Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of the DRACO Particle-in-Cell Code using Busek 200W Hall Thruster Experimental Data

Abstract : The thesis discusses developments to the electric propulsion plume code DRACO as well as validation and sensitivity analysis of the code. DRACO is a PIC code that models particles kinematically while using finite differences schemes to solve the electric potential and field. The DRACO ode has been recently modified. A particle source has been added to use the Hall Thruster device code HPHall as input to model Hall Thrusters. The code is capable of using a non-uniform mesh that uses any combination of uniform, linear and exponential stretching schemes in any of three directions. A stretched mesh can be used to refine simulation results in certain areas or improve performance by reducing the number of cells in a mesh. Finally, DRACO has the capability of using a DSMC collision scheme as well as performing recombination collisions. A sensitivity analysis of the upgraded DRACO code was performed to test experimental data gathered using a Busek 200 W Hall Thruster. A simulation was created that attempts to numerically recreate the experiment; the validation is performed by comparing the plasma potential, polytropic temperature, ion number density of the thruster plume as well as Faraday and ExB probe results. The study compares the HPHall source with older source models and also compares variations of the HPHall source. The field solver and collision model used are compared to determine how to achieve the best results. Finally, both uniform and non-uniform meshes are tested to determine if a non-uniform mesh can be properly implemented to improve simulation results and performance. Results from the validation and sensitivity study show the DRACO code can be used to recreate a vacuum chamber simulation using a Hall Thruster. The best results occur when the HPHall source is used with a MCC collision scheme using a projected background neutral density and CEX collision tracking. A stretched mesh was tested and proved results that are as accurate as a uniform mesh.
OrfPredictor: predicting protein-coding regions in EST-derived sequences

OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at .
Detecting Fracture Related Voids and Abandoned Lead/Zinc Mines and Appraising the Subsidence Potential

Summary Historical lead/zinc mining activities have left surface scars and underground hazardsacross a portion of southeastern Kansas, southwestern Missouri, and northeastern Oklahoma,known as the Tri-State Lead/Zinc Mining District. Fractures and voids in otherwise competentnear-surface rock layers can pose a stability risk to overlying surface structure. Confidentdetection and delineation of voids or open fractures prior to surface expression permits theevaluation and possible reduction in risk such features pose to people and property. Surfacegrowth associated with a sinkhole located within 100 ft of State Line Road and a gas meteringstation south of Baxter Springs, Kansas, raised concerns for public safety and prompted anextensive drilling and geophysical investigation. The mine workings of interest ranged in depthfrom 100 to over 150 ft below ground surface and are in an area where Mississippian Limestoneacts as both host and roof rock. Overlying the limestone is a soil and clay layer varying in thick-ness from 10 to 20 ft. Subsidence in this area has a historical precedent dating back prior to themid-twentieth century.Abandoned lead/zinc mines (drifts) known from mine maps to pass beneath State LineRoad and generally coincident with the sinkhole of concern were the primary targets of this studyand were suggested to embody a risk to surface structures in this area. Extensive drilling in theimmediate area provided excellent 1-D ground truth but lacked the lateral resolution necessary tomap the subsurface extent of fracture zones and voids. Surface wave imaging detected lateralvariations in rock rigidity at depths and locations generally consistent with mine maps and drill-encountered sediment-filled and open fractures. Stable voids, regardless of origin, represent norisk to public safety; however, if stable voids begin to grow and surpass a size or roof span thatcan be supported by its roof rock, subsidence will occur. At the present time, science providesno method to confidently predict subsidence rates, extent, and volume. However, by usinggeophysical methods such as surface wave imaging as a monitoring tool, iterative “snap shots” ofthe subsurface allow discrimination of change and estimates of current subsidence rates.Surface wave analysis using MASW allowed relatively quick and accurate (in relation toother geophysical methods) acoustic images to be produced of the upper 50 ft to 150 ft.
Pose Estimation of Known Objects by Efficient Silhouette Matching

Pose estimation is essential for automated handling of objects. In many computer vision applications only the object silhouettes can be acquired reliably, because untextured or slightly transparent objects do not allow for other features. We propose a pose estimation method for known objects, based on hierarchical silhouette matching and unsupervised clustering. The search hierarchy is created by an unsupervised clustering scheme, which makes the method less sensitive to parametrization, and still exploits spatial neighborhood for efficient hierarchy generation. Our evaluation shows a decrease in matching time of 80% compared to an exhaustive matching and scalability to large models.
Assessing Signal-Driven Mechanisms in Neonates: Brain Responses to Temporally and Spectrally Different Sounds

