2,223 results on '"Sundaresan, P."'
Search Results
202. Publisher Correction: A pipeline for malignancy and therapy agnostic assessment of cancer drug response using cell mass measurements
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Kimmerling, Robert J., Stevens, Mark M., Olcum, Selim, Minnah, Anthony, Vacha, Madeleine, LaBella, Rachel, Ferri, Matthew, Wasserman, Steven C., Fujii, Juanita, Shaheen, Zayna, Sundaresan, Srividya, Ribadeneyra, Drew, Jayabalan, David S., Agte, Sarita, Aleman, Adolfo, Criscitiello, Joseph A., Niesvizky, Ruben, Luskin, Marlise R., Parekh, Samir, Rosenbaum, Cara A., Tamrazi, Anobel, and Reid, Clifford A.
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- 2023
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203. Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network
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Pacheco, Jennifer A., Rasmussen, Luke V., Wiley, Jr., Ken, Person, Thomas Nate, Cronkite, David J., Sohn, Sunghwan, Murphy, Shawn, Gundelach, Justin H., Gainer, Vivian, Castro, Victor M., Liu, Cong, Mentch, Frank, Lingren, Todd, Sundaresan, Agnes S., Eickelberg, Garrett, Willis, Valerie, Furmanchuk, Al’ona, Patel, Roshan, Carrell, David S., Deng, Yu, Walton, Nephi, Satterfield, Benjamin A., Kullo, Iftikhar J., Dikilitas, Ozan, Smith, Joshua C., Peterson, Josh F., Shang, Ning, Kiryluk, Krzysztof, Ni, Yizhao, Li, Yikuan, Nadkarni, Girish N., Rosenthal, Elisabeth A., Walunas, Theresa L., Williams, Marc S., Karlson, Elizabeth W., Linder, Jodell E., Luo, Yuan, Weng, Chunhua, and Wei, WeiQi
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- 2023
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204. A design of experiments screen reveals that Clostridium novyi-NT spore germinant sensing is stereoflexible for valine and its analogs
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Sundaresan, Ajitha, Le Ngoc, Mai, Wew, Marvell Ung, Ramkumar, Varsha, Raninga, Prahlad, Sum, Rongji, and Cheong, Ian
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- 2023
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205. Subgroup and subtype-specific outcomes in adult medulloblastoma.
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Coltin, Hallie, Sundaresan, Lakshmikirupa, Smith, Kyle, Skowron, Patryk, Massimi, Luca, Eberhart, Charles, Schreck, Karisa, Gupta, Nalin, Weiss, William, Tirapelli, Daniela, Carlotti, Carlos, Li, Kay, Ryzhova, Marina, Golanov, Andrey, Zheludkova, Olga, Absalyamova, Oksana, Okonechnikov, Konstantin, Stichel, Damian, von Deimling, Andreas, Giannini, Caterina, Raskin, Scott, Van Meir, Erwin, Chan, Jennifer, Fults, Daniel, Chambless, Lola, Kim, Seung-Ki, Vasiljevic, Alexandre, Faure-Conter, Cecile, Vibhakar, Rajeev, Jung, Shin, Leary, Sarah, Mora, Jaume, McLendon, Roger, Pollack, Ian, Hauser, Peter, Grajkowska, Wieslawa, Rubin, Joshua, van Veelen, Marie-Lise, French, Pim, Kros, Johan, Liau, Linda, Pfister, Stefan, Kool, Marcel, Kijima, Noriyuki, Taylor, Michael, Packer, Roger, Northcott, Paul, Korshunov, Andrey, and Ramaswamy, Vijay
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Adult ,DNA methylation profiling ,Medulloblastoma ,Molecular groups ,Risk stratification ,Adolescent ,Adult ,Biomarkers ,Tumor ,Cerebellar Neoplasms ,Cohort Studies ,Female ,Humans ,Male ,Medulloblastoma ,Progression-Free Survival ,Risk Factors ,Young Adult - Abstract
Medulloblastoma, a common pediatric malignant central nervous system tumour, represent a small proportion of brain tumours in adults. Previously it has been shown that in adults, Sonic Hedgehog (SHH)-activated tumours predominate, with Wingless-type (WNT) and Group 4 being less common, but molecular risk stratification remains a challenge. We performed an integrated analysis consisting of genome-wide methylation profiling, copy number profiling, somatic nucleotide variants and correlation of clinical variables across a cohort of 191 adult medulloblastoma cases identified through the Medulloblastoma Advanced Genomics International Consortium. We identified 30 WNT, 112 SHH, 6 Group 3, and 41 Group 4 tumours. Patients with SHH tumours were significantly older at diagnosis compared to other subgroups (p
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- 2021
206. SpaceBeam
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Woodford, Timothy, Zhang, Xinyu, Chai, Eugene, Sundaresan, Karthikeyan, and Khojastepour, Amir
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Information and Computing Sciences ,Communications Engineering ,Engineering - Published
- 2021
207. Genetic diversity and population structure assessment of Hellenia speciosa from Indian agro-ecological regions using inter-simple sequence repeat markers
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Prabhu, Kamasamudra N., Rodrigues, Vereena, Kumar, Amit, Kumar, Manish, Srivastava, Sharad, Shukla, Ashutosh K., and Sundaresan, Velusamy
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- 2023
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208. Perceptions towards Engagement: The Case of Thai English Majors in an International Higher Education Environment
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Loo, Daron Benjamin, Keough, Wendy, Sundaresan, Anita, and Thomas, Darrin
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This study examines Thai English majors' perceptions towards engagement. The aim of this study is to be better informed of the English language learning experience of students in an international environment where English is used as a foreign language. A mixed methods approach was employed. A modified version of the National Survey of Student Engagement (NSSE) was used to collect quantitative data, while qualitative data was collected through a focus group interview. Correlation scores and one-way ANOVA were calculated to examine the survey data. Results indicated that almost all the categories of engagement were significantly correlated, except for the correlation between supportive learning environment and faculty interaction. The one-way ANOVA test, on the other hand, revealed that students' year of study had a significant effect on at least three components of engagement. The quantitative results were further informed by data collected from a focus group interview. From the interview, students were able to describe the classroom atmosphere, teachers' pedagogical strategies, as well as challenges they faced in their studies. From the findings, it was evident that the Thai students were open to different pedagogical approaches, and that they were not culturally constrained. This may be the hallmark of international education, wherein students take on a contextualized approach to learning, aside from being in a context where a foreign language is used.
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- 2018
209. Relapsed Multiple Myeloma with Anaplastic Transformation
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Sundaresan, Durgadevi, Bhagat, Snehvarsha, Sreedharanunni, Sreejesh, Sachdeva, Man Updesh Singh, Malhotra, Pankaj, and Sharma, Praveen
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- 2024
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210. Investigation of the magnetic ground state of the ordered double perovskite Sr2YbRuO6: a tale of two transitions
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Sharma, Shivani, Adroja, D. T., Ritter, C., Khalyavin, D., Manuel, P., Stenning, Gavin B. G., Sundaresan, A., Hillier, A. D., Deen, P. P., Khomskii, D. I., and Langridge, S.
