Development of protein engineered enzymes for the study of galactosaminoglycan neuromedicine

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006."June 2006."Includes bibliographical references.Glycans are chemically heterogeneous macromolecules that have profound importance in a variety of biological processes. Located at the surfaces of cells, deposited in the extracellular matrix, or attached to soluble signaling agents, these molecules are characterized by a structural complexity that has thus far prevented their widespread exploitation in biomedicine. Insight into the fine structure and sequence of these complex biomolecules provides a novel niche for the development of therapeutic interventions. Such an understanding is rapidly accumulating via the molecular cloning, recombinant genetic expression, and protein purification of glycosaminoglycan-degrading enzymes. To this end, enzymes from the chondroitinase family of Pedobacter heparinus and Proteus vulgaris were developed. This library of enzymatic tools will reveal glycoconjugate structure-function motifs, allowed for by structural elucidation of glycan species using coupled bioinformatics/analytical chemistry techniques centered on mass spectrometry, nuclear magnetic resonance, and capillary electrophoresis.(cont.) Biochemical characterization of these enzymes has allowed for the rational genetic manipulation of substrate recognition and binding site amino acid residues, producing site-directed protein engineered mutants with altered action pattern and substrate specificity. Progress in these areas will allow for the elucidation of critical roles of glycans in the biological regulation of growth factors, morphogens, cytokines, and cell-surface proteins. This extension of the capabilities of glycan analytical biotechnologies will help to translate basic science glycobiology to applied glycomedicine and drug discovery.by Vikas Prabhakar.Ph.D

Closed Form Expressions for Delay to Ramp Inputs for On-Chip VLSI RC Interconnect

In high speed digital integrated circuits, interconnects delay can be significant and should be included for accurate analysis. Delay analysis for interconnect has been done widely by using moments of the impulse response, from the explicit Elmore delay (the first moment of the impulse response) expression, to moment matching methods which creates reduced order trans impedance and transfer function approximations. However, the Elmore delay is fast becoming ineffective for deep submicron technologies, and reduced order transfer function delays are impractical for use as early-phase design metrics or as design optimization cost functions. This paper describes an approach for fitting moments of the impulse response to probability density functions so that delay can be estimated accurately at an early physical design stage. For RC trees it is demonstrated that the inverse gamma function provides a provably stable approximation. We used the PERI [13] (Probability distribution function Extension for Ramp Inputs) technique that extends delay metrics for ramp inputs to the more general and realistic non-step inputs. The accuracy of our model is justified with the results compared with that of SPICE simulations. Keywords¾ Moment Matching, On-Chip Interconnect, Probability Distribution function, Cumulative Distribution function, Delay calculation, Slew Calculation, Beta Distribution, VLSI

Evaluation of left ventricular ejection fraction using through-time radial GRAPPA

BACKGROUND: The determination of left ventricular ejection fraction using cardiovascular magnetic resonance (CMR) requires a steady cardiac rhythm for electrocardiogram (ECG) gating and multiple breathholds to minimize respiratory motion artifacts, which often leads to scan times of several minutes. The need for gating and breathholding can be eliminated by employing real-time CMR methods such as through-time radial GRAPPA. The aim of this study is to compare left ventricular cardiac functional parameters obtained using current gold-standard breathhold ECG-gated functional scans with non-gated free-breathing real-time imaging using radial GRAPPA, and to determine whether scan time or the occurrence of artifacts are reduced when using this real-time approach. METHODS: 63 patients were scanned on a 1.5T CMR scanner using both the standard cardiac functional examination with gating and breathholding and the real-time method. Total scan durations were noted. Through-time radial GRAPPA was employed to reconstruct images from the highly accelerated real-time data. The blood volume in the left ventricle was assessed to determine the end systolic volume (ESV), end diastolic volume (EDV), and ejection fraction (EF) for both methods, and images were rated for the presence of artifacts and quality of specific image features by two cardiac readers. Linear regression analysis, Bland-Altman plots and two-sided t-tests were performed to compare the quantitative parameters. A two-sample t-test was performed to compare the scan durations, and a two-sample test of proportion was used to analyze the presence of artifacts. For the reviewers´ ratings the Wilcoxon test for the equality of the scores’ distributions was employed. RESULTS: The differences in EF, EDV, and ESV between the gold-standard and real-time methods were not statistically significant (p-values of 0.77, 0.82, and 0.97, respectively). Additionally, the scan time was significantly shorter for the real-time data collection (p<0.001) and fewer artifacts were reported in the real-time images (p<0.01). In the qualitative image analysis, reviewers marginally preferred the standard images although some features including cardiac motion were equivalently rated. CONCLUSION: Real-time functional CMR with through-time radial GRAPPA performed without ECG-gating under free-breathing can be considered as an alternative to gold-standard breathhold cine imaging for the evaluation of ejection fraction in patients

