Miracle-dz/UniFAR-FTUs huggingface dataset:
Aliasing Detection and Reduction Scheme on Angularly Undersampled Light Fields

When using plenoptic camera for digital refocusing, angular undersampling can cause severe (angular) aliasing artifacts. Previous approaches have focused on avoiding aliasing by pre-processing the acquired light field via prefiltering, demosaicing, reparameterization, and so on. In this paper, we present a different solution that first detects and then removes angular aliasing at the light field refocusing stage. Different from previous frequency domain aliasing analysis, we carry out a spatial domain analysis to reveal whether the angular aliasing would occur and uncover where in the image it would occur. The spatial analysis also facilitates easy separation of the aliasing versus non-aliasing regions and angular aliasing removal. Experiments on both synthetic scene and real light field data sets (camera array and Lytro camera) demonstrate that our approach has a number of advantages over the classical prefiltering and depth-dependent light field rendering techniques.
Bias correction in species distribution models: pooling survey and collection data for multiple species

Presence‐only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence–absence or count data collected in systematic, planned surveys are more reliable but typically less abundant. We proposed a probabilistic model to allow for joint analysis of presence‐only and survey data to exploit their complementary strengths. Our method pools presence‐only and presence–absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence‐only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence‐only data. We evaluate our model's performance on data for 36 eucalypt species in south‐eastern Australia. We find that presence‐only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data‐pooling technique substantially improves the out‐of‐sample predictive performance of our model when the amount of available presence–absence data for a given species is scarce If we have only presence‐only data and no presence–absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species' geographic range.
ImsInnovation - experiences of an IMS testbed

The IP Multimedia Subsystem (IMS) defined by the 3rd Generation Partnership Project (3GPP) is the architecture merging the Internet and mobile worlds. The IMS enables new business models and allows third-party developers to make their applications available to all IMS users. This paper introduces an IMS testbed called ImsInnovation, which was launched in Summer 2008. The objective of the testbed project is to ease the development of new third-party applications for the IMS. As part of this project we provide web developers with Java APIs (Application Programming Interfaces) that exploit the functionality of the IMS both for the Java Mobile Edition (ME) and the Java Enterprise Edition (EE). The provided APIs are based on existing SIP and IMS Java Specification Requests defined by the Java Community Process (JCP). In this paper we also discuss our experiences from the testbed project and describe a couple of applications deployed in the testbed.
Planning walking patterns for a biped robot

Biped robots have better mobility than conventional wheeled robots, but they tend to tip over easily. To be able to walk stably in various environments, such as on rough terrain, up and down slopes, or in regions containing obstacles, it is necessary for the robot to adapt to the ground conditions with a foot motion, and maintain its stability with a torso motion. When the ground conditions and stability constraint are satisfied, it is desirable to select a walking pattern that requires small torque and velocity of the joint actuators. We first formulate the constraints of the foot motion parameters. By varying the values of the constraint parameters, we can produce different types of foot motion to adapt to ground conditions. We then propose a method for formulating the problem of the smooth hip motion with the largest stability margin using only two parameters, and derive the hip trajectory by iterative computation. Finally, the correlation between the actuator specifications and the walking patterns is described through simulation studies, and the effectiveness of the proposed methods is confirmed by simulation examples and experimental results.
Trifluoroethanol and binding to model membranes stabilize a predicted turn in a peptide corresponding to the first extracellular loop of the angiotensin II AT(1A) receptor.

Homology modeling of the angiotensin II AT(1A) receptor based on rhodopsin's crystal structure has assigned the 92-100 (YRWPFGNHL) sequence of the receptor to its first extracellular loop. Solution and membrane-bound conformational properties of a peptide containing this sequence (EL1) were examined by CD, fluorescence, and (1)H-NMR. CD spectra in aqueous solution revealed an equilibrium between less organized and folded conformers. NMR spectra indicated the coexistence of trans and cis isomers of the Trp(3)-Pro(4) bond. A positive band at 226 nm in the CD spectra suggested aromatic ring stacking, modulated by EL1's ionization degree. CD spectra showed that trifluoroethanol (TFE), or binding to detergent micelles and phospholipid bilayers, shifted the equilibrium toward conformers with higher secondary structure content. Different media gave rise to spectra suggestive of different beta-turns. Chemical shift changes in the NMR spectra corroborated the stabilization of different conformations. Thus, environments of lower polarity or binding to interfaces probably favored the formation of hydrogen bonds, stabilizing beta-turns, predicted for this sequence in the whole receptor. Increases in Trp(3) fluorescence intensity and anisotropy, blue shifts of the maximum emission wavelength, and pK changes also evinced the interaction between EL1 and model membranes. Binding was seen to depend on both hydrophobic and electrostatic interactions, as well as lipid phase packing. Studies with water-soluble and membrane-bound fluorescence quenchers demonstrated that Trp(3) is located close to the water-membrane interface. The results are discussed with regard to possible implications in receptor folding and function.
Getting Things in Order: An Introduction to the R Package seriation

Seriation, i.e., finding a suitable linear order for a set of objects given data and a loss or merit function, is a basic problem in data analysis. Caused by the problem's combinatorial nature, it is hard to solve for all but very small sets. Nevertheless, both exact solution methods and heuristics are available. In this paper we present the package seriation which provides an infrastructure for seriation with R. The infrastructure comprises data structures to represent linear orders as permutation vectors, a wide array of seriation methods using a consistent interface, a method to calculate the value of various loss and merit functions, and several visualization techniques which build on seriation. To illustrate how easily the package can be applied for a variety of applications, a comprehensive collection of examples is presented.
Foot Modeling and Smart Plantar Pressure Reconstruction from Three Sensors

