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Shankar SS, Rai A, Ahmad A, Sastry M. Rapid synthesis of Au, Ag, and bimetallic Au core-Ag shell nanoparticles using Neem (Azadirachta indica) leaf broth. J Colloid Interface Sci 2004; 275:496-502. [PMID: 15178278 DOI: 10.1016/j.jcis.2004.03.003] [Citation(s) in RCA: 1174] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2003] [Accepted: 03/04/2004] [Indexed: 11/27/2022]
Abstract
We report on the use of Neem (Azadirachta indica) leaf broth in the extracellular synthesis of pure metallic silver and gold nanoparticles and bimetallic Au/Ag nanoparticles. On treatment of aqueous solutions of silver nitrate and chloroauric acid with Neem leaf extract, the rapid formation of stable silver and gold nanoparticles at high concentrations is observed to occur. The silver and gold nanoparticles are polydisperse, with a large percentage of gold particles exhibiting an interesting flat, platelike morphology. Competitive reduction of Au3+ and Ag+ ions present simultaneously in solution during exposure to Neem leaf extract leads to the synthesis of bimetallic Au core-Ag shell nanoparticles in solution. Transmission electron microscopy revealed that the silver nanoparticles are adsorbed onto the gold nanoparticles, forming a core-shell structure. The rates of reduction of the metal ions by Neem leaf extract are much faster than those observed by us in our earlier studies using microorganisms such as fungi, highlighting the possibility that nanoparticle biological synthesis methodologies will achieve rates of synthesis comparable to those of chemical methods.
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21 |
1174 |
2
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Shankar SS, Rai A, Ankamwar B, Singh A, Ahmad A, Sastry M. Biological synthesis of triangular gold nanoprisms. NATURE MATERIALS 2004; 3:482-8. [PMID: 15208703 DOI: 10.1038/nmat1152] [Citation(s) in RCA: 802] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 04/21/2004] [Indexed: 05/20/2023]
Abstract
The optoelectronic and physicochemical properties of nanoscale matter are a strong function of particle size. Nanoparticle shape also contributes significantly to modulating their electronic properties. Several shapes ranging from rods to wires to plates to teardrop structures may be obtained by chemical methods; triangular nanoparticles have been synthesized by using a seeded growth process. Here, we report the discovery that the extract from the lemongrass plant, when reacted with aqueous chloroaurate ions, yields a high percentage of thin, flat, single-crystalline gold nanotriangles. The nanotriangles seem to grow by a process involving rapid reduction, assembly and room-temperature sintering of 'liquid-like' spherical gold nanoparticles. The anisotropy in nanoparticle shape results in large near-infrared absorption by the particles, and highly anisotropic electron transport in films of the nanotriangles.
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21 |
802 |
3
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Shankar SS, Ahmad A, Sastry M. Geranium leaf assisted biosynthesis of silver nanoparticles. Biotechnol Prog 2003; 19:1627-31. [PMID: 14656132 DOI: 10.1021/bp034070w] [Citation(s) in RCA: 494] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Development of biologically inspired experimental processes for the synthesis of nanoparticles is evolving into an important branch of nanotechnology. In this paper, we report on the use of Geranium (Pelargonium graveolens) leaf extract in the extracellular synthesis of silver nanoparticles. On treating aqueous silver nitrate solution with geranium leaf extract, rapid reduction of the silver ions is observed leading to the formation of highly stable, crystalline silver nanoparticles in solution. Transmission electron microscopy analysis of the silver particles indicated that they ranged in size from 16 to 40 nm and were assembled in solution into quasilinear superstructures. The rate of reduction of the silver ions by the geranium leaf extract is faster than that observed by us in an earlier study using a fungus, Fusarium oxysporum, thus highlighting the possibility that nanoparticle biosynthesis methodologies will achieve rates of synthesis comparable to those of chemical methods. This study also represents an important advance in the use of plants over microorganisms in the biosynthesis of metal nanoparticles.
