 diabetes or related phenotypes would also confer risk for gestational diabetes mellitus. MATERIALS AND METHODS In 1,881 unrelated pregnant Scandinavian women (649 women with gestational diabetes mellitus, 1,232 non-diabetic control subjects) we genotyped the transcription factor 7-like 2 (TCF7L2 rs7903146), adiponectin (ADIPOQ +276G > T), peroxisome-proliferator activated receptor, gamma 2 (PPARG Pro12Ala), PPARG-coactivator, 1 alpha (PPARGC1A Gly482Ser), forkhead box C2 (FOXC2 -512C > T) and beta3-adrenergic receptor (ADRB3 Trp64Arg) polymorphisms using TaqMan allelic discrimination assay or RFLP. RESULTS The CC, CT and TT genotype frequencies of the TCF7L2 rs7903146 variant differed significantly between women with gestational diabetes mellitus and control women (46.3, 43.6 and 10.1% vs 58.5, 35.3 and 6.2%, p = 3.7 x 10(-6), corrected p value [Pc] for multiple testing Pc = 2.2 x 10(-5)). The T-allele was associated with an increased risk of gestational diabetes mellitus (odds ratio 1.49 [95% CI 1.28-1.75], p = 4.9 x 10(-7) [Pc = 2.8 x 10(-6)]). Compared with wild-type CC-genotype carriers, heterozygous (CT-genotype) and homozygous (TT-genotype) carriers had a 1.6-fold (95% CI 1.26-1.93, p = 3.7 x 10(-5) [Pc = 0.0002]) and a 2.1-fold (95% CI 1.41-2.99, p = 0.0001 [Pc = 0.0008]) increased risk of gestational diabetes mellitus, respectively. The other polymorphisms studied were not significantly associated with gestational diabetes mellitus (ADIPOQ +276G > T: 1.17 [1.01-1.36], p = 0.039 [Pc = 0.23]; PPARG Pro12Ala: 1.06 [0.87-1.29], p = 0.53; PPARGC1A Gly482Ser: 0.96 [0.83-1.10], p = 0.54; FOXC2 -512C > T: 1.01 [0.87-1.16], p = 0.94; and ADRB3 Trp64Arg: 1.22 [0.95-1.56], p = 0.12). CONCLUSIONS/INTERPRETATION The TCF7L2 rs7903146 variant is associated with an increased risk of gestational diabetes mellitus in Scandinavian women.
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Affiliation(s)
- N Shaat
- Department of Clinical Sciences/Diabetes & Endocrinology, Malmö University Hospital, Lund University, Malmö, Sweden.
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Wang L, Koynova R, Parikh H, MacDonald RC. Transfection activity of binary mixtures of cationic o-substituted phosphatidylcholine derivatives: the hydrophobic core strongly modulates physical properties and DNA delivery efficacy. Biophys J 2006; 91:3692-706. [PMID: 16935955 PMCID: PMC1630455 DOI: 10.1529/biophysj.106.092700] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [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: 11/18/2022] Open
Abstract
A combination of two cationic lipid derivatives having the same headgroup but tails of different chain lengths has been shown to have considerably different transfection activity than do the separate molecules. Such findings point to the importance of investigating the hydrophobic portions of cationic amphiphiles. Hence, we have synthesized a variety of cationic phosphatidylcholines with unusual hydrophobic moieties and have evaluated their transfection activity and that of their mixtures with the original molecule of this class, dioleoyl-O-ethylphosphatidylcholine (EDOPC). Four distinct relationships between transfection activity and composition of the mixture (plotted as percent of the new compound added to EDOPC) were found, namely: with a maximum or minimum; with a proportional change; or with essentially no change. Relevant physical properties of the lipoplexes were also examined; specifically, membrane fusion (by fluorescence resonance energy transfer between cationic and anionic lipids) and DNA unbinding (measured as accessibility of DNA to ethidium bromide by electrophoresis and by fluorescence resonance energy transfer between DNA and cationic lipid), both after the addition of negatively charged membrane lipids. Fusibility increased with increasing content of second cationic lipid, regardless of the transfection pattern. However, the extent of DNA unbinding after addition of negatively charged membrane lipids did correlate with extent of transfection. The phase behavior of cationic lipids per se as well as that of their mixtures with membrane lipids revealed structural differences that may account for and support the hypothesis that a membrane lipid-triggered, lamellar-->nonlamellar phase transition that facilitates DNA release is critical to efficient transfection by cationic lipids.
