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Computing Marginals Using MapReduce [article]

Foto Afrati, Shantanu Sharma, Jeffrey D. Ullman, Jonathan R. Ullman
2015 arXiv   pre-print
We consider the problem of computing the data-cube marginals of a fixed order k (i.e., all marginals that aggregate over k dimensions), using a single round of MapReduce. The focus is on the relationship between the reducer size (number of inputs allowed at a single reducer) and the replication rate (number of reducers to which an input is sent). We show that the replication rate is minimized when the reducers receive all the inputs necessary to compute one marginal of higher order. That
more » ... tion lets us view the problem as one of covering sets of k dimensions with sets of a larger size m, a problem that has been studied under the name "covering numbers." We offer a number of constructions that, for different values of k and m meet or come close to yielding the minimum possible replication rate for a given reducer size.
arXiv:1509.08855v1 fatcat:lq5ne24hkff5xj4taqgbjo7sim

Exploiting Data Sensitivity on Partitioned Data [article]

Sharad Mehrotra, Kerim Yasin Oktay, Shantanu Sharma
2018 arXiv   pre-print
Several researchers have proposed solutions for secure data outsourcing on the public clouds based on encryption, secret-sharing, and trusted hardware. Existing approaches, however, exhibit many limitations including high computational complexity, imperfect security, and information leakage. This chapter describes an emerging trend in secure data processing that recognizes that an entire dataset may not be sensitive, and hence, non-sensitivity of data can be exploited to overcome some of the
more » ... itations of existing encryption-based approaches. In particular, data and computation can be partitioned into sensitive or non-sensitive datasets - sensitive data can either be encrypted prior to outsourcing or stored/processed locally on trusted servers. The non-sensitive dataset, on the other hand, can be outsourced and processed in the cleartext. While partitioned computing can bring new efficiencies since it does not incur (expensive) encrypted data processing costs on non-sensitive data, it can lead to information leakage. We study partitioned computing in two contexts - first, in the context of the hybrid cloud where local resources are integrated with public cloud resources to form an effective and secure storage and computational platform for enterprise data. In the hybrid cloud, sensitive data is stored on the private cloud to prevent leakage and a computation is partitioned between private and public clouds. Care must be taken that the public cloud cannot infer any information about sensitive data from inter-cloud data access during query processing. We then consider partitioned computing in a public cloud only setting, where sensitive data is encrypted before outsourcing. We formally define a partitioned security criterion that any approach to partitioned computing on public clouds must ensure in order to not introduce any new vulnerabilities to the existing secure solution.
arXiv:1812.01741v1 fatcat:hdjemyygzfa4plgzb3tjdvqn4i

Guanine quadruplex DNA structure restricts methylation of CpG dinucleotides genome-wide

Rashi Halder, Kangkan Halder, Priyanka Sharma, Gaurav Garg, Shantanu Sengupta, Shantanu Chowdhury
2010 Molecular Biosystems  
doi:10.1039/c0mb00009d pmid:20877913 fatcat:snifngvqefat7a4d4anu4be74u

Plasmacytoma of the Skull-base: A Rare Tumor

Abhilasha Siyag, Tej P Soni, Anil K Gupta, Lalit M Sharma, Naresh Jakhotia, Shantanu Sharma
2018 Cureus  
Madhawi Sharma (MD, Senior Pathologist, Lab Head, SRL Ltd., Fortis Escorts Hospital, Jaipur, India.  ... 
doi:10.7759/cureus.2073 pmid:29552435 pmcid:PMC5854301 fatcat:hbryln6aw5dbxg4c6f4ti62h5u

Incomplete Immunization Coverage in Delhi: Reasons and Solutions

Shantanu Sharma, Charu Kohli, Nandini Sharma, Devika Mehra
2016 Primary Health Care Open Access  
From the list, all defaulters were then Shantanu Sharma, Charu Kohli, Nandini Sharma and Devika Mehra International Journal of Basic and Applied Biology p-ISSN: 2394-5820, e-ISSN: 2349-2539, Volume 3,  ... 
doi:10.4172/2167-1079.1000240 fatcat:q5lrcgd2xfbndds6ukuqbkybji

Assignment of Different-Sized Inputs in MapReduce [article]

