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Lee D, Nayak S, Martin SW, Heatherington AC, Vicini P, Hua F. A quantitative systems pharmacology model of blood coagulation network describes in vivo biomarker changes in non-bleeding subjects. J Thromb Haemost 2016; 14:2430-2445. [PMID: 27666750 DOI: 10.1111/jth.13515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 09/01/2016] [Indexed: 01/03/2023]
Abstract
Essentials Baseline coagulation activity can be detected in non-bleeding state by in vivo biomarker levels. A detailed mathematical model of coagulation was developed to describe the non-bleeding state. Optimized model described in vivo biomarkers with recombinant activated factor VII treatment. Sensitivity analysis predicted prothrombin fragment 1 + 2 and D-dimer are regulated differently. SUMMARY Background Prothrombin fragment 1 + 2 (F1 + 2 ), thrombin-antithrombin III complex (TAT) and D-dimer can be detected in plasma from non-bleeding hemostatically normal subjects or hemophilic patients. They are often used as safety or pharmacodynamic biomarkers for hemostatis-modulating therapies in the clinic, and provide insights into in vivo coagulation activity. Objectives To develop a quantitative systems pharmacology (QSP) model of the blood coagulation network to describe in vivo biomarkers, including F1 + 2 , TAT, and D-dimer, under non-bleeding conditions. Methods The QSP model included intrinsic and extrinsic coagulation pathways, platelet activation state-dependent kinetics, and a two-compartment pharmacokinetics model for recombinant activated factor VII (rFVIIa). Literature data on F1 + 2 and D-dimer at baseline and changes with rFVIIa treatment were used for parameter optimization. Multiparametric sensitivity analysis (MPSA) was used to understand key proteins that regulate F1 + 2 , TAT and D-dimer levels. Results The model was able to describe tissue factor (TF)-dependent baseline levels of F1 + 2 , TAT and D-dimer in a non-bleeding state, and their increases in hemostatically normal subjects and hemophilic patients treated with different doses of rFVIIa. The amount of TF required is predicted to be very low in a non-bleeding state. The model also predicts that these biomarker levels will be similar in hemostatically normal subjects and hemophilic patients. MPSA revealed that F1 + 2 and TAT levels are highly correlated, and that D-dimer is more sensitive to the perturbation of coagulation protein concentrations. Conclusions A QSP model for non-bleeding baseline coagulation activity was established with data from clinically relevant in vivo biomarkers at baseline and changes in response to rFVIIa treatment. This model will provide future mechanistic insights into this system.
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Satyam L, Poddutoori R, Mukherjee S, Marappan S, Gopinath S, Pothuganti M, Nayak S, Kaza L, Nandish C, Amith A, Ravindra M, Nagaraju A, Antony T, Pandit C, Chelur S, Daginakatte G, Samajdar S, Ramachandra M. Potent and selective inhibition of CDK7 by novel covalent inhibitors. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32978-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nayak S, Lenka PK, Equebal A, Biswas A. Custom-made silicone hand prosthesis: A case study. HAND SURGERY & REHABILITATION 2016; 35:299-303. [PMID: 27781997 DOI: 10.1016/j.hansur.2016.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/16/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
Up to now, a cosmetic glove was the most common method for managing transmetacarpal (TMC) and carpometacarpal (CMC) amputations, but it is devoid of markings and body color. At this amputation level, it is very difficult to fit a functional prosthesis because of the short available length, unsightly shape, grafted skin, contracture and lack of functional prosthetic options. A 30-year-old male came to our clinic with amputation at the 1st to 4th carpometacarpal level and a 5th metacarpal that was projected laterally and fused with the carpal bone. The stump had grafted skin, redness, and an unhealed suture line. He complained of pain projected over the metacarpal and suture area. The clinical team members decided to fabricate a custom-made silicone hand prosthesis to accommodate the stump, protect the grafted skin, improve the hand's appearance and provide some passive function. The custom silicone hand prosthesis was fabricated with modified flexible wires to provide passive interphalangeal movement. Basic training, care and maintenance instructions for the prosthesis were given to the patient. The silicone hand prosthesis was able to restore the appearance of the lost digits and provide some passive function. His pain (VAS score) was reduced. Improvement in activities of daily living was found in the DASH questionnaire and Jebsen-Taylor Hand Function test. A silicone glove is a good option for more distal amputations, as it can accommodate any deformity, protect the skin, enhance the appearance and provide functional assistance. This case study provides a simple method to get passively movable fingers after proximal hand amputation.