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Condensed Matter - Strongly Correlated Electrons - Abstract
Comprehensive muon spin rotation/relaxation (muSR) and neutron powder diffraction (NPD) studies supported via bulk measurements have been performed on the ordered double perovskite Sr2YbRuO6 to investigate the nature of the magnetic ground state. Two sharp transitions at TN1 ~ 42 K and TN2 ~ 36 K have been observed in the static and dynamic magnetization measurements, coinciding with the heat capacity data. In order to confirm the origin of the observed phase transitions and the magnetic ground state, microscopic evidences are presented here. An initial indication of long-range magnetic ordering comes from a sharp drop in the muon initial asymmetry and a peak in the relaxation rate near TN1. NPD confirms that the magnetic ground state of Sr2YbRuO6 consists of an antiferromagnetic (AFM) structure with interpenetrating lattices of parallel Yb3+ and Ru5+ moments lying in the ab-plane and adopting a A-type AFM structure. Intriguingly, a small but remarkable change is observed in the long-range ordering parameters at TN2 confirming the presence of a weak spin reorientation (i.e. change in spin configuration) transition of Ru and Yb moments, as well as a change in the magnetic moment evolution of the Yb3+ spins at TN2. The temperature dependent behaviour of the Yb3+ and Ru5+ moments suggests that the 4d-electrons of Ru5+ play a dominating role in stabilizing the long range ordered magnetic ground state in the double perovskite Sr2YbRuO6 whereas only the Yb3+ moments show an arrest at TN2. The observed magnetic structure and the presence of a ferromagnetic interaction between Ru- and Yb- ions are explained with use of the Goodenough-Kanamori-Anderson (GKA) rules. Possible reasons for the presence of the second magnetic phase transition and of a compensation point in the magnetization data are linked to competing mechanisms of magnetic anisotropy., Comment: 28 pages, 12 figures
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- 2020
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211. The Erlang Weighted Tree, A New Branching Process
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Moharrami, Mehrdad, Subramanian, Vijay, Liu, Mingyan, and Sundaresan, Rajesh
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Mathematics - Probability ,60J80, 05C80, 60K35 - Abstract
In this paper, we study a new discrete tree and the resulting branching process, which we call the \textbf{E}rlang \textbf{W}eighted \textbf{T}ree(\textbf{EWT}). The EWT appears as the local weak limit of a random graph model proposed in~\cite{La2015}. In contrast to the local weak limit of well-known random graph models, the EWT has an interdependent structure. In particular, its vertices encode a multi-type branching process with uncountably many types. We derive the main properties of the EWT, such as the probability of extinction, growth rate, etc. We show that the probability of extinction is the smallest fixed point of an operator. We then take a point process perspective and analyze the growth rate operator. We derive the Krein--Rutman eigenvalue $\beta_0$ and the corresponding eigenfunctions of the growth operator, and show that the probability of extinction equals one if and only if $\beta_0 \leq 1$.
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- 2020
212. Plant zygote development: recent insights and applications to clonal seeds
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Khanday, Imtiyaz and Sundaresan, Venkatesan
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Biotechnology ,Reproductive health and childbirth ,Animals ,Crops ,Agricultural ,Diploidy ,Gene Expression Regulation ,Plant ,Haploidy ,Seeds ,Zygote ,Biochemistry and Cell Biology ,Microbiology ,Plant Biology ,Plant Biology & Botany - Abstract
In flowering plants, haploid gametes - an egg cell and a sperm cell fuse to form the first diploid cell - the zygote. The zygote is the progenitor stem cell that gives rise to all the embryonic and post embryonic tissues and organs. Unlike animals, both maternal and paternal gene products participate in the initial development of zygotes in plants. Here, we discuss recent advances in understanding of the zygotic transition and embryo initiation in angiosperms, including the role of parental contributions to gene expression in the zygote. We further discuss utilization of this knowledge in agricultural biotechnology through synthetic apomixis. Parthenogenesis obtained by manipulation of embryogenic factors, combined with mutations that bypass meiosis, enables clonal propagation of hybrid crops through seeds.
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- 2021
213. Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays).
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Murphy, Katherine M, Edwards, Joseph, Louie, Katherine B, Bowen, Benjamin P, Sundaresan, Venkatesan, Northen, Trent R, and Zerbe, Philipp
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Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges, including interactions with soil-dwelling microbial communities. However, the role of specialized metabolites in modulating plant-microbiome interactions often remains elusive. In this study, we report that maize (Zea mays) diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 (anther ear 2), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. The Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other large-scale metabolome alterations. Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.
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- 2021
214. DEFECTIVE EMBRYO AND MERISTEMS genes are required for cell division and gamete viability in Arabidopsis
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Lee, Chin Hong, Hawker, Nathaniel P, Peters, Jonathan R, Lonhienne, Thierry GA, Gursanscky, Nial R, Matthew, Louisa, Brosnan, Christopher A, Mann, Christopher WG, Cromer, Laurence, Taochy, Christelle, Ngo, Quy A, Sundaresan, Venkatesan, Schenk, Peer M, Kobe, Bostjan, Borges, Filipe, Mercier, Raphael, Bowman, John L, and Carroll, Bernard J
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Biochemistry and Cell Biology ,Biological Sciences ,Contraception/Reproduction ,Genetics ,Aetiology ,1.1 Normal biological development and functioning ,2.1 Biological and endogenous factors ,Underpinning research ,Generic health relevance ,Alleles ,Arabidopsis ,Arabidopsis Proteins ,Cell Division ,Cell Survival ,Evolution ,Molecular ,Gene Dosage ,Gene Expression Regulation ,Plant ,Genes ,Essential ,Genes ,Plant ,Genetic Complementation Test ,Germ Cells ,Meiosis ,Multigene Family ,Organ Specificity ,Pollen ,RNA ,Messenger ,RNA-Binding Proteins ,Seeds ,Transgenes ,ran GTP-Binding Protein ,Developmental Biology - Abstract
The DEFECTIVE EMBRYO AND MERISTEMS 1 (DEM1) gene encodes a protein of unknown biochemical function required for meristem formation and seedling development in tomato, but it was unclear whether DEM1's primary role was in cell division or alternatively, in defining the identity of meristematic cells. Genome sequence analysis indicates that flowering plants possess at least two DEM genes. Arabidopsis has two DEM genes, DEM1 and DEM2, which we show are expressed in developing embryos and meristems in a punctate pattern that is typical of genes involved in cell division. Homozygous dem1 dem2 double mutants were not recovered, and plants carrying a single functional DEM1 allele and no functional copies of DEM2, i.e. DEM1/dem1 dem2/dem2 plants, exhibit normal development through to the time of flowering but during male reproductive development, chromosomes fail to align on the metaphase plate at meiosis II and result in abnormal numbers of daughter cells following meiosis. Additionally, these plants show defects in both pollen and embryo sac development, and produce defective male and female gametes. In contrast, dem1/dem1 DEM2/dem2 plants showed normal levels of fertility, indicating that DEM2 plays a more important role than DEM1 in gamete viability. The increased importance of DEM2 in gamete viability correlated with higher mRNA levels of DEM2 compared to DEM1 in most tissues examined and particularly in the vegetative shoot apex, developing siliques, pollen and sperm. We also demonstrate that gamete viability depends not only on the number of functional DEM alleles inherited following meiosis, but also on the number of functional DEM alleles in the parent plant that undergoes meiosis. Furthermore, DEM1 interacts with RAS-RELATED NUCLEAR PROTEIN 1 (RAN1) in yeast two-hybrid and pull-down binding assays, and we show that fluorescent proteins fused to DEM1 and RAN1 co-localize transiently during male meiosis and pollen development. In eukaryotes, RAN is a highly conserved GTPase that plays key roles in cell cycle progression, spindle assembly during cell division, reformation of the nuclear envelope following cell division, and nucleocytoplasmic transport. Our results demonstrate that DEM proteins play an essential role in cell division in plants, most likely through an interaction with RAN1.