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Affiliation(s)
- Li Wang
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois, USA
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Shah MS, Shah DS, Tomar G, Parikh H, Shah J, Shah B. Radiological quiz - tuberous sclerosis. Indian J Radiol Imaging 2006. [DOI: 10.4103/0971-3026.29026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- MS Shah
- From the N.H.L. Municipal Medical College, Ahmedabad, India
| | - DS Shah
- From the N.H.L. Municipal Medical College, Ahmedabad, India
| | - G Tomar
- From the N.H.L. Municipal Medical College, Ahmedabad, India
| | - H Parikh
- From the N.H.L. Municipal Medical College, Ahmedabad, India
| | - J Shah
- From the N.H.L. Municipal Medical College, Ahmedabad, India
| | - B Shah
- From the N.H.L. Municipal Medical College, Ahmedabad, India
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Shaat N, Karlsson E, Lernmark A, Ivarsson S, Lynch K, Parikh H, Almgren P, Berntorp K, Groop L. Common variants in MODY genes increase the risk of gestational diabetes mellitus. Diabetologia 2006; 49:1545-51. [PMID: 16752173 DOI: 10.1007/s00125-006-0258-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [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] [Received: 01/06/2006] [Accepted: 02/28/2006] [Indexed: 12/18/2022]
Abstract
AIMS/HYPOTHESIS Impaired beta cell function is the hallmark of gestational diabetes mellitus (GDM) and MODY. In addition, women with MODY gene mutations often present with GDM, but it is not known whether common variants in MODY genes contribute to GDM. SUBJECTS AND METHODS We genotyped five common variants in the glucokinase (GCK, commonly known as MODY2), hepatocyte nuclear factor 1-alpha (HNF1A, commonly known as MODY3) and 4-alpha (HNF4A commonly known as MODY1) genes in 1,880 Scandinavian women (648 women with GDM and 1,232 pregnant non-diabetic control women). RESULTS The A allele of the GCK -30G-->A polymorphism was more common in GDM women than in control subjects (odds ratio [OR] 1.28 [95% CI 1.06-1.53], p=0.008, corrected p value, p=0.035). Under a recessive model [AA vs GA+GG], the OR increased further to 2.12 (95% CI 1.21-3.72, p=0.009). The frequency of the L allele of the HNF1A I27L polymorphism was slightly higher in GDM than in controls (1.16 [95% CI 1.001-1.34], p=0.048, corrected p value, p=0.17). However, the OR increased under a dominant model (LL+IL vs II; 1.31 [95% CI 1.08-1.60], p=0.007). The rs2144908, rs2425637 and rs1885088 variants, which are located downstream of the primary beta cell promoter (P2) of HNF4A, were not associated with GDM. CONCLUSIONS/INTERPRETATION The -30G-->A polymorphism of the beta-cell-specific promoter of GCK and the I27L polymorphism of HNF1A seem to increase the risk of GDM in Scandinavian women.
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Affiliation(s)
- N Shaat
- Department of Clinical Sciences/Diabetes and Endocrinology, Malmö University Hospital, Lund University, Malmö, Sweden.
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Daum RS, Zenko CE, Given GZ, Ballanco GA, Parikh H, Germino K. Magnitude of interference after diphtheria-tetanus toxoids-acellular pertussis/Haemophilus influenzae type b capsular polysaccharide-tetanus vaccination is related to the number of doses administered. J Infect Dis 2001; 184:1293-9. [PMID: 11679918 DOI: 10.1086/324007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/31/2001] [Indexed: 11/04/2022] Open
Abstract
We compared the antibody response to Haemophilus influenzae type b capsular polysaccharide (PRP) after 1, 2, or 3 doses of a diphtheria-tetanus toxoids-acellular pertussis (DTaP) vaccine combined with a PRP-tetanus conjugate (PRP-T) vaccine, followed by separate injections of DTaP and PRP-T vaccines for the last 1 or 2 doses. Healthy infants were recruited from pediatric practices and were immunized according to recommended schedules. A significant decrease in the mean anti-PRP (from 5.25 to 2.68 microg/mL) and anti-tetanus toxoid antibody responses (from 0.13 to 0.09 Eq/mL) was observed as the number of doses of the DTaP/PRP-T combination vaccine increased (P<.02 and P=.01, respectively). In contrast, the mean anti-diphtheria toxoid antibody response increased with increasing numbers of DTaP/PRP-T doses (P=.0001). The effects of interference were not eliminated by the completion of the primary series with 1 or 2 doses of the DTaP and PRP-T vaccines given separately.
