Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactive Hausdorff distance computation for general polygonal models

We present a simple algorithm to compute the Hausdorff distance between complicated, polygonal models at interactive rates. The algorithm requires no assumptions about the underlying topology and geometry. To avoid the high computational and implementation complexity of exact Hausdorff distance calculation, we approximate the Hausdorff distance within a user-specified error bound. The main ingredient of our approximation algorithm is a novel polygon subdivision scheme, called Voronoi subdivision, combined with culling between the models based on bounding volume hierarchy (BVH). This cross-culling method relies on tight yet simple computation of bounds on the Hausdorff distance, and it discards unnecessary polygon pairs from each of the input models alternatively based on the distance bounds. This algorithm can approximate the Hausdorff distance between polygonal models consisting of tens of thousands triangles with a small error bound in real-time, and outperforms the existing algorithm by more than an order of magnitude. We apply our Hausdorff distance algorithm to the measurement of shape similarity, and the computation of penetration depth for physically-based animation. In particular, the penetration depth computation using Hausdorff distance runs at highly interactive rates for complicated dynamics scene.
Carotenoid-based coloration predicts resistance to oxidative damage during immune challenge

SUMMARY Many animal ornaments may have evolved as signals advertising the quality of the bearer. The honesty of the information content of these signals would rely on the costs associated with their expression, these being relatively greater for low-quality than for high-quality individuals. Given the physiological functions of carotenoids, carotenoid-based ornaments could indicate individual immunocompetence, and possibly the ability to mount an immune response at a lower cost. We evaluated whether the red carotenoid-based coloration of male red-legged partridges (Alectoris rufa) predicts the capacity of the individual to counteract the oxidative stress generated by a cell-mediated immune response. Individuals were subcutaneously injected with phytohaemagglutinin (PHA) or phosphate buffer solution (PBS) as a control. We found that eye ring pigmentation predicted the change in the amount of peroxidized lipids (TBARS) in blood after the PHA-induced inflammatory challenge. The degree of pigmentation of this carotenoid-based ornament was also negatively related to individual changes in γ-glutamyl transferase (GGT), another biomarker of oxidative stress involved in antioxidant metabolism (i.e. glutathione recycling). However, changes in circulating carotenoids did not significantly explain changes in lipid peroxidation or GGT levels, suggesting that the higher resistance to oxidative stress of those individuals with more pigmented eye rings was not directly mediated by their greater circulating levels of carotenoids. Our results indicate that carotenoid-based coloration can predict not only immune responsiveness (more coloured males mount greater responses) but also an individual's ability to counter the oxidative stress generated during immune challenge (more coloured males experience less oxidative damage when mounting an immune response).
Local search methods for l1-minimization in a data compression problem

We consider the problem of finding a linear combination of at most t out of K column vectors in a matrix, such that a target vector is approximated as closely as possible. The motivation of the model is to find a lower-dimensional representation of a given signal vector (target) while minimizing loss of accuracy. We point out the computational intractability of this problem, and suggest some local search heuristics for the unit norm case. The heuristics, all of which are based on pivoting schemes in a related linear program, are compared experimentally with respect to speed and accuracy.
The Association Between Clinical Features Seen on Fundus Photographs and Glaucomatous Damage Detected on Visual Fields and Optical Coherence Tomography Scans