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Patra S, Nayak S, Pradhan S, Bara D, Sarangi C, Mohapatra C. Multiple variations in the external features of a single cadaveric liver – A case report. J ANAT SOC INDIA 2016. [DOI: 10.1016/j.jasi.2016.08.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Gurawalia J, Nayak S. 529. Retrospective study of modified video-endoscopic versus open inguinal lymphadenectomy. Eur J Surg Oncol 2016. [DOI: 10.1016/j.ejso.2016.06.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Nayak S, Chakraverty S. Numerical solution of fuzzy stochastic differential equation. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2016. [DOI: 10.3233/ifs-162168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kumar M, Ghosh S, Nayak S, Das A. Recent advances in biosensor based diagnosis of urinary tract infection. Biosens Bioelectron 2016; 80:497-510. [DOI: 10.1016/j.bios.2016.02.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/06/2016] [Accepted: 02/08/2016] [Indexed: 12/16/2022]
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Nayak S, Siddiqui JK, Varner JD. Modelling and analysis of an ensemble of eukaryotic translation initiation models. IET Syst Biol 2016; 5:2. [PMID: 21261397 DOI: 10.1049/iet-syb.2009.0065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Programmed protein synthesis plays an important role in the cell cycle. Deregulated translation has been observed in several cancers. In this study, the authors constructed an ensemble of mathematical models describing the integration of growth factor signals with translation initiation. Using these models, the authors estimated critical structural features of the translation architecture. Sensitivity and robustness analysis with and without growth factors suggested that a balance between competing regulatory programmes governed translation initiation. Proteins such as Akt and mTor promoted initiation by integrating growth factor signals with the assembly of the 80S initiation complex. However, negative regulators such as PTEN and 4EBP1 restrained initiation in the absence of stimulation. Other proteins such as eIF4E were also found to be structurally critical as deletion of amplification of these components resulted in a network incapable of nominal operation. These findings could help understand the molecular basis of translation deregulation observed in cancer and perhaps lead to new anti-cancer therapeutic strategies. [Includes supplementary material].
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Ahmed A, Nayak S, Babu S, Vyakarnam A. Impact of Type I IFN dysregulation in M. tuberculosis infection on T cell responses. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.02.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Dangre G, Mudey A, Tankhiwale N, Nayak S. Point surveillance of staphylococcus aureus nasal carriage among health care workers in rural tertiary care center of Central India. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.02.612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Makroo R, Nayak S, Chowdhry M, Jasuja S, Sagar G, Rosamma N, Thakur U. Role of therapeutic plasma exchange in reducing ABO titers in patients undergoing ABO-incompatible renal transplant. APOLLO MEDICINE 2016. [DOI: 10.1016/j.apme.2016.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Nayak S, Chakraverty S. Numerical Solution of Stochastic Point-Kinetics Neutron Equation with Fuzzy Parameters. NUCL TECHNOL 2016. [DOI: 10.13182/nt15-63] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Selvakumar R, Chase S, Thomas JK, Kota A, Nayak S. Idiopathic Spontaneous Intraperitoneal Haemorrhage - a rare initial presentation of Haemophilia B. ACTA ACUST UNITED AC 2016; 37:75-6. [PMID: 29668189 DOI: 10.7869/tg.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ghosh SB, Bhattacharya K, Nayak S, Mukherjee P, Salaskar D, Kale SP. Identification of different species of Bacillus isolated from Nisargruna Biogas Plant by FTIR, UV-Vis and NIR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 148:420-426. [PMID: 25930088 DOI: 10.1016/j.saa.2015.03.104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 03/13/2015] [Accepted: 03/27/2015] [Indexed: 06/04/2023]
Abstract
Definitive identification of microorganisms, including pathogenic and non-pathogenic bacteria, is extremely important for a wide variety of applications including food safety, environmental studies, bio-terrorism threats, microbial forensics, criminal investigations and above all disease diagnosis. Although extremely powerful techniques such as those based on PCR and microarrays exist, they require sophisticated laboratory facilities along with elaborate sample preparation by trained researchers. Among different spectroscopic techniques, FTIR was used in the 1980s and 90s for bacterial identification. In the present study five species of Bacillus were isolated from the aerobic predigester chamber of Nisargruna Biogas Plant (NBP) and were identified to the species level by biochemical and molecular biological (16S ribosomal DNA sequence) methods. Those organisms were further checked by solid state spectroscopic absorbance measurements using a wide range of electromagnetic radiation (wavelength 200 nm to 25,000 nm) encompassing UV, visible, near Infrared and Infrared regions. UV-Vis and NIR spectroscopy was performed on dried bacterial cell suspension on silicon wafer in specular mode while FTIR was performed on KBr pellets containing the bacterial cells. Consistent and reproducible species specific spectra were obtained and sensitivity up to a level of 1000 cells was observed in FTIR with a DTGS detector. This clearly shows the potential of solid state spectroscopic techniques for simple, easy to implement, reliable and sensitive detection of bacteria from environmental samples.