Past studies have found that, in adults, the acoustic properties of sound signals (such as fast versus slow temporal features) differentially activate the left and right hemispheres, and some have hypothesized that left-lateralization for speech processing may follow from left-lateralization to rapidly changing signals. Here, we tested whether newborns’ brains show some evidence of signal-specific lateralization responses using near-infrared spectroscopy (NIRS) and auditory stimuli that elicits lateralized responses in adults, composed of segments that vary in duration and spectral diversity. We found significantly greater bilateral responses of oxygenated hemoglobin (oxy-Hb) in the temporal areas for stimuli with a minimum segment duration of 21 ms, than stimuli with a minimum segment duration of 667 ms. However, we found no evidence for hemispheric asymmetries dependent on the stimulus characteristics. We hypothesize that acoustic-based functional brain asymmetries may develop throughout early infancy, and discuss their possible relationship with brain asymmetries for language.
Composite Binary Losses

We study losses for binary classification and class probability estimation and extend the understanding of them from margin losses to general composite losses which are the composition of a proper loss with a link function. We characterise when margin losses can be proper composite losses, explicitly show how to determine a symmetric loss in full from half of one of its partial losses, introduce an intrinsic parametrisation of composite binary losses and give a complete characterisation of the relationship between proper losses and "classification calibrated" losses. We also consider the question of the "best" surrogate binary loss. We introduce a precise notion of "best" and show there exist situations where two convex surrogate losses are incommensurable. We provide a complete explicit characterisation of the convexity of composite binary losses in terms of the link function and the weight function associated with the proper loss which make up the composite loss. This characterisation suggests new ways of "surrogate tuning" as well as providing an explicit characterisation of when Bregman divergences on the unit interval are convex in their second argument. Finally, in an appendix we present some new algorithm-independent results on the relationship between properness, convexity and robustness to misclassification noise for binary losses and show that all convex proper losses are non-robust to misclassification noise.
Presentation of a Game Semantics for First-Order Propositional Logic

Game semantics aim at describing the interactive behaviour of proofs by interpreting formulas as games on which proofs induce strategies. In this article, we introduce a game semantics for a fragment of first order propositional logic. One of the main difficulties that has to be faced when constructing such semantics is to make them precise by characterizing definable strategies – that is strategies which actually behave like a proof. This characterization is usually done by restricting to the model to strategies satisfying subtle combinatory conditions such as innocence, whose preservation under composition is often difficult to show. Here, we present an original methodology to achieve this task which requires to combine tools from game semantics, rewriting theory and categorical algebra. We introduce a diagrammatic presentation of definable strategies by the means of generators and relations: those strategies can be generated from a finite set of “atomic” strategies and that the equality between strategies generated in such a way admits a finite axiomatization. These generators satisfy laws which are a variation of bialgebras laws, thus bridging algebra and denotational semantics in a clean and unexpected way.
The throughput of data switches with and without speedup

In this paper we use fluid model techniques to establish two results concerning the throughput of data switches. For an input-queued switch (with no speedup) we show that a maximum weight algorithm for connecting inputs and outputs delivers a throughput of 100%, and for combined input- and output-queued switches that run at a speedup of 2 we show that any maximal matching algorithm delivers a throughput of 100%. The only assumptions on the input traffic are that it satisfies the strong law of large numbers and that it does not oversubscribe any input or any output.
Phosphorylation of the AP2 μ subunit by AAK1 mediates high affinity binding to membrane protein sorting signals

During receptor-mediated endocytosis, AP2 complexes act as a bridge between the cargo membrane proteins and the clathrin coat by binding to sorting signals via the μ2 subunit and to clathrin via the β subunit. Here we show that binding of AP2 to sorting signals in vitro is regulated by phosphorylation of the μ2 subunit of AP2. Phosphorylation of μ2 enhances the binding affinity of AP2 for sorting motifs as much as 25-fold compared with dephosphorylated AP2. The recognition of sorting signals was not affected by the phosphorylation status of the α or β2 subunit, suggesting that phosphorylation of μ2 is critical for regulation of AP2 binding to sorting signals. Phosphorylation of μ2 occurs at a single threonine residue (Thr-156) and is mediated by the newly discovered adaptor-associated kinase, AAK1, which copurifies with AP2. We propose that phosphorylation of the AP2 μ2 subunit by AAK1 ensures high affinity binding of AP2 to sorting signals of cargo membrane proteins during the initial steps of receptor-mediated endocytosis.
The cost of exactly simulating quantum entanglementwith classical communicationGilles

