Miracle-dz/UniFAR-FTUs huggingface dataset:
A Constant Speed Changing Rate and Constant Turn Rate Model for Maneuvering Target Tracking

This paper addresses the problem of modeling maneuvering target motion in tracking applications. A target trajectory can typically be divided into segments with different dynamic motion modes, such as a constant velocity motion, a constant acceleration motion or a constant turn rate motion. To integrate the different motion modes into a uniform model, a Constant Speed Changing Rate and Constant Turn Rate (CSCRCTR) model is proposed. A new state vector is defined, and the state transition function is derived. Based on the CSCRCTR model, we present a tracking algorithm using a particle filter. The performances of the CSCRCTR model, the uniform model (UM) and the interacting multiple model (IMM) for tracking a simulated maneuvering target are compared and show that the CSCRCTR model maintains a good consistency for different types of motions and achieves better accuracy than UM and IMM when maneuvers occur.
On approximability of the minimum-cost k-connected spanning subgraph problem

We present the first truly pojynomial-time approximation scheme (PTAS) for the mimmum-cost k-vertex(or: kedge-) connected spanning subgraph problem for complete Euclidean graphs in Rd. Previously it was known for every positive constant E how to construct in a polynomial time a graph on a superset of the input points which is k-vertex connected with respect to the input points, and whose cost is within (1 +E) of the minimum-cost of a k-vertex connected graph spanning the input points. We subsume that result by showing for every positive constant E how to construct m a polynomial-time a k-connected subgraph spanning the input points without any Steiner points and having the cost within (1 + E) of the minimum. We also studv hardness of annroximations for the minimum-cost k-v”ertexand k-edge-connected spanning subrrrauh oroblems. The. onlv inannroximabilitv result kno&*so far for the minimumrcost k-vertexand-k-edgeconnected spanning subgraph problems states that the kedge-connectivity problem in unweighted graphs does not have a PTAS unless P = NP, even for k = 2. We present a simpler proof of this result that holds even for aranhs of bounded degree, and provide the first proof that Vfnhing a PTAS for the k-vertex-connectivitv nroblem in unweiehted graphs is NP-hard even for k = 2 aid for graphs of bocnded degree. We further show that our algorithmic results for Euclidean graphs cannot be extended to arbitrarily high dimensions. -We prove that for weighted graphs tfiere-is no PTAS for the k-vertexand the k-edne-connectivitv oroblem unless P = NP, even for Euclidealgraphs in W”g ’ and k = 2.
Phylogenetic Analysis of Staphylococcus aureus CC398 Reveals a Sub-Lineage Epidemiologically Associated with Infections in Horses

In the early 2000s, a particular MRSA clonal complex (CC398) was found mainly in pigs and pig farmers in Europe. Since then, CC398 has been detected among a wide variety of animal species worldwide. We investigated the population structure of CC398 through mutation discovery at 97 genetic housekeeping loci, which are distributed along the CC398 chromosome within 195 CC398 isolates, collected from various countries and host species, including humans. Most of the isolates in this collection were received from collaborating microbiologists, who had preserved them over years. We discovered 96 bi-allelic polymorphisms, and phylogenetic analyses revealed that an epidemic sub-clone within CC398 (dubbed ‘clade (C)’) has spread within and between equine hospitals, where it causes nosocomial infections in horses and colonises the personnel. While clade (C) was strongly associated with S. aureus from horses in veterinary-care settings (p = 2×10−7), it remained extremely rare among S. aureus isolates from human infections.
Evidence of carotid artery wall hypertrophy in homozygous homocystinuria.