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- 2021
215. Pythia: AI-assisted Code Completion System
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Svyatkovskiy, Alexey, Zhao, Ying, Fu, Shengyu, and Sundaresan, Neel
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Computer Science - Software Engineering ,Computer Science - Machine Learning - Abstract
In this paper, we propose a novel end-to-end approach for AI-assisted code completion called Pythia. It generates ranked lists of method and API recommendations which can be used by software developers at edit time. The system is currently deployed as part of Intellicode extension in Visual Studio Code IDE. Pythia exploits state-of-the-art large-scale deep learning models trained on code contexts extracted from abstract syntax trees. It is designed to work at a high throughput predicting the best matching code completions on the order of 100 $ms$. We describe the architecture of the system, perform comparisons to frequency-based approach and invocation-based Markov Chain language model, and discuss challenges serving Pythia models on lightweight client devices. The offline evaluation results obtained on 2700 Python open source software GitHub repositories show a top-5 accuracy of 92\%, surpassing the baseline models by 20\% averaged over classes, for both intra and cross-project settings., Comment: Published in Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD '19)
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- 2019
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216. Large Time Behaviour and the Second Eigenvalue Problem for Finite State Mean-Field Interacting Particle Systems
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Yasodharan, Sarath and Sundaresan, Rajesh
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Mathematics - Probability ,Mathematics - Optimization and Control ,60F10, 60K35 (Primary) 47A75, 60J75, 68M20 (Secondary) - Abstract
This article examines large time behaviour of finite state mean-field interacting particle systems. Our first main result is a sharp estimate (in the exponential scale) on the time required for convergence of the empirical measure process of the $N$-particle system to its invariant measure; we show that when time is of the order of $\exp\{N\Lambda\}$ for a suitable constant $\Lambda \geq 0$, the process has mixed well and it is close to its invariant measure. We then obtain large-$N$ asymptotics of the second largest eigenvalue of the generator associated with the empirical measure process when it is reversible with respect to its invariant measure. We show that its absolute value scales as $\exp\{-N\Lambda\}$. The main tools used in establishing our results are the large deviation properties of the empirical measure process from its large-$N$ limit. As an application of the study of large time behaviour, we also show convergence of the empirical measure of the system of particles to a global minimum of a certain `entropy' function when particles are added over time in a controlled fashion. The controlled addition of particles is analogous to the cooling schedule associated with the search for a global minimum of a function using the simulated annealing algorithm., Comment: 33 pages. Added references and re-organised the introduction
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- 2019
217. Linear magnetoelectric effect in the antiferromagnetic Sm2BaCuO5
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Yanda, Premakumar, Ter-Oganessian, N. V., and Sundaresan, A.
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Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Materials Science - Abstract
We report the discovery of linear magnetoelectric effect in the well-known green phase compound, Sm2BaCuO5, which crystallizes in the centrosymmetric orthorhombic (Pnma) structure. Magnetization and specific heat measurements reveal the long-range antiferromagnetic ordering of Cu2+ and Sm3+-ions moments at TN1 = 23 K and TN2 = 5 K, respectively. Applied magnetic field induces dielectric anomaly at TN1 whose magnitude increases with field, which results in significant (1.7%) magnetocapacitance effect. On the other hand, the dielectric anomaly observed in zero-applied magnetic field at TN2 shows a small (0.4%) magnetocapacitance effect. Interestingly, applied magnetic field induces an electric polarization below TN1 and the polarization varies linearly up to the maximum applied field of 9 T with the magnetoelectric coefficient {\alpha} ~ 4.4 ps/m, demonstrating high magnetoelectric coupling. Below TN2, the electric polarization decreases from 35 to 29 {\mu}C/m2 at 2 K and 9 T due to ordering of Sm-sublattice. The observed linear magnetoelectricity in Sm2BaCuO5 is explained using symmetry analysis., Comment: 22 pages, 5 figures (to be published in Phys. Rev. B)
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- 2019
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218. Muon spin rotation and neutron scattering investigations of the B-site ordered double perovskite Sr2DyRuO6
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Adroja, D. T., Sharma, Shivani, Ritter, C., Hillier, A. D., Tomy, C. V., Singh, R., Smith, R. I., Koza, M., Sundaresan, A., and Langridge, S.
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Condensed Matter - Strongly Correlated Electrons - Abstract
The magnetic ground state of double perovskite Sr2DyRuO6 has been investigated using muon spin rotation and relaxation (muSR), neutron powder diffraction (NPD) and inelastic neutron scattering (INS), in addition to heat capacity and magnetic susceptibility (ac and dc) measurements. A clear signature of a long-range ordered magnetic ground state has been observed in the heat capacity data, which exhibit two sharp anomalies at 39.5 and 36 K found as well in the magnetic data. Further confirmation of long-range magnetic ordering comes from a sharp drop in the muon initial asymmetry and a peak in the relaxation rate at 40 K, along with a weak anomaly near 36 K. Based on temperature dependent NPD, the low temperature magnetic structure contains two interpenetrating lattices of Dy and Ru5, forming an antiferromagnetic ground state below 39.5 K with magnetic propagation vector k = (0,0,0). The magnetic moments of Dy and Ru at 3.5 K are pointing along the crystallographic b-axis with values of muDy = 4.92(10) muB and muRu = 1.94(7) muB, respectively. The temperature dependence of the Ru moments follows a mean field type behaviour, while that of the Dy moments exhibits a deviation indicating that the primary magnetic ordering is induced by the order of the 4d electrons of Ru rather than that of its proper 4f Dy electrons. The origin of the second anomaly observed in the heat capacity data at 36.5 K must be connected to a very small spin reorientation as the NPD studies do not reveal any clear change in the observed magnetic Bragg peaks positions or intensities between these two transitions. INS measurements reveal the presence of crystal field excitations (CEF) in the paramagnetic state with overall CEF splitting of 73.8 meV, in agreement with the point change model calculations., Comment: 25 pages, 14 figures
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- 2019
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219. Verifying Multipartite Entangled GHZ States via Multiple Quantum Coherences
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Wei, Ken X., Lauer, Isaac, Srinivasan, Srikanth, Sundaresan, Neereja, McClure, Douglas T., Toyli, David, McKay, David C., Gambetta, Jay M., and Sheldon, Sarah
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Quantum Physics - Abstract
The ability to generate and verify multipartite entanglement is an important benchmark for near-term quantum devices devices. We develop a scalable entanglement metric based on multiple quantum coherences, and demonstrate experimentally on a 20-qubit superconducting device - the IBM Q System One. We report a state fidelity of 0.5165$\pm$0.0036 for an 18-qubit GHZ state, indicating multipartite entanglement across all 18 qubits. Our entanglement metric is robust to noise and only requires measuring the population in the ground state; it can be readily applied to other quantum devices to verify multipartite entanglement., Comment: 7+4 pages, comments welcome
