Miracle-dz/UniFAR-FTUs huggingface dataset:
International Journal of Computational Geometry & Applications C World Scientiic Publishing Company Decision Trees for Geometric Models

1 ABSTRACT A fundamental problem in model-based computer vision is that of identifying which of a given set of geometric models is present in an image. Considering a \probe" to be an oracle that tells us whether or not a model is present at a given point, we study the problem of computing eecient strategies (\decision trees") for probing an image, with the goal to minimize the number of probes necessary (in the worst case) to determine which single model is present. We show that a dlgke height binary decision tree always exists for k polygonal models (in xed position), provided (1) they are non-degenerate (do not share boundaries) and (2) they share a common point of intersection. Further, we give an eecient algorithm for constructing such decision tress when the models are given as a set of polygons in the plane. We show that constructing a minimum height tree is NP-complete if either of the two assumptions is omitted. We provide an eecient greedy heuristic strategy and show that, in the general case, it yields a decision tree whose height is at most dlgke times that of an optimal tree. Finally, we discuss some restricted cases whose special structure allows for improved results.
Some modeling and estimation issues in control of heterogeneous networks

Heterogeneous communication networks with their variety of application demands, uncertain time-varying trafc load, and mixture of wired and wireless links pose several challenging problem in modeling and control. In this paper we focus on the round-trip time (RTT), which is a particularly important variable for efficient end-to-end congestion control. Based on a simple aggregated model of the network, an algorithm combining a Kalman lter and a change detection algorithm is proposed for RTT estimation. It is illustrated on real data that this algorithm provides estimates of significantly better accuracy as compared to the RTT estimator currently used in TCP.We also analyze how wireless links affect the RTT distribution. Link re-transmissions induce delays which do not conform to the assumptions on which the transport protocol is based. This causes undesired TCP control actions which reduce throughput. A link layer solution based on adding carefully selected delays to certain packets is proposed to counteract this problem.
Improve Sentiment Analysis Accuracy using Multiple Kernel Approach

Sentiment Analysis has become an indispensible part of product reviews in present scenario. Sentiment Analysis is a very well studied field, but the scale remains limited to not more than a few hundred researchers. The problem of analyzing the overall sentiment of a document using Machine learning techniques has been considered. Results have been improved using multiple kernel approach and compared with previously used techniques.The present research is a comparison and extension of the work proposed by Mullen and Collier (2003). The system consists of a feature Extraction phase and a learning phase; on the basis of which the overall sentiment of the document is analyzed. The present work uses the movie review data set used by Pang (2002). The approach significantly outperforms the previous methods attaining 90% and 92% accuracy using 5 fold cross validation 10 fold cross validation respectively. General Terms Machine Learning, Information Retrieval.
Collective extraction from heterogeneous web lists

Automatic extraction of structured records from inconsistently formatted lists on the web is challenging: different lists present disparate sets of attributes with variations in the ordering of attributes; many lists contain additional attributes and noise that can confuse the extraction process; and formatting within a list may be inconsistent due to missing attributes or manual formatting on some sites. We present a novel solution to this extraction problem that is based on i) collective extraction from multiple lists simultaneously and ii) careful exploitation of a small database of seed entities. Our approach addresses the layout homogeneity within the individual lists, content redundancy across some snippets from different sources, and the noisy attribute rendering process. We experimentally evaluate variants of this algorithm on real world data sets and show that our approach is a promising direction for extraction from noisy lists, requiring mild and thus inexpensive supervision suitable for extraction from the tail of the web.
Domain Knowledge Articulation using Integration Graphs

In order to be queried and reused, different domain knowledge bases must be shared using the same representation. In this paper, we introduce a graph-based knowledge model to articulate independently developed ontologies that describe the same application domain. Our knowledge representation formalism is based on a new type of graphs denoted as “hierarchical graphs”. This representation provides a basis for the heuristic inferences and for the logical deductions that are used to detect semantic mismatches between domain knowledge bases whenever they must be composed. Integration graphs can also be viewed as a suitable data modelling formalism for information integration.
Acrolein-Exposed Normal Human Lung Fibroblasts in Vitro: Cellular Senescence, Enhanced Telomere Erosion, and Degradation of Werner’s Syndrome Protein

