1,732,634 research outputs found
Structural and dynamical insights on HLA-DRB1: peptide complexes which confer resistance and susceptibility to multiple sclerosis in sardinia: a molecular dynamics simulation study
No full textMicroscale Dynamics in Suspensions of Non-Spherical Particles
No full textSubmitted by Amit Kumar ([email protected]) on 2010-05-13T20:29:09Z
No. of bitstreams: 1
kumar_amit.pdf: 5973919 bytes, checksum: c8d359ddf609b573aa42556bc9fb3d89 (MD5)Approved for entry into archive by Sarah Shreeves([email protected]) on 2010-05-13T20:43:09Z (GMT) No. of bitstreams: 1
kumar_amit.pdf: 5973919 bytes, checksum: c8d359ddf609b573aa42556bc9fb3d89 (MD5)Made available in DSpace on 2010-05-13T20:43:09Z (GMT). No. of bitstreams: 1
kumar_amit.pdf: 5973919 bytes, checksum: c8d359ddf609b573aa42556bc9fb3d89 (MD5)
Previous issue date: 201
Dynamical footprint of cross-reactivity in a human autoimmune T-cell receptor
Full text linkThe present work focuses on the dynamical aspects of cross-reactivity between myelin based protein (MBP) self-peptide and two microbial peptides (UL15, PMM) for Hy.1B11 T-cell receptor (TCR). This same TCR was isolated from a patient suffering from multiple sclerosis (MS). The study aims at highlighting the chemical interactions underlying recognition mechanisms between TCR and the peptides presented by Major Histocompatibility Complex (MHC) proteins, which form a crucial component in adaptive immune response against foreign antigens. Since the ability of a TCR to recognize different peptide antigens presented by MHC depends on its cross-reactivity, we used molecular dynamics methods to obtain atomistic detail on TCR-peptide-MHC complexes. Our results show how the dynamical basis of Hy.1B11 TCR's cross-reactivity is rooted in a similar bridging interaction pattern across the TCR-peptide-MHC interface. Our simulations confirm the importance of TCR CDR3α E98 residue interaction with MHC and a predominant role of P6 peptide residue in MHC binding affinity. Altogether, our study provides energetic and dynamical insights into factors governing peptide recognition by the cross-reactive Hy.1B11 TCR, found in MS patient
A comparative study of stress intensity factor extraction techniques for the generalized finite element method
Full text linkGeneralized Finite Element Method (GFEM) is a Partition of Unity Method where
shape functions are constructed by the product of standard finite element shape
function and some additional shape functions. These additional shape functions
take the benefit of some prior knowledge of the solution. They are especially useful
in fracture mechanics problems where crack singularities are addressed. A
crack can be represented with the help of discontinuous and singular shape functions.
This gives a great flexibility to the user in a choice of an appropriate mesh.
Stress intensity factor is an important quantity in fracture mechanics which is used
to predict the stress state around a crack front. This report presents a comprehensive
study of stress intensity factor extraction techniques: The Contour Integral
Method (CIM), the Cut-off Function Method (CFM) and the Displacement Correlation
Method (DCM). A few techniques are also shown to improve Displacement
Correlation Method with the use of additional sampling points.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-05-01The student, Amit Kumar Dhankhar, accepted the attached license on 2016-04-26 at 22:10.The student, Amit Kumar Dhankhar, submitted this Thesis for approval on 2016-04-26 at 22:20.This Thesis was approved for publication on 2016-04-28 at 09:07.DSpace SAF Submission Ingestion Package generated from Vireo submission #9536 on 2016-07-07 at 14:18:07Made available in DSpace on 2016-07-07T21:18:08Z (GMT). No. of bitstreams: 2
DHANKHAR-THESIS-2016.pdf: 7148295 bytes, checksum: a0e016df9ef345d5a4322910df32a270 (MD5)
LICENSE.txt: 4216 bytes, checksum: b50dd402df436de69f00f40f547f7c07 (MD5)
Previous issue date: 2016-04-28Embargo set by: Seth Robbins for item 93323
Lift date: 2018-07-07T21:18:16Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemLimited Restriction Lifted for Item 93323 on 2018-07-08T09:15:29Z
Clustering What Matters in Constrained Settings: Improved Outlier to Outlier-Free Reductions
Full text linkConstrained clustering problems generalize classical clustering formulations, e.g., k-median, k-means, by imposing additional constraints on the feasibility of a clustering. There has been significant recent progress in obtaining approximation algorithms for these problems, both in the metric and the Euclidean settings. However, the outlier version of these problems, where the solution is allowed to leave out m points from the clustering, is not well understood. In this work, we give a general framework for reducing the outlier version of a constrained k-median or k-means problem to the corresponding outlier-free version with only (1+ε)-loss in the approximation ratio. The reduction is obtained by mapping the original instance of the problem to f(k, m, ε) instances of the outlier-free version, where f(k, m, ε) = ((k+m)/ε)^O(m). As specific applications, we get the following results:
- First FPT (in the parameters k and m) (1+ε)-approximation algorithm for the outlier version of capacitated k-median and k-means in Euclidean spaces with hard capacities.