BACKGROUND We aimed to determine whether intima-media thickness (IMT) was increased in the carotid artery of subjects with homocystinuria to better understand the in vivo contribution of homocysteine to early atherogenesis. METHODS AND RESULTS We investigated ultrasonographically the right common carotid artery in 14 subjects with homozygous homocystinuria aged 3 to 34 years (mean, 13 years) and in 15 of their heterozygous parents aged 32 to 47 years (mean, 41 years) by comparison with 2 control groups of 15 healthy subjects of the same age. Far-wall IMT and lumen diameter were measured with a computerized program, and the cross-sectional area of the intima-media complex (CSA-IMC) was calculated from IMT and diameter. Comparison with their respective controls, adjusted for body surface area or height, showed that homozygotes had greater IMT (P<0.001) and CSA-IMC (P<0.05) and smaller diameter (P<0.05), whereas heterozygotes had values similar to their controls. Multivariate analysis of the arterial parameters with age, body surface area (or height), and plasma total homocysteine in the homozygous and heterozygous groups combined showed that IMT was related to age (P<0.05) and homocysteine (P<0.01), diameter was related to body surface area (P<0.001) or height (P<0.05), and CSA-IMC was related to age (P<0.05), body surface area (P<0.05) (but not height), and homocysteine (P<0.05). CONCLUSIONS Homozygous homocystinuria was associated with common carotid wall hypertrophy, whereas heterozygous disease was not. Such hypertrophy may reflect a smooth muscle proliferation induced by hyperhomocysteinemia and represent a promising target for testing vascular effects of therapeutic measures to lower homocysteine.
Mycobacterium kansasii pericarditis in a kidney transplant recipient: a case report and comprehensive review of the literature

Mycobacterium kansasii is the second most common non‐tuberculous mycobacteria in kidney transplant recipients (KTRs) and has been reported to cause disseminated infection in KTRs. We report the first case to our knowledge of M. kansasii pericarditis after kidney transplantation in a 54‐year‐old man. The patient was admitted with a 2‐month history of intermittent fever and myalgia, treated with oral prednisolone and mycophenolate mofetil prior to admission. Chest computed tomography showed enlarged mediastinal lymph node and small amount of pericardial effusion. Mediastinoscopic biopsy of mediastinal lymph node revealed reactive hyperplasia, without evidence of granuloma, but acid‐fast bacilli stain of pericardial fluid reported positive finding and pericardial fluid culture identified M. kansasii. The patient has been treated successfully with rifabutin‐based combination therapy. All available cases of M. kansasii infection in kidney transplant patients and M. kansasii pericarditis in human immunodeficiency virus‐infected patients are comprehensively reviewed.
Salicylic acid modulates levels of phosphoinositide dependent-phospholipase C substrates and products to remodel the Arabidopsis suspension cell transcriptome

Basal phosphoinositide-dependent phospholipase C (PI-PLC) activity controls gene expression in Arabidopsis suspension cells and seedlings. PI-PLC catalyzes the production of phosphorylated inositol and diacylglycerol (DAG) from phosphoinositides. It is not known how PI-PLC regulates the transcriptome although the action of DAG-kinase (DGK) on DAG immediately downstream from PI-PLC is responsible for some of the regulation. We previously established a list of genes whose expression is affected in the presence of PI-PLC inhibitors. Here this list of genes was used as a signature in similarity searches of curated plant hormone response transcriptome data. The strongest correlations obtained with the inhibited PI-PLC signature were with salicylic acid (SA) treatments. We confirm here that in Arabidopsis suspension cells SA treatment leads to an increase in phosphoinositides, then demonstrate that SA leads to a significant 20% decrease in phosphatidic acid, indicative of a decrease in PI-PLC products. Previous sets of microarray data were re-assessed. The SA response of one set of genes was dependent on phosphoinositides. Alterations in the levels of a second set of genes, mostly SA-repressed genes, could be related to decreases in PI-PLC products that occur in response to SA action. Together, the two groups of genes comprise at least 40% of all SA-responsive genes. Overall these two groups of genes are distinct in the functional categories of the proteins they encode, their promoter cis-elements and their regulation by DGK or phospholipase D. SA-regulated genes dependent on phosphoinositides are typical SA response genes while those with an SA response that is possibly dependent on PI-PLC products are less SA-specific. We propose a model in which SA inhibits PI-PLC activity and alters levels of PI-PLC products and substrates, thereby regulating gene expression divergently.
Chapter 2 GAME THEORY IN SUPPLY CHAIN ANALYSIS