Foto Afrati, Shlomi Dolev, Ephraim Korach, Shantanu Sharma, Jeffrey D. Ullman
2015 arXiv   pre-print
A MapReduce algorithm can be described by a mapping schema, which assigns inputs to a set of reducers, such that for each required output there exists a reducer that receives all the inputs that participate in the computation of this output. Reducers have a capacity, which limits the sets of inputs that they can be assigned. However, individual inputs may vary in terms of size. We consider, for the first time, mapping schemas where input sizes are part of the considerations and restrictions.
more » ... of the significant parameters to optimize in any MapReduce job is communication cost between the map and reduce phases. The communication cost can be optimized by minimizing the number of copies of inputs sent to the reducers. The communication cost is closely related to the number of reducers of constrained capacity that are used to accommodate appropriately the inputs, so that the requirement of how the inputs must meet in a reducer is satisfied. In this work, we consider a family of problems where it is required that each input meets with each other input in at least one reducer. We also consider a slightly different family of problems in which, each input of a set, X, is required to meet each input of another set, Y, in at least one reducer. We prove that finding an optimal mapping schema for these families of problem is NP-hard, and present several approximation algorithms for finding a near optimal mapping schema.
arXiv:1501.06758v1 fatcat:u3x56cwltbgjpj6f25acymhxty

Multiscale Modeling of Nucleosome Dynamics

Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan
2007 Biophysical Journal  
Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid discrete molecular dynamics simulations and an all-atom model for detailed structural investigation.
more » ... a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperatures, suggesting a mechanism of chromatin structural organization whereby histone tails regulate inter-and intranucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed "cold sites", which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A interhistone interfaces, indicating the necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows that bending across the H3-H3 is a prominent mode of intranucleosomal dynamics. We postulate that effects of salts on mononucleosomes can be modeled in discrete molecular dynamics by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mononucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin structure, mediated by salt-bridge interactions with adjacent DNA.
doi:10.1529/biophysj.106.094805 pmid:17142268 pmcid:PMC1796817 fatcat:25ea6ue4xbag5nordhek32zsia

Probing protein aggregation using discrete molecular dynamics

Shantanu Sharma
2008 Frontiers in Bioscience  
Shantanu Sharma is supported by UNC Integrated Biomedical Research Training Program (5T90DA022857-02).  ... 
doi:10.2741/3039 pmid:18508545 pmcid:PMC2497428 fatcat:y4r4yxhiqzbabbbjfutwxm5sce

A Survey on 5G: The Next Generation of Mobile Communication [article]

Nisha Panwar, Shantanu Sharma, Awadhesh Kumar Singh
2015 arXiv   pre-print
The rapidly increasing number of mobile devices, voluminous data, and higher data rate are pushing to rethink the current generation of the cellular mobile communication. The next or fifth generation (5G) cellular networks are expected to meet high-end requirements. The 5G networks are broadly characterized by three unique features: ubiquitous connectivity, extremely low latency, and very high-speed data transfer. The 5G networks would provide novel architectures and technologies beyond
more » ... -the-art architectures and technologies. In this paper, our intent is to find an answer to the question: "what will be done by 5G and how?" We investigate and discuss serious limitations of the fourth generation (4G) cellular networks and corresponding new features of 5G networks. We identify challenges in 5G networks, new technologies for 5G networks, and present a comparative study of the proposed architectures that can be categorized on the basis of energy-efficiency, network hierarchy, and network types. Interestingly, the implementation issues, e.g., interference, QoS, handoff, security-privacy, channel access, and load balancing, hugely effect the realization of 5G networks. Furthermore, our illustrations highlight the feasibility of these models through an evaluation of existing real-experiments and testbeds.
arXiv:1511.01643v1 fatcat:fl6xmpjd55g3dcqq2ypstd5h6i

Security and Privacy Aspects in MapReduce on Clouds: A Survey [article]

Philip Derbeko, Shlomi Dolev, Ehud Gudes, Shantanu Sharma
2016 arXiv   pre-print
MapReduce is a programming system for distributed processing large-scale data in an efficient and fault tolerant manner on a private, public, or hybrid cloud. MapReduce is extensively used daily around the world as an efficient distributed computation tool for a large class of problems, e.g., search, clustering, log analysis, different types of join operations, matrix multiplication, pattern matching, and analysis of social networks. Security and privacy of data and MapReduce computations are
more » ... sential concerns when a MapReduce computation is executed in public or hybrid clouds. In order to execute a MapReduce job in public and hybrid clouds, authentication of mappers-reducers, confidentiality of data-computations, integrity of data-computations, and correctness-freshness of the outputs are required. Satisfying these requirements shield the operation from several types of attacks on data and MapReduce computations. In this paper, we investigate and discuss security and privacy challenges and requirements, considering a variety of adversarial capabilities, and characteristics in the scope of MapReduce. We also provide a review of existing security and privacy protocols for MapReduce and discuss their overhead issues.
arXiv:1605.00677v1 fatcat:32i6kmqxinetbe63i7p7fl7glu