We investigate the amount of communication that must augment classical local hidden variable models in order to simulate the behaviour of entangled quantum systems. We consider the scenario where a bipartite measurement is given from a set of possibilities and the goal is to obtain exactly the same correlations that arise when the actual quantum system is measured. We show that, in the case of a single pair of qubits in a Bell state, a constant number of bits of communication is always suucient|regardless of the number of measurements under consideration. We also show that, in the case of a system of n Bell states, a constant times 2 n bits of communication are necessary.
Interactive Off-Line Handwritten Text Transcription Using On-Line Handwritten Text as Feedback

Handwritten Text Recognition is a problem that has gained attention in the last years mainly due to the interest in the transcription of historical documents. However, the automatic transcription is ineffectual in unconstrained handwritten documents. Thus, human intervention is typically needed to correct the results. Given that a post-editing approach is inefficient and uncomfortable, multimodal interactive approaches have begun to emerge in the last years. In this scheme, the user interacts with the system by means of an e-pen. This multimodal feedback, on the one hand, allows to improve the accuracy of the system and, on the other hand, increases user acceptability. In this work, we present a new approach on interaction based on character sequences. Here we present developments that allow taking advantage of interaction-derived context to significantly improve feedback decoding accuracy. Empirical tests suggest that, despite the loss of the deterministic accuracy of traditional peripherals, this approach can save significant amounts of user effort with respect to non-interactive post-editing correction.
Entanglement-Assisted Local Manipulation of Pure Quantum States

We demonstrate that local transformations on a composite quantum system can be enhanced in the presence of certain entangled states. These extra states act much like catalysts in a chemical reaction: they allow otherwise impossible local transformations to be realized, without being consumed in any way. In particular, we show that this effect can considerably improve the efficiency of entanglement concentration procedures for finite states.
H/Direct: a binary foreign language interface for Haskell

H/Direct is a foreign-language interface for the purely functional language Haskell. Rather than rely on host-language type signatures, H/Direct compiles Interface Definition Language (IDL) to Haskell stub code that marshals data across the interface. This approach allows Haskell to call both C and COM, and allows a Haskell component to be wrapped in a C or COM interface. IDL is a complex language and language mappings for IDL are usually described informally. In contrast, we provide a relatively formal and precise definition of the mapping between Haskell and IDL.
micro+e- micro-e+ transitions via neutral scalar bosons.

With $\mu\to e\gamma$ decay forbidden by multiplicative lepton number conservation, we study muonium--antimuonium transitions induced by neutral scalar bosons. Pseudoscalars do not induce conversion for triplet muonium, while for singlet muonium, pseudoscalar and scalar contributions add constructively. This is in contrast to the usual case of doubly charged scalar exchange, where the conversion rate is the same for both singlet and triplet muonium. Complementary to muonium conversion studies, high energy $\mu^+e^- \to \mu^- e^+$ and $e^-e^- \to \mu^- \mu^-$ collisions could reveal spectacular resonance peaks for the cases of neutral and doubly charged scalars, respectively.
Observational signatures and non-Gaussianities of general single-field inflation

We perform a general study of primordial scalar non-Gaussianities in single-field inflationary models in Einstein gravity. We consider models where the inflaton Lagrangian is an arbitrary function of the scalar field and its first derivative, and the sound speed is arbitrary. We find that under reasonable assumptions, the non-Gaussianity is completely determined by five parameters. In special limits of the parameter space, one finds distinctive ‘shapes’ of the non-Gaussianity. In models with a small sound speed, several of these shapes would become potentially observable in the near future. Different limits of our formulae recover various previously known results.
Efficient Bayesian methods for clustering.