Game theory has become an essential tool in the analysis of supply chains with multiple agents, often with conflicting objectives. This chapter surveys the applications of game theory to supply chain analysis and outlines game-theoretic concepts that have potential for future application. We discuss both non-cooperative and cooperative game theory in static and dynamic settings. Careful attention is given to techniques for demonstrating the existence and uniqueness of equilibrium in non-cooperative games. A newsvendor game is employed throughout to demonstrate the application of various tools.
Novel phylogenetic relationships of the enigmatic brevicipitine and scaphiophrynine toads as revealed by sequences from the nuclear Rag–1 gene

Owing to a general paucity of characters and an apparently high level of homoplasy, the systematics of frogs have remained disputed. A phylogeny based on the single-copy nuclear Rag–1 gene revealed unexpected placements of scaphiophrynine and brevicipitine toads. The former have usually been considered as sister group to all other extant microhylids or are even classified as a separate family. Their basal position among microhylids was weakly indicated in our analysis; but they clearly are part of a strongly supported clade composed of representatives from five other microhylid subfamilies. By contrast, the brevicipitines, a group that hitherto was unanimously considered to belong to the Microhylidae, were highly divergent and placed as a sister group to the arthroleptoid clade. These novel phylogenetic placements are best reflected by a classificatory status of the Scaphiophryninae as a subfamily of the Microhylidae, whereas the brevicipitines may merit recognition as a distinct family. Our findings seem to corroborate a high degree of morphological homoplasy in frogs and suggest that even highly derived morphological states, such as the hydrostatic tongue of microhylids, hemisotids and brevicipitines, may be subject to convergent evolution, parallelism or character reversal.
Use of an optical flow algorithm to quantify and correct patient motion during tomographic acquisition

We have developed an automatic procedure for the detection, quantification and correction of translational motion during single photon emission computerized tomography (SPECT). The method computes the optical flow vector field between two successive views. The optical flow vector field assigns to each pixel of a tomographic view a two dimensional velocity that describes its motion across the image plane between two successive views. Motion can be corrected by shifting the moved views back by the amount of the measured motion distance. The method is applied to human studies where obvious motion was detected from visual inspection of a rotating cine display. Visually artifactual perfusion defects are eliminated after motion correction. The optical flow method can accurately detect the presence of motion, localize the camera angle at which motion occurred and measure the distance of motion.
Automatically Identifying Vocal Expressions for Music Transcription

Music transcription has many uses ranging from music information retrieval to better education tools. An important component of automated transcription is the identification and labeling of different kinds of vocal expressions such as vibrato, glides, and riffs. In Indian Classical Music such expressions are particularly important since a raga is often established and identified by the correct use of these expressions. It is not only important to classify what the expression is, but also when it starts and ends in a vocal rendition. Some examples of such expressions that are key to Indian music are Meend (vocal glides) and Andolan (very slow vibrato). In this paper, we present an algorithm for the automatic transcription and expression identification of vocal renditions with specific application to North Indian Classical Music. Using expert human annotation as the ground truth, we evaluate this algorithm and compare it with two machinelearning approaches. Our results show that we correctly identify the expressions and transcribe vocal music with 85% accuracy. As a part of this effort, we have created a corpus of 35 voice recordings, of which 12 recordings are annotated by experts. The corpus is available for download 1 .
Bayesian estimation from few samples: community detection and related problems

We propose an efficient meta-algorithm for Bayesian estimation problems that is based on low-degree polynomials, semidefinite programming, and tensor decomposition. The algorithm is inspired by recent lower bound constructions for sum-of-squares and related to the method of moments. Our focus is on sample complexity bounds that are as tight as possible (up to additive lower-order terms) and often achieve statistical thresholds or conjectured computational thresholds. Our algorithm recovers the best known bounds for community detection in the sparse stochastic block model, a widely-studied class of estimation problems for community detection in graphs. We obtain the first recovery guarantees for the mixed-membership stochastic block model (Airoldi et el.) in constant average degree graphs---up to what we conjecture to be the computational threshold for this model. We show that our algorithm exhibits a sharp computational threshold for the stochastic block model with multiple communities beyond the Kesten--Stigum bound---giving evidence that this task may require exponential time. The basic strategy of our algorithm is strikingly simple: we compute the best-possible low-degree approximation for the moments of the posterior distribution of the parameters and use a robust tensor decomposition algorithm to recover the parameters from these approximate posterior moments.
Dynamics of the neuronal intermediate filaments

