Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient Packing of Unit Squares in a Square

Let $s(N)$ denote the edge length of the smallest square in which one can pack $N$ unit squares. A duality method is introduced to prove that $s(6)=s(7)=3$. Let $n_r$ be the smallest integer $n$ such that $s(n^2+1)\le n+{1/r}$. We use an explicit construction to show that $n_r\le 27r^3/2+O(r^2)$, and also that $n_2\le43$.
CAHIER DU LAMSADE 307 Mars 2011 On the MAX k-VERTEX COVER problem

Given a graph G(V,E) of order n and a constant k 6 n, the max k-vertex cover problem consists of determining k vertices that cover the maximum number of edges in G. In its (standard) parameterized version, max k-vertex cover can be stated as follows: “given G, k and parameter l, does G contain k vertices that cover at least l edges? ”. We first devise moderately exponential exact algorithms for max k-vertex cover, with complexity exponential to n (note that the known results concerned time bounds of the form n) by developing a branch and reduce method based upon the measure-and-conquer technique. We then prove that, interestingly enough, although max k-vertex cover is non fixed parameter tractable with respect to l, it is fixed parameter tractable with respect to the size τ of a minimum vertex cover of G. We also point out that the same happens for a lot of well-known problems quite different from max k-vertex cover. We finally study approximation of max k-vertex cover by moderately exponential algorithms. The general goal of the issue of moderately exponential approximation is to catch-up on polynomial inapproximability, by providing algorithms achieving, with worst-case running times importantly smaller than those needed for exact computation, approximation ratios unachievable in polynomial time.
Gene prediction with a hidden Markov model and a new intron submodel

MOTIVATION The problem of finding the genes in eukaryotic DNA sequences by computational methods is still not satisfactorily solved. Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons. RESULTS We have developed a new program, AUGUSTUS, for the ab initio prediction of protein coding genes in eukaryotic genomes. The program is based on a Hidden Markov Model and integrates a number of known methods and submodels. It employs a new way of modeling intron lengths. We use a new donor splice site model, a new model for a short region directly upstream of the donor splice site model that takes the reading frame into account and apply a method that allows better GC-content dependent parameter estimation. AUGUSTUS predicts on longer sequences far more human and drosophila genes accurately than the ab initio gene prediction programs we compared it with, while at the same time being more specific. AVAILABILITY A web interface for AUGUSTUS and the executable program are located at http://augustus.gobics. de.
Towards an objective evaluation of underactuated gripper designs

In this paper we explore state-of-the-art underactuated, compliant robot gripper designs through looking at their performance on a generic grasping task. Starting from a state of the art open gripper design, we propose design modifications,and importantly, evaluate all designs on a grasping experiment involving a selection of objects resulting in 3600 object-gripper interactions. Interested in non-planned grasping but rather on a design's generic performance, we explore the influence of object shape, pose and orientation relative to the gripper and its finger number and configuration. Using open-loop grasps we achieved up to 75% success rate over our trials. The results indicate and support that under motion constraints and uncertainties and without involving grasp planning, a 2-fingered underactuated compliant hand outperforms higher multi-fingered configurations. To our knowledge this is the first extended objective comparison of various multi-fingered underactuated hand designs under generic grasping conditions.
High Fibroblast Growth Factor 23 Levels Associated With Low Hemoglobin Levels in Patients With Chronic Kidney Disease Stages 3 and 4

