Miracle-dz/UniFAR-FTUs huggingface dataset:
Approximation Algorithms for Geometric Separation Problems

In computer graphics and solid modeling, one is interested in representing complex geometric objects with combinatorially simpler ones. It turns out that via a “fattening” transformation, one obtains a formulation of the approximation problem in terms of separation: Find a minimumcomplexity surface that separates two sets. In this paper, we provide approximation algorithms for several geometric separation problems, including: • Given a set of triangles T and a set S of points that lie within the union of the triangles, find a minimum-cardinality set, T , of pairwise-disjoint triangles, each contained within some triangle of T , that cover the point set S. • Given finite sets of “red” and “blue” points in the plane, determine a simple polygon of fewest edges that separates the red points from the blue points. More generally, given finite sets of points of many color classes, determine a planar “separating” subdivision of minimum combinatorial complexity, which has the property that each face of the subdivision contains points of at most one color class; • Given two polyhedral terrains, P and Q, over a common support set (e.g., the unit square), with P lying above Q, compute a nested polyhedral terrain R that lies between P and Q such that R has a minimum number of facets. Exact solution of the above problems in polynomial time is highly unlikely: The decision versions of all three problems are known to be NP-hard. We provide polynomial-time algorithms that are guaranteed to produce an answer within a logarithmic factor (O(log n), where n is the complexity of the input problem instance) of optimal. (The error factor is constant in the orthogonal case — coverage by disjoint aligned rectangles, or separation of orthohedral terrains.) We also discuss extensions to higher dimensions.
Fredkin-Enabled Transformation-Based Reversible Logic Synthesis

Reversible computation is gaining increasing relevance in the context of several post-CMOS technologies, the most prominent of those being quantum computing. The problem of implementing a given Boolean function using a set of elementary reversible logic gates is known as reversible logic synthesis. Due to the presumed hardness of the reversible circuit synthesis problem, different heuristics have been proposed in the literature to reduce quantum cost (QC), gate count, and logical depth without using ancillary lines. Interestingly, none of these heuristics systematically utilize Fredkin gates. In this paper, we demonstrate, both theoretically and empirically, that accommodating Fredkin gates significantly improves the performance of reversible circuits.
Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa.

The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed L-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH.carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the -CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O.O separation of 2.918 (4) A and an O.O.O angle of 148.5 (2) degrees ; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7) degrees . Elsewhere in the structure one NH.O interaction reaches an N.O separation of 2.691 (13) A at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate L-serine-II. The OH.OH hydrogen-bonded chains of L-serine-I are replaced in L-serine-II by shorter OH.carboxyl interactions, which have an O.O separation of 2.62 (2) A. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCalphaCO torsion angle from -178.1 (2) degrees at 4.8 GPa to -156.3 (10) degrees at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to L-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH.O hydrogen bonding in both phases relative to L-serine-I at ambient pressure.
Characterizing commercial intent

Understanding the intent underlying user's queries may help personalize search results and therefore improve user satisfaction. We develop a methodology for using the content of search engine result pages (SERPs) along with the information obtained from query strings to study characteristics of query intent, with a particular focus on sponsored search. This work represents an initial step towards the development and evaluation of an ontology for commercial search, considering queries that reference specific products, brands and retailers. The characteristics of query categories are studied with respect to aggregated user's clickthrough behavior on advertising links. We present a model for clickthrough behavior that considers the influence of such factors as the location of ads and the rank of ads, along with query category. We evaluate our work using a large corpus of clickthrough data obtained from a major commercial search engine. Our findings suggest that query based features, along with the content of SERPs, are effective in detecting query intent. The clickthrough behavior is found to be consistent with the classification for the general categories of query intent, while for product, brand and retailer categories, all is true to a lesser extent.
Effects of different carbon fluxes on G1 phase duration, cyclin expression, and reserve carbohydrate metabolism in Saccharomyces cerevisiae