We have analyzed the dynamics of neuronal intermediate filaments in living neurons by using the method of photobleaching of fluorescently- labeled neurofilament L protein and immunoelectron microscopy of incorporation sites of biotinylated neurofilament L protein. Low-light- level imaging and photobleaching of growing axons of mouse sensory neurons did not affect the rate of either axonal growth or the addition of intermediate filament structures at the axon terminal, suggesting that any perturbations caused by these optical methods would be minimal. After laser photobleaching, recovery of fluorescence did occur slowly with a recovery half-time of 40 min. Furthermore, we observed a more rapid fluorescence recovery in growing axons than in quiescent ones, indicating a growth-dependent regulation of the turnover rate. Incorporation sites of biotin-labeled neurofilament L protein were localized as numerous discrete sites along the axon, and they slowly elongated to become continuous arrays 24 h after injection. Collectively, these results indicate that neuronal intermediate filaments in growing axons turn over within the small area of the axoplasm possibly by the mechanism of lateral and segmental incorporation of new subunits.
Contingent Planning via Heuristic Forward Search witn Implicit Belief States

Contingent planning is the task of generating a conditional plan given uncertainty about the initial state and action effects, but with the ability to observe some aspects of the current world state. Contingent planning can be transformed into an And-Or search problem in belief space, the space whose elements are sets of possible worlds. In (Brafman & Hoffmann 2004), we introduced a method for implicitly representing a belief state using a propositional formula that describes the sequence of actions leading to that state. This representation trades off space for time and was shown to be quite effective for conformant planning within a heuristic forward-search planner based on the FF system. In this paper we apply the same architecture to contingent planning. The changes required to adapt the search space representation are small. More effort is required to adapt the relaxed planning problems whose solution informs the forward search algorithm. We propose the targeted use of an additional relaxation, mapping the relaxed contingent problem into a relaxed conformant problem. Experimental results show that the resulting planning system, Contingent-FF, is highly competitive with the state-of-the-art contingent planners POND and MBP.
Prediction of protein domain boundaries from inverse covariances

It has been known even since relatively few structures had been solved that longer protein chains often contain multiple domains, which may fold separately and play the role of reusable functional modules found in many contexts. In many structural biology tasks, in particular structure prediction, it is of great use to be able to identify domains within the structure and analyze these regions separately. However, when using sequence data alone this task has proven exceptionally difficult, with relatively little improvement over the naive method of choosing boundaries based on size distributions of observed domains. The recent significant improvement in contact prediction provides a new source of information for domain prediction. We test several methods for using this information including a kernel smoothing‐based approach and methods based on building alpha‐carbon models and compare performance with a length‐based predictor, a homology search method and four published sequence‐based predictors: DOMCUT, DomPRO, DLP‐SVM, and SCOOBY‐DOmain. We show that the kernel‐smoothing method is significantly better than the other ab initio predictors when both single‐domain and multidomain targets are considered and is not significantly different to the homology‐based method. Considering only multidomain targets the kernel‐smoothing method outperforms all of the published methods except DLP‐SVM. The kernel smoothing method therefore represents a potentially useful improvement to ab initio domain prediction. Proteins 2013. © 2012 Wiley Periodicals, Inc.
HéNon Map: Simple Sinks Gaining Coexistence as B → 1

