cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
MOESM6 of Exploration of carbohydrate binding behavior and anti-proliferative activities of Arisaema tortuosum lectin
Creators: name: Kshema Thakur
name: Tarnjeet Kaur
name: Manpreet Kaur
name: Hora, Rachna
name: Singh, Jatinder
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: Additional file 6: Table S4. Taxonomical division of lectins included in phylogenetic analysis.
The Role of Social Context in Modulating Gene Expression, Neural Activity, and Neuroendocrine Response in Individuals of Varying Social Status
Creators: Williamson, Caitlin
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Psychology
subject: FOS: Psychology
subject: Gene expression
subject: Neurobiology--Social aspects
subject: Social status
subject: Neurosciences--Social aspects
subject: Social behavior in animals

description: Social context, which includes both the direct social experience of individuals as well as the characteristics of their social network as a whole, has been shown to be an important modulator of behavior across species. However, relatively little is known about the role of social context in regulating the complex relationships between neurobiology, neuroendocrine response, and behavior in mammals. Historically, the neurobiology of social behavior has been studied at the dyadic level, looking at brief social interactions between pairs of individuals. Given that all social species live in groups, rather than pairs, it is essential that we begin to understand the role social context at the group level plays in regulating physiology. Throughout this thesis, I use a novel behavioral housing system to study how the characteristics of stable social groups and how instances of social opportunity, when individuals are ascending up a social hierarchy, are associated with differential brain gene expression, neuroendocrine output, and behavior. I first extensively analyze the social dynamics of male dominance hierarchies, showing that they are both consistent, in that males reliably form significantly linear dominance hierarchies, and unique, in that the characteristics of these hierarchies vary from group to group. I further prove that mice living in these social hierarchies are extremely socially competent, displaying the ability to respond appropriately to individuals of varying social status. I demonstrate that females are capable of forming dominance hierarchies as well, but that their hierarchies differ from those of males. I then use this foundational knowledge to investigate how these different hierarchy characteristics can lead to differences in physiology, how one’s social status is associated with brain gene expression and neuroendocrine response, and how disruption of a hierarchy through removal of the alpha male leads to robust behavioral as well as physiological consequences. Finally, I use the insights gained from this immediate early gene work to demonstrate the crucial role of the infralimbic/prelimbic region of the medial prefrontal cortex in regulating socially competent response to changing social contexts. Taken together, this work establishes the broad role social context plays in regulating the complex relationships between behavior, brain gene expression, neural activation, and neuroendocrine output.
AI MEET BIOINFORMATICS: INTERPRETING BIOMEDICAL DATA USING DEEP LEARNING
Creators: name: Tang, Ziyang
Publisher: name: Purdue University Graduate School
Year: 2024
Subjects: classificationCode: 461103
subject: Deep learning

description: Artificial Intelligence driven approaches, especially  based on deep learning algorithms, provided an alternative perspective in summarizing the common features in large-scale and complex datasets and aided the human professions in discovering novel features in cross-domain research. In this dissertation, the author proposed his research of developing AI-driven algorithms to reveal the real relation of complex medical data. The author started to identify the abnormal structures from the radiology images. When the abnormal structure was detected, the author built a model to explore the domain layers or cell phenotype of the specific tissues. Finally, the author evaluated cell-cell communication for the downstream tasks.

In his first research, the author applied IResNet, a two-stage prediction-interpretation Convolution Neural Network, to assist clinicians in the early diagnosis of Autism Spectrum Disorders (ASD). IresNet first predicted the input sMRI scan to one of the two categories: (1) ASD group or (2) Normal Control group, and interpret the prediction using a \textit{post-hoc} approach and visualized the abnormal structures on top of the raw inputs. The proposed method can be applied to other neural diseases such as Alzheimer's Disease. 

When the abnormal structure was detected, the author proposed a method to reveal the latent relation at the tissue level. Thus the author proposed SiGra, an unsupervised learning paradigm to identify the domain layers and cellular phenotype in a particular tissue slide based on the corresponding gene expression matrix and the morphology representations. SiGra outperformed other benchmarking algorithms in three different tissue slides from three commercialized single-cell platforms.

At last, the author measured the potential interactions between two cells. The proposed spaCI, measured the correlation of a Ligand-Receptor interaction in the high-dimension latent space and predicted the interactive $L-R$ pair for downstream analysis. 