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Affiliation(s)
- R S Daum
- Department of Pediatrics, Section of Infectious Diseases and General Pediatrics, University of Chicago, Chicago, IL 60637, USA.
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Ray SD, Parikh H, Hickey E, Bagchi M, Bagchi D. Differential effects of IH636 grape seed proanthocyanidin extract and a DNA repair modulator 4-aminobenzamide on liver microsomal cytochrome 4502E1-dependent aniline hydroxylation. Mol Cell Biochem 2001; 218:27-33. [PMID: 11330834 DOI: 10.1023/a:1007272611915] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [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: 11/12/2022]
Abstract
Previous studies from our laboratories have linked the protective abilities of IH636 grape seed proanthocyanidin extract (GSPE) with inactivation of anti-apoptotic gene bcl-XL, and modification of several other critical molecular targets such as DNA-damage/DNA-repair, lipid peroxidation and intracellular Ca2+ homeostasis. Especially, GSPE provided dramatic protection against acetaminophen (APAP)-induced hepatotoxicity, significantly increased bcl-XL expression in the liver, and antagonized both necrotic and apoptotic deaths of liver cells in vivo. However, it was not clear from this study whether anti-apoptogenic and anti-necrotic effects of GSPE were: (i) due to its interference with endonuclease activity, (ii) due to its antioxidant effect, or, (iii) due to its ability to inhibit microsomal drug metabolizing enzyme(s), such as CYP-4502E1. Since CYP-4502E1 primarily metabolizes acetaminophen in mice and rats, this study specifically focused on CYP-4502E1's catalytic activity in vitro. Overall this investigation compared the in vitro aniline hydroxylation patterns of: (i) in vivo GSPE-exposed and unexposed (control) mouse liver microsomes, (ii) induced (1% acetone in drinking water for 3 days) and uninduced rat liver microsomes in the presence and absence of GSPE in vitro, and (iii) control rat liver microsomes in the presence of an anti-APAP agent 4-aminobenzamide (4-AB) in vitro. For the in vivo assessment, male B6C3F1 mice were fed GSPE diet (ADI 100 mg/kg body wt) for 4 weeks, and liver microsomes were isolated from both control and GSPE-fed mice for aniline hydroxylation, a specific marker of CYP-4502E1 activity. Data show that hydroxylation was 40% less in microsomes from GSPE-exposed livers compared to control microsomes. Similarly, when rat liver microsomes were incubated with various concentrations of GSPE in vitro (100 and 250 microg/ml), aniline hydroxylation was inhibited to various degrees (uninduced: 40 and 60% and induced: 25 and 50%, respectively with 100 and 250 microg/ml). Influence of GSPE on hydroxylation patterns were compared with another hepatoprotective agent 4-aminobenzamide (4-AB), a well-known modulator of nuclear enzyme poly(ADP-ribose) polymerase, and the data shows that 4-AB did not alter aniline hydroxylation at all. Collectively, these results may suggest that GSPE has the ability to inhibit CYP-4502E1, and this is an additional cytoprotective attribute, in conjunction with its novel antioxidant and/or antiendonucleolytic potential.
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Affiliation(s)
- S D Ray
- Department of Pharmacology, Toxicology and Medicinal Chemistry, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York 11201, USA.