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- 2019
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220. Reputation-Based Information Design for Inducing Prosocial Behavior
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Reiffers-Masson, Alexandre and Sundaresan, Rajesh
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Computer Science - Social and Information Networks ,Computer Science - Computer Science and Game Theory - Abstract
We study the idea of information design for inducing prosocial behavior in the context of electricity consumption. We consider a continuum of agents. Each agent has a different intrinsic motivation to reduce her power consumption. Each agent models the power consumption of the others via a distribution. Using this distribution, agents will anticipate their reputational benefit and choose a power consumption by trading off their own intrinsic motivation to do a prosocial action, the cost of this prosocial action and their reputation. Initially, the service provider can provide two types of quantized feedbacks of the power consumption. We study their advantages and disadvantages. For each feedback, we characterize the corresponding mean field equilibrium, using a fixed point equation. Besides computing the mean field equilibrium, we highlight the need for a systematic study of information design, by showing that revealing less information to the society can lead to more prosociality. In the last part of the paper, we introduce the notion of privacy and provide a new quantized feedback, more flexible than the previous ones, that respects agents' privacy concern but at the same time improves prosociality. The results of this study are also applicable to generic resource sharing problems., Comment: 24 pages, 10 figures
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- 2019
221. Learning to Detect an Odd Markov Arm
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Karthik, P. N. and Sundaresan, Rajesh
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Computer Science - Information Theory - Abstract
A multi-armed bandit with finitely many arms is studied when each arm is a homogeneous Markov process on an underlying finite state space. The transition law of one of the arms, referred to as the odd arm, is different from the common transition law of all other arms. A learner, who has no knowledge of the above transition laws, has to devise a sequential test to identify the index of the odd arm as quickly as possible, subject to an upper bound on the probability of error. For this problem, we derive an asymptotic lower bound on the expected stopping time of any sequential test of the learner, where the asymptotics is as the probability of error vanishes. Furthermore, we propose a sequential test, and show that the asymptotic behaviour of its expected stopping time comes arbitrarily close to that of the lower bound. Prior works deal with independent and identically distributed arms, whereas our work deals with Markov arms. Our analysis of the rested Markov setting is a key first step in understanding the difficult case of restless Markov setting, which is still open.
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- 2019
222. Compact Scene Graphs for Layout Composition and Patch Retrieval
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Tripathi, Subarna, Sridhar, Sharath Nittur, Sundaresan, Sairam, and Tang, Hanlin
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Structured representations such as scene graphs serve as an efficient and compact representation that can be used for downstream rendering or retrieval tasks. However, existing efforts to generate realistic images from scene graphs perform poorly on scene composition for cluttered or complex scenes. We propose two contributions to improve the scene composition. First, we enhance the scene graph representation with heuristic-based relations, which add minimal storage overhead. Second, we use extreme points representation to supervise the learning of the scene composition network. These methods achieve significantly higher performance over existing work (69.0% vs 51.2% in relation score metric). We additionally demonstrate how scene graphs can be used to retrieve pose-constrained image patches that are semantically similar to the source query. Improving structured scene graph representations for rendering or retrieval is an important step towards realistic image generation., Comment: To appear in CVPRW 2019 (CEFRL)
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- 2019
223. Highly tunable magnetic spirals and electric polarization in Gd$_{0.5}$Dy$_{0.5}$MnO$_3$
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De, Chandan, Bag, Rabindranath, Singh, Surjeet, Orlandi, Fabio, Manuel, P., Langridge, Sean, Sanyal, Milan K, Rao, C. N. R., Mostovoy, Maxim, and Sundaresan, A.
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Condensed Matter - Strongly Correlated Electrons - Abstract
Recent progress in the field of multiferroics led to the discovery of many new materials in which ferroelectricity is induced by cycloidal spiral orders. The direction of the electric polarization is typically constrained by spin anisotropies and magnetic field. Here, we report that the mixed rare-earth manganite, Gd$_{0.5}$Dy$_{0.5}$MnO$_3$, exhibits a spontaneous electric polarization along a general direction in the crystallographic ac-plane, which is suppressed below 10 K but re-emerges in an applied magnetic field. Neutron diffraction measurements show that the polarization direction results from a large tilt of the spiral plane with respect to the crystallographic axes and that the suppression of ferroelectricity is caused by the transformation of a cycloidal spiral into a helical one, a unique property of this rare-earth manganite. The freedom in the orientation of the spiral plane allows for a fine magnetic control of ferroelectricity, i.e. a rotation as well as a strong enhancement of the polarization depending on the magnetic field direction. We show that this unusual behavior originates from the coupling between the transition metal and rare-earth magnetic subsystems., Comment: 20 pages, 8 figures (to be published in Physical Review Materials)
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- 2019
224. In silico and In vitro Analysis of Nigella sativa Bioactives Against Chorismate Synthase of Listeria monocytogenes: a Target Protein for Biofilm Inhibition
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Vanajothi, Ramar, Bhavaniramya, Sundaresan, Vijayakumar, Rajendran, Alothaim, Abdulaziz S., Alqurashi, Yaser E., Vishnupriya, Selvaraju, Vaseeharan, Baskaralingam, and Umadevi, Muthu
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- 2023
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225. Quantum Chemical and Electrochemical Evaluation of Isoperthiocyanic Acid Derivatives as Novel Corrosion Inhibitors of Mild Steel in 2 M Hydrochloric Acid
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Murthy, Ram, Vedarajan, Raman, and Sundaresan, C. N.
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- 2022
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226. Machinability of Nimonic Alloy 90 in µ-Titanium Carbide Mixed Electrical Discharge Machining
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Sundaresan, Dinesh, Marappan, Loganathan, Thangavelu, Karthikeyan, and Venkatraman, Vijayan
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- 2022
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227. Evidence of a cluster spin-glass state in the B-site disordered perovskite SrTi0.5Mn0.5O3
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Sharma, Shivani, Yadav, Poonam, Sau, Tusita, Yanda, Premakumar, Baker, Peter J., da Silva, Ivan, Sundaresan, A., and Lalla, N. P.