In summary, the author presented three end-to-end AI-driven frameworks to facilitate clinicians and pathologists in better understanding the latent connections of complex diseases and tissues.
Bi-Hamiltonian manifolds, quasi-bi-Hamiltonian systems and separation variables
Creators: name: Tondo, G.
name: Morosi, C.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: We discuss from a bi-Hamiltonian point of view the Hamilton-Jacobi separability of a few dynamical systems. They are shown to admit, in their natural phase space, a quasi-bi-Hamiltonian formulation of Pfaffian type. This property allows us to straightforwardly recover a set of separation variables for the corresponding Hamilton-Jacobi equation.
description: 12 pages, no figures, LaTeX 2.09, to be published in Report on Mathematical Physics
Perturbative--nonperturbative connection in quantum mechanics and field theory
Creators: name: Dunne, Gerald V.
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: On the occasion of this ArkadyFest, celebrating Arkady Vainshtein's 60th birthday, I review some selected aspects of the connection between perturbative and nonperturbative physics, a subject to which Arkady has made many important contributions. I first review this connection in quantum mechanics, which was the subject of Arkady's very first paper. Then I discuss this issue in relation to effective actions in field theory, which also touches on Arkady's work on operator product expansions. Finally, I conclude with a discussion of a special quantum mechanical system, a quasi-exactly solvable model with energy-reflection duality, which exhibits an explicit duality between the perturbative and nonperturbative sectors, without invoking supersymmetry.
description: 17 pp, 9 figures; Review talk at ArkadyFest Symposium, May 2002, Minneapolis
The Role of SRGAP2 in Modulating Synaptic Dynamics in Adult Sensory Cortex
Creators: Tsai, Joseph
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Neurosciences
subject: FOS: Clinical medicine
subject: Neurobiology
subject: Somatosensory cortex
subject: Synapses

description: Human brain evolution granted us cognitive and behavioral capabilities that are unique amongst animals. SRGAP2 is a gene that was specifically duplicated in the human lineage and plays roles in the regulation of cortical development and synapse dynamics. As paralogs of one of the few known genes that regulates excitatory and inhibitory synapses concurrently, the duplications of SRGAP2 were well-positioned during human evolution to gain novel functions leading to the cognitive and behavioral phenotypes exhibited in humans. SRGAP2C, a human-specific paralog of the ancestral SRGAP2 gene, inhibits every known function of SRGAP2 and induces a phenotype similar to SRGAP2 knockdown. This induces neoteny in the maturation of synapses in mice, allowing us to study a putatively “human-like” phenotype in the mouse brain. While studies have been conducted on the effects of SRGAP2 manipulation in juvenile and young adult mice, its effects on older mice has yet to be determined.
      In this dissertation, we perform longitudinal imaging experiments to determine the effects of SRGAP2 manipulation in the cortex of adult mice. In Chapter 3, we first examine the effects of SRGAP2 knockdown on the spine dynamics on apical dendrites of layer 5 pyramidal cells in the barrel cortex of adult mice, determining how it regulates spine density, turnover, and survival at baseline and in response to sensory deprivation. In Chapter 4, we study how SRGAP2 knockdown affects the clustered formations of new dendritic spines on the apical dendrites of layer 5 pyramidal cells in the barrel cortex of adult mice. Together, these results represent the first demonstration of SRGAP2 regulating on synapse dynamics in vivo and show that SRGAP2 knockdown can be used to model human brain evolution in adult mice.
MOESM3 of Exploration of carbohydrate binding behavior and anti-proliferative activities of Arisaema tortuosum lectin
Creators: name: Kshema Thakur
name: Tarnjeet Kaur
name: Manpreet Kaur
name: Hora, Rachna
name: Singh, Jatinder
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology