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Patra S, Mohapatra C, Sarangi C, Biswal R, Panda M, Pradhan S, Bara D, Nayak S. Incidence of accessory mandibular foramen and its clinical significance. J ANAT SOC INDIA 2015. [DOI: 10.1016/j.jasi.2015.07.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Nayak S. O-002 developing an interventional stroke service: improving clinical outcomes and reducing cost and delivering great cost saving benefits to health economy. J Neurointerv Surg 2015. [DOI: 10.1136/neurintsurg-2015-011917.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nayak S, Leung V, Woo T, Sastry A. E-067 management of tandem intracranial and extracranial occlusion causing hyper acute ischemic stroke with extracranial cervical stenting in conjunction with mechanical thrombectomy. J Neurointerv Surg 2015. [DOI: 10.1136/neurintsurg-2015-011917.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nayak S, Sastry A, Leung V, Roffe C, Woo T. E-065 differences in clinical, radiological and interventional factors predicting outcome and mortality after mechanical thrombectomy for acute large vessel stroke comparing over and under 70 age groups - a five year retrospective study. J Neurointerv Surg 2015. [DOI: 10.1136/neurintsurg-2015-011917.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Nayak S, Lally F, Soorani M, Jadun C, Yang Y, McCrudden J, Naire S, Roffe C. E-066 in vitroexperiments of cerebral blood flow during aspiration thrombectomy. J Neurointerv Surg 2015. [DOI: 10.1136/neurintsurg-2015-011917.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nayak S, Lee D, Patel-Hett S, Pittman DD, Martin SW, Heatherington AC, Vicini P, Hua F. Using a Systems Pharmacology Model of the Blood Coagulation Network to Predict the Effects of Various Therapies on Biomarkers. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2015; 4:396-405. [PMID: 26312163 PMCID: PMC4544053 DOI: 10.1002/psp4.50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/23/2015] [Indexed: 01/09/2023]
Abstract
A number of therapeutics have been developed or are under development aiming to modulate the coagulation network to treat various diseases. We used a systems model to better understand the effect of modulating various components on blood coagulation. A computational model of the coagulation network was built to match in-house in vitro thrombin generation and activated Partial Thromboplastin Time (aPTT) data with various concentrations of recombinant factor VIIa (FVIIa) or factor Xa added to normal human plasma or factor VIII-deficient plasma. Sensitivity analysis applied to the model revealed that lag time, peak thrombin concentration, area under the curve (AUC) of the thrombin generation profile, and aPTT show different sensitivity to changes in coagulation factors' concentrations and type of plasma used (normal or factor VIII-deficient). We also used the model to explore how variability in concentrations of the proteins in coagulation network can impact the response to FVIIa treatment.