AbstractIn chronic kidney disease (CKD), decreased erythropoietin production, low serum active vitamin D levels, and high renin-angiotensin-aldosterone activities had been regarded as major causes of renal anemia. At present, no clinical data are available to elucidate the association between renal anemia and fibroblast growth factor 23 (FGF23) levels in CKD. This study aimed to access whether FGF23 is involved in the pathogenesis of renal anemia.This cross-sectional observational study included 53 stable outpatients with CKD stages 3 and 4. Our primary predictor was serum FGF23 levels and outcome was hemoglobin levels. Measurements contained hemoglobin, FGF23, 25-hydroxyvitamin D, intact parathyroid hormone, plasma renin, serum aldosterone, HbA1C levels, lipid and iron profiles, and serum and urine electrolytes.Mean age of our patients was 66.4 ± 12.8 (SD) years, mean estimated glomerular filtration rate 33.5 ± 13.9 mL/min/1.73 m2, median FGF23 level 200 (25th–75th percentile, 124–303) pg/mL, vitamin D level 19.5 (25th–75th percentile, 14.0–25.9) ng/mL, and hemoglobin level 12.7 (25th–75th percentile, 10.7–13.75) g/dL. Even after adjusting multiple variables, lower hemoglobin levels correlated significantly with FGF23 levels that were higher than the median value (>200 pg/mL). Moreover, after adjusting for aldosterone, but not 25-hydroxyvitamin D, it decreased the association with FGF23 that higher than median level and hemoglobin levels. We also observed a significant decrease of hemoglobin level in the higher FGF23 group who had a diabetes history.High FGF23 levels were observed to be associated with low hemoglobin levels, which may be partially mediated through the effects of serum aldosterone levels in our patients with CKD stages 3 and 4. Furthermore, we also presumed that diabetes itself may have an impact on the loop among FGF23, hemoglobin, and aldosterone levels in these CKD patients.
Limitations of ordinary least squares models in analyzing repeated measures data.

PURPOSE To a) introduce and present the advantages of linear mixed models using generalized least squares (GLS) when analyzing repeated measures data; and b) show how model misspecification and an inappropriate analysis using repeated measures ANOVA with ordinary least squares (OLS) methodology can negatively impact the probability of occurrence of Type I error. METHODS The effects of three strength-training groups were simulated. Strength gains had two slope conditions: null (no gain), and moderate (moderate gain). Ten subjects were hypothetically measured at five time points, and the correlation between measurements within a subject was modeled as compound symmetric (CS), autoregressive lag 1 (AR(1)), and random coefficients (RC). A thousand data sets were generated for each correlation structure. Then, each was analyzed four times--once using OLS, and three times using GLS, assuming the following variance/covariance structures: CS, AR(1), and RC. RESULTS OLS produced substantially inflated probabilities of Type I errors when the variance/covariance structure of the data set was not CS. The RC model was less affected by the actual variance/covariance structure of the data set, and gave good estimates across all conditions. CONCLUSIONS Using OLS to analyze repeated measures data is inappropriate when the covariance structure is not known to be CS. Random coefficients growth curve models may be useful when the variance/covariance structure of the data set is unknown.
Some Bounds on the Complexity of Gradients, Jacobians, and Hessians

The evaluation or approximation of derivatives is an important part of many nonlinear computations. The cost of evaluating rst-and second-derivative matrices is often assumed to grow linearly and quadratically with the number of independent variables, respectively. It is shown here that much tighter bounds can be achieved through the exploitation of partial function-and argument-separability in combination with the forward and reverse mode of computational , or automatic, diierentiation. The new separability concepts facilitate the reduction of chromatic numbers and maximal row lengths, which determine the complexity of the Curtis-Powell-Reid and Newsam-Ramsdell schemes for estimating sparse derivative matrices. Because of the duality between the forward and reverse modes these techniques can be applied to Jacobians as well as their transposes and the associated row-intersection graphs. In contrast to diierencing, computational diierentiation yields derivative values free of truncation errors and without any parameter dependence. A key result presented in this paper is that gradients and Hessians of partially separable functions can also be obtained surprisingly cheaply in the easily implemented forward mode as well as in the more sophisticated reverse mode of computational diierentiation.
Chemical Data Assimilation—An Overview