description: Additional file 2: Figure S1. Full length coding sequence of lectin genes from mRNA of ATL. Numbers indicate ORF. Deduced amino acid sequence in one letter code are mentioned below the coding sequence. The start and stop codons are highlighted in bold and shade. The upright arrow indicates predicted cleavage site for signal peptide. Italicised amino acid sequence represents conserved bulb-type lectin DOM 1 and 2. Adjacent cysteins predicted to be involved in disulphide linkage in respective domains are highlighted in shadow. Conserved CRS [QXDXNXVXY] are indicated in bold and are boxed.
Short-depth circuits for efficient expectation value estimation
Creators: name: Roggero, Alessandro
name: Baroni, Alessandro
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The evaluation of expectation values $Tr\left[ρO\right]$ for some pure state $ρ$ and Hermitian operator $O$ is of central importance in a variety of quantum algorithms. Near optimal techniques developed in the past require a number of measurements $N$ approaching the Heisenberg limit $N=\mathcal{O}\left(1/ε\right)$ as a function of target accuracy $ε$. The use of Quantum Phase Estimation requires however long circuit depths $C=\mathcal{O}\left(1/ε\right)$ making their implementation difficult on near term noisy devices. The more direct strategy of Operator Averaging is usually preferred as it can be performed using $N=\mathcal{O}\left(1/ε^2\right)$ measurements and no additional gates besides those needed for the state preparation. In this work we use a simple but realistic model to describe the bound state of a neutron and a proton (the deuteron) and show that the latter strategy can require an overly large number of measurement in order to achieve a reasonably small relative target accuracy $ε_r$. We propose to overcome this problem using a single step of QPE and classical post-processing. This approach leads to a circuit depth $C=\mathcal{O}\left(ε^μ\right)$ (with $μ\geq0$) and to a number of measurements $N=\mathcal{O}\left(1/ε^{2+ν}\right)$ for $0
Spectral Difference Equations Satisfied by KP Soliton Wavefunctions
Creators: name: Kasman, Alex
Publisher: name: arXiv
Year: 1998
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: The Baker-Akhiezer (wave) functions corresponding to soliton solutions of the KP hierarchy are shown to satisfy eigenvalue equations for a commutative ring of translational operators in the spectral parameter. In the rational limit, these translational operators converge to the differential operators in the spectral parameter previously discussed as part of the theory of "bispectrality". Consequently, these translational operators can be seen as demonstrating a form of bispectrality for the non-rational solitons as well.
description: to appear in "Inverse Problems"
Exact spectrum and partition function of SU(m|n) supersymmetric Polychronakos model
Creators: name: Basu-Mallick, B.
name: Ujino, H.
name: Wadati, M.
Publisher: name: arXiv
Year: 1999
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: By using the fact that Polychronakos-like models can be obtained through the `freezing limit' of related spin Calogero models, we calculate the exact spectrum as well as partition function of SU(m|n) supersymmetric Polychronakos (SP) model. It turns out that, similar to the non-supersymmetric case, the spectrum of SU(m|n) SP model is also equally spaced. However, the degeneracy factors of corresponding energy levels crucially depend on the values of bosonic degrees of freedom (m) and fermionic degrees of freedom (n). As a result, the partition functions of SP models are expressed through some novel q-polynomials. Finally, by interchanging the bosonic and fermionic degrees of freedom, we obtain a duality relation among the partition functions of SP models.
description: Latex, 20 pages, no figures, minor typos corrected
MOESM2 of Exploration of carbohydrate binding behavior and anti-proliferative activities of Arisaema tortuosum lectin
Creators: name: Kshema Thakur
name: Tarnjeet Kaur
name: Manpreet Kaur
name: Hora, Rachna
name: Singh, Jatinder
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Pharmacology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Additional file 3: Table S2. Predicted physico-chemical properties of ATL.
Additional file 2 of Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea
Creators: name: Zhao, Hong-Yan
name: Wen, Lin
name: Miao, Yu-Feng
name: Du, Yu
name: Sun, Yan
name: Yin, Yin
name: Lin, Chi-Xian
name: Lin, Long-Hui
name: Ji, Xiang
name: Gao, Jian-Fang
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Original images of the SDS-PAGE profiles of venom fractions separated by RP-HPLC (1–11 peak number). Figure S2. Original images of SDS-PAGE profiles of whole venom protein (left panel) and cross-reaction between H. curtus venom and commercial antivenoms by western blotting (right panel) (Hcu: H. curtus).
Q-deformed KP hierarchy: Its additional symmetries and infinitesimal Bäcklund transformations
Creators: name: Tu, Ming-Hsien
Publisher: name: arXiv
Year: 1998
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: We study the additional symmetries associated with the $q$-deformed Kadomtsev-Petviashvili ($q$-KP) hierarchy. After identifying the resolvent operator as the generator of the additional symmetries, the $q$-KP hierarchy can be consistently reduced to the so-called $q$-deformed constrained KP ($q$-cKP) hierarchy. We then show that the additional symmetries acting on the wave function can be viewed as infinitesimal Bäcklund transformations by acting the vertex operator on the tau-function of the $q$-KP hierarchy. This establishes the Adler-Shiota-van Moerbeke formula for the $q$-KP hierarchy.
description: 9 pages, Revtex, no figures
Scylla: A Mesos Framework for Container Based MPI Jobs
Creators: name: Saha, Pankaj
name: Beltre, Angel
name: Govindaraju, Madhusudhan
Publisher: name: arXiv
Year: 2019