DNA Sequence Mediates Nucleosome Structure and Stability

Shantanu Sharma, Nikolay V. Dokholyan
2008 Biophysical Journal  
Nucleosomes form the fundamental repeating unit of eukaryotic chromatin. Subtle modifications in nucleosome structure and histone tails regulate chromatin states; hence, a comprehensive understanding of alterations in nucleosome structure is of fundamental importance in chromatin biophysics. The nature of core histone organization and nucleosome dynamics have been extensively studied using biophysical experiments, multiscale computational models, and simulations ((1,2) and references therein).
more » ... owever, the precise mechanisms of how DNA sequence mediates nucleosome structure and stability remains to be completely understood. The eviction of H2A/H2B core histones from the histone octamer is known to expose nucleosomal DNA for transcription. In this issue of Biophysical Journal, Kelbauskas et al. (3) have investigated the sequence dependence of H2A/H2B eviction mediated by histone chaperone yNAP-1 using single-molecule Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) experiments. Single molecule experiments have gained a newfound interest in probing chromatin dynamics, in part, because of their ability to study subtle variations in chromatin dynamics at a single nucleosome level, rather than probing population-averaged properties (1,4-6). H2A/H2B dimers interact with nearly 30 basepairs of nucleosomal DNA, thus depletion of H2A/H2B dimers from the nucleosomes results in significant exposure of the nucleosomal DNA. Understanding H2A/H2B depletion is of special significance in chromatin biophysics as loss of H2A/H2B histones is associated with important cellular processes, including transcription elongation, ATP-dependent nucleosome remodeling, and function of RNA polymerase. In a previous study (7) , Kelbauskas et al. used FRET and FCS assays to study the sequence dependence of mononucleosome structure and stability of chromatin reconstitution in bulk solution conditions. This sequence dependence was tested in nucleosomes having three physiologically relevant DNA sequences: 1), sea urchin 5S rDNA; 2), DNA from yeast GAL10 promoter sequence; and 3), DNA Mouse Mammary Tumor Virus promoter DNA (MMTV-B). While GAL10 and MMTV-B nucleosomes are known to exhibit significant conformational dynamics associated with gene activation in vivo, sea urchin 5S rDNA is extensively used as a template DNA for in vitro studies of nucleosome dynamics. Nucleosome stability was tested by analyzing the conformation-dependent FRET response in the three nucleosomes, with FRET donor and acceptor fluorophores attached to nucleosomal DNA. The authors showed that upon dilution to subnanomolar concentrations (corresponding to single-molecule studies), the efficiency of FRET signals from MMTV-B and GAL10 nucleosomes is reduced by as much as 35%, while that from 5S nucleosomes remains undiminished. The in vitro FCS assays showed that the relative diffusion coefficient for 5S nucleosomes was higher than that of MMTV-B and GAL10 nucleosomes, suggesting that under ambient conditions, 5S nucleosomes are more compact, as compared to MMTV-B and GAL10 nucleosomes. Similar results are observed for the three sets of nucleosomes at elevated temper-atures (42°C) and upon treatment with high salt concentrations. These observations suggest that 5S nucleosomes are more stable than MMTV-B and GAL10 nucleosomes. In coherence with genomic regulatory mechanisms, these differences in nucleosome structure and stability may mediate nucleosome recognition and histone modifications. In this issue, Kelbauskas et al. (3) report that treatment with histone chaperone yNAP-1 causing H2A/H2B histone eviction leads to the same FRET changes as observed in corresponding subnanomolar dilution assays. Notably, in both assays, the extent of reduction in FRET signal was also similar for MMTV-B and GAL10 nucleosomes. Furthermore, salt stability assays suggest that while yNAP-1 histone chaperone was acting on each of the three nucleosomes, 5S nucleosomes exhibit no FRET change. These results reinforce the previous studies that H2A/ H2B release causes sequence-dependent FRET responses. The yNAP1 assay also suggests that the three mono-nucleosomes follow two-state dynamics with folded and unfolded states. While the two-state behavior is most pronounced in 5S nucleosomes, the rate of nucleosomal DNA dynamics is enhanced in GAL10 and MMTV-B nucleosomes. Simulations of a nucleosome core particle having Xenopus laevis core histones and a palindromic DNA from human a-satellite sequence (2) also suggest specific interactions between H2A-H2B histones and nucleosomal DNA. Functionally important interactions are reported at interface of H4-H2A and H4-H2B histones (2), suggesting that the sequence-dependent eviction of H2A-H2B dimers may also be evolutionarily conserved in higher eukaryotes. Kelbauskas et al. (3) analyze two possible hypotheses for the biophysical mechanism leading to differences in FRET response in these nucleosomes under subnanomolar concentrations: the first hypothesis suggesting differences
doi:10.1529/biophysj.107.119172 pmid:17933872 pmcid:PMC2134875 fatcat:xu5gms4p2zakzixowr2ghlsoq4