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Comparative Study |
22 |
494 |
4
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Chinnaiyan AM, Prasad U, Shankar S, Hamstra DA, Shanaiah M, Chenevert TL, Ross BD, Rehemtulla A. Combined effect of tumor necrosis factor-related apoptosis-inducing ligand and ionizing radiation in breast cancer therapy. Proc Natl Acad Sci U S A 2000; 97:1754-9. [PMID: 10677530 PMCID: PMC26508 DOI: 10.1073/pnas.030545097] [Citation(s) in RCA: 384] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potent endogenous activator of the cell death pathway and functions by activating the cell surface death receptors 4 and 5 (DR4 and DR5). TRAIL is nontoxic in vivo and preferentially kills neoplastically transformed cells over normal cells by an undefined mechanism. Radiotherapy is a common treatment for breast cancer as well as many other cancers. Here we demonstrate that ionizing radiation can sensitize breast carcinoma cells to TRAIL-induced apoptosis. This synergistic effect is p53-dependent and may be the result of radiation-induced up-regulation of the TRAIL-receptor DR5. Importantly, TRAIL and ionizing radiation have a synergistic effect in the regression of established breast cancer xenografts. Changes in tumor cellularity and extracellular space were monitored in vivo by diffusion-weighted magnetic resonance imaging (diffusion MRI), a noninvasive technique to produce quantitative images of the apparent mobility of water within a tissue. Increased water mobility was observed in combined TRAIL- and radiation-treated tumors but not in tumors treated with TRAIL or radiation alone. Histological analysis confirmed the loss of cellularity and increased numbers of apoptotic cells in TRAIL- and radiation-treated tumors. Taken together, our results provide support for combining radiation with TRAIL to improve tumor eradication and suggest that efficacy of apoptosis-inducing cancer therapies may be monitored noninvasively, using diffusion MRI.
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research-article |
25 |
384 |
5
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Hatridge M, Shankar S, Mirrahimi M, Schackert F, Geerlings K, Brecht T, Sliwa KM, Abdo B, Frunzio L, Girvin SM, Schoelkopf RJ, Devoret MH. Quantum back-action of an individual variable-strength measurement. Science 2013; 339:178-81. [PMID: 23307736 DOI: 10.1126/science.1226897] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Measuring a quantum system can randomly perturb its state. The strength and nature of this back-action depend on the quantity that is measured. In a partial measurement performed by an ideal apparatus, quantum physics predicts that the system remains in a pure state whose evolution can be tracked perfectly from the measurement record. We demonstrated this property using a superconducting qubit dispersively coupled to a cavity traversed by a microwave signal. The back-action on the qubit state of a single measurement of both signal quadratures was observed and shown to produce a stochastic operation whose action is determined by the measurement result. This accurate monitoring of a qubit state is an essential prerequisite for measurement-based feedback control of quantum systems.
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Research Support, U.S. Gov't, Non-P.H.S. |
12 |
191 |
6
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Shankar S, Teyler TJ, Robbins N. Aging differentially alters forms of long-term potentiation in rat hippocampal area CA1. J Neurophysiol 1998; 79:334-41. [PMID: 9425202 DOI: 10.1152/jn.1998.79.1.334] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Long-term potentiation (LTP) of the Schaffer collateral/commissural inputs to CA1 in the hippocampus was shown to consist of N-methyl-D-aspartate receptor (NMDAR) and voltage-dependent calcium channel (VDCC) dependent forms. In this study, the relative contributions of these two forms of LTP in in vitro hippocampal slices from young (2 mo) and old (24 mo) Fischer 344 rats were examined. Excitatory postsynaptic potentials (EPSP) were recorded extracellularly from stratum radiatum before and after a tetanic stimulus consisting of four 200-Hz, 0.5-s trains given 5 s apart. Under control conditions, a compound LTP consisting of both forms was induced and was similar, in both time course and magnitude, in young and old animals. NMDAR-dependent LTP (nmdaLTP), isolated by the application of 10 microM nifedipine (a voltage-dependent calcium channel blocker), was significantly reduced in magnitude in aged animals. The VDCC dependent form (vdccLTP), isolated by the application of 50 microM D,L-2-amino-5-phosphonvalerate (APV), was significantly larger in aged animals. Although both LTP forms reached stable values 40-60 min posttetanus in young animals, in aged animals vdccLTP increased and nmdaLTP decreased during this time. In both young and old animals, the sum of the two isolated LTP forms approximated the magnitude of the compound LTP, and application of APV and nifedipine or genestein (a tyrosine kinase inhibitor) together blocked potentiation. These results suggest that aging causes a shift in synaptic plasticity from NMDAR-dependent mechanisms to VDCC-dependent mechanisms. The data are consistent with previous findings of increased L-type calcium current and decreased NMDAR number in aged CA1 cells and may help explain age-related deficits in learning and memory.