By controlled addition of galactose to synchronized galactose-limited Saccharomyces cerevisiae cultures, the growth rate could be regulated while external conditions were kept constant. By using this method, the G1 phase duration was modulated and expression of cell cycle-regulated genes was investigated. The expression of the cyclin genes CLN1 and CLN2 was always induced just before bud emergence, indicating that this event marks the decision to pass Start. Thus, G1 phase elongation was not due to a slower accumulation of the CLN1 and CLN2 mRNA levels. Only small differences in CLN3 expression levels were observed. The maximal SWI4 expression preceded maximal CLN1 and CLN2 expression under all conditions, as expected for a transcriptional activator. But whereas SWI4 was expressed at about 10 to 20 min, before CLN1 and CLN2 expression at high growth rates, this time increased to about 300 min below a particular consumption rate at which the G1 phase strongly elongated. In the slower-growing cultures, also an increase in SWI6 expression was observed in the G1 phase. The increase in G1 phase duration below a particular consumption rate was accompanied by a strong increase in the reserve carbohydrate levels. These carbohydrates were metabolized again before bud emergence, indicating that below this consumption rate, a transient increase in ATP flux is required for progression through the cell cycle. Since Start occurred at different cell sizes under different growth conditions, it is not just a certain cell size that triggers passage through Start.
In Vitro Drug-Drug Interaction Screens for Canine Veterinary Medicines: Evaluation of Cytochrome P450 Reversible Inhibition

Little information regarding the metabolic pathways of pharmaceutical agents administered to dogs, or the inhibition of those metabolic pathways, is available. Without this information, it is difficult to assess how combinations of drugs, whether new or old or approved or nonapproved, may increase the risk for metabolic drug-drug interactions in dogs. Because mammalian xenobiotic metabolism pathways often involve the hepatic cytochrome P450 (P450) monooxgenases, canine liver microsome P450 inhibition screens were tested to evaluate the potential metabolic drug interaction risk of commonly used veterinary medicines. A probe substrate cocktail was developed for four of the five major hepatic canine P450s and used to evaluate their inhibition by 45 canine therapeutic agents in a single-point IC50 screen. Moderate inhibitors (>25%) were further characterized with an automated ninepoint IC50 assay that identified ketoconazole, clomipramine, and loperamide as submicromolar CYP2D15 inhibitors. Additional inhibitors belonged to the antiemetic, antimitotic, and anxiolytic therapeutic classes. According to the marker activities, the relative frequency of P450 inhibition by isoform followed the sequence CYP2D15 > CYP2B11 > CYP2C21/41 > CYP3A12/26 > CYP1A1/2. The findings presented suggest there is some overlap in canine and human P450 inhibition specificity. However, occasional differences may give human drugs used off-label in dogs unexpected P450 inhibition profiles and, therefore, cause an unexpected drug-drug interaction risk.
A test of the generalizability of a recently suggested conceptual model for assessment center ratings

ABSTRACT The present study replicated and extended research concerning a recently suggested conceptual model of the underlying factors of dimension ratings in assessment centers (ACs) proposed by Hoffman, Melchers, Blair, Kleinmann, and Ladd that includes broad dimension factors, exercise factors, and a general performance factor. We evaluated the criterion-related validity of these different components and expanded their nomological network. Results showed that all components (i.e., broad dimensions, exercises, general performance) were significant predictors of training performance. Furthermore, broad dimensions showed incremental validity beyond exercises and general performance. Finally, relationships between the AC factors and individual difference constructs (e.g., Big Five, core self-evaluations, positive and negative affectivity) supported the construct-related validity of broad dimensions and provided further insights in the nature of the different AC components.
On Taylor Expansion Methods for Multivariate Integral Equations of the Second Kind

A new Taylor series method that the authors originally developed for the solution of one-dimensional integral equations is extended to solve multivariate integral equations. In this paper, the new method is applied to the solution of multivariate Fredholm equations of the second kind. A comparison is given of the new method and the traditional Taylor series method of solving integral equations. The new method is adapted to parallel computation and can therefore be highly efficient on modern computers. The method also gives highly accurate approximations for all derivatives of the solution up to the order of the Taylor series approximation. Numerical examples are given to illustrate the efficiency and accuracy of the method. Keywords—Taylor-Series Expansion Method, Multivariate Fredholm Integral Equations, Galerkin Method, Collocation Method.
Verbal persuasion and resilience of parenting self-efficacy: Preliminary findings of an experimental approach