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Nayak S, Edwards DL, Saleh AA, Greenspan SL. Systematic review and meta-analysis of the performance of clinical risk assessment instruments for screening for osteoporosis or low bone density. Osteoporos Int 2015; 26:1543-54. [PMID: 25644147 PMCID: PMC4401628 DOI: 10.1007/s00198-015-3025-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 01/02/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED We performed a systematic review and meta-analysis of the performance of clinical risk assessment instruments for screening for DXA-determined osteoporosis or low bone density. Commonly evaluated risk instruments showed high sensitivity approaching or exceeding 90% at particular thresholds within various populations but low specificity at thresholds required for high sensitivity. Simpler instruments, such as OST, generally performed as well as or better than more complex instruments. INTRODUCTION The purpose of the study is to systematically review the performance of clinical risk assessment instruments for screening for dual-energy X-ray absorptiometry (DXA)-determined osteoporosis or low bone density. METHODS Systematic review and meta-analysis were performed. Multiple literature sources were searched, and data extracted and analyzed from included references. RESULTS One hundred eight references met inclusion criteria. Studies assessed many instruments in 34 countries, most commonly the Osteoporosis Self-Assessment Tool (OST), the Simple Calculated Osteoporosis Risk Estimation (SCORE) instrument, the Osteoporosis Self-Assessment Tool for Asians (OSTA), the Osteoporosis Risk Assessment Instrument (ORAI), and body weight criteria. Meta-analyses of studies evaluating OST using a cutoff threshold of <1 to identify US postmenopausal women with osteoporosis at the femoral neck provided summary sensitivity and specificity estimates of 89% (95%CI 82-96%) and 41% (95%CI 23-59%), respectively. Meta-analyses of studies evaluating OST using a cutoff threshold of 3 to identify US men with osteoporosis at the femoral neck, total hip, or lumbar spine provided summary sensitivity and specificity estimates of 88% (95%CI 79-97%) and 55% (95%CI 42-68%), respectively. Frequently evaluated instruments each had thresholds and populations for which sensitivity for osteoporosis or low bone mass detection approached or exceeded 90% but always with a trade-off of relatively low specificity. CONCLUSIONS Commonly evaluated clinical risk assessment instruments each showed high sensitivity approaching or exceeding 90% for identifying individuals with DXA-determined osteoporosis or low BMD at certain thresholds in different populations but low specificity at thresholds required for high sensitivity. Simpler instruments, such as OST, generally performed as well as or better than more complex instruments.
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Thota S, Narang V, Nayak S, Sambasivam S, Choi BC, Sarkar T, Andersson MS, Mathieu R, Seehra MS. On the nature of magnetic state in the spinel Co₂SnO₄. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:166001. [PMID: 25817434 DOI: 10.1088/0953-8984/27/16/166001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the spinel Co2SnO4, coexistence of ferrimagnetic ordering below T(N) ≃ 41 K followed by a spin glass state below T(SG) ≃ 39 K was proposed recently based on the temperature dependence of magnetization M(T) data. Here new measurements of the temperature dependence of the specific heat C(P)(T), ac-susceptibilities χ'(T) and χ″(T) measured at frequencies between 0.51 and 1.2 kHz, and the hysteresis loop parameters (coercivity H(C)(T) and remanence M(R)(T)) in two differently prepared samples of Co2SnO4 are reported. The presence of the Co(2+) and Sn(4+) states is confirmed by x-ray photoelectron spectroscopy (XPS) yielding the structure: Co2SnO4 = [Co(2+)][Co(2+)Sn(4+)]O4. The data of C(P) versus T shows only an inflection near 39 K characteristic of spin-glass ordering. The analysis of the frequency dependence of ac-magnetic susceptibility data near 39 K using the Vogel-Fulcher law and the power-law of the critical slowing-down suggests the presence of spin clusters in the system which is close to a spin-glass state. With a decrease in temperature below 39 K, the temperature dependence of the coercivity H(C) and remanence M(R) for the zero-field cooled samples show both H(C) and M(R) reaching their peak magnitudes near 25 K, then decreasing with decreasing T and becoming negligible below 15 K. The plot of C(P)/T versus T also yields a weak inflection near 15 K. This temperature dependence of H(C) and remanence M(R) is likely associated with the different magnitudes of the magnetic moments of Co(2+) ions on the 'A' and 'B' sites and their different temperature dependence.
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Nayak S, Chakraverty S. Fuzzy finite element analysis of multi-group neutron diffusion equation with imprecise parameters. ACTA ACUST UNITED AC 2015. [DOI: 10.1504/ijnest.2015.067801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Orton L, Pennington A, Nayak S, Whitehead M, Petticrew M, White M, Sowden A. The health inequalities impact of low control in the living environment: a theory-led systematic review of observational studies. Eur J Public Health 2014. [DOI: 10.1093/eurpub/cku162.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Panja S, Nayak S, Ghosh SK, Selvakumar M, Chattopadhyay S. Self-assembly of a biodegradable branched PE-PCL-b-PEC amphiphilic polymer: synthesis, characterization and targeted delivery of doxorubicin to cancer cells. RSC Adv 2014. [DOI: 10.1039/c4ra08351b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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