Subjects: subject: Performance (cs.PF)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Open source cloud technologies provide a wide range of support for creating customized compute node clusters to schedule tasks and managing resources. In cloud infrastructures such as Jetstream and Chameleon, which are used for scientific research, users receive complete control of the Virtual Machines (VM) that are allocated to them. Importantly, users get root access to the VMs. This provides an opportunity for HPC users to experiment with new resource management technologies such as Apache Mesos that have proven scalability, flexibility, and fault tolerance. To ease the development and deployment of HPC tools on the cloud, the containerization technology has matured and is gaining interest in the scientific community. In particular, several well known scientific code bases now have publicly available Docker containers. While Mesos provides support for Docker containers to execute individually, it does not provide support for container inter-communication or orchestration of the containers for a parallel or distributed application. In this paper, we present the design, implementation, and performance analysis of a Mesos framework, Scylla, which integrates Mesos with Docker Swarm to enable orchestration of MPI jobs on a cluster of VMs acquired from the Chameleon cloud [1]. Scylla uses Docker Swarm for communication between containerized tasks (MPI processes) and Apache Mesos for resource pooling and allocation. Scylla allows a policy-driven approach to determine how the containers should be distributed across the nodes depending on the CPU, memory, and network throughput requirement for each application.
Correlated random walks with a finite memory range
Creators: name: Bidaux, Roger
name: Boccara, Nino
Publisher: name: arXiv
Year: 1999
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: We study a family of correlated one-dimensional random walks with a finite memory range M.These walks are extensions of the Taylor's walk as investigated by Goldstein, which has a memory range equal to one. At each step, with a probability p, the random walker moves either to the right or to the left with equal probabilities, or with a probability q=1-p performs a move, which is a stochastic Boolean function of the M previous steps. We first derive the most general form of this stochastic Boolean function, and study some typical cases which ensure that the average value of the walker's location after n steps is zero for all values of n. In each case, using a matrix technique, we provide a general method for constructing the generating function of the probability distribution of R_n; we also establish directly an exact analytic expression for the step-step correlations and the variance of the walk. From the expression of , which is not straightforward to derive from the probability distribution, we show that, for n going to infinity, the variance of any of these walks behaves as n, provided p>0. Moreover, in many cases, for a very small fixed value of p, the variance exhibits a crossover phenomenon as $n$ increases from a not too large value. The crossover takes place for values of $n$ around 1/p. This feature may mimic the existence of a non-trivial Hurst exponent, and induce a misleading analysis of numerical data issued from mathematical or natural sciences experiments.
description: 18 figures
Entropy of Constant Curvature Black Holes in General Relativity
Creators: name: Creighton, Jolien D. E.
name: Mann, Robert B.
Publisher: name: arXiv
Year: 1997
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We consider the thermodynamic properties of the constant curvature black hole solution recently found by Banados. We show that it is possible to compute the entropy and the quasilocal thermodynamics of the spacetime using the Einstein-Hilbert action of General Relativity. The constant curvature black hole has some unusual properties which have not been seen in other black hole spacetimes. The entropy of the black hole is not associated with the event horizon; rather it is associated with the region between the event horizon and the observer. Further, surfaces of constant internal energy are not isotherms so the first law of thermodynamics exists only in an integral form. These properties arise from the unusual topology of the Euclidean black hole instanton.
description: 4 pages LaTeX2e (RevTeX), 2 PostScript figures. Small corrections in the text and the references
Real-Time Charge Initialization of Diamond Nitrogen-Vacancy Centers for Enhanced Spin Readout
Creators: name: Hopper, David A.
name: Lauigan, Joseph D.
name: Huang, Tzu-Yung
name: Bassett, Lee C.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A common impediment to qubit performance is imperfect state initialization. In the case of the diamond nitrogen-vacancy (NV) center, the initialization fidelity is limited by fluctuations in the defect's charge state during optical pumping. Here, we use real-time control to deterministically initialize the NV center's charge state at room temperature. We demonstrate a maximum charge initialization fidelity of 99.4$\pm$0.1% and present a quantitative model of the initialization process that allows for systems-level optimization of the spin-readout signal-to-noise ratio. Even accounting for the overhead associated with the initialization sequence, increasing the charge initialization fidelity from the steady-state value of 75% near to unity allows for a factor-of-two speedup in experiments while maintaining the same signal-to-noise-ratio. In combination with high-fidelity readout based on spin-to-charge conversion, real-time initialization enables a factor-of-20 speedup over traditional methods, resulting in an ac magnetic sensitivity of 1.3 nT/Hz$^{1/2}$ for our single NV-center spin. The real-time control method is immediately beneficial for quantum sensing applications with NV centers as well as probing charge-dependent physics, and it will facilitate protocols for quantum feedback control over multi-qubit systems.
description: 21 pages including supplementary information
Interlibrary loan and document delivery through the internet in academic libraries: American and British case studies
Creators: name: Diomidi, Eleni N.
Publisher: name: Loughborough University
Year: 2021
Subjects: subject: 89999 Information and Computing Sciences not elsewhere classified
subject: FOS: Computer and information sciences