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27 |
170 |
7
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Heidt S, Hester J, Shankar S, Friend PJ, Wood KJ. B cell repopulation after alemtuzumab induction-transient increase in transitional B cells and long-term dominance of naïve B cells. Am J Transplant 2012; 12:1784-92. [PMID: 22420490 PMCID: PMC3387484 DOI: 10.1111/j.1600-6143.2012.04012.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In organ transplantation, the composition of the B-cell compartment is increasingly identified as an important determinant for graft outcome. Whereas naïve and transitional B cells have been associated with long-term allograft survival and operational tolerance, memory B cells have been linked to decreased allograft survival. Alemtuzumab induction therapy effectively depletes B cells, but is followed by rapid repopulation up to levels exceeding base line. The characteristics of the repopulating B cells are currently unknown. We studied the phenotypic and functional characteristics of B cells longitudinally in 19 kidney transplant recipients, before and at 6, 9 and 12 months after alemtuzumab induction therapy. A transient increase in transitional B cells and cells with phenotypic characteristics of regulatory B cells, as well as a long-term dominance in naïve B cells was found in alemtuzumab-treated kidney transplant recipients, which was not influenced by conversion from tacrolimus to sirolimus. At all time-points after treatment, B cells showed unaltered proliferative and IgM-producing capacity as compared to pretransplant samples, whereas the ability to produce IgG was inhibited long-term. In conclusion, induction therapy with alemtuzumab results in a long-term shift toward naïve B cells with altered phenotypic and functional characteristics.
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research-article |
13 |
106 |
8
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Wallace VP, Fitzgerald AJ, Shankar S, Flanagan N, Pye R, Cluff J, Arnone DD. Terahertz pulsed imaging of basal cell carcinoma ex vivo and in vivo. Br J Dermatol 2004; 151:424-32. [PMID: 15327550 DOI: 10.1111/j.1365-2133.2004.06129.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Terahertz radiation lies between the infrared and microwave regions of the electromagnetic spectrum and can be used to excite large amplitude vibrational modes of molecules and probe the weak interactions between them. Terahertz pulsed imaging (TPI) is a noninvasive imaging technique that utilises this radiation. OBJECTIVES To determine whether TPI could differentiate between basal cell carcinoma (BCC) and normal tissue and to test whether it can help facilitate delineation of tumour margins prior to surgery. METHODS A portable TPI system was used in the clinic to image 18 BCCs ex vivo and five in vivo. RESULTS The diseased tissue showed a change in terahertz properties compared with normal tissue, manifested through a broadening of the reflected terahertz pulse. Regions of disease identified in the terahertz image correlated well with histology. CONCLUSIONS This study has confirmed the potential of TPI to identify the extent of BCC in vivo and to delineate tumour margins. Further clinical study of TPI as a surgical tool is now required.
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Research Support, Non-U.S. Gov't |
21 |
102 |
9
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Xie ZD, Hershberger CD, Shankar S, Ye RW, Chakrabarty AM. Sigma factor-anti-sigma factor interaction in alginate synthesis: inhibition of AlgT by MucA. J Bacteriol 1996; 178:4990-6. [PMID: 8759865 PMCID: PMC178284 DOI: 10.1128/jb.178.16.4990-4996.1996] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Conversion from the nonmucoid to the mucoid phenotype is a typical feature of Pseudomonas aeruginosa strains causing chronic pulmonary infections in cystic fibrosis patients. One of the key genetic controls in this conversion to mucoidy is from the algT(U)-mucA-mucB(algN) locus, located at 67.5 min on the standard P. aeruginosa chromosomal map. The algT gene promotes conversion to mucoidy and encodes an alternative sigma factor (sigma E) which belongs to the ECF (for extracytoplasmic function) family. On the other hand, the mucA and mucB (algN) genes suppress conversion to mucoidy. Loss-of-function mutations in mucA have been postulated to be the cause of mucoidy in some P. aeruginosa strains isolated from cystic fibrosis patients. We expressed and purified the protein products from the mucA and mucB open reading frames. The purified MucA protein abolishes the in vitro transcription specified by AlgT and the ability of AlgT to compete with an Escherichia coli sigma factor, FliA, suggesting that inhibiting AlgT-dependent transcription could be the mechanism by which mucA suppresses mucoidy in vivo. Enzyme-linked immunosorbent assay and glycerol density gradient sedimentation experiments suggest that MucA physically interacts with AlgT.