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Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons - Abstract
SrTi0.5Mn0.5O3 (STMO) is a chemically disordered perovskite having random distribution of Ti and Mn over 1b site. Striking discrepancies about the structural and magnetic properties of STMO demands detailed analysis which is addressed. To explore the magnetic ground state of STMO, static and dynamic magnetic properties were studied over a broad temperature range (2-300 K). The dc, ac magnetization show a cusp like peak at Tf ~ 14 K, which exhibits field and frequency dependence. The thermoremanent magnetization is characterized by using stretched exponential function and characteristic time suggests the existence of spin clusters. Also the other features observed in magnetic memory effect, muon spin resonance/rotation and neutron powder diffraction confirm the existence of cluster spin glass state in STMO, rather than the long range ordered ground state. Intriguingly, the observed spin relaxation can be attributed to the dilute magnetism due to non-magnetic doping at Mn-site and competing antiferromagnetic and ferromagnetic interactions resulting from the site disorder., Comment: 17 pages, 7 figures
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- 2019
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228. A Mean-field Approach for Controlling Singularly Perturbed Multi-population SIS Epidemics
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T., Akhil P., Altman, Eitan, and Sundaresan, Rajesh
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Mathematics - Optimization and Control - Abstract
We consider a multi-population epidemic model with one or more (almost) isolated communities and one mobile community. Each of the isolated communities has contact within itself and, in addition, contact with the outside world but only through the mobile community. The contact rate between the mobile community and the other communities is assumed to be controlled. We first derive a multidimensional ordinary differential equation (ODE) as a mean-field fluid approximation to the process of the number of infected nodes, after appropriate scaling. We show that the approximation becomes tight as the sizes of the communities grow. We then use a singular perturbation approach to reduce the dimension of the ODE and identify an optimal control policy on this system over a fixed time horizon via Pontryagin's minimum principle. We then show that this policy is close to optimal, within a certain class, on the original problem for large enough communities. From a phenomenological perspective, we show that the epidemic may sustain in time in all communities (and thus the system has a nontrivial metastable regime) even though in the absence of the mobile nodes the epidemic would die out quickly within each of the isolated communities., Comment: 16 pages (two column format), 4 figures
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- 2019
229. Double-Auction Mechanisms for Resource Trading Markets
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Naveen, K P and Sundaresan, Rajesh
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Computer Science - Networking and Internet Architecture ,Computer Science - Computer Science and Game Theory - Abstract
We consider a double-auction mechanism, which was recently proposed in the context of rate allocation in mobile data-offloading markets. Network operators (users) derive benefit from offloading their traffic to third party WiFi or femtocell networks (link-suppliers). Link-suppliers experience costs for the additional capacity that they provide. Users and link-suppliers (collectively referred to as agents) have their pay-offs and cost functions as private knowledge. A network-manager decomposes the problem into a network problem and agent problems. The surrogate pay-offs and cost functions are modulated by the agents' bids. Agents' payoffs and costs are then determined by the allocations and prices set by the network-manager. Under this design, so long as the agents do not anticipate the effect of their actions on the prices set by the network-manager (i.e., price-taking agents), a competitive equilibrium exists as a solution to the network and agent problems, and this equilibrium optimizes the sum utility of all agents. However, this design fails when the agents are all strategic (price-anticipating). Specifically, the presence of a strategic link-supplier drives the system to an undesirable equilibrium with zero participation resulting in an efficiency loss of 100%. This is in stark contrast to an earlier setting where the users alone are strategic but the link-supplier is not - the efficiency loss is known to be at most 34%. The paper then proposes a Stackelberg game modification where the efficiency loss can be characterized in terms of the link-supplier's cost function when the users' pay-off functions are linear. Specifically, when the link-supplier's cost function is quadratic, the worst case efficiency loss is 25%. Further, the loss in efficiency improves for polynomial cost functions of higher degree.
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- 2019
230. COVID-19: Optimal Design of Serosurveys for Disease Burden Estimation
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Athreya, Siva, Babu, Giridhara R., Iyer, Aniruddha, S., Mohammed Minhaas B., Rathod, Nihesh, Shriram, Sharad, Sundaresan, Rajesh, Vaidhiyan, Nidhin Koshy, and Yasodharan, Sarath
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- 2022
- Full Text
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231. Pharyngocutaneous Fistula Following Primary and Salvage Laryngectomy: Aetiology and Predictive Factors
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Michael, Rajiv C., Das, Sukamal, Mani, Suresh, Arunagiri, Sabarinath, Thomas, Regi, Vediappan, Rajan Sundaresan, and Philip, Dona Maria
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- 2022
- Full Text
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232. Trends in breast and prostate cancer screening and diagnostic procedures during the COVID-19 pandemic in central Massachusetts
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Epstein, Mara M., Sundaresan, Devi, Fair, Meagan, Fouayzi, Hassan, Warner, Erica T., Garber, Lawrence D., Gurwitz, Jerry H., and Field, Terry S.
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- 2022
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233. Cytocompatibility of Pluronics F-127 on adenocarcinomic human alveolar basal epithelial cells (A549 cells)
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Megha, Kizhakkepurakkal Balachandran, Swathi, Sundaresan, Joseph, Xavier, Vandana, Unnikrishnan, and Mohanan, Parayanthala Valappil
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- 2022
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234. Burden Among Caregivers of Pediatric Patients with Neurofibromatosis Type 1 (NF1) and Plexiform Neurofibroma (PN) in the United States: A Cross-Sectional Study
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Yang, Xiaoqin, Yoo, Hyun Kyoo, Amin, Suvina, Cheng, Wendy Y., Sundaresan, Sanjana, Zhang, Lujia, and Duh, Mei S.
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- 2022
- Full Text
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235. Multiple timescale contact charging
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Shinbrot, T., Ferdowsi, B., Sundaresan, S., and Araujo, N. A. M.
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
Contact charging between insulators is one of the most basic, yet least well understood, of physical processes. For example we have no clear theory for how insulators recruit enough charge carriers to deposit charge but not enough to discharge. In this letter we note that charging and discharging kinetics may be distinct, and from this observation we develop a mathematical model. The model surprisingly predicts that charging can decrease as contact frequency increases: we confirm this prediction experimentally and propose future steps.
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- 2018
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236. Simultaneous Small Noise Limit for Singularly Perturbed Slow-Fast Coupled Diffusions
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Athreya, Siva R., Borkar, Vivek S., Kumar, K. Suresh, and Sundaresan, Rajesh
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Mathematics - Probability ,60J60, 60G35 - Abstract
We consider a simultaneous small noise limit for a singularly perturbed coupled diffusion described by \begin{eqnarray*} dX^{\varepsilon}_t &=& b(X^{\varepsilon}_t, Y^{\varepsilon}_t)dt + \varepsilon^{\alpha}dB_t, dY^{\varepsilon}_t &=& - \frac{1}{\varepsilon} \nabla_yU(X^{\varepsilon}_t, Y^{\varepsilon}_t)dt + \frac{s(\varepsilon)}{\sqrt{\varepsilon}} dW_t, \end{eqnarray*} where $B_t, W_t$ are independent Brownian motions on ${\mathbb R}^d$ and ${\mathbb R}^m$ respectively, $b : \mathbb{R}^d \times \mathbb{R}^m \rightarrow \mathbb{R}^d$, $U : \mathbb{R}^d \times \mathbb{R}^m \rightarrow \mathbb{R}$ and $s :(0,\infty) \rightarrow (0,\infty)$. We impose regularity assumptions on $b$, $U$ and let $0 < \alpha < 1.$ When $s(\varepsilon)$ goes to zero slower than a prescribed rate as $\varepsilon \rightarrow 0$, we characterize all weak limit points of $X^{\varepsilon}$, as $\varepsilon \rightarrow 0$, as solutions to a differential equation driven by a measurable vector field. Under an additional assumption on the behaviour of $U(x, \cdot)$ at its global minima we characterize all limit points as Filippov solutions to the differential equation., Comment: Added References and Corrected Typos