description: Interlibrary loan and document delivery through the internet in academic libraries: American and British case studies
The Role of T-box Transcription Factors in the Development and Plasticity of Natural Killer Cell Lineages
Creators: Pikovskaya, Olga
Publisher: name: Columbia University
Year: 2016
Subjects: subject: Killer cells
subject: Lymphocytes
subject: Immunology
subject: FOS: Clinical medicine
subject: Immunogenetics
subject: Transcription factors

description: Type 1 innate lymphocytes comprise two developmentally divergent lineages, type 1 helper innate lymphoid cells (hILC1s) and conventional NK (cNK) cells. All type 1 innate lymphocytes (ILCs) express the transcription factor T-bet, but cNK cells additionally express Eomesodermin (Eomes). We show that deletion of Eomes alleles at the onset of type 1 ILC maturation using NKp46-Cre imposes a substantial block in cNK cell development. Formation of the entire lymphoid and non-lymphoid type 1 ILC compartment appears to require the semi-redundant action of both T-bet and Eomes. To determine if Eomes is sufficient to redirect hILC1 development to a cNK cell fate, we generated transgenic mice that express Eomes when and where T-bet is expressed using Tbx21 locus control to drive expression of Eomes codons. Ectopic Eomes expression induces cNK cell-like properties across the lymphoid and non-lymphoid type 1 ILC compartments. To investigate if T-bet is sufficient to direct type 1 ILC development into the hILC1 lineage, we also generated transgenic mice in which Tbx21 locus control drives expression of T-bet codons. Enforced T-bet expression, however, does not appear sufficient to induce hILC1-like attributes among type 1 ILCs. Subsequent to their divergent lineage specification, hILC1s and cNK cells possess substantial developmental plasticity elicited by the absence or presence of Eomes.
Protected Multiplets of M-Theory on a Plane Wave
Creators: name: Dasgupta, Keshav
name: Sheikh-Jabbari, Mohammad M.
name: Van Raamsdonk, Mark
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We show that the symmetry algebra governing the interacting part of the matrix model for M-theory on the maximally supersymmetric pp-wave is the basic classical Lie superalgebra SU(4|2). We determine the SU(4|2) multiplets present in the exact spectrum in the limit where μ(the mass parameter) becomes infinite, and find that these include infinitely many BPS multiplets. Using the representation theory of SU(4|2), we demonstrate that some of these BPS multiplets, including all of the vacuum states of the matrix model plus certain infinite towers of excited states, have energies which are exactly protected non-perturbatively for any value of μ> 0. In the large N limit, these lead to exact quantum states of M-theory on the pp-wave. We also show explicitly that there are certain BPS multiplets which do receive energy corrections by combining with other BPS multiplets to form ordinary multiplets.
description: Latex file, 30 eps figures, 42 pages. v3: Minor corrections in section 7
Totalistic two-dimensional cellular automata exhibiting global periodic behavior
Creators: name: Boccara, Nino
name: Roger, Michel
Publisher: name: arXiv
Year: 1999
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: We have determined families of two-dimensional deterministic totalistic cellular automaton rules whose stationary density of active sites exhibits a period two in time. Each family of deterministic rules is characterized by an ``average probabilistic totalistic rule'' exhibiting the same periodic behavior.
description: 8 figures
Tromino: Demand and DRF Aware Multi-Tenant Queue Manager for Apache Mesos Cluster
Creators: name: Saha, Pankaj
name: Beltre, Angel
name: Govindaraju, Madhusudhan
Publisher: name: arXiv
Year: 2019
Subjects: subject: Performance (cs.PF)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Apache Mesos, a two-level resource scheduler, provides resource sharing across multiple users in a multi-tenant cluster environment. Computational resources (i.e., CPU, memory, disk, etc. ) are distributed according to the Dominant Resource Fairness (DRF) policy. Mesos frameworks (users) receive resources based on their current usage and are responsible for scheduling their tasks within the allocation. We have observed that multiple frameworks can cause fairness imbalance in a multiuser environment. For example, a greedy framework consuming more than its fair share of resources can deny resource fairness to others. The user with the least Dominant Share is considered first by the DRF module to get its resource allocation. However, the default DRF implementation, in Apache Mesos' Master allocation module, does not consider the overall resource demands of the tasks in the queue for each user/framework. This lack of awareness can result in users without any pending task receiving more resource offers while users with a queue of pending tasks starve due to their high dominant shares. We have developed a policy-driven queue manager, Tromino, for an Apache Mesos cluster where tasks for individual frameworks can be scheduled based on each framework's overall resource demands and current resource consumption. Dominant Share and demand awareness of Tromino and scheduling based on these attributes can reduce (1) the impact of unfairness due to a framework specific configuration, and (2) unfair waiting time due to higher resource demand in a pending task queue. In the best case, Tromino can significantly reduce the average waiting time of a framework by using the proposed Demand-DRF aware policy.
The Role of Texts in the Formation of the Geluk School in Tibet during the Mid-Fourteenth and Fifteenth Centuries
Creators: Tsering, Sonam
Publisher: name: Columbia University
Year: 2020
Subjects: Buddhism
Buddhist literature, Tibetan
Buddhist monks