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research-article |
29 |
96 |
10
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Kim HY, Schlictman D, Shankar S, Xie Z, Chakrabarty AM, Kornberg A. Alginate, inorganic polyphosphate, GTP and ppGpp synthesis co-regulated in Pseudomonas aeruginosa: implications for stationary phase survival and synthesis of RNA/DNA precursors. Mol Microbiol 1998; 27:717-25. [PMID: 9515698 DOI: 10.1046/j.1365-2958.1998.00702.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The regulatory protein AlgR2 in Pseudomonas aeruginosa positively regulates nucleoside diphosphate kinase (Ndk) and succinyl-CoA synthetase, enzymes critical in nucleoside triphosphate (NTP) formation. AlgR2 positively regulates the production of alginate, GTP, ppGpp and inorganic polyphosphate (poly P). An algR2 mutant with low levels of these metabolites has them restored by introducing and overexpressing either the algR2 or the ndk gene into the algR2 mutant. Thus, Ndk is involved in the formation of these compounds and largely prevents the death of the algR2 mutant, which occurs early in the stationary phase. We demonstrate that the 12 kDa Ndk-pyruvate kinase (Pk) complex, previously shown to generate predominantly GTP instead of all the NTPs, has a low affinity for the deoxynucleoside diphosphates and cannot generate the dNTPs needed for DNA replication and cell division; this complex may thus be involved in regulating the levels of both NTPs and dNTPs that modulate cell division and survival in the stationary phase.
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27 |
72 |
11
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Shankar S, Hatridge M, Leghtas Z, Sliwa KM, Narla A, Vool U, Girvin SM, Frunzio L, Mirrahimi M, Devoret MH. Autonomously stabilized entanglement between two superconducting quantum bits. Nature 2013; 504:419-22. [PMID: 24270808 DOI: 10.1038/nature12802] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/22/2013] [Indexed: 12/27/2022]
Abstract
Quantum error correction codes are designed to protect an arbitrary state of a multi-qubit register from decoherence-induced errors, but their implementation is an outstanding challenge in the development of large-scale quantum computers. The first step is to stabilize a non-equilibrium state of a simple quantum system, such as a quantum bit (qubit) or a cavity mode, in the presence of decoherence. This has recently been accomplished using measurement-based feedback schemes. The next step is to prepare and stabilize a state of a composite system. Here we demonstrate the stabilization of an entangled Bell state of a quantum register of two superconducting qubits for an arbitrary time. Our result is achieved using an autonomous feedback scheme that combines continuous drives along with a specifically engineered coupling between the two-qubit register and a dissipative reservoir. Similar autonomous feedback techniques have been used for qubit reset, single-qubit state stabilization, and the creation and stabilization of states of multipartite quantum systems. Unlike conventional, measurement-based schemes, the autonomous approach uses engineered dissipation to counteract decoherence, obviating the need for a complicated external feedback loop to correct errors. Instead, the feedback loop is built into the Hamiltonian such that the steady state of the system in the presence of drives and dissipation is a Bell state, an essential building block for quantum information processing. Such autonomous schemes, which are broadly applicable to a variety of physical systems, as demonstrated by the accompanying paper on trapped ion qubits, will be an essential tool for the implementation of quantum error correction.
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Research Support, U.S. Gov't, Non-P.H.S. |
12 |
64 |
12
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Shankar S, Gulati M, Kang M, Gupta S, Suri S. Image-guided percutaneous drainage of thoracic empyema: can sonography predict the outcome? Eur Radiol 2000; 10:495-9. [PMID: 10757003 DOI: 10.1007/s003300050083] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The aim of this study was to assess the safety and efficacy of image-guided percutaneous catheter drainage (IGPCD) of thoracic empyemas, and to correlate the outcome of IGPCD with the pre-procedural sonographic appearance. One hundred three patients (74 males and 29 females) with thoracic empyema (age range 1 month to 70 years, median age 28 years) underwent IGPCD. In 63 (61.17%) patients, IGPCD was the primary treatment modality; in 40 (38.84%) patients it was used after unsuccessful intercostal chest tube drainage (ICTD). Ultrasound was the main modality used for guidance; CT guidance was used in only 7 patients (6.8%). Eight- to 12-F pigtail catheters or 10- to 14-F Malecot catheters were used. The outcome was correlated with the pre-procedural US appearance (anechoic, complex non-septated or complex septated) of the empyema. The IGPCD technique was successful in 80 of 102 patients. Based on the US appearance, IGPCD was successful in 12 of 13 (92.3%) patients with anechoic empyemas; 53 of 65 (81.54%) patients with complex non-septated empyemas, and in 15 of 24 (62.5%) patients with complex septated empyemas. A statistically significant difference (p < 0.01) was seen in the outcome of IGPCD in the three categories. Twenty-two patients required further treatment: ICTD (n = 9; 2 of them later also underwent surgery); and surgery (n = 15). The duration of catheter drainage ranged from 2-60 days. No major complications were encountered. Percutaneous catheter drainage of thoracic empyemas with imaging guidance ensures accurate catheter placement with a high success and a low complication rate. Pre-procedural US can predict the likelihood of success of IGPCD.