Verbal persuasion may be the least preferable way to enhance parenting self-efficacy as it may undermine resilience against failures inevitable in parenting. To test this, 55 parents participated in two tasks. First, a cry interpretation task led a random half of the participants to believe they mastered this skill and would do well on the subsequent task, while the other half was told their skill was low. In the second task parents chose appropriate responses to stop infant crying which exposed them to randomly assigned success rates (20%, 40%, 50%, or 80%). Parenting self-efficacy was rated before and after the second task. Results showed that positive persuasion led to higher parenting self-efficacy than negative persuasion. Crucially, parents who received positive persuasion were vulnerable to decreases in self-efficacy due to failure. These findings are a preliminary suggestion that verbal persuasion may heighten parenting self-efficacy in the short-term, but undermine its long-term resilience.
Circular Mixture Modeling of Color Distribution for Blind Stain Separation in Pathology Images

In digital pathology, to address color variation and histological component colocalization in pathology images, stain decomposition is usually performed preceding spectral normalization and tissue component segmentation. This paper examines the problem of stain decomposition, which is a naturally nonnegative matrix factorization (NMF) problem in algebra, and introduces a systematical and analytical solution consisting of a circular color analysis module and an NMF-based computation module. Unlike the paradigm of existing stain decomposition algorithms where stain proportions are computed from estimated stain spectra using a matrix inverse operation directly, the introduced solution estimates stain spectra and stain depths via probabilistic reasoning individually. Since the proposed method pays extra attentions to achromatic pixels in color analysis and stain co-occurrence in pixel clustering, it achieves consistent and reliable stain decomposition with minimum decomposition residue. Particularly, aware of the periodic and angular nature of hue, we propose the use of a circular von Mises mixture model to analyze the hue distribution, and provide a complete color-based pixel soft-clustering solution to address color mixing introduced by stain overlap. This innovation combined with saturation-weighted computation makes our study effective for weak stains and broad-spectrum stains. Extensive experimentation on multiple public pathology datasets suggests that our approach outperforms state-of-the-art blind stain separation methods in terms of decomposition effectiveness.
The production and perception of sub-phonemic vowel contrasts and the role of the listener in sound change

In his work on the role of the listener in language change, Ohala (1981) suggests that acoustic byproducts of physiological linguistic processes may sometimes be perceived by listeners as linguistically important information, creating a cycle which may ultimately lead to language change. To explore this issue, we investigated anticipatory vowel-to-vowel coarticulation in English, which previous work has shown can exert influence over as much as three vowels’ distance. The perceptibility of such effects at various distances from the influencing vowel was tested using event-related-potentials (ERP) and behavioral methodologies. Even the longest-distance effects were perceptible to some listeners. This group of listeners also provided production data. While the strongest support for a language-change hypothesis like that discussed here would come from a production-perception correlation, this was not found. However, we argue that even in the absence of such a correlation, the present findings are broadly consistent with such an account.
On the cut rule in the calculus of structures

We investigate the proof complexity of analytic subsystems of the deep inference proof system SKSg (the calculus of structures). Exploiting the fact that the so-called cut rule of SKSg does not correspond to cut in the sequent calculus, but to the ¬ -left rule, we establish that the “analytic” system KSg + c ↑ has essentially the same complexity as the monotone Gentzen calculus MLK . In particular, KSg + c ↑ quasipolynomially simulates SKSg , and admits polynomial-size proofs of some variants of the pigeonhole principle.
The Puzzling Evolution of the Home Bias, Information Processing and Financial Openness

This paper presents a rational expectations model of asset prices with rationally inattentive investors that, unlike previous papers, can explain both the substantial amount of equity wealth invested domestically and the puzzling time series behavior of the home bias - an initial plateau before 1985, then a decrease until 1994 followed by stabilization on another plateau. When there is a financial liberalization, investors exploit past information to predict current asset payoffs. The resulting endogenous local information advantage generates a gradual decrease of the home bias until its steady state. In the long run, the home bias remains large due to the interaction of the optimal attention allocation with the optimal portfolio choice. Using measures for information capacity, informational advantages and ? financial openness as explanatory variables, we are able to explain at least 46.8% of the variation of the home bias for 19 developed countries from 1988 until 2004. Our estimates show that both variables are significant, with home bias decreasing with financial openness and increasing with information capacity, as predicted by our model.
Jupiter: a toolkit for interactive large model visualization

The fast increasing size of datasets in scientific computing, mechanical engineering, or virtual medicine is quickly exceeding the graphics capabilities of modern computers. Toolkits for the large model visualization address this problem by combining efficient geometric techniques, such as occlusion and visibility culling, mesh reduction, and efficient rendering. We introduce Jupiter, a toolkit for the interactive visualization of large models which exploits the above mentioned techniques. Jupiter was originally developed by Hewlett-Packard and EAI, and it has been equipped with new functionality by the University of Tubingen, as being part, of the Kelvin project. An initial version of Jupiter has been released as open source.
Downregulation of E3 ubiquitin ligases and mitophagy-related genes in skeletal muscle of physically inactive, frail older women: a cross-sectional comparison.