description: The dissertation delineates how the writings compiled in The Collected Works (Gsung ’bum) of Jey Tsongkhapa Lobzang Drakpa (1357–1419), the founder of the Geluk School of Tibetan Buddhism, constitute the centrality of the Geluk thought and philosophy and have contributed towards the school’s formation. It details how the texts have played a prominent role in establishing doctrinal authority, defining philosophical boundaries, postulating intellectual identity, and reorienting monastic education for the school. These texts have also considerably enhanced the intellectual, spiritual, and charismatic authority of Jey Tsongkhapa as a teacher and philosopher. This dissertation bases its approach on the premise that the life and writings of Tsongkhapa define the core identity of the Geluk School and that an explicit rejection of either tantamount to an outright abnegation of its membership. The dissertation begins with a critical retelling of Tibet’s religious history to contextualize the subject. The second chapter presents the culture and practice of life writing in Tibet to inform about the mechanism employed in traditional auto/biographies. Given the enormous attention drawn by the study of Jesus Christ (c. 4 BCE–c. 33 CE) in western academia, the chapter includes a literary review of contemporary studies and research for their emulation in the study of Tibetan hagiographies. The life story of Tsongkhapa is recounted in the third chapter. The fourth chapter details significant historical events that helped recenter Tsongkhapa in the Tibetan religio-cultural landscape. The fifth chapter presents his oeuvre—The Collected Works, the first extensive xylographic work printed in Tibet in the early fifteenth century. It also outlines the volume contents, presents sample texts, and chronicles the history of its publication and printing. The sixth chapter illustrates the centrality of Jey Tsongkhapa’s writings and its integration into the Geluk monastic educational system. The seventh chapter explicates on the topic of textual transmission and demonstrates how the texts were passed down through unbroken lineages to this day. The dissertation concludes with an epilogue and other back matters, including a list of transliteration of names, which are phoneticized in the main body for the ease of reading.
Estimating the Algorithmic Variance of Randomized Ensembles via the Bootstrap
Creators: name: Lopes, Miles E.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Statistics Theory (math.ST)
subject: Machine Learning (stat.ML)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: Although the methods of bagging and random forests are some of the most widely used prediction methods, relatively little is known about their algorithmic convergence. In particular, there are not many theoretical guarantees for deciding when an ensemble is "large enough" --- so that its accuracy is close to that of an ideal infinite ensemble. Due to the fact that bagging and random forests are randomized algorithms, the choice of ensemble size is closely related to the notion of "algorithmic variance" (i.e. the variance of prediction error due only to the training algorithm). In the present work, we propose a bootstrap method to estimate this variance for bagging, random forests, and related methods in the context of classification. To be specific, suppose the training dataset is fixed, and let the random variable $Err_t$ denote the prediction error of a randomized ensemble of size $t$. Working under a "first-order model" for randomized ensembles, we prove that the centered law of $Err_t$ can be consistently approximated via the proposed method as $t\to\infty$. Meanwhile, the computational cost of the method is quite modest, by virtue of an extrapolation technique. As a consequence, the method offers a practical guideline for deciding when the algorithmic fluctuations of $Err_t$ are negligible.
description: 53 pages
The Role of Videogame Glitch in Adult Learning
Creators: Albuquerque Mendes, Beatriz
Publisher: name: Columbia University
Year: 2018
Subjects: Educational technology
Adult education
Media literacy
Video games
Problem solving

description: This research investigates the responses of three individuals engaging with the Super Mario World (SMW) platform videogame glitches, and how they learned to solve the problem without formal help. This investigation was chosen because it explores connections between media literacy, critical thinking, and play in adults in the context of responding to unexpected technological errors. At the core of this study is the question of how encounters with arbitrary glitches can motivate and elicit critical thinking. Following a case study model, data were collected as the three subjects played SMW and encountered glitches. Questions regarding the (glitchy) game play experience were addressed in the first interview immediately following. The subjects were asked to create a visual essay and keep personal journals, which were gathered after 30 days, and a second interview at that time focused on the overall experience.
      Several results emerged from the data. Each of the subjects identified and solved for glitches in a way that suggested critical thinking processes. In addition, they all reflected in various ways on the challenges that glitches presented, making connections to larger issues and their everyday lives. The data also showed the importance of memory in these processes. The results suggest that while subjects approached and solved a technological glitch in SMW game play, they simultaneously acquired, developed, and—at least for the duration of the study—sustained new literacy skills and expanded their proficiency with critical thinking. This holds some potential implications for the value of incorporating glitch experiences both inside and outside the classroom, suggesting that videogame play—and particularly glitches in play—can be considered valuable opportunities for learners and teachers alike.
Free evolution of nonlinear scalar field collapse in double-null coordinates
Creators: name: Burko, Lior M.
Publisher: name: arXiv
Year: 1997
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study numerically the fully nonlinear spherically-symmetric collapse of a self-gravitating, minimally-coupled, massless scalar field. Our numerical code is based on double-null coordinates and on free evolution of the metric functions and the scalar field. The numerical code is stable and second-order accurate. We use this code to study the late-time asymptotic behavior at fixed $r$ (outside the black hole), along the event horizon, and along future null infinity. In all three asymptotic regions we find that, after the decay of the quasi-normal modes, the perturbations are dominated by inverse power-law tails. The corresponding power indices agree with the integer values predicted by linearized theory. We also study the case of a charged black hole nonlinearly perturbed by a (neutral) self-gravitating scalar field, and find the same type of behavior---i.e., quasi-normal modes followed by inverse power-law tails, with the same indices as in the uncharged case.
description: 4 pages. Talk presented at the Eighth Marcel Grossmann Meeting, June 22 - June 27, 1997, Jerusalem, Israel
The anomaly in the central charge of the supersymmetric kink from dimensional regularization and reduction
Creators: name: Rebhan, A.
name: van Nieuwenhuizen, P.
name: Wimmer, R.
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We show that the anomalous contribution to the central charge of the 1+1-dimensional N=1 supersymmetric kink that is required for BPS saturation at the quantum level can be linked to an analogous term in the extra momentum operator of a 2+1-dimensional kink domain wall with spontaneous parity violation and chiral domain wall fermions. In the quantization of the domain wall, BPS saturation is preserved by nonvanishing quantum corrections to the momentum density in the extra space dimension. Dimensional reduction from 2+1 to 1+1 dimensions preserves the unbroken N=1/2 supersymmetry and turns these parity-violating contributions into the anomaly of the central charge of the supersymmetric kink. On the other hand, standard dimensional regularization by dimensional reduction from 1 to (1-epsilon) spatial dimensions, which also preserves supersymmetry, obtains the anomaly from an evanescent counterterm.
description: LATeX, 19 pages, v2: significantly extended section 4 on dimensional reduction and evanescent counterterms
The Role of Urinary Catheters in Development of Nosocomial Urinary Tract-Related Bacteremia
Creators: Conway, Laurie Jean
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Nursing
subject: FOS: Health sciences
subject: Epidemiology
subject: Bacteremia
subject: Urinary catheterization
subject: Nosocomial infections--Epidemiology
subject: Intensive care units