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Comparative Study |
25 |
63 |
13
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Abstract
Haemorrhage is a life-threatening complication in pancreatic disease. Twenty-five patients with this complication are described; 15 had major bleeding, nine had minor bleeding and one patient had a pseudoaneurysm identified at operation. Of the 15 patients with major bleeding, six presented with this complication and in nine cases it followed pancreatic resection. Of the six patients who presented with major bleeding, five underwent resection with one death while the patient managed conservatively died. The nine patients who had major bleeding after pancreatic resection were managed by ligation of the bleeding artery in six cases with one death, and one patient who rebled after ligation of the bleeding artery was successfully managed by further resection. Three patients with postresection major bleeding were managed conservatively with one death. All minor haemorrhages were managed conservatively without mortality. Deaths after major bleeding were a result of sepsis in three cases and respiratory failure in one. The severity of the underlying pancreatitis was an important factor in two patients. Pseudocysts and pancreatic fistulae were important underlying factors leading to the complication. It is recommended that patients with sepsis, a pancreatic fistula or severe underlying pancreatitis should have their haemorrhage treated by pancreatic resection, while those patients with bleeding following pancreatic resection without such complications can be managed by ligation.
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36 |
57 |
14
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Kattamis AC, Shankar S, Cohen AR. Neurologic complications of treatment of childhood acute immune thrombocytopenic purpura with intravenously administered immunoglobulin G. J Pediatr 1997; 130:281-3. [PMID: 9042132 DOI: 10.1016/s0022-3476(97)70355-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We studied the incidence, associated morbidity, and impact on health care charges of neurologic complications in 38 children with acute immune thrombocytopenic purpura (ITP) treated with intravenously administered IgG. Thirteen patients (34%) had transient neurologic complications, manifested by severe headache, nausea, and, rarely, aseptic meningitis. Computed tomography was performed in nine patients. Twelve patients were hospitalized longer than was required for their ITP alone. Neurologic complications caused by the IgG preparations used in the treatment of childhood ITP occur more frequently than has previously been suggested and may substantially increase the cost of treatment.
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MESH Headings
- Acute Disease
- Adolescent
- Child
- Child, Preschool
- Costs and Cost Analysis
- Female
- Hospitalization/economics
- Humans
- Immunoglobulins, Intravenous/administration & dosage
- Immunoglobulins, Intravenous/adverse effects
- Immunoglobulins, Intravenous/economics
- Incidence
- Infant
- Male
- Nervous System Diseases/economics
- Nervous System Diseases/epidemiology
- Nervous System Diseases/etiology
- Purpura, Thrombocytopenic, Idiopathic/complications
- Purpura, Thrombocytopenic, Idiopathic/economics
- Purpura, Thrombocytopenic, Idiopathic/therapy
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Comparative Study |
28 |
55 |
15
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El Yacoubi B, Brunings AM, Yuan Q, Shankar S, Gabriel DW. In planta horizontal transfer of a major pathogenicity effector gene. Appl Environ Microbiol 2007; 73:1612-21. [PMID: 17220258 PMCID: PMC1828793 DOI: 10.1128/aem.00261-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas citri pv. citri is a clonal group of strains that causes citrus canker disease and appears to have originated in Asia. A phylogenetically distinct clonal group that causes identical disease symptoms on susceptible citrus, X. citri pv. aurantifolii, arose more recently in South America. Genomes of X. citri pv. aurantifolii strains carry two DNA fragments that hybridize to pthA, an X. citri pv. citri gene which encodes a major type III pathogenicity effector protein that is absolutely required to cause citrus canker. Marker interruption mutagenesis and complementation revealed that X. citri pv. aurantifolii strain B69 carried one functional pthA homolog, designated pthB, that was required to cause cankers on citrus. Gene pthB was found among 38 open reading frames on a 37,106-bp plasmid, designated pXcB, which was sequenced and annotated. No additional pathogenicity effectors were found on pXcB, but 11 out of 38 open reading frames appeared to encode a type IV transfer system. pXcB transferred horizontally in planta, without added selection, from B69 to a nonpathogenic X. citri pv. citri (pthA::Tn5) mutant strain, fully restoring canker. In planta transfer efficiencies were very high (>0.1%/recipient) and equivalent to those observed for agar medium with antibiotic selection, indicating that pthB conferred a strong selective advantage to the recipient strain. A single pathogenicity effector that can confer a distinct selective advantage in planta may both facilitate plasmid survival following horizontal gene transfer and account for the origination of phylogenetically distinct groups of strains causing identical disease symptoms.