Purpose: To classify the appearance of the optic disc seen on fundus photographs of healthy subjects and patients with or suspected glaucoma whose diagnosis was based upon visual fields (VFs) and spectral-domain optical coherence tomography (sdOCT) results. Patients and Methods: One eye of 100 patients with or suspected glaucoma and 62 healthy subjects were prospectively tested with 24-2 and 10-2 VF and macular and disc sdOCT cube scans. All eyes with or suspected glaucoma had a 24-2 mean deviation better than −6.0 dB and an abnormal appearing disc on stereophotographs. The retinal ganglion cell plus inner plexiform layer (RGC+) from the macular scans and the retinal nerve fiber layer (RNFL) from the macular and disc scans were segmented and converted to probabilities plots. An eye was considered “glaucoma” if the sdOCT probability plots showed an abnormality in a region that corresponded to a defect seen on the 24-2 and/or 10-2 VF total deviation plot. Similarly, an eye was considered “suspect” only if both the sdOCT and VF plots were normal. Healthy subjects (normal VFs and sdOCT) were classified as “controls” and used as reference for comparisons. Glaucoma specialists reviewed the stereophotographs and classified eyes based on the presence of signs suggestive of glaucomatous optic neuropathy. Results: The pattern of clinical signs of glaucomatous optic neuropathy seen on stereophotographs was statistically different between glaucoma (P<0.001) and suspects (P<0.001) vs. controls and explained up to 68% of the total variance of the diagnosis based upon sdOCT and VFs. Vertical cup-to-disc>0.6, focal neuroretinal rim thinning, focal RNFL loss, and violation of the ISNT rule had the best performance to differentiate glaucoma and suspects from controls. Compared with the suspect group, glaucoma eyes (abnormal sdOCT and VF tests) were more likely to have vertical cup-to-disc>0.6 (92% vs. 69%, P=0.003), diffuse rim (53% vs. 9%, P<0.001) and RNFL (61% vs. 26%, P<0.001) thinning, and &bgr;-zone parapapillary atrophy (68% vs. 17%, P<0.001). Conclusions: Focal and diffuse signs of glaucoma damage seen on stereophotographs often match damage shown on VFs and sdOCT. In addition, damage shown on VFs and sdOCT is often missed during clinical evaluation. Longitudinal studies ought to differentiate focal signs of glaucoma damage seen on stereophotography from false-positives or very early loss.
Active power filter operation of an electric vehicle applied to single-phase networks

This work proposes the application of a battery or plug-in electric vehicle powertrain on the mitigation of possible residential electricity network power quality problems by means of the integration of a shunt active power filter into its power electronics circuitry. The integration of additional functions to an electric vehicle is a very desirable feature, since it can result on cost reduction (in comparison to the separately implementation of the integrated functions). Simulation results provide evidence of the possible employment of power electronics converters, inherent to the vehicle propulsion system, in order to reduce harmonic content and improve power factor in single-phased electric networks.
LAMMER Kinase LkhA Plays Multiple Roles in the Vegetative Growth and Asexual and Sexual Development of Aspergillus nidulans

LAMMER kinase plays pivotal roles in various physiological processes in eukaryotes; however, its function in filamentous fungi is not known. We performed molecular studies on the function of the Aspergillus nidulans LAMMER kinase, LkhA, and report its involvement in multiple developmental processes. The gene for LkhA was highly expressed during reproductive organ development, such as that of conidiophores and cleistothecia. During vegetative growth, the patterns of germ tube emergence and hyphal polarity were changed and septation was increased by lkhA deletion. Northern analyses showed that lkhA regulated the transcription of brlA, csnD, and ppoA, which supported the detrimental effect of lkhA-deletion on asexual and sexual differentiation. LkhA also affected expression of cyclin-dependent kinase NimXcdc2, a multiple cell cycle regulator, and StuA, an APSES family of fungal transcription factors that play pivotal roles in multiple differentiation processes. Here, for the first time, we present molecular evidence showing that LAMMER kinase is involved in A. nidulans development by modulating the expression of key regulators of developmental processes.
Manualized Group Cognitive-Behavioral Therapy for Social Anxiety in At-Risk Mental State and First Episode Psychosis: A Pilot Study of Feasibility and Outcomes