Chemical data assimilation is the process by which models use measurements to produce an optimal representation of the chemical composition of the atmosphere. Leveraging advances in algorithms and increases in the available computational power, the integration of numerical predictions and observations has started to play an important role in air quality modeling. This paper gives an overview of several methodologies used in chemical data assimilation. We discuss the Bayesian framework for developing data assimilation systems, the suboptimal and the ensemble Kalman filter approaches, the optimal interpolation (OI), and the three and four dimensional variational methods. Examples of assimilation real observations with CMAQ model are presented.
Insight into Glycoside Hydrolases for Debranched Xylan Degradation from Extremely Thermophilic Bacterium Caldicellulosiruptor lactoaceticus

Caldicellulosiruptor lactoaceticus 6A, an anaerobic and extremely thermophilic bacterium, uses natural xylan as carbon source. The encoded genes of C. lactoaceticus 6A for glycoside hydrolase (GH) provide a platform for xylan degradation. The GH family 10 xylanase (Xyn10A) and GH67 α-glucuronidase (Agu67A) from C. lactoaceticus 6A were heterologously expressed, purified and characterized. Both Xyn10A and Agu67A are predicted as intracellular enzymes as no signal peptides identified. Xyn10A and Agu67A had molecular weight of 47.0 kDa and 80.0 kDa respectively as determined by SDS-PAGE, while both appeared as homodimer when analyzed by gel filtration. Xyn10A displayed the highest activity at 80°C and pH 6.5, as 75°C and pH 6.5 for Agu67A. Xyn10A had good stability at 75°C, 80°C, and pH 4.5–8.5, respectively, and was sensitive to various metal ions and reagents. Xyn10A possessed hydrolytic activity towards xylo-oligosaccharides (XOs) and beechwood xylan. At optimum conditions, the specific activity of Xyn10A was 44.6 IU/mg with beechwood xylan as substrate, and liberated branched XOs, xylobiose, and xylose. Agu67A was active on branched XOs with methyl-glucuronic acids (MeGlcA) sub-chains, and primarily generated XOs equivalents and MeGlcA. The specific activity of Agu67A was 1.3 IU/mg with aldobiouronic acid as substrate. The synergistic action of Xyn10A and Agu67A was observed with MeGlcA branched XOs and xylan as substrates, both backbone and branched chain of substrates were degraded, and liberated xylose, xylobiose, and MeGlcA. The synergism of Xyn10A and Agu67A provided not only a thermophilic method for natural xylan degradation, but also insight into the mechanisms for xylan utilization of C. lactoaceticus.
D S ] 2 2 O ct 2 00 4 Optimal Free-Space Management and Routing-Conscious Dynamic Placement for Reconfigurable Computers ∗

We describe algorithmic results on two crucial aspects of allocating resources on array-based hardware devices with partial reconfigurability. By using methods from the field of computational geometry, we derive a method that allows correct maintainance of free and occupied space of a set of n rectangular modules in time O(n log n); previous approaches needed a time of O(n) for correct results and O(n) for heuristic results. We also show a matching lower bound of Ω(n log n), so our approach is optimal. We also show that finding an optimal feasible communicationconscious placement (which minimizes the total weighted Manhattan distance between the new module and existing demand points) can be computed with Θ(n log n). Both resulting algorithms are practically easy to implement and show convincing experimental behavior. ACM Classification: C.1. 3: Reconfigurable Hardware; F.2. 2.c: Geometrical problems and computations
Grounding: Bonding to Earth: We Leave Out Something Big When We Just Say \"Bonding\"

Returning to basics, grounding is bonding to earth. While grounding electrodes are the only true bonds to earth, the term "grounding" has been traditionally applied when bonding to extended conducting bodies such as the ground bus in an electrical panel. That tradition is presently under fire, with suggestions that what is referred to as the equipment grounding conductor (EGC) should be renamed the equipment bonding conductor. Beyond semantics, the term "bonding" alone compared to grounding (bonding to earth) presents a clear omission, which is the reference to earth. This article challenges that omission, presenting the multifaceted approach for the reduction of electrical hazards that is provided by bonding to earth rather than simply bonding.
Test-driven development of web and enterprise agents