description: This dissertation examines risk factors for bacteremia secondary to catheter-associated bacteriuria (CAB), specifically the potential risk of continued catheter presence, and assesses the degree to which hospitals in the United States (US) have implemented strategies to reduce unnecessary use of urinary catheters. In Chapter One, the problems of urinary tract-related bacteremia and unnecessary use of urinary catheters are introduced and their significance is described. In Chapter Two, a systematic review of the literature identifying risk factors for bacteremia secondary to CAB among adults in acute care settings is reported. In Chapter Three, a case control study elucidating risk factors for secondary bacteremia among adult patients with nosocomial CAB is reported, including an assessment of the risk posed by the continued presence of a urinary catheter after the onset of CAB. In Chapter Four, the prevalence and predictors of urinary catheter reduction policies in US hospitals is reported. In Chapter Five, findings of the three studies are summarized and overarching conclusions are provided including strengths, limitations, and implications for research, practice, and policy.
Chloridium humicola T. P. Wei & Y. L. Jiang 2022, comb. nov.
Creators: name: Wei, Tian-Peng
name: Wang, Kun-Ying
name: Zhang, Hong
name: Luo, Ming-Yan
name: Jia, Wei-Yu
name: Zeng, Yan
name: Jiang, Yu-Lan
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Fungi
Ascomycota
Sordariomycetes
Chaetosphaeriales
Chaetosphaeriaceae
Chloridium
Chloridium humicola

description: Chloridium humicola (S.C. Jong & E.E. Davis) T.P. Wei & Y.L. Jiang, comb. nov.
MycoBank: MB 842520
 Basionym:— Phialocephala humicola S.C. Jong & E.E. Davis, Mycologia 64 (6): 1352 (1972).
Description:— Jong & Davis (1972).
 Notes:— Phialocephala humicola was initially reported as saprophytes on soil in New Jersey, USA (Jong & Davis 1972). Although we did not isolate the type strains, we have examined the DNA sequence data from ex-type culture and another culture deposited under that species name in GenBank. Multi-locus phylogenetic analyses indicate that this species formed a well-supported monophyletic lineage in Chloridium, and can be differentiated from the other species in Chloridium by its morphological characteristics and DNA sequence data (Fig 1, 2; Jong & Davis 1972). Based on morphological characters and phylogenetic analyses, we therefore transferred P. humicola to Chloridium as a new combination.
description: Published as part of Wei, Tian-Peng, Wang, Kun-Ying, Zhang, Hong, Luo, Ming-Yan, Jia, Wei-Yu, Zeng, Yan & Jiang, Yu-Lan, 2022, A new species and a new combination of Chloridium from southwest China, pp. 67-76 in Phytotaxa 549 (1) on page 72, DOI: 10.11646/phytotaxa.549.1.5, http://zenodo.org/record/6605361
Additional file 1: of Inclusive engagement for health and development or â political theatreâ : results from case studies examining mechanisms for country ownership in Global Fund processes in Malawi, Tanzania and Zimbabwe
Creators: name: Armstrong, Russell
name: White, Arlette Campbell
name: Chinyamuchiko, Patrick
name: Chizimbi, Steven
name: Rush, Sarah Hamm
name: Poku, Nana
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: File contains three supplementary tables showing detailed financial data from which percentage calculations in Figs.Â 2, 3 and 4 in the main manuscript were derived. (DOCX 55 kb)
Terminology for the description of the shape of pottery fragments from Hellenistic and Roman contexts
Creators: name: High-Steskal, Nicole
name: Rembart, Laura
name: Katzjäger, Denise
Publisher: name: Zenodo
Year: 2019
Subjects: English-German terminology
pottery studies
archaeology
digital humanities