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Journal Article |
18 |
49 |
16
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Sundin GW, Shankar S, Chugani SA, Chopade BA, Kavanaugh-Black A, Chakrabarty AM. Nucleoside diphosphate kinase from Pseudomonas aeruginosa: characterization of the gene and its role in cellular growth and exopolysaccharide alginate synthesis. Mol Microbiol 1996; 20:965-79. [PMID: 8809750 DOI: 10.1111/j.1365-2958.1996.tb02538.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report the cloning and determination of the nucleotide sequence of the gene encoding nucleoside diphosphate kinase (Ndk) from Pseudomonas aeruginosa. The amino acid sequence of Ndk was highly homologous with other known bacterial and eukaryotic Ndks (39.9 to 58.3% amino acid identity). We have previously reported that P. aeruginosa strains with mutations in the genes algR2 and algR2 algH produce extremely low levels of Ndk and, as a consequence, are defective in their ability to grow in the presence of Tween 20, a detergent that inhibits a kinase which can substitute for Ndk. Hyperexpression of ndk from the clone pGWS95 in trans in the P. aeruginosa algR2 and algR2 algH double mutant restored Ndk production to levels which equalled or exceeded wild-type levels and enabled these strains to grow in the presence of Tween 20. Hyperexpression of ndk from pGWS95 in the P. aeruginosa algR2 mutant also restored alginate production to levels that were approximately 60% of wild type. Nucleoside diphosphate kinase activity was present in both the cytosolic and membrane-associated fractions of P. aeruginosa. The cytosolic Ndk was non-specific in its transfer activity of the terminal phosphate from ATP to other nucleoside diphosphates. However, the membrane form of Ndk was more active in the transfer of the terminal phosphate from ATP to GDP resulting in the predominant formation of GTP. We report in this work that pyruvate kinase and Ndk form a complex which alters the specificity of Ndk substantially to GTP. The significance of GTP in signal transduction events within the cell and in the production of GDP-mannose, an essential alginate precursor, clearly indicates the importance of Ndk in cellular processes as well as in alginate synthesis.
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29 |
49 |
17
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Nigg SE, Paik H, Vlastakis B, Kirchmair G, Shankar S, Frunzio L, Devoret MH, Schoelkopf RJ, Girvin SM. Black-box superconducting circuit quantization. PHYSICAL REVIEW LETTERS 2012; 108:240502. [PMID: 23004246 DOI: 10.1103/physrevlett.108.240502] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Indexed: 06/01/2023]
Abstract
We present a semiclassical method for determining the effective low-energy quantum Hamiltonian of weakly anharmonic superconducting circuits containing mesoscopic Josephson junctions coupled to electromagnetic environments made of an arbitrary combination of distributed and lumped elements. A convenient basis, capturing the multimode physics, is given by the quantized eigenmodes of the linearized circuit and is fully determined by a classical linear response function. The method is used to calculate numerically the low-energy spectrum of a 3D transmon system, and quantitative agreement with measurements is found.
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13 |
48 |
18
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Shankar S, Gander RE, Brandell BR. Changes in the myoelectric signal (MES) power spectra during dynamic contractions. ELECTROENCEPHALOGRAPHY AND CLINICAL NEUROPHYSIOLOGY 1989; 73:142-50. [PMID: 2473881 DOI: 10.1016/0013-4694(89)90193-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Power spectra of surface myoelectric signals (MES) have been estimated during dynamic contractions of the biceps brachii. The effect of applied torque, velocity of contraction and muscle length have been studied with respect to median frequency and total spectral power. The results of the investigation carried out thus far can be summarised as follows: (1) The median frequency is observed to vary with the applied torque and the muscle length but not with the velocity of contraction. (2) The expected dependence of the MES power with the applied torque, velocity and muscle length was confirmed. These results suggest that the power spectrum could be used to reveal changes in the electrophysiological characteristics of a muscle during dynamic contractions as is the case with static contractions.