BACKGROUND AND OBJECTIVES Reduced lean mass and physical function is a characteristic of frailty. However, it is currently unknown if proteolysis through the E3 ubiquitin ligases and the autophagic lysosomal pathway is dysregulated in inactive frail older women. The purpose of this study was to determine the expression of key markers of ubiquitin-mediated and autophagic lysosomal proteolysis in inactive (N = 7) compared with active (N = 7) older women. METHODS Strength, mobility, leg lean mass, and physical activity assessment were used to characterize activity levels and frailty in older women. Vastus lateralis biopsies were collected after an overnight fast and were assessed for gene and protein targets related to E3 ubiquitin ligases and the autophagic lysosomal system. RESULTS We found that AMP-activated protein kinase alpha (Thr172) was increased (p = .045), and forkhead box O3A (FOXO3A) gene expression (p = .047) was lower in inactive frail older women. Foxo3a (Ser253), Beclin1 (Ser93/96), and class III phosphatidylinositol-3-kinase (VPS34) protein expression were not different between the groups (p > .05). Neural precursor cell-expressed developmentally downregulated protein 4, muscle ring finger 1, muscle atrophy F-box, and the autophagy/mitophagy gene expression markers, Beclin1, autophagy-related-7, BCL2/adenovirus E1B 19 kDa interacting protein 3 (BNIP3), dynamin-related protein 1, and Parkinson protein 2 (PARKIN) were lower in inactive frail older women (p < .05). Autophagy/mitophagy markers were positively correlated with the 6-minute walk and leg lean mass (p < .05). CONCLUSIONS We conclude that physical inactivity in frail older women is associated with a downregulation of ubiquitin-mediated and autophagic lysosomal skeletal muscle gene expression, perhaps related to low muscle mass and poor physical function.
Discovery of a Large-Scale Filament Connected to the Massive Galaxy Cluster MACS J0717.5+3745 at z = 0.55

We report the detection of a 4 h Mpc long large-scale filament leading into the massive galaxy cluster MACS J0717.5+3745. The extent of this object well beyond the cluster's nominal virial radius (~2.3 Mpc) rules out prior interaction between its constituent galaxies and the cluster and makes it a prime candidate for a genuine filament as opposed to a merger remnant or a double cluster. The structure was discovered as a pronounced overdensity of galaxies selected to have V-R colors close to the cluster red sequence. Extensive spectroscopic follow-up of over 300 of these galaxies in a region covering the filament and the cluster confirms that the entire structure is located at the cluster redshift of z = 0.545. Featuring galaxy surface densities of typically 15 Mpc-2 down to luminosities of 0.13L, the most diffuse parts of the filament are comparable in density to the clumps of red galaxies found around A851 in the only similar study carried out to date (Kodama et al.). Our direct detection of an extended large-scale filament funneling matter onto a massive distant cluster provides a superb target for in-depth studies of the evolution of galaxies in environments of greatly varying density and supports the predictions from theoretical models and numerical simulations of structure formation in a hierarchical picture.
IMDE: An easy-to-use web server for missing data estimation

Missing value imputation is crucial for the microarray data analysis since the missing values would degrade the performance of the downstream analysis, e.g. differentially expressed genes identification, gene clustering or classification. Although many missing value imputation algorithms has been proposed, convenient software tools are still lacking. The existing tools are not easy to use and cannot tell users how to choose the optimal imputation algorithm for their dataset. In this paper, we present an easy-to-use web server named IMDE (Impute Missing Data Easily). IMDE has two unique features. First, it provides much more missing value imputation algorithms than any existing tool. Second, it can suggest the optimal imputation algorithm for users' dataset after doing the performance evaluation.We used four different datasets to show that different optimal algorithms may be chosen for different datasets and for different selection schemes. We expect that IMDE will be a very useful server for solving the missing value problem in the microarray data.