description: Collection of terms used to describe the general shape of a vessel as well as the rim of pottery fragments. The collection was created to improve the translation of German terms into English and make several datasets interoperable.
Structure of the Cauchy horizon singularity
Creators: name: Burko, Lior M.
Publisher: name: arXiv
Year: 1997
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study the Cauchy horizon (CH) singularity of a spherical charged black hole perturbed nonlinearly by a self-gravitating massless scalar field. We show numerically that the singularity is weak both at the early and at the late sections of the CH, where the focusing of the area coordinate $r$ is strong. In the early section the metric perturbations vanish, and the fields behave according to perturbation analysis. We find exact analytical expressions for the gradients of $r$ and of the scalar field, which are valid at both sections. We then verify these analytical results numerically.
description: 4 pages. Talk presented at the Eighth Marcel Grossmann Meeting, June 22 - June 27, 1997, Jerusalem, Israel
Exploring the Fairness and Resource Distribution in an Apache Mesos Environment
Creators: name: Saha, Pankaj
name: Beltre, Angel
name: Govindaraju, Madhusudhan
Publisher: name: arXiv
Year: 2019
Subjects: subject: Performance (cs.PF)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Apache Mesos, a cluster-wide resource manager, is widely deployed in massive scale at several Clouds and Data Centers. Mesos aims to provide high cluster utilization via fine grained resource co-scheduling and resource fairness among multiple users through Dominant Resource Fairness (DRF) based allocation. DRF takes into account different resource types (CPU, Memory, Disk I/O) requested by each application and determines the share of each cluster resource that could be allocated to the applications. Mesos has adopted a two-level scheduling policy: (1) DRF to allocate resources to competing frameworks and (2) task level scheduling by each framework for the resources allocated during the previous step. We have conducted experiments in a local Mesos cluster when used with frameworks such as Apache Aurora, Marathon, and our own framework Scylla, to study resource fairness and cluster utilization. Experimental results show how informed decision regarding second level scheduling policy of frameworks and attributes like offer holding period, offer refusal cycle and task arrival rate can reduce unfair resource distribution. Bin-Packing scheduling policy on Scylla with Marathon can reduce unfair allocation from 38\% to 3\%. By reducing unused free resources in offers we bring down the unfairness from to 90\% to 28\%. We also show the effect of task arrival rate to reduce the unfairness from 23\% to 7\%.
MOESM1 of Exploration of carbohydrate binding behavior and anti-proliferative activities of Arisaema tortuosum lectin
Creators: name: Kshema Thakur
name: Tarnjeet Kaur
name: Manpreet Kaur
name: Hora, Rachna
name: Singh, Jatinder
Publisher: name: figshare
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified

description: Additional file 1: Table S1. Thermodynamic parameters for the interaction of ATL with asialofetuin.
The Role of the Clustered Protocadherins in the Assembly of Olfactory Neural Circuits
Creators: Mountoufaris, George
Publisher: name: Columbia University
Year: 2016
Subjects: subject: Olfactory nerve
subject: Cadherins
subject: Neural circuitry
subject: Neurosciences
subject: FOS: Clinical medicine

description: The clustered protocadherins (Pcdh α, β & γ) provide individual neurons with cell surface diversity. However, the importance of Pcdh mediated diversity in neural circuit assembly and how it may promote neuronal connectivity remains largely unknown. Moreover, to date, Pcdh in vivo function has been studied at the level of individual gene clusters; whole cluster-wide function has not been addressed. Here I examine the role of all three Pcdh gene clusters in olfactory sensory neurons (OSNs); a neuronal type that expressed all three types of Pcdhs and in addition I address the role of Pcdh mediate diversity in their wiring. When OSNs share a dominant single Pcdh identity (α, β & γ) their axons fail to form distinct glomeruli, suggestive of inappropriate self-recognition of neighboring axons (loss of non-self-discrimination). By contrast, deletion of the entire α, β,γ Pcdh gene cluster, but not of each individual cluster alone, leads to loss of self-recognition and self-avoidance thus, OSN axons fail to properly arborize. I conclude that Pcdh-expression is necessary for self-recognition in OSNs, whereas its diversity allows distinction between self and non-self. Both of these functions are required for OSNs to connect and assembly into functional circuits in the olfactory bulb. My results, also reveal neuron-type specific differences in the requirement of specific Pcdh gene clusters and demonstrate significant redundancy between Pcdh isoforms in the olfactory system.