Background: Acrolein is a ubiquitous environmental hazard to human health. Acrolein has been reported to activate the DNA damage response and induce apoptosis. However, little is known about the effects of acrolein on cellular senescence. Objectives: We examined whether acrolein induces cellular senescence in cultured normal human lung fibroblasts (NHLF). Methods: We cultured NHLF in the presence or absence of acrolein and determined the effects of acrolein on cell proliferative capacity, senescence-associated β-galactosidase activity, the known senescence-inducing pathways (e.g., p53, p21), and telomere length. Results: We found that acrolein induced cellular senescence by increasing both p53 and p21. The knockdown of p53 mediated by small interfering RNA (siRNA) attenuated acrolein-induced cellular senescence. Acrolein decreased Werner’s syndrome protein (WRN), a member of the RecQ helicase family involved in DNA repair and telomere maintenance. Acrolein-induced down-regulation of WRN protein was rescued by p53 knockdown or proteasome inhibition. Finally, we found that acrolein accelerated p53-mediated telomere shortening. Conclusions: These results suggest that acrolein induces p53-mediated cellular senescence accompanied by enhanced telomere attrition and WRN protein down-regulation. Citation: Jang JH, Bruse S, Huneidi S, Schrader RM, Monick MM, Lin Y, Carter AB, Klingelhutz AJ, Nyunoya T. 2014. Acrolein-exposed normal human lung fibroblasts in vitro: cellular senescence, enhanced telomere erosion, and degradation of Werner’s syndrome protein. Environ Health Perspect 122:955–962; http://dx.doi. org/10.1289/ehp.1306911
Tracking of extended object or target group using random matrix — Part I: New model and approach

The approach of using a random matrix for extended object and group target tracking (EOT and GTT) is efficient. Designing and effectively applying this approach rely on modeling the extended object and group targets accurately. To describe complex dynamical variation and practical observation distortion of the extension in size, shape and orientation, two random matrix based models are proposed. True measurement noise can also be incorporated into the measurement model easily. Facilitated by special properties of the models, an approximate Bayesian approach is proposed to estimate the kinematic state and the extension jointly. For maneuvering EOT and GTT, a multiple-model approach is derived by moment matching. To evaluate what is proposed, simulation results of a scenario for maneuvering EOT are also given. The results illustrate the effectiveness of the proposed models and approach.
Dispersion-Equalization Techniques for Substrate Integrated Waveguide Interconnects

This paper demonstrates dispersion-equalization techniques for substrate integrated waveguide (SIW) interconnects using tapered SIW terminations. Two system arrangements are introduced. It is shown that a properly designed tapered SIW section operating as a reflective equalizer along with a 3-dB coupler or a circulator can be used to equalize the dispersion that occurs in an SIW interconnect. Time-delay characteristics of the SIW interconnect and the designed tapered equalizer section are presented, and the two dispersion-equalization systems are evaluated in the time and frequency domains. Testing of the systems with a 1-Gb/s digital input demonstrates the efficacy of the dispersion-equalization techniques in the region directly above the cutoff frequency.
Neuron-specific Sumo1-3 knockdown in mice impairs episodic and fear memories.

BACKGROUND Growing evidence suggests that small ubiquitin-like modifier (SUMO) conjugation plays a key role in brain plasticity by modulating activity-dependent synaptic transmission. However, these observations are based largely on cell culture experiments. We hypothesized that episodic and fear memories would be affected by silencing SUMO1-3 expression. METHODS To investigate the role of SUMO conjugation in neuronal functioning in vivo, we generated a novel Sumo transgenic mouse model in which a Thy1 promoter drives expression of 3 distinct microRNAs to silence Sumo1-3 expression, specifically in neurons. Wild-type and Sumo1-3 knockdown mice were subjected to a battery of behavioural tests to elucidate whether Sumoylation is involved in episodic and emotional memory. RESULTS Expression of Sumo1-3 microRNAs and the corresponding silencing of Sumo expression were particularly pronounced in hippocampal, amygdala and layer V cerebral cortex neurons. The Sumo knockdown mice displayed anxiety-like responses and were impaired in episodic memory processes, contextual and cued fear conditioning and fear-potentiated startle. LIMITATIONS Since expression of Sumo1-3 was silenced in this mouse model, we need to verify in future studies which of the SUMO paralogues play the pivotal role in episodic and emotional memory. CONCLUSION Our results indicate that a functional SUMO conjugation pathway is essential for emotionality and cognition. This novel Sumo knockdown mouse model and the technology used in generating this mutant may help to reveal novel mechanisms that underlie a variety of neuropsychiatric conditions associated with anxiety and impairment of episodic and emotional memory.
Comparative Sequence and Structure Analysis Reveals the Conservation and Diversity of Nucleotide Positions and Their Associated Tertiary Interactions in the Riboswitches