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- 2018
237. Augmenting Max-Weight with Explicit Learning for Wireless Scheduling with Switching Costs
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Krishnasamy, Subhashini, T, Akhil P, Arapostathis, Ari, Sundaresan, Rajesh, and Shakkottai, Sanjay
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Electrical Engineering and Systems Science - Systems and Control - Abstract
In small-cell wireless networks where users are connected to multiple base stations (BSs), it is often advantageous to switch off dynamically a subset of BSs to minimize energy costs. We consider two types of energy cost: (i) the cost of maintaining a BS in the active state, and (ii) the cost of switching a BS from the active state to inactive state. The problem is to operate the network at the lowest possible energy cost (sum of activation and switching costs) subject to queue stability. In this setting, the traditional approach -- a Max-Weight algorithm along with a Lyapunov-based stability argument -- does not suffice to show queue stability, essentially due to the temporal co-evolution between channel scheduling and the BS activation decisions induced by the switching cost. Instead, we develop a learning and BS activation algorithm with slow temporal dynamics, and a Max-Weight based channel scheduler that has fast temporal dynamics. We show using convergence of time-inhomogeneous Markov chains, that the co-evolving dynamics of learning, BS activation and queue lengths lead to near optimal average energy costs along with queue stability., Comment: A shorter version of this paper appeared in the Proceedings of IEEE Conference on Computer Communications (IEEE Infocom 2017)
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- 2018
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238. On the Impact of Guest Traffic in Open-Access Domestic Broadband Sharing Schemes
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Lenas, Sotiris, Tsaoussidis, Vassilis, Sundaresan, Srikanth, Sathiaseelan, Arjuna, and Crowcroft, Jon
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Computer Science - Networking and Internet Architecture - Abstract
Open-access domestic broadband connection sharing constitutes a voluntary practice that is associated with societal, economic and public-safety benefits. Despite this fact, broadband subscribers are usually hesitant to freely share their broadband connection with guests for a multitude of reasons; one of them being sharing their network might hinder their own broadband quality of experience. In this paper, we investigate experimentally the impact of uplink guest traffic on the sharer's broadband quality of experience under both generic and broadband-sharing-specific packet scheduling policies. Both guest-user traffic and access point profiles employed in our study are developed by analyzing real-world traffic traces and measurements, captured from actual broadband sharing networking environments. Our results validate the suitability of hybrid packet scheduling policies for broadband sharing schemes and show that only a few dozen kilobytes per second of uplink guest traffic can be tolerated by sharers without hampering their broadband quality of experience. In this context, we show that the selection of the most appropriate packet scheduling policy for broadband sharing, as well as its respective configuration, depend largely on the capacity of the broadband connection and the policy's packet-dropping behavior on guest traffic.
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- 2018
239. A Multi-Modal Approach to Infer Image Affect
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Sundaresan, Ashok, Murugesan, Sugumar, Davis, Sean, Kappaganthu, Karthik, Jin, ZhongYi, Jain, Divya, and Maunder, Anurag
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Learning ,Statistics - Machine Learning - Abstract
The group affect or emotion in an image of people can be inferred by extracting features about both the people in the picture and the overall makeup of the scene. The state-of-the-art on this problem investigates a combination of facial features, scene extraction and even audio tonality. This paper combines three additional modalities, namely, human pose, text-based tagging and CNN extracted features / predictions. To the best of our knowledge, this is the first time all of the modalities were extracted using deep neural networks. We evaluate the performance of our approach against baselines and identify insights throughout this paper.
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- 2018
240. Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters.
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Liechty, Zachary, Santos-Medellín, Christian, Edwards, Joseph, Nguyen, Bao, Mikhail, David, Eason, Shane, Phillips, Gregory, and Sundaresan, Venkatesan
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endosphere ,fermentation ,methane ,methanogenesis ,microbiome ,rhizoplane ,rhizosphere ,rice ,root - Abstract
Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2 These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions.IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.
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- 2020
241. Genome-wide redistribution of 24-nt siRNAs in rice gametes
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Li, Chenxin, Xu, Hengping, Fu, Fang-Fang, Russell, Scott D, Sundaresan, Venkatesan, and Gent, Jonathan I
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Plant Biology ,Biological Sciences ,Genetics ,Contraception/Reproduction ,DNA Methylation ,Gene Expression Regulation ,Plant ,Gene Silencing ,Genome ,Plant ,Germ Cells ,Heterochromatin ,Nucleosomes ,Oryza ,RNA ,Small Interfering ,Sex Determination Processes ,Transcriptome ,Medical and Health Sciences ,Bioinformatics - Abstract
Gametes constitute a critical stage of the plant life cycle during which the genome undergoes reprogramming in preparation for embryogenesis. Here, we examined genome-wide distributions of small RNAs in the sperm and egg cells of rice. We found that 24-nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants, were depleted from heterochromatin boundaries in both gametes relative to vegetative tissues, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm cells, 24-nt siRNAs were spread across heterochromatic regions, while in egg cells, 24-nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, especially at loci which also produced siRNAs in other tissues. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale redistribution in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs.
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- 2020
242. Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota
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Edwards, Joseph, Santos-Medellín, Christian, Nguyen, Bao, Kilmer, John, Liechty, Zachary, Veliz, Esteban, Ni, Jiadong, Phillips, Gregory, and Sundaresan, Venkatesan
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Agriculture ,Land and Farm Management ,Agricultural ,Veterinary and Food Sciences ,Crop and Pasture Production ,Biological Sciences ,Zero Hunger ,Domestication ,Microbiota ,Oryza ,Plant Roots ,Soil Microbiology ,Environmental Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundSoils are a key component of agricultural productivity, and soil microbiota determine the availability of many essential plant nutrients. Agricultural domestication of soils, that is, the conversion of previously uncultivated soils to a cultivated state, is frequently accompanied by intensive monoculture, especially in the developing world. However, there is limited understanding of how continuous cultivation alters the structure of prokaryotic soil microbiota after soil domestication, including to what extent crop plants impact soil microbiota composition, and how changes in microbiota composition arising from cultivation affect crop performance.ResultsWe show here that continuous monoculture (> 8 growing seasons) of the major food crop rice under flooded conditions is associated with a pronounced shift in soil bacterial and archaeal microbiota structure towards a more consistent composition, thereby domesticating microbiota of previously uncultivated sites. Aside from the potential effects of agricultural cultivation practices, we provide evidence that rice plants themselves are important drivers of the domestication process, acting through selective enrichment of specific taxa, including methanogenic archaea, in their rhizosphere that differ from those of native plants growing in the same environment. Furthermore, we find that microbiota from soils domesticated by rice cultivation contribute to plant-soil feedback, by imparting a negative effect on rice seedling vigor.ConclusionsSoil domestication through continuous monoculture cultivation of rice results in compositional changes in the soil microbiota, which are in part driven by the rice plants. The consequences include a negative impact on plant performance and increases in greenhouse gas emitting microbes.