- First FPT (in the parameters k and m) (3+ε) and (9+ε) approximation algorithms for the outlier version of capacitated k-median and k-means, respectively, in general metric spaces with hard capacities.
- First FPT (in the parameters k and m) (2-δ)-approximation algorithm for the outlier version of the k-median problem under the Ulam metric.
Our work generalizes the results of Bhattacharya et al. and Agrawal et al. to a larger class of constrained clustering problems. Further, our reduction works for arbitrary metric spaces and so can extend clustering algorithms for outlier-free versions in both Euclidean and arbitrary metric spaces
Positive intercropping effects on biomass production are species-specific and involve rhizosphere enzyme activities: Evidence from a field study
No full text<jats:title>Abstract</jats:title><jats:p>Less attention has been given to soil enzymes that contribute to beneficial rhizosphere interactions in intercropping systems. Therefore, we performed a field experiment by growing faba bean, lupine, and maize in mono and mixed cultures in a moderately fertile soil. We measured shoot biomass and the kinetic parameters (maximal velocity (<jats:italic>V</jats:italic><jats:sub>max</jats:sub>) and Michaelis-constant (<jats:italic>K</jats:italic><jats:sub><jats:italic>m</jats:italic></jats:sub>)) of three key enzymes in the rhizosphere: Leucine-aminopeptidase (LAP), β-1,4-N-acetylglucosaminidase (NAG), and phosphomonoesterase (PHO). Faba bean benefitted in mixed cultures by greater shoot biomass production with both maize and lupine compared to its expected biomass in monoculture. Next, LAP and NAG kinetic parameters were less responsive to mono and mixed cultures across the crop species. In contrast, both the <jats:italic>V</jats:italic><jats:sub>max</jats:sub> and <jats:italic>K</jats:italic><jats:sub><jats:italic>m</jats:italic></jats:sub> values of PHO increased in the faba bean rhizosphere when grown in mixed cultures with maize and lupine. A positive relative interaction index for shoot P and N uptake for faba bean showed its net facilitative interactions in the mixed cultures. Overall, these results suggest that over-productivity in intercropping is crop-specific and the positive intercropping effects could be modulated by P availability. We argue that the enzyme activities involved in nutrient cycling should be incorporated in further research.</jats:p>
A new approach for prediction of foliar dust in a coal mining region and its impacts on vegetation physiological processes using multi‐source satellite data sets
No full textEstimating foliar dust (FD) is essential in understanding the complex interaction between FD, vegetation, and the environment. The elevated FD has a significant impacts on vegetation physiological processes. The present study aims to explore the potential of multi-sensor optical satellite data sets (e.g., Landsat-8, 9; Sentinel-2B, and PlanetScope) in conjunction with in situ data sets for FD estimation over the Jharsuguda coal mining region in Eastern India. The efficacy of different spectral bands and various radiometric indices (RIs) was tested using linear regression models for FD estimation. Furthermore, the study attempts to quantify the impacts of FD on vegetation's physiological processes (e.g., carbon uptake, transpiration, water use efficiency, leaf temperature) through proxy data sets. The key findings of the study uncovered sensor-specific and common trends in vegetation spectral profiles under varying FD concentrations. A saturation threshold was observed around 50 g/m
2 of FD concentration, beyond which additional FD concentration exhibited limited impact on spectral reflectance. On the other hand, the assessment of FD estimation models revealed distinct performances and shared trends across various satellite sensors. Notably, near-infrared and shortwave infrared-1 bands, along with certain RIs, such as the Global Environmental Monitoring Index and the Non-Linear Index, emerged as pivotal for accurate FD estimation. Besides, the study results revealed that vegetation-associated carbon uptake experienced a ∼2 to 3 gC reduction for every additional gram of FD per square meter. Moreover, the vegetation transpiration reduction per unit of FD ranged from approximately 0.0005 to 0.0006 mm/m
2/day, highlighting a moderate impact on transpiration levels. These findings aid a significant evidence base to our understanding of FD's impact on vegetation physiological processes.</p
sj-docx-2-pie-10.1177_09544089221087821 - Supplemental material for Design and development of a rapid prototyping system combining traditional fused deposition modeling and reconfigurable pins platform
No full textSupplemental material, sj-docx-2-pie-10.1177_09544089221087821 for Design and development of a rapid prototyping system combining traditional fused deposition modeling and reconfigurable pins platform by Vikrant Charak and Amit Kumar Sinha in Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering</p
sj-docx-3-pie-10.1177_09544089221087821 - Supplemental material for Design and development of a rapid prototyping system combining traditional fused deposition modeling and reconfigurable pins platform
No full textSupplemental material, sj-docx-3-pie-10.1177_09544089221087821 for Design and development of a rapid prototyping system combining traditional fused deposition modeling and reconfigurable pins platform by Vikrant Charak and Amit Kumar Sinha in Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering</p
sj-docx-4-pie-10.1177_09544089221087821 - Supplemental material for Design and development of a rapid prototyping system combining traditional fused deposition modeling and reconfigurable pins platform
No full textSupplemental material, sj-docx-4-pie-10.1177_09544089221087821 for Design and development of a rapid prototyping system combining traditional fused deposition modeling and reconfigurable pins platform by Vikrant Charak and Amit Kumar Sinha in Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering</p
- …