An easily recoverable and recyclable homogeneous polyester-based Pd catalytic system for the hydrogenation of alpha,beta-unsaturated carbonyl compounds

Abstract Homogeneous catalysis is an efficient tool to carry out hydrogenation processes but the major drawback is represented by the separation of the expensive catalyst from the product mixture. In this view we prepared a polyester-based Pd catalytic system that offers the advantages of both homogenous and heterogeneous catalyses: efficacy, selectivity and recyclability. Here its application in the hydrogenation of selected α,β-unsaturated carbonyl compounds is described.Homogeneous catalysis is an efficient tool to carry out hydrogenation processes but the major drawback is represented by the separation of the expensive catalyst from the product mixture. In this view we prepared a polyester-based Pd catalytic system that offers the advantages of both homogenous and heterogeneous catalyses: efficacy, selectivity and recyclability. Here its application in the hydrogenation of selected alpha,beta-unsaturated carbonyl compounds is described. (C) 2015 Elsevier B.V. All rights reserved

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe

Knowledge models in agropedia indica

This paper refers to the creation of multilingual agricultural knowledge models (KMs) in the context of the Agropedia Indica project. We present the reasons and the requirements for the development of such KMs, the choices made in terms of modeling tools and modeling solutions, and we detail the content of some of the models

Tuberculosis of the foot: An osteolytic variety

Background: Foot involvement in osteoarticular tuberculosis is uncommon and isolated bony involvement of foot bones with an osteolytic defect is even more rare; diagnostic and therapeutic delays can occur, worsening the prognosis. We present a retrospective series of osteolytic variety of foot tuberculosis. Materials and Methods: We present 24 osteolytic variety of foot tuberculosis (Eleven calcaneus, four cuboid, two cunieforms, one talus, three metatarsals, three phalanges) out of 92 foot TB cases collected over last 20 years. There were 16 adults and eight children. Tissue diagnosis was established in 23 of 24 cases based on PCR AFB staining, culture, and histopathology. Surgical intervention was reserved for patients with either a juxtaarticular focus threatening to involve a joint or an impending collapse of a midfoot bone with cystic destruction. Results: Fifteen cases had an osteolytic lesion on the radiographs resembling a space-occupying lesion, five had patchy osteolysis, while four showed coke like sequestra; one patient had a lesion in two bones. Antitubercular chemotherapy after biopsy was sufficient to heal the lesion in 19 cases, while in five cases surgical debridement needed to be done. The lesions healed eventually. At an average followup of 8.3 years, (range 2-15 years) there were no recurrences and all patients were free from pain, with no restriction of movements. Six patients complained of occasional pain during walking on uneven ground. Conclusion: When tuberculous pathology is limited to the bone, the prognosis is better than in articular disease, as there is less deformity, and hence, less residual pain and disability

Tuberculosis of the elbow: A clinicoradiological analysis

Background: The incidence of Tuberculosis (TB) of elbow is 2-5% of all skeletal locations. Most reports of TB elbow have focused attention on the diagnosis. The management options and classification has been missing. We present a retrospective clinicoradiological analysis of 38 cases (40 elbows) of TB of elbow joint. Materials and Methods: The patients presented with pain, swelling and loss of motion. Two cases had bilateral involvement. The average delay between onset of symptoms and presentation was 8 months. The elbows were classified according to modified Martini′s radiological classification, which distinguishes between osseous lesions close to joint line (e.g. coronoid, condyles) and lesions away from the joint line (e.g. epicondyles, olecranon). We modified the classification to subdivide into para-articular bony lesions that had invaded the joint and those that were threatening to invade joint. All patients received antitubercular chemotherapy and immobilization in above-elbow plaster slab for 4-8 weeks. Twenty patients underwent surgical interventions (synovectomy, intraarticular debridement). Results: The average followup period was 5.3 years (range 1.5-14.2 years). The range of movement at final followup averaged 107° for stage 2, 90° for stage 3A, 47° for stage 3B and 32° for stage 4. Range of supination and pronation was less satisfactory as compared to flexion and extension and all elbows with bony involvement had less than 90° arc of supination and pronation. Conclusion: Surgical intervention could appreciably alter the outcome especially in patients with extra-articular involvement close to the joint. We have classified this subgroup separately