The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand’s functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch.
A Systems Approach to Countermeasures in Credibility Assessment Interviews

Countermeasures, or techniques for hiding guilt during a credibility assessment examination, have long been an important topic in cognitive psychology and criminal justice fields. With recent IS research on automated screening systems, understanding the potential for countermeasures in this new paradigm is of increasing importance. This paper reports on a large experiment examining countermeasures in an automated deception detection screening context. The effectiveness of traditional countermeasure types (mental and physical) are examined, as well as an exploratory approach of trying several countermeasures at once. The exploratory approach was tested to investigate a proposed novel systems-inspired solution to countermeasures—triangulating on deception likelihood using multiple sensors measuring multiple behavioral and psychophysiological anomalies. The findings give credence to the proposition that monitoring multiple heterogeneous cues to deception may be a viable solution for mitigating the effectiveness of countermeasures.
CD73 Is Dispensable for the Regulation of Inflationary CD8+ T-Cells after Murine Cytomegalovirus Infection and Adenovirus Immunisation

The ecto-5'-nucleotidase (CD73) is expressed by T-cell subsets, myeloid derived suppressive cells and endothelial cells. It works in conjunction with CD39 to regulate the formation and degradation of adenosine in vivo. Adenosine has previously been shown to suppress the proliferation and cytokine secretion of T-cells and recent evidence suggests that inhibition of CD73 has the potential to enhance T-cell directed therapies. Here we utilised a CD73 knockout mouse model to assess the suppressive ability of CD73 on CD8+ T-cell classical memory and memory “inflation”, induced by murine cytomegalovirus (MCMV) infection and adenovirus immunisation. We show that CD73 is dispensable for normal CD8+ T-cell differentiation and function in both models. Thus CD73 as a suppressor of CD8+ T-cells is unlikely to play a deterministic role in the generation and functional characteristics of antiviral memory in these settings.
Lytic: synthesizing high-dimensional algorithmic analysis with domain-agnostic, faceted visual analytics

We present Lytic, a domain-independent, faceted visual analytic (VA) system for interactive exploration of large datasets. It combines a flexible UI that adapts to arbitrary character-separated value (CSV) datasets with algorithmic preprocessing to compute unsupervised dimension reduction and cluster data from high-dimensional fields. It provides a variety of visualization options that require minimal user effort to configure and a consistent user experience between visualization types and underlying datasets. Filtering, comparison and visualization operations work in concert, allowing users to hop seamlessly between actions and pursue answers to expected and unexpected data hypotheses.
The pelvic kidney of male Ambystoma maculatum (Amphibia, urodela, ambystomatidae) with special reference to the sexual collecting ducts

This study details the gross and microscopic anatomy of the pelvic kidney in male Ambystoma maculatum. The nephron of male Ambystoma maculatum is divided into six distinct regions leading sequentially away from a renal corpuscle: (1) neck segment, which communicates with the coelomic cavity via a ventrally positioned pleuroperitoneal funnel, (2) proximal tubule, (3) intermediate segment, (4) distal tubule, (5) collecting tubule, and (6) collecting duct. The proximal tubule is divided into a vacuolated proximal region and a distal lysosomic region. The basal plasma membrane is modified into intertwining microvillus lamellae. The epithelium of the distal tubule varies little along its length and is demarcated by columns of mitochondria with their long axes oriented perpendicular to the basal lamina. The distal tubule possesses highly interdigitating microvillus lamellae from the lateral membranes and pronounced foot processes of the basal membrane that are not intertwined, but perpendicular to the basal lamina. The collecting tubule is lined by an epithelium with dark and light cells. Light cells are similar to those observed in the distal tuble except with less mitochondria and microvillus lamellae of the lateral and basal plasma membrane. Dark cells possess dark euchromatic nuclei and are filled with numerous small mitochondria. The epithelium of the neck segment, pleuroperitoneal funnel, and intermediate segment is composed entirely of ciliated cells with cilia protruding from only the central portion of the apical plasma membrane. The collecting duct is lined by a highly secretory epithelium that produces numerous membrane bound granules that stain positively for neutral carbohydrates and proteins. Apically positioned ciliated cells are intercalated between secretory cells. The collecting ducts anastomose caudally and unite with the Wolffian duct via a common collecting duct. The Wolffian duct is secretory, but not to the extent of the collecting duct, synthesizes neutral carbohydrates and proteins, and is also lined by apical ciliated cells intercalated between secretory cells. Although functional aspects associated with the morphological variation along the length of the proximal portions of the nephron have been investigated, the role of a highly secretory collecting duct has not. Historical data that implicated secretory activity concordant with mating activity, and similarity of structure and chemistry to sexual segments of the kidneys in other vertebrates, lead us to believe that the collecting duct functions as a secondary sexual organ in Ambystoma maculatum. J. Morphol. , 2010. © 2010 Wiley‐Liss, Inc.
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