Test-driven development asserts that the test code is equally important as the production code. In this paper we propose a new unit testing framework in which the unit of work is an agent. The framework has emerged as a necessity during the development of our enterprise-scale multiagent middleware, and has therefore been designed as a practical solution. It includes a message-based and an interceptor-based architecture, and supports simultaneous testing of both client-side and server-side agents.
Identification of an epithelial protein related to the desmosome and intermediate filament network

Using a mAb, referred to as 08L, we have identified a protein, of M(r) approximately 140,000, associated with desmosomes of epithelial cells. The 08L antibody stained the intracellular side of lateral cell margins of monolayer epithelial cells but did not stain cell margins free of cell contact. Immunoelectron microscopy revealed that the 08L antigen was localized to the cytosolic surface of the desmosomal plaque near points of intermediate filament convergence with apparently little staining of the desmosomal plaque proper. Western blots revealed the 08L antigen to be a protein, of M(r) approximately 140,000, found in the Triton-X 100 insoluble pellet. High salt-containing buffers extracted the 08L antigen from the insoluble material. Examination of the assembly of 08L to the desmosome complex, in cells grown in low confluent culture or in calcium-switch assays, by double immunofluorescence with 08L and anti-desmoplakin antibody, revealed that 08L was recruited to morphologically identifiable desmosomes. 08L antigen may exist in a cytosolic pool prior to assembly to the cell surface. The solubility of 08L in low calcium and normal calcium conditions, however, was similar. 08L association to the desmosome was correlated with increased organization of the intermediate filament network. We suggest that the 08L antigen may be involved in the organization and stabilization of the desmosome-IF complexes of epithelia.
Perturbative superluminal censorship and the null energy condition

We argue that “effective” superluminal travel, potentially caused by the tipping over of light cones in Einstein gravity, is always associated with violations of the null energy condition (NEC). This is most easily seen by working perturbatively around Minkowski spacetime, where we use linearized Einstein gravity to show that the NEC forces the light cones to contract (narrow). Given the NEC, the Shapiro time delay in any weak gravitational field is always a delay relative to the Minkowski background, and never an advance. Furthermore, any object travelling within the lightcones of the weak gravitational field is similarly delayed with respect to the minimum traversal time possible in the background Minkowski geometry.
2LIPGarden: 3D hypermedia for everyone

The early Web was hailed for being easy to use, and what is more important, giving people a chance to participate in its growth. The Web3D was believed to have potential to be the next step in the Web's evolution, since it could benefit from graphics hardware and provide users with new and exciting experiences. Nevertheless, Virtual Reality Markup Language (VRML), the first Web3D standard, and its successor X3D, did not generate commercial success. These languages were excessively complex for average Internet users. In this paper, we propose 2LIPGarden, a 3D Hypermedia publishing framework that lets individuals who only know basic HTML - those same enthusiasts who could write pages for the early Web - create simple, easy to use yet interactive 3D web pages. Our framework builds upon 2-Layer Interface Paradigm (2LIP), an attempt to marry advantages of 3D experience with the advantages of narrative structure of hypertext. We introduce c-link to HTML, a new type of hyperlink, which connects text with its 3D visualization.
Web Application Testing with Customized Test Requirements - An Experimental Comparison Study

Test suite reduction uses test requirement coverage to determine if the reduced test suite maintains the original suite's requirement coverage. Based on observations from our previous experimental studies on test suite reduction, we believe there is a need for customized test requirements for Web applications. In this paper, we examine usage-based customized test requirements for the test suite reduction problem in Web application testing. We conduct an extensive experimental study to evaluate the tradeoffs between five classes of customized requirements with respect to reduced test suite size, program coverage and fault detection effectiveness. Our results show that the reduced suites' program coverage and fault detection effectiveness increases with the context or data associated with the reduction requirement. Based on our experimental results, we provide guidance to testers on the most useful test requirement for Web applications in general and provide intuition on factors testers need to consider when selecting test requirements
Real-time biosignal quality analysis of ambulatory ECG for detection of myocardial ischemia