ABSTRACT Social anxiety has received scant attention in studies of schizophrenia and related psychoses. However, some data suggest it may be an obstacle to vocational and functional outcome. This pilot study investigated the feasibility of a group-based cognitive behavioral therapy (CBGT) to reduce social anxiety in those at risk for developing psychosis or in the early phase. Twenty-nine patients with first-episode psychosis (FEP) or at ultra high risk for developing psychosis or often referred to as at-risk mental state (ARMS) with comorbid social anxiety attended a CBGT intervention weekly for 14 weeks in 90-minute sessions. Baseline, post-treatment, and follow-up ratings of social anxiety were measured using the Social Interaction Anxiety Scale, the Social Phobia Inventory, and the Brief Social Phobia Scale. Psychotic symptoms and general psychopathology were also measured before and after the intervention. Results suggest that the proposed CBGT is feasible and beneficial for socially anxious patients at risk, or with experience of, psychosis. Participants significantly improved on three outcome measures of social anxiety after completing this intervention (all p’s < .002). Participants who completed treatment also showed a significant reduction on measures of depression and negative symptoms. Future research should examine the relative efficacy of this brief manualized CBGT intervention for the treatment of social anxiety and psychotic symptoms in a larger randomized controlled trial.
A generalized composition algorithm for weighted finite-state transducers

This paper describes a weighted finite-state transducer composition algorithm that generalizes the concept of the composition filter and presents filters that remove useless epsilon paths and push forward labels and weights along epsilon paths. This filtering permits the compostion of large speech recognition contextdependent lexicons and language models much more efficiently in time and space than previously possible. We present experiments on Broadcast News and a spoken query task that demonstrate an∼5% to 10% overhead for dynamic, runtime composition compared to a static, offline composition of the recognition transducer. To our knowledge, this is the first such system with so little overhead.
Model-Free Reinforcement Learning of Impedance Control in Stochastic Environments

For humans and robots, variable impedance control is an essential component for ensuring robust and safe physical interaction with the environment. Humans learn to adapt their impedance to specific tasks and environments; a capability which we continually develop and improve until we are well into our twenties. In this article, we reproduce functionally interesting aspects of learning impedance control in humans on a simulated robot platform. As demonstrated in numerous force field tasks, humans combine two strategies to adapt their impedance to perturbations, thereby minimizing position error and energy consumption: 1) if perturbations are unpredictable, subjects increase their impedance through cocontraction; and 2) if perturbations are predictable, subjects learn a feed-forward command to offset the perturbation. We show how a 7-DOF simulated robot demonstrates similar behavior with our model-free reinforcement learning algorithm PI2, by applying deterministic and stochastic force fields to the robot's end-effector. We show the qualitative similarity between the robot and human movements. Our results provide a biologically plausible approach to learning appropriate impedances purely from experience, without requiring a model of either body or environment dynamics. Not requiring models also facilitates autonomous development for robots, as prespecified models cannot be provided for each environment a robot might encounter.
A practical means for the optimization of structured light system calibration parameters

This paper presents a novel approach for the optimization of calibration parameters in structured light system (SLS). Different with conventional calibration algorithms, the proposed optimization algorithm is implemented in 3D space instead of 2D image space. The object used for parameter optimization can be a simple plane with some markers. A global optimal function is constructed to contain all the intrinsic and extrinsic parameters of the SLS. Using the primary calibration parameters by conventional methods as initial values, the optimal function can be solved by minimizing the 3D measurement errors like distance, angle between markers, and the planarity of the reference plane. Experimental results show that, 3D reconstruction accuracy can be greatly improved by the proposed approach in comparison with traditional SLS calibration methods.
Anvaya: An Algorithm and Case-Study on Improving the Goodness of Software Process Models Generated by Mining Event-Log Data in Issue Tracking Systems

Issue Tracking Systems (ITS) such as Bugzilla can be viewed as Process Aware Information Systems (PAIS) generating event-logs during the life-cycle of a bug report. Process Mining consists of mining event logs generated from PAIS for process model discovery, conformance and enhancement. We apply process map discovery techniques to mine event trace data generated from ITS of open source Firefox browser project to generate and study process models. Bug life-cycle consists of diversity and variance. Therefore, the process models generated from the event-logs are spaghetti-like with large number of edges, inter-connections and nodes. Such models are complex to analyse and difficult to comprehend by a process analyst. We improve the Goodness (fitness and structural complexity) of the process models by splitting the event-log into homogeneous subsets by clustering structurally similar traces. We adapt the K-Medoid clustering algorithm with two different distance metrics: Longest Common Subsequence (LCS) and Dynamic Time Warping (DTW). We evaluate the goodness of the process models generated from the clusters using complexity and fitness metrics. We study back-forth and self-loops, bug reopening, and bottleneck in the clusters obtained and show that clustering enables better analysis. We also propose an algorithm to automate the clustering process-the algorithm takes as input the event log and returns the best cluster set.
Interleukin‐1B 31 C>T polymorphism combined with Helicobacter pylori‐modified gastric cancer susceptibility: evidence from 37 studies