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- 2019
243. Genome-Wide Association Study of Apparent Treatment-Resistant Hypertension in the CHARGE Consortium: The CHARGE Pharmacogenetics Working Group
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Irvin, Marguerite R, Sitlani, Colleen M, Floyd, James S, Psaty, Bruce M, Bis, Joshua C, Wiggins, Kerri L, Whitsel, Eric A, Sturmer, Til, Stewart, James, Raffield, Laura, Sun, Fangui, Liu, Ching-Ti, Xu, Hanfei, Cupples, Adrienne L, Tanner, Rikki M, Rossing, Peter, Smith, Albert, Zilhão, Nuno R, Launer, Lenore J, Noordam, Raymond, Rotter, Jerome I, Yao, Jie, Li, Xiaohui, Guo, Xiuqing, Limdi, Nita, Sundaresan, Aishwarya, Lange, Leslie, Correa, Adolfo, Stott, David J, Ford, Ian, Jukema, J Wouter, Gudnason, Vilmundur, Mook-Kanamori, Dennis O, Trompet, Stella, Palmas, Walter, Warren, Helen R, Hellwege, Jacklyn N, Giri, Ayush, O'donnell, Christopher, Hung, Adriana M, Edwards, Todd L, Ahluwalia, Tarunveer S, Arnett, Donna K, and Avery, Christy L
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Biomedical and Clinical Sciences ,Cardiovascular Medicine and Haematology ,Clinical Sciences ,Hypertension ,Human Genome ,Cardiovascular ,Genetics ,Black or African American ,Aged ,Antihypertensive Agents ,Blood Pressure ,Case-Control Studies ,DNA (Cytosine-5-)-Methyltransferases ,DNA Methyltransferase 3A ,DNA-Binding Proteins ,Drug Resistance ,Dystrophin-Associated Proteins ,Europe ,Female ,Genetic Loci ,Genome-Wide Association Study ,Humans ,Male ,Middle Aged ,Myosin Heavy Chains ,Myosin Type V ,Neuropeptides ,Pharmacogenetics ,Pharmacogenomic Variants ,Polymorphism ,Single Nucleotide ,Risk Assessment ,Risk Factors ,Transcription Factors ,United States ,White People ,blood pressure ,hypertension ,genome-wide association study ,severe hypertension ,treatment-resistant hypertension ,Cardiovascular System & Hematology ,Cardiovascular medicine and haematology ,Clinical sciences - Abstract
BackgroundOnly a handful of genetic discovery efforts in apparent treatment-resistant hypertension (aTRH) have been described.MethodsWe conducted a case-control genome-wide association study of aTRH among persons treated for hypertension, using data from 10 cohorts of European ancestry (EA) and 5 cohorts of African ancestry (AA). Cases were treated with 3 different antihypertensive medication classes and had blood pressure (BP) above goal (systolic BP ≥ 140 mm Hg and/or diastolic BP ≥ 90 mm Hg) or 4 or more medication classes regardless of BP control (nEA = 931, nAA = 228). Both a normotensive control group and a treatment-responsive control group were considered in separate analyses. Normotensive controls were untreated (nEA = 14,210, nAA = 2,480) and had systolic BP/diastolic BP < 140/90 mm Hg. Treatment-responsive controls (nEA = 5,266, nAA = 1,817) had BP at goal (
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- 2019
244. Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice.
- Author
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Han, Lin, Madan, Vikas, Mayakonda, Anand, Dakle, Pushkar, Woon, Teoh, Shyamsunder, Pavithra, Nordin, Hazimah, Cao, Zeya, Sundaresan, Janani, Lei, Ienglam, Wang, Zhong, and Koeffler, H
- Subjects
Animals ,Cell Differentiation ,Cell Line ,Tumor ,Cell Lineage ,Chromatin ,Chromatin Assembly and Disassembly ,DNA-Binding Proteins ,Hematopoiesis ,Humans ,Mice ,Mice ,Inbred C57BL ,Myeloid Cells ,Transcription Factors - Abstract
Precise regulation of chromatin architecture is vital to physiological processes including hematopoiesis. ARID1A is a core component of the mammalian SWI/SNF complex, which is one of the ATP-dependent chromatin remodeling complexes. To uncover the role of ARID1A in hematopoietic development, we utilized hematopoietic cell-specific deletion of Arid1a in mice. We demonstrate that ARID1A is essential for maintaining the frequency and function of hematopoietic stem cells and its loss impairs the differentiation of both myeloid and lymphoid lineages. ARID1A deficiency led to a global reduction in open chromatin and ensuing transcriptional changes affected key genes involved in hematopoietic development. We also observed that silencing of ARID1A affected ATRA-induced differentiation of NB4 cells, suggesting its role in granulocytic differentiation of human leukemic cells. Overall, our study provides a comprehensive elucidation of the function of ARID1A in hematopoiesis and highlights the central role of ARID1A-containing SWI/SNF complex in maintaining chromatin dynamics in hematopoietic cells.
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- 2019
245. Mechanisms by which sialylated milk oligosaccharides impact bone biology in a gnotobiotic mouse model of infant undernutrition
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Cowardin, Carrie A, Ahern, Philip P, Kung, Vanderlene L, Hibberd, Matthew C, Cheng, Jiye, Guruge, Janaki L, Sundaresan, Vinaik, Head, Richard D, Barile, Daniela, Mills, David A, Barratt, Michael J, Huq, Sayeeda, Ahmed, Tahmeed, and Gordon, Jeffrey I
- Subjects
Biochemistry and Cell Biology ,Biomedical and Clinical Sciences ,Biological Sciences ,Pediatric ,Prevention ,Breastfeeding ,Lactation and Breast Milk ,Digestive Diseases ,Nutrition ,2.1 Biological and endogenous factors ,Zero Hunger ,Animals ,Bacteria ,Bone and Bones ,Cattle ,Diet ,Disease Models ,Animal ,Feces ,Gastrointestinal Microbiome ,Germ-Free Life ,Humans ,Infant ,Intestine ,Small ,Male ,Malnutrition ,Mice ,Mice ,Inbred C57BL ,Milk ,Human ,Oligosaccharides ,Osteoblasts ,Osteoclasts ,Signal Transduction ,childhood undernutrition ,stunting ,gut microbiota ,bone growth ,breast milk oligosaccharides - Abstract
Undernutrition in children is a pressing global health problem, manifested in part by impaired linear growth (stunting). Current nutritional interventions have been largely ineffective in overcoming stunting, emphasizing the need to obtain better understanding of its underlying causes. Treating Bangladeshi children with severe acute malnutrition with therapeutic foods reduced plasma levels of a biomarker of osteoclastic activity without affecting biomarkers of osteoblastic activity or improving their severe stunting. To characterize interactions among the gut microbiota, human milk oligosaccharides (HMOs), and osteoclast and osteoblast biology, young germ-free mice were colonized with cultured bacterial strains from a 6-mo-old stunted infant and fed a diet mimicking that consumed by the donor population. Adding purified bovine sialylated milk oligosaccharides (S-BMO) with structures similar to those in human milk to this diet increased femoral trabecular bone volume and cortical thickness, reduced osteoclasts and their bone marrow progenitors, and altered regulators of osteoclastogenesis and mediators of Th2 responses. Comparisons of germ-free and colonized mice revealed S-BMO-dependent and microbiota-dependent increases in cecal levels of succinate, increased numbers of small intestinal tuft cells, and evidence for activation of a succinate-induced tuft cell signaling pathway linked to Th2 immune responses. A prominent fucosylated HMO, 2'-fucosyllactose, failed to elicit these changes in bone biology, highlighting the structural specificity of the S-BMO effects. These results underscore the need to further characterize the balance between, and determinants of, osteoclastic and osteoblastic activity in stunted infants/children, and suggest that certain milk oligosaccharides may have therapeutic utility in this setting.