This work is part of an on-going effort to implement real-time biosignal quality analysis for electrocardiograms (ECG). Biosignal quality analysis can provide an estimate of the signal-to-noise ratio (SNR), which can be used to gate alarms for myocardial ischemia, as indicated by ST deviations in ambulatory ECG. Currently, the false alarm rate is high due to contaminants in the ECG, such as motion artifact. In the proposed algorithm, ECG data are segmented into 16-beat analysis windows. Within an analysis window, the heart's PQRST complexes are segmented, aligned, and averaged to form an estimate of the true PQRST complex output by the heart. A SNR is estimated for each beat by comparing the PQRST complex of each beat to the average PQRST complex; the lowest SNR across all beats in the analysis window is the SNR assigned to the analysis window. Performance of the algorithm is evaluated using ECG data contaminated with various levels of motion artifact. The algorithm provides SNR estimates that are correlated with true SNR (r = 0.89). Leveraging the repeatability of the PQRST complex, it derives these estimates solely from the recorded ECG and does not require a noise free period or any supplementary signals. Results indicate that this algorithm may be a viable method for gating myocardial alarms for reduction of the false alarm rate.
3D reconstruction based on light field information

As an important branch of computational photography, light field photography combines the hardware design of optical system with key algorithm of signal processing quite well. Unlike traditional photography which can only record light ray's two-dimensional position, light field photography system can record four-dimensional position and direction. Therefore, much more image information can be obtained from light field photography. With the development of 3D display technology, light field based autofocus and 3D display technology is becoming more and more popular. In this paper, a light field based new 3D reconstruction algorithm for buildings and office environment is proposed by applying Wavelet Transform and SVM (Support Vector Machine) model to obtain the image focusing quality assessment, along with the Mean Shift Algorithm and Random Field Model to get the depth map of the scene. Firstly, light field image is captured by using a light field camera. Secondly, we use frequency domain digital refocus algorithm to manipulate light field image and obtain several serialized refocused images with different focus. Thirdly, wavelet features are extracted from each refocused image, and then an image focusing quality assessment is conducted by using RBF (Radial Basis Function) kernel based SVM model. Finally, we use Mean Shift algorithm to realize color clustering of the original light field image, and then build MRF (Markov Random Field) Model with color nodes. By iterating the likelihood depth result obtained from real scenario depth calibrations according to image focusing quality assessment, finally the depth map of the scene is reconstructed. Experiments are conducted to prove the feasibility of the proposed 3D reconstructed algorithm based on light field. And the experimental results on real datasets demonstrate good performance of this algorithm.
Women’s and men’s role in culture of honor endorsement within families

In this article, we analyze the patterns of culture of honor within Spanish families. Each member of 271 Spanish four-member families (parents and two children each, total N = 1084) completed a questionnaire containing scales for the culture of honor and for sociodemographic variables (gender, order born and age). The results show that intra-family similarities emerge. However, path analyses show that the gender and birth order of the child are relevant in predicting this similarity. In particular, the first-born child converges with their mother to a higher extent than the father regardless of their gender. However, for the second-born child both parents instill their ideas about culture of honor in a gender congruent way (father–boy and mother–girl). Furthermore, there are higher similarities within younger families, indicating a stronger influence from parents to children. Results are discussed in view of social role and gender social learning theories.
Visualization of mandarin articulation driven by ultrasound data

In this paper, we construct a three-dimensional visualization system for Chinese phoneme driven by ultrasound data, which is expected to provide intuitive and accurate visualization of articulatory movements. Our visualization system is is developed based on two data sets, one is three-dimensional (3D) articulatory data which is obtained using physiological articulatory model, and the other is ultrasound images recorded during production of sustained Chinese vowels. In this study, we analyzed configurations of 7 Chinese phonemes based on an ultrasound database. About 150,000 muscle activation patterns were designed to generate variety of 3D tongue shapes via the physiological articulatory model. The preliminary results showed the pronunciation visualization can be presented properly.