One of the most important goals of unsupervised learning is to discover meaningful clusters in data. Clustering algorithms strive to discover groups, or clusters, of data points which belong together because they are in some way similar. The research presented in this thesis focuses on using Bayesian statistical techniques to cluster data. We take a model-based Bayesian approach to defining a cluster, and evaluate cluster membership in this paradigm. Due to the fact that large data sets are increasingly common in practice, our aim is for the methods in this thesis to be efficient while still retaining the desirable properties which result from a Bayesian paradigm. We develop a Bayesian Hierarchical Clustering (BHC) algorithm which efficiently addresses many of the drawbacks of traditional hierarchical clustering algorithms. The goal of BHC is to construct a hierarchical representation of the data, incorporating both finer to coarser grained clusters, in such a way that we can also make predictions about new data points, compare different hierarchies in a principled manner, and automatically discover interesting levels of the hierarchy to examine. BHC can also be viewed as a fast way of performing approximate inference in a Dirichlet Process Mixture model (DPM), one of the cornerstones of nonparametric Bayesian Statistics. We create a new framework for retrieving desired information from large data collections, Bayesian Sets, using Bayesian clustering techniques. Unlike current retrieval methods, Bayesian Sets provides a principled framework which leverages the rich and subtle information provided by queries in the form of a set of examples. Whereas most clustering algorithms are completely unsupervised, here the query provides supervised hints or constraints as to the membership of a particular cluster. We call this "clustering on demand", since it involves forming a cluster once some elements of that cluster have been revealed. We use Bayesian Sets to develop a content-based image retrieval system. We also extend Bayesian Sets to a discriminative setting and use this to perform automated analogical reasoning. Lastly, we develop extensions of clustering in order to model data with more complex structure than that for which traditional clustering is intended. Clustering models traditionally assume that each data point belongs to one and only one cluster, and although they have proven to be a very powerful class of models, this basic assumption is somewhat limiting. For example, there may be overlapping regions where data points actually belong to multiple clusters, like movies which can each belong to multiple genres. We extend traditional mixture models to create a statistical model for overlapping clustering, the Infinite Overlapping Mixture Model (IOMM), in a non-parametric Bayesian setting, using the Indian Buffet Process (IBP). We also develop a Bayesian Partial Membership model (BPM), which allows data points to have partial membership in multiple clusters via a continuous relaxation of a finite mixture model.
Colloid suspension stability and transport through unsaturated porous media

Contaminant transport is traditionally modeled in a two-phase system: a mobile aqueous phase and an immobile solid phase. Over the last 15 years, there has been an increasing awareness of a third, mobile solid phase. This mobile solid phase, or mobile colloids, are organic or inorganic submicron-sized particles that move with groundwater flow. When colloids are present, the net effect on radionuclide transport is that radionuclides can move faster through the system. It is not known whether mobile colloids exist in the subsurface environment of the Hanford Site. Furthermore, it is not known if mobile colloids would likely exist in a plume emanating from a Low Level Waste (LLW) disposal site. No attempt was made in this study to ascertain whether colloids would form. Instead, experiments and calculations were conducted to evaluate the likelihood that colloids, if formed, would remain in suspension and move through saturated and unsaturated sediments. The objectives of this study were to evaluate three aspects of colloid-facilitated transport of radionuclides as they specifically relate to the LLW Performance Assessment. These objectives were: (1) determine if the chemical conditions likely to exist in the near and far field of the proposed disposal site are prone to induce flocculation (settling of colloids from suspension) or dispersion of naturally occurring Hanford colloids, (2) identify the important mechanisms likely involved in the removal of colloids from a Hanford sediment, and (3) determine if colloids can move through unsaturated porous media.
Cell face velocity alternatives in a structured colocated grid for the unsteady Navier–Stokes equations

The use of a colocated variable arrangement for the numerical solution of fluid flow is becoming more and more popular due to its coding simplicity. The inherent decoupling of the pressure and velocity fields in this arrangement can be handled via a special interpolation procedure for the calculation of the cell face velocity named pressure‐weighted interpolation method (PWIM) (AIAA J. 1983; 21(11):1525–1532). In this paper a discussion on the alternatives to extend PWIM to unsteady flows is presented along with a very simple criterion to ascertain if a given interpolation practice will produce steady results that are relaxation dependent or time step dependent. Following this criterion it will be shown that some prior schemes presented as time step independent are actually not, although by using special interpolations can be readily adapted to be. A systematic way of deriving different cell face velocity expressions will be presented and new formulae free of Δt dependence will be derived. Several computational exercises will accompany the theoretical discussion to support our claims. Copyright © 2009 John Wiley & Sons, Ltd.
Geo-replicated storage with scalable deferred update replication

Many current online services are deployed over geographically distributed sites (i.e., datacenters). Such distributed services call for geo-replicated storage, that is, storage distributed and replicated among many sites. Geographical distribution and replication can improve locality and availability of a service. Locality is achieved by moving data closer to the users. High availability is attained by replicating data in multiple servers and sites. This paper considers a class of scalable replicated storage systems based on deferred update replication with transactional properties. The paper discusses different ways to deploy scalable deferred update replication in geographically distributed systems, considers the implications of these deployments on user-perceived latency, and proposes solutions. Our results are substantiated by a series of microbenchmarks and a social network application.