Gastric cancer is one of the most common malignancies worldwide. Interleukin‐1‐beta (IL‐1β) is a pro‐inflammatory cytokine and potent inhibitor of gastric acid secretion. Some studies provided evidence of the association between IL‐1B 31 polymorphism and gastric cancer risk while other studies did not. Therefore, we conducted a comprehensive meta‐analysis to reassess the association. A systematic literature search of the PubMed and EMBASE databases identified 37 studies with 6108 cases and 8980 controls for this meta‐analysis. The crude odd ratios (ORs) and the 95% confidence intervals (CIs) were calculated to evaluate the strength of the association. Meta‐regression was used to determine the major source of heterogeneity across the studies. The pooled analysis did not suggest the significant association of IL‐1B 31 C>T polymorphism with gastric cancer risk. Stratified analysis was performed by ethnicity, source of control, genotype method, and indicated a significantly increased gastric cancer risk associated with IL‐1B 31T variant in the population‐based subgroup (heterozygous model: OR = 1.22, 95% CI = 1.03–1.45). Moreover, stratified analysis by Helicobacter pylori infection status indicated that IL‐1B 31 polymorphism increased gastric cancer risk in infection‐positive subgroup (homozygous model: OR = 1.35, 95% CI = 1.02–1.78; heterozygous model: OR = 1.31, 95% CI = 1.04–1.66; recessive model: OR = 1.29, 95% CI = 1.04–1.61). The study suggested that IL‐1B 31 polymorphism might confer susceptibility to gastric cancer in the presence of H. pylori infection, indicating a gene–environment interaction in gastric carcinogenesis.
Mining Revision History to Assess Trustworthiness of Article Fragments

Wikis are a type of collaborative repository system that enables users to create and edit shared content on the Web. The popularity and proliferation of Wikis have created a new set of challenges for trust research because the content in a Wiki can be contributed by a wide variety of users and can change rapidly. Nevertheless, most Wikis lack explicit trust management to help users decide how much they should trust an article or a fragment of an article. In this paper, we investigate the dynamic nature of revisions as we explore ways of utilizing revision history to develop an article fragment trust model. We use our model to compute trustworthiness of articles and article fragments. We also augment Wikis with a trust view layer with which users can visually identify text fragments of an article and view trust values computed by our model
Plasticity of both planar cell polarity and cell identity during the development of Drosophila

Drosophila has helped us understand the genetic mechanisms of pattern formation. Particularly useful have been those organs in which different cell identities and polarities are displayed cell by cell in the cuticle and epidermis (Lawrence, 1992; Bejsovec and Wieschaus, 1993; Freeman, 1997). Here we use the pattern of larval denticles and muscle attachments and ask how this pattern is maintained and renewed over the larval moult cycles. During larval growth each epidermal cell increases manyfold in size but neither divides nor dies. We follow individuals from moult to moult, tracking marked cells and find that, as cells are repositioned and alter their neighbours, their identities change to compensate and the pattern is conserved. Single cells adopting a new fate may even acquire a new polarity: an identified cell that makes a forward-pointing denticle in the first larval stage may make a backward-pointing denticle in the second and third larval stages. DOI: http://dx.doi. org/10.7554/eLife.01569. 001
Latent Semantics of Action Verbs Reflect Phonetic Parameters of Intensity and Emotional Content