The quadratic map of the interval displays one attractor for each parameter value. Conservative maps of the plane display infinite coexistence of stability islands around periodic orbits. Between these two extremes, dissipative systems of the plane are known to have infinite coexistence of sinks as a generic property, yet very hard to detect. We investigate how more and more coexistence is gained as the area-contraction rate b → 1. In this paper, we show a sequence of simple sinks gaining coexistence, and investigate the convergence properties of its bifurcation values. The sinks are simple, or primary, due to their geometrical structure.
Location of variable and conserved epitopes among the multiple serotypes of streptococcal M protein

In studies primarily confined to the amino-terminal region of the fibrillar group A streptococcal M protein, only limited immunological crossreactions have been observed among M serotypes. In this investigation, two monoclonal antibodies generated against nearly the entire M6 molecule (LysM6) were used to determine the extent of crossreactions among M serotyping strains and to localize their epitopes on the M molecule. Colony blot and immunoblot analyses revealed that an epitope responsible for crossreactions among 5 of the 56 strains of different M serotypes tested is located in the amino- terminal half of the molecule, distal to the cell surface. In contrast, a more common crossreactive epitope, reacting with 20 of the 56 strains, is located near the middle of the M molecule. These studies also reveal that the more conserved determinant, located more proximally to the cell surface, is accessible to the immune system, even on the whole organism, and, thus, may be useful in devising means to protect against infections by multiple group A streptococcal M serotypes.
Depressive Symptoms in People with and without Alcohol Abuse: Factor Structure and Measurement Invariance of the Beck Depression Inventory (BDI-II) Across Groups

This study explored differences in the factor structure of depressive symptoms in patients with and without alcohol abuse, and differences in the severity of depressive symptoms between the two groups. In a sample of 358 patients without alcohol problems and 167 patients with comorbid alcohol problems, confirmatory factor analysis revealed that the same factor structures, Beck et al.'s two-factor Somatic Affective-Cognitive (SA-C) model, and Buckley et al.'s three-factor Cognitive-Affective- Somatic (C-A-S) model, demonstrated the best fit to the data in both groups. The SA-C model was preferred due to its more parsimonious nature. Evidence for strict measurement invariance across the two groups for the SA-C model was found. MIMIC (multiple-indicator-multiple-cause) modeling showed that the level of depressive symptoms was found to be highest on both factors in the group with comorbid alcohol problems. The magnitude of the differences in latent mean scores suggested a moderate difference in the level of depressive symptoms between the two groups. It is argued that patients with comorbid depression and alcohol abuse should be offered parallel and adequate treatment for both conditions.
Imaging of zymogen granules in fully wet cells. Evidence for restricted mechanism of granule growth

The introduction of wet SEM imaging technology permits electron microscopy of wet samples. Samples are placed in sealed specimen capsules and are insulated from the vacuum in the SEM chamber by an impermeable, electron‐transparent membrane. The complete insulation of the sample from the vacuum allows direct imaging of fully hydrated, whole‐mount tissue. In the current work, we demonstrate direct inspection of thick pancreatic tissue slices (above 400 μm). In the case of scanning of the pancreatic surface, the boundaries of intracellular features are seen directly. Thus no unfolding is required to ascertain the actual particle size distribution based on the sizes of the sections. This method enabled us to investigate the true granule size distribution and confirm early studies of improved conformity to a Poisson‐like distribution, suggesting that the homotypic granule growth results from a mechanism, which favors the addition of a single unit granule to mature granules. Microsc. Res. Tech., 2007. © 2007 Wiley‐Liss, Inc.
Monotone Graph Limits and Quasimonotone Graphs

Abstract The recent theory of graph limits gives a powerful framework for understanding the properties of suitable (convergent) sequences (Gn ) of graphs in terms of a limiting object that may be represented by a symmetric function W on [0, 1]2, i.e., a kernel or graphon. In this context it is natural to wish to relate specific properties of the sequence to specific properties of the kernel. Here we show that the kernel is monotone (i.e., increasing in both variables) if and only if the sequence satisfies a “quasimonotonicity” property defined by a certain functional tending to zero. As a tool we prove an inequality relating the cut and L 1 norms of kernels of the form W 1−W 2 with W 1 and W 2 monotone that may be of interest in its own right; no such inequality holds for general kernels.