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36 |
47 |
19
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Geerlings K, Leghtas Z, Pop IM, Shankar S, Frunzio L, Schoelkopf RJ, Mirrahimi M, Devoret MH. Demonstrating a driven reset protocol for a superconducting qubit. PHYSICAL REVIEW LETTERS 2013; 110:120501. [PMID: 25166782 DOI: 10.1103/physrevlett.110.120501] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Indexed: 06/03/2023]
Abstract
Qubit reset is crucial at the start of and during quantum information algorithms. We present the experimental demonstration of a practical method to force qubits into their ground state, based on driving appropriate qubit and cavity transitions. Our protocol, called the double drive reset of population, is tested on a superconducting transmon qubit in a three-dimensional cavity. Using a new method for measuring population, we show that we can prepare the ground state with a fidelity of at least 99.5% in less than 3 μs; faster times and higher fidelity are predicted upon parameter optimization.
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Shankar S, Mohapatra B, Suri A. Cloning of a novel human testis mRNA specifically expressed in testicular haploid germ cells, having unique palindromic sequences and encoding a leucine zipper dimerization motif. Biochem Biophys Res Commun 1998; 243:561-5. [PMID: 9480848 DOI: 10.1006/bbrc.1997.7943] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel gene coding for a human sperm surface protein (HSS) has been cloned from a human testis cDNA library. The 2.5 kb cDNA (hss) contains five direct repeats, three mirror repeats, three possible stem loop structures and three unique palindromic motifs located at functionally relevant positions. Open reading frame encodes a protein of 766 amino acids. The deduced protein analysis revealed a NH2 terminus extracellular domain having a leucine zipper (LZ) motif, a transmembrane helical domain and a cytoplasmic domain at the COOH terminus. Tissue specific expression studies demonstrated the presence of hss transcript only in testis. Cell type expression of hss mRNA was observed only on the round spermatids suggesting haploid germ cell expression.
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Shankar S, Theis B, Russell RC. Management of the stump of the pancreas after distal pancreatic resection. Br J Surg 1990; 77:541-4. [PMID: 2354339 DOI: 10.1002/bjs.1800770525] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The optimal management of the stump of the pancreas following distal resection remains controversial. To determine whether there was an advantage in draining the stump of the pancreas into a Roux-en-Y loop of jejunum, a retrospective survey of 113 patients who had a distal pancreatectomy for chronic pancreatitis or complications of acute pancreatitis in the non-acute phase was undertaken. The decision to perform a drainage procedure was determined on the basis of the pancreatogram, the size of the pancreatic duct and technical factors at the time of the operation. Sixty-seven patients had no drainage procedure and 46 patients had a drainage procedure. The two groups were comparable in all respects before surgery. The postoperative outcome in the short- and long-term was similar in both groups. It is concluded that caudal pancreatic drainage confers no benefit following distal pancreatic resection.
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Shankar SS, Bhargava S, Sastry M. Synthesis of gold nanospheres and nanotriangles by the Turkevich approach. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2005; 5:1721-7. [PMID: 16245535 DOI: 10.1166/jnn.2005.192] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Gold nanoparticles of triangular morphology possess interesting optical properties with potential application in medicine and infrared absorbing coatings, however, little is known about conditions that favor their growth. In this paper, we have reinvestigated a time-tested recipe for the formation of gold nanospheres by citrate reduction of aqueous gold ions under boiling conditions (Turkevich recipe). Our principle findings are that gold nanotriangle formation is kinetically controlled and is highly favored at low temperatures. Furthermore, the presence of chloride ions from the precursor chloroaurate ions plays a major role in promoting the growth of <111> oriented triangular/truncated triangular particles. The presence of bromide and iodide ions that possess the ability to replace surface-bound chloride ions inhibits triangle formation to varying degrees.
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Schlictman D, Kubo M, Shankar S, Chakrabarty AM. Regulation of nucleoside diphosphate kinase and secretable virulence factors in Pseudomonas aeruginosa: roles of algR2 and algH. J Bacteriol 1995; 177:2469-74. [PMID: 7730279 PMCID: PMC176906 DOI: 10.1128/jb.177.9.2469-2474.1995] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Alginate is an important virulence factor for Pseudomonas aeruginosa during infection of the lungs of cystic fibrosis patients. The genes encoding enzymes for alginate production by P. aeruginosa are normally silent. They are activated in response to several environmental conditions, including high osmolarity, exposure to ethanol, or long-term growth under conditions of nutrient deprivation. Several genes which participate in the activation of alginate gene promoters have been identified; among these is the algR2 (algQ) gene. AlgR2 is an 18-kDa protein which has been shown to regulate the critical algD gene encoding GDP-mannose dehydrogenase as well as to regulate the levels of a tricarboxylic acid cycle enzyme, i.e., succinyl coenzyme A synthetase, and nucleoside diphosphate kinase (Ndk), an enzyme involved in nucleoside triphosphate synthesis. Succinyl coenzyme A synthetase and Ndk form a complex in P. aeruginosa. While algR2 is required for alginate synthesis at 37 degrees C, an algR2 insertion mutant was still able to make alginate slowly at 37 or at 30 degrees C. We used this observation to identify and clone a gene, termed algH. A strain with mutations in both algR2 and algH is unable to produce alginate at either 37 or 30 degrees C, and it is fully defective in Ndk production.