Conjuring up our thoughts, language reflects statistical patterns of word co-occurrences which in turn come to describe how we perceive the world. Whether counting how frequently nouns and verbs combine in Google search queries, or extracting eigenvectors from term document matrices made up of Wikipedia lines and Shakespeare plots, the resulting latent semantics capture not only the associative links which form concepts, but also spatial dimensions embedded within the surface structure of language. As both the shape and movements of objects have been found to be associated with phonetic contrasts already in toddlers, this study explores whether articulatory and acoustic parameters may likewise differentiate the latent semantics of action verbs. Selecting 3 × 20 emotion-, face-, and hand-related verbs known to activate premotor areas in the brain, their mutual cosine similarities were computed using latent semantic analysis LSA, and the resulting adjacency matrices were compared based on two different large scale text corpora: HAWIK and TASA. Applying hierarchical clustering to identify common structures across the two text corpora, the verbs largely divide into combined mouth and hand movements versus emotional expressions. Transforming the verbs into their constituent phonemes, and projecting them into an articulatory space framed by tongue height and formant frequencies, the clustered small and large size movements appear differentiated by front versus back vowels corresponding to increasing levels of arousal. Whereas the clustered emotional verbs seem characterized by sequences of close versus open jaw produced phonemes, generating up- or downwards shifts in formant frequencies that may influence their perceived valence. Suggesting, that the latent semantics of action verbs reflect parameters of intensity and emotional polarity that appear correlated with the articulatory contrasts and acoustic characteristics of phonemes.
Automorphisms of a polynomial ring which admit reductions of type I

Recently, Shestakov-Umirbaev solved Nagata's conjecture on an automorphism of a polynomial ring. To solve the conjecture, they defined notions called reductions of types I--IV for automorphisms of a polynomial ring. An automorphism admitting a reduction of type I was first found by Shestakov-Umirbaev. Using a computer, van den Essen--Makar-Limanov--Willems gave a family of such automorphisms. In this paper, we present a new construction of such automorphisms using locally nilpotent derivations. As a consequence, we discover that there exists an automorphism admitting a reduction of type I which satisfies some degree condition for each possible value.
Association between Milk and Milk Product Consumption and Anthropometric Measures in Adult Men and Women in India: A Cross-Sectional Study

Background The nutritional aetiology of obesity remains unclear, especially with regard to the role of dairy products in developing countries. Objective To examine whether milk/milk product consumption is associated with obesity and high waist circumference among adult Indians. Methods Information on plain milk, tea, curd and buttermilk/lassi consumption assessed using a Food Frequency Questionnaire was obtained from the cross-sectional sib-pair designed Indian Migration Study (3698 men and 2659 women), conducted at four factory locations across north, central and south India. The anthropometric measures included were Body Mass Index (BMI) and Waist Circumference (WC). Mixed-effect logistic regression models were conducted to accommodate sib-pair design and adjust for potential confounders. Results After controlling for potential confounders, the risk of being obese (BMI≥25 kg/m2) was lower among women (OR = 0.57;95%CI:0.43−0.76;p≤0.0001) and men (OR = 0.67;95%CI: 0.51−0.87;p = 0.005), and the risk of a high WC (men: >90 cm; women: >80 cm) was lower among men (OR = 0.71;95%CI:0.54−0.93;p = 0.005) and women (OR = 0.79;95%CI:0.59−1.05;p>0.05) who consume ≥1 portions of plain milk daily than those who do not consume any milk. The inverse association between daily plain milk consumption and obesity was also confirmed in sibling-pair analyses. Daily tea consumption of ≥1 portion was associated with obesity (OR = 1.51;95%CI:1.00−2.25;p>0.050) and high WC (OR = 1.65;95%CI:1.08−2.51;p>0.019) among men but not among women but there was no strong evidence of association of curd and buttermilk/lassi consumption with obesity and high waist circumference among both men and women. Conclusions The independent, inverse association of daily plain milk consumption with the risk of being obese suggests that high plain milk intake may lower the risk of obesity in adult Indians. However, this is an observational finding and uncontrolled confounding cannot be excluded as an explanation for the association. Therefore, confirmatory studies are needed to clarify this relationship.