Clinical correlation of vitamin D in depression

Nitin Sharma, Shantanu Bharti, Abdul Qadir Jilani, Anju Agarwal, Saloni Singh, Ruchita Sharma
2019 International Journal of Advances in Medicine  
Literature has substantially advanced our understanding of the action of vitamin D in depression, much is still unknown concerning how vitamin D relates to dimensions of depression. Hence, authors aimed to examine the relationship of vitamin D in patients of depression, its correlation with the severity of depression and different symptom domains of depression.Methods: This Hospital based case control study included 75 patients with depression and 50 controls who were age and gender matched.
more » ... k's Depression Inventory II was used to assess the severity and symptom domains of depression. Vitamin D levels was assessed using Enhanced Chemiluminescence Technique.Results: Vitamin D deficiency was found significantly (<0.001*) among cases than controls. Significant (0.003*) inverse correlation was observed between severity of depression and vitamin D level.In cognitive symptoms, pessimism, punishment feeling, self-criticism, suicidal thoughts and worthlessness were found significantly higher among vitamin D deficient patients. However, in somatic-affective symptoms, crying, indecisiveness, loss of energy, irritability, concentration difficulty and being tired were the significant by prominent symptoms in vitamin D deficient patients.Conclusions: Vitamin D (<50 nmol/L) was found to be significantly associated with depressive symptoms with cognitive and somatic-affective symptoms being affected by vitamin D deficiency.
doi:10.18203/2349-3933.ijam20193251 fatcat:vqy3mu46vfh5be7454hidl7vgy

Partitioned Data Security on Outsourced Sensitive and Non-sensitive Data [article]

Sharad Mehrotra, Shantanu Sharma, Jeffrey D. Ullman, Anurag Mishra
2018 arXiv   pre-print
Despite extensive research on cryptography, secure and efficient query processing over outsourced data remains an open challenge. This paper continues along the emerging trend in secure data processing that recognizes that the entire dataset may not be sensitive, and hence, non-sensitivity of data can be exploited to overcome limitations of existing encryption-based approaches. We propose a new secure approach, entitled query binning (QB) that allows non-sensitive parts of the data to be
more » ... ced in clear-text while guaranteeing that no information is leaked by the joint processing of non-sensitive data (in clear-text) and sensitive data (in encrypted form). QB maps a query to a set of queries over the sensitive and non-sensitive data in a way that no leakage will occur due to the joint processing over sensitive and non-sensitive data. Interestingly, in addition to improve performance, we show that QB actually strengthens the security of the underlying cryptographic technique by preventing size, frequency-count, and workload-skew attacks.
arXiv:1812.09233v1 fatcat:epxyephd75f5pc7x5se7vnt3iu

The path of DNA in the kinetochore

Kerry Bloom, Shantanu Sharma, Nikolay V. Dokholyan
2006 Current Biology  
E-mail: joshz@helix.nih.gov Correspondences The path of DNA in the kinetochore Kerry Bloom 1 , Shantanu Sharma 2 , and Nikolay V. Dokholyan 2 USA.  ... 
doi:10.1016/j.cub.2006.03.054 pmid:16631569 pmcid:PMC2112771 fatcat:rcvfpyu5wfdwlm7t5bvi5meqba

Depression and anxiety in patients with epilepsy

Sanyam Gupta, Nitin Sharma, Shantanu Bharti, Ruchita Sharma, Ajay Kohli, Anju Agarwal, Abdul Qadir Jilani, Ritu Shukla
2018 International Journal of Advances in Medicine  
Anxiety and depression are commonly found in epileptic patients. However, the etiology behind the mechanism remains multifactorial, mostly because of variability in study settings. In order to fill the knowledge gap, we investigated the prevalence of anxiety and depression among epileptic patients and their correlation with certain demographic variables.Methods: In a Cross Sectional Out Patient Based Study, a total of 147 patients with epilepsy were recruited and evaluated for inclusion and
more » ... usion criterion. Participants who met the inclusion criterion were assessed using standardized scales HARS and HADS rating scale for anxiety and depressive symptoms respectively.Results: 100 participants were included with mean age of 33.63 years for men and 30.16 years for females. 27% showed mild to severe anxiety and 21% had mild to moderate depression. Prevalence of both anxiety and depression was found more among females, singles, participants from urban background and having partial epilepsy. Significantly (p-0.020*) higher anxiety was seen in patients with partial epilepsy than those with generalized epilepsy.Conclusions: Individuals with partial epilepsy are more prone to get affected from comorbid disorder like anxiety and depression, especially females, singles and those from urban domicile.
doi:10.18203/2349-3933.ijam20183906 fatcat:456woocdtndevan7k7v5xzljfe
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