Significance Defining a core functional proteome supporting the living process has importance for both developing fundamental understanding of cell functions and for synthetic biology applications. Comparative genomics has been the primary approach to achieve such a definition. Here, we use genome-scale models to define a core proteome that computationally supports basic cellular function. This core proteome for metabolism and protein expression, defined through systems biology methods, is validated and characterized by using multiple disparate data types. Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation) and exhibit significantly more complex transcriptional and posttranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5′UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated by using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it de facto defines a paleome.
Effects of light and the regulatory B-subunit composition of protein phosphatase 2A on the susceptibility of Arabidopsis thaliana to aphid (Myzus persicae) infestation

The interactions between biotic and abiotic stress signaling pathways are complex and poorly understood but protein kinase/phosphatase cascades are potentially important components. Aphid fecundity and susceptibility to Pseudomonas syringae infection were determined in the low light-grown Arabidopsis thaliana wild type and in mutant lines defective in either the protein phosphatase (PP)2A regulatory subunit B'γ (gamma; pp2a-b'γ) or B'ζ (zeta; pp2a-b'ζ1-1 and pp2a-b'ζ 1-2) and in gamma zeta double mutants (pp2a-b'γζ) lacking both subunits. All the mutants except for pp2a-b'ζ 1-1 had significantly lower leaf areas than the wild type. Susceptibility to P. syringae was similar in all genotypes. In contrast, aphid fecundity was significantly decreased in the pp2a-b'γ mutant relative to the wild type but not in the pp2a-b'γζ double mutant. A high light pre-treatment, which led to a significant increase in rosette growth in all mutant lines but not in the wild type, led to a significant decrease in aphid fecundity in all genotypes. The high light pre-treatment abolished the differences in aphid resistance observed in the pp2a-b'γ mutant relative to the wild type. The light and CO2 response curves for photosynthesis were changed in response to the high light pre-treatment, but the high light effects were similar in all genotypes. These data demonstrate that a pre-exposure to high light and the composition of B-subunits on the trimeric PP2A holoenzymes are important in regulating plant resistance to aphids. The functional specificity for the individual regulatory B-subunits may therefore limit aphid colonization, depending on the prevailing abiotic stress environment.
Perturbative Analysis of Adaptive Smoothing Methods in Quantifying Large-Scale Structure

Smoothing operation to make a continuous density field from the observed pointlike distribution of galaxies is crucially important for topological or morphological analysis of the large-scale structure, such as the genus statistics or the area statistics (or, equivalently, the level-crossing statistics). It has been pointed out that the adaptive smoothing filters are more efficient tools to resolve cosmic structures than the traditional spatially fixed filters. We study weakly nonlinear effects caused by two representative adaptive methods often used in smoothed hydrodynamical particle (SPH) simulations. Using the framework of second-order perturbation theory, we calculate the generalized skewness parameters for the adaptive methods in the case of fluctuations that are initially power-law fluctuations. Then we apply the multidimensional Edgeworth expansion method and investigate the weakly nonlinear evolution of the genus statistics and the area statistics. Isodensity contour surfaces are often parameterized by the volume fraction of the regions above a given density threshold. We also discuss this parameterization method in perturbative manner.