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Daum RS, Zenko CE, Given GZ, Ballanco GA, Parikh H, Vidor E, Liu X. Absence of a significant interaction between a Haemophilus influenzae conjugate vaccine combined with a diphtheria toxoid, tetanus toxoid and acellular pertussis vaccine in the same syringe and inactivated polio vaccine. Pediatr Infect Dis J 2000; 19:710-7. [PMID: 10959738 DOI: 10.1097/00006454-200008000-00008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND We compared the antibody response to Haemophilus influenzae type b capsular polysaccharide (PRP) after three doses of a diphtheria toxoid, tetanus toxoid and acellular pertussis vaccine (DTaP) combined with a PRP-tetanus conjugate (PRP-T) in infants randomized to receive oral polio vaccine (OPV) or inactivated polio vaccine (IPV). The polio vaccine was given separately at the same visit. METHODS Three hundred fifty-six infants from pediatric practices in suburban Chicago and New Orleans were randomized into two groups. Group A received OPV at 2 and 4 months of age; Group B received IPV at 2 and 4 months of age. Both groups received DTaP/PRP-T at 2, 4 and 6 months of age and hepatitis B vaccine at 2 and 4 months of age. A serum sample was obtained before immunization (age 2 months) and 1 month after 3 doses of DTaP/PRP-T (age 7 months). Sera were assayed for antibody responses to all relevant vaccine antigens. RESULTS No significant vaccine antigen interference was found when polio immunization was provided by IPV or OPV for anti-PRP, diphtheria, tetanus or pertussis antibodies. OPV recipients had a significantly higher mean antibody response to serotype 1 (P = 0.03) and 2 (P = 0.0001) poliovirus. CONCLUSION Whether polio immunization was accomplished with IPV or OPV did not significantly influence the antibody responses in sera obtained at 7 months of age for anti-PRP, anti-diphtheria and anti-tetanus toxoid antibodies and antibodies to pertussis antigens, when DTaP/PRP-T was given in the primary series.
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Affiliation(s)
- R S Daum
- Department of Pediatric Infectious Diseases, The University of Chicago, IL, USA
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Parikh H, Lesseps A. Incrustation of the thread of an intrauterine contraceptive device. J OBSTET GYNAECOL 2000; 20:439-40. [PMID: 15512616 DOI: 10.1080/01443610050112255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- H Parikh
- Department of Obstetrics and Gynaecology, Gravesend and North Kent Hospital, UK.
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Abstract
The genomic sequence of Hoxa-7 (encoding the HOXa-7 homeobox protein), including the coding region (0.7 kb), flanked by a 5'-upstream region (2.8 kb), a 3'-downstream region (1 kb) and interrupted by an intron (995 bp), was determined. Northern blot analysis indicated the transcript size of Hoxa-7 to be 2.1-2.4 kb. Reverse transcription-PCR and primer extension analysis established the 5'-boundary of the mRNA to be in the region 1166 nt upstream from the start codon. Transient transfection of various Hoxa-7::cat constructs in NIH 3T3 cells was used to characterize the transcriptional activity of the 5'-flanking region of the gene. Constructs containing 544, 274 and 71 bp of the region upstream from the transcription start point (tsp) exhibited 78, 203 and 407%, respectively, of the activity shown by a control construct containing 739 bp of the upstream region. These data suggested the presence of negative regulatory elements in the region from 544 to 71 bp upstream from the tsp.
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Affiliation(s)
- H Parikh
- Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
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Halal F, Chitayat D, Parikh H, Rosenblatt B, Tranchemontagne J, Vekemans M, Potier M. Ring chromosome 20 and possible assignment of the structural gene encoding human carboxypeptidase-L to the distal segment of the long arm of chromosome 20. Am J Med Genet 1992; 43:576-9. [PMID: 1605251 DOI: 10.1002/ajmg.1320430314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We report on a 14-year-old boy with ring chromosome 20. Clinical manifestations included postnatal growth retardation, epilepsy, microcephaly, behaviour disorder, minor facial anomalies, small sella turcica, possible partial growth hormone deficiency, and mental retardation. A decreased activity of enzyme carboxypeptidase-L/protective protein (CP/PP) in cultured fibroblasts was demonstrated in our patient and a patient with a karyotype 46,XY,-14, + der(14)t(14;20)(14pter----14q32.3::20q13.1----20qter)m at. This suggests possible assignment of the CP/PP gene to the distal segment of 20q.
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Affiliation(s)
- F Halal
- Department of Pediatrics, Hôpital Ste-Justine, Université de Montréal, Quebec, Canada
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