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- 2019
246. Long-term effect of thymectomy plus prednisone versus prednisone alone in patients with non-thymomatous myasthenia gravis: 2-year extension of the MGTX randomised trial
- Author
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Wolfe, Gil I, Kaminski, Henry J, Aban, Inmaculada B, Minisman, Greg, Kuo, Hui-Chien, Marx, Alexander, Ströbel, Philipp, Mazia, Claudio, Oger, Joel, Cea, J Gabriel, Heckmann, Jeannine M, Evoli, Amelia, Nix, Wilfred, Ciafaloni, Emma, Antonini, Giovanni, Witoonpanich, Rawiphan, King, John O, Beydoun, Said R, Chalk, Colin H, Barboi, Alexandru C, Amato, Anthony A, Shaibani, Aziz I, Katirji, Bashar, Lecky, Bryan RF, Buckley, Camilla, Vincent, Angela, Dias-Tosta, Elza, Yoshikawa, Hiroaki, Waddington-Cruz, Márcia, Pulley, Michael T, Rivner, Michael H, Kostera-Pruszczyk, Anna, Pascuzzi, Robert M, Jackson, Carlayne E, Verschuuren, Jan JGM, Massey, Janice M, Kissel, John T, Werneck, Lineu C, Benatar, Michael, Barohn, Richard J, Tandan, Rup, Mozaffar, Tahseen, Silvestri, Nicholas J, Conwit, Robin, Sonett, Joshua R, Jaretzki, Alfred, Newsom-Davis, John, Cutter, Gary R, Group, MGTX Study, Cutter, Gary, Aban, Inmaculada, Feese, Michelle, Wolfe, Gil, Kaminski, Henry, Sonett, Joshua, Saluto, Valeria, Rosenberg, Moises, Alvarez, Valeria, Rey, Lisa, King, John, Butzkueven, Helmut, Goldblatt, John, Carey, John, Pollard, John, Reddel, Stephen, Handel, Nicholas, McCaughan, Brian, Pallot, Linda, Novis, Ricardo, Boasquevisque, Carlos, Morato-Fernandez, Rubens, Ximenes, Manoel, Werneck, Lineu, Scola, Rosana, Soltoski, Paulo, Chalk, Colin, Moore, Fraser, Mulder, David, Wadup, Lisa, Mezei, Michele, Evans, Kenneth, Jiwa, Theresa, Schaffar, Anne, White, Chris, Toth, Cory, Gelfand, Gary, Wood, Susan, Pringle, Elizabeth, Zwicker, Jocelyn, Maziak, Donna, Shamji, Farid, and Sundaresan, Sudhir
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Neurosciences ,Myasthenia Gravis ,Autoimmune Disease ,Rare Diseases ,Clinical Research ,Clinical Trials and Supportive Activities ,Evaluation of treatments and therapeutic interventions ,6.1 Pharmaceuticals ,Adult ,Female ,Humans ,Longitudinal Studies ,Male ,Prednisone ,Thymectomy ,Treatment Outcome ,Young Adult ,MGTX Study Group ,Neurology & Neurosurgery ,Clinical sciences - Abstract
BackgroundThe Thymectomy Trial in Non-Thymomatous Myasthenia Gravis Patients Receiving Prednisone (MGTX) showed that thymectomy combined with prednisone was superior to prednisone alone in improving clinical status as measured by the Quantitative Myasthenia Gravis (QMG) score in patients with generalised non-thymomatous myasthenia gravis at 3 years. We investigated the long-term effects of thymectomy up to 5 years on clinical status, medication requirements, and adverse events.MethodsWe did a rater-blinded 2-year extension study at 36 centres in 15 countries for all patients who completed the randomised controlled MGTX and were willing to participate. MGTX patients were aged 18 to 65 years at enrolment, had generalised non-thymomatous myasthenia gravis of less than 5 years' duration, had acetylcholine receptor antibody titres of 1·00 nmol/L or higher (or concentrations of 0·50-0·99 nmol/L if diagnosis was confirmed by positive edrophonium or abnormal repetitive nerve stimulation, or abnormal single fibre electromyography), had Myasthenia Gravis Foundation of America Clinical Classification Class II-IV disease, and were on optimal anticholinesterase therapy with or without oral corticosteroids. In MGTX, patients were randomly assigned (1:1) to either thymectomy plus prednisone or prednisone alone. All patients in both groups received oral prednisone at doses titrated up to 100 mg on alternate days until they achieved minimal manifestation status. The primary endpoints of the extension phase were the time-weighted means of the QMG score and alternate-day prednisone dose from month 0 to month 60. Analyses were by intention to treat. The trial is registered with ClinicalTrials.gov, number NCT00294658. It is closed to new participants, with follow-up completed.FindingsOf the 111 patients who completed the 3-year MGTX, 68 (61%) entered the extension study between Sept 1, 2009, and Aug 26, 2015 (33 in the prednisone alone group and 35 in the prednisone plus thymectomy group). 50 (74%) patients completed the 60-month assessment, 24 in the prednisone alone group and 26 in the prednisone plus thymectomy group. At 5 years, patients in the thymectomy plus prednisone group had significantly lower time-weighted mean QMG scores (5·47 [SD 3·87] vs 9·34 [5·08]; p=0·0007) and mean alternate-day prednisone doses (24 mg [SD 21] vs 48 mg [29]; p=0·0002) than did those in the prednisone alone group. 14 (42%) of 33 patients in the prednisone group, and 12 (34%) of 35 in the thymectomy plus prednisone group, had at least one adverse event by month 60. No treatment-related deaths were reported during the extension phase.InterpretationAt 5 years, thymectomy plus prednisone continues to confer benefits in patients with generalised non-thymomatous myasthenia gravis compared with prednisone alone. Although caution is appropriate when generalising our findings because of the small sample size of our study, they nevertheless provide further support for the benefits of thymectomy in patients with generalised non-thymomatous myasthenia gravis.FundingNational Institutes of Health, National Institute of Neurological Disorders and Stroke.
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- 2019
247. The role of patient-reported outcome measures in the continuum of cancer clinical care: ESMO Clinical Practice Guideline
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Di Maio, M., Basch, E., Denis, F., Fallowfield, L.J., Ganz, P.A., Howell, D., Kowalski, C., Perrone, F., Stover, A.M., Sundaresan, P., Warrington, L., Zhang, L., Apostolidis, K., Freeman-Daily, J., Ripamonti, C.I., and Santini, D.
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- 2022
- Full Text
- View/download PDF
248. Clinical and humanistic burden among pediatric patients with neurofibromatosis type 1 and plexiform neurofibroma in the USA
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Yang, Xiaoqin, Yoo, Hyun Kyoo, Amin, Suvina, Cheng, Wendy Y., Sundaresan, Sanjana, Zhang, Lujia, and Duh, Mei Sheng
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- 2022
- Full Text
- View/download PDF
249. Rapid Adaptation of Cancer Education in Response to the COVID-19 Pandemic: Evaluation of a Live Virtual Statistics and Research Skills Workshop for Oncology Trainees
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Turner, Sandra, Pham, Trang, Robledo, Kristy, Turner, Sara, Brown, Chris, and Sundaresan, Purnima
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- 2022
- Full Text
- View/download PDF
250. LWCNN: a lightweight convolutional neural network for agricultural crop protection
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Raman, Sundaresan, Soni, Manan, Ramaprasad, Rohit, and Chamola, Vinay
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- 2022
- Full Text
- View/download PDF
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