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Chopade BA, Shankar S, Sundin GW, Mukhopadhyay S, Chakrabarty AM. Characterization of membrane-associated Pseudomonas aeruginosa Ras-like protein Pra, a GTP-binding protein that forms complexes with truncated nucleoside diphosphate kinase and pyruvate kinase to modulate GTP synthesis. J Bacteriol 1997; 179:2181-8. [PMID: 9079902 PMCID: PMC178953 DOI: 10.1128/jb.179.7.2181-2188.1997] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We report the purification and characterization of a protein from the membrane fraction of Pseudomonas aeruginosa showing intrinsic guanosine triphosphatase (GTPase) activity. The protein was purified as a 48-kDa polypeptide capable of binding and hydrolyzing GTP. The N-terminal sequence of the purified protein revealed its similarity to the Escherichia coli Ras-like protein (Era), and the protein cross-reacted with anti-Era antibodies. This protein was named Pseudomonas Ras-like protein (Pra). Anti-Pra antibodies also cross-reacted with E. coli Era protein. Pra is autophosphorylated in vitro, with phosphotransfer of the terminal phosphate from [gamma-32P]GTP but not [gamma-32P]ATP. Pra is capable of complex formation with the truncated 12-kDa form of nucleoside diphosphate kinase (Ndk) but not with the 16-kDa form. Purified Pra was also shown to physically interact with pyruvate kinase (Pk); Pk and Pra can form a complex, but when the 12-kDa Ndk, Pk, and Pra are all present, Pk has a higher affinity than Pra for forming a complex with the 12-kDa Ndk. The 12-kDa Ndk-Pra complex catalyzed increased synthesis of GTP and dGTP and diminished synthesis of CTP and UTP or dCTP and dTTP relative to their synthesis by uncomplexed Ndk. Moreover, the complex of Pra with Pk resulted in the specific synthesis of GTP as well when Pra was present in concentrations in excess of that of Pk. Membrane fractions from cells harvested in the mid-log phase demonstrated very little nucleoside triphosphate (NTP)-synthesizing activity and no detectable Ndk. Membranes from cells harvested at late exponential phase showed NTP-synthesizing activity and the physical presence of Ndk but not of Pk or Pra. In contrast, membrane fractions of cells harvested at early to late stationary phase showed predominant GTP synthesis and the presence of increasing amounts of Pk and Pra. It is likely that the association of Pra with Ndk and/or Pk restricts its intrinsic GTPase activity, which may modulate stationary-phase gene expression and the survival of P. aeruginosa by modulating the level of GTP.
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Kang M, Gupta S, Khandelwal N, Shankar S, Gulati M, Suri S. CT-guided fine-needle aspiration biopsy of spinal lesions. Acta Radiol 1999; 40:474-8. [PMID: 10485234 DOI: 10.3109/02841859909175570] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE A retrospective study of CT-guided fine-needle aspiration biopsies (FNABs) of spinal lesions performed over a period of 6 years was carried out with the aim of assessing the safety and efficacy of the procedure and to analyse the various approaches used. MATERIAL AND METHODS Ninety-three FNABs were performed in 87 patients, 4-70 years of age, under CT guidance. Lytic or mixed vertebral lesions with or without a paraspinal soft tissue component were included in the study. The approach depended on the anatomic region and part of the vertebra involved. RESULTS A definite cytological diagnosis was obtained in 77 patients (88.5%); of these, 47 patients had benign lesions and 30 patients had neoplasms. The most common pathologies encountered were tuberculosis (n=33) and metastases (n=17). There were 10 inconclusive FNABs; these showed blood only, necrotic material or scanty material insufficient for diagnosis. There were no procedure-related complications. CONCLUSION CT-guided FNAB is a safe and effective technique for the evaluation of spinal lesions and is helpful in planning therapy. Choosing the appropriate approach results in a low complication rate.
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