In order to monitor pressure under feet, this study presents a biomechanical model of the human foot. The main elements of the foot that induce the plantar pressure distribution are described. Then the link between the forces applied at the ankle and the distribution of the plantar pressure is established. Assumptions are made by defining the concepts of a 3D internal foot shape, which can be extracted from the plantar pressure measurements, and a uniform elastic medium, which describes the soft tissues behaviour. In a second part, we show that just 3 discrete pressure sensors per foot are enough to generate real time plantar pressure cartographies in the standing position or during walking. Finally, the generated cartographies are compared with pressure cartographies issued from the F-SCAN system. The results show 0.01 daN (2% of full scale) average error, in the standing position.
Strategies for recruitment of relatives of BRCA mutation carriers to a genetic testing program in the Bahamas

The prevalence of BRCA1 and BRCA2 mutations among unselected breast cancer patients in the Bahamas is 23%. It is beneficial to advise relatives of mutation carriers that they are candidates for genetic testing. Women who test positive are then eligible for preventive interventions, such as oophorectomy. It is not clear how often relatives of women with a mutation in the Bahamas wish to undergo genetic testing for the family mutation. Furthermore, it is not clear how best to communicate this sensitive information to relatives in order to maximize patient compliance. We offered genetic testing to 202 first‐degree relatives of 58 mutation carriers. Of 159 women who were contacted by the proband or other family member, only 14 made an appointment for genetic testing (9%). In contrast, among 32 relatives who were contacted directly by the genetic counselor, 27 came for an appointment (84%). This study suggests that for recruitment of relatives in the Bahamas, direct contact by counselor is preferable to using the proband as an intermediary.
Effect of mercury and Gpi‐2 genotype on standard metabolic rate of eastern mosquitofish (Gambusia holbrooki)

Previous studies demonstrated differential mortality among mosquitofish of different Gpi‐2 genotypes during acute mercury and arsenate exposures. Mercury‐exposed mosquitofish also had Gpi‐2 genotype‐specific differences in glycolytic and Krebs cycle metabolite pools. The mortality and metabolite data suggested that mosquitofish bearing specific Gpi‐2 genotypes might differ in metabolic efficiency, with less efficient Gpi‐2 genotypes having higher standard metabolic rates (SMRs) and shorter times to death during acute mercury exposure. Effect of Gpi‐2 genotype on SMR was assessed with a factorial arrangement of six Gpi‐2 genotypes and two exposure sequences (Control — Control; Control — 100 μg/L Hg). The SMRs were estimated by measuring oxygen consumption using an indirect, closed‐circuit, computer‐controlled respirometer. A 48‐h exposure to 100 μg/L of mercury resulted in a 16.7% elevation of SMR above control levels (p = 0.001). The Gpi‐2 genotype and the number of heterozygous loci per individual had no significant effect on SMR in mercury‐exposed mosquitofish. The experimental results do not support the hypothesis that Gpi‐2 genotype‐specific differences in glycolytic and Krebs cycle metabolite pools and mortality in mosquitofish exposed to mercury are associated with differences in SMR.
Interfacial adhesion and toughness of nanostructured diamond coatings

Microwave plasma chemical vapor deposition was used to deposit ultrasmooth nanostructured diamond films (roughness of 14 nm) on a titanium alloy (Ti–6Al–4V) by employing a feedgas mixture containing a high methane fraction (15% by volume) in nitrogen and hydrogen. Of particular interest in this study is the exceptional adhesion of the 4-μm-thick diamond coatings to the metal substrates as observed by indentation testing up to 150 kg load with a 1/8-in. -diameter tungsten carbide ball. No film delamination was observed up to 150 kg indentation load for each of 5 samples grown under the same processing conditions. Scanning electron microscopy of the film surrounding the indentations revealed circumferential microcracking beginning at loads ranging from 60 kg to as high as 150 kg. The strain to cause film microcracking was estimated from calculations of indentation surface areas to be as high as 1.9 ± 0.2%, which represents a significant improvement in toughness over other ceramic coatings.
Molecular Analysis of Ring Y Chromosome in a 10-Year-Old Boy with Mixed Gonadal Dysgenesis and Growth Hormone Deficiency

Molecular Analysis of Ring Y Chromosome in a 10-Year-Old Boy with Mixed Gonadal Dysgenesis and Growth Hormone Deficiency Ring Y chromosome is a very rare chromosomal aberration. The published mixed gonadal dysgenesis (MGD) patients with a ring Y chromosome are short in stature, but are not growth hormone (GH) deficient. We present the molecular cytogenetic and molecular characterization of ring Y chromosome mosaicism in a 10-year-old boy with MGD whose short stature could be explained by the high percentage of cells monosomic for the X-chromosome, but also by the presence of severe GH deficiency. The ring Y chromosome in our patient is a de novo structural aberration. The father's karyotype was normal.
E-CELL: software environment for whole-cell simulation

MOTIVATION Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.
Predicting Effect of Temperature Field on Sensitization of Alloy 690 Weldments

The present study develops two 3-D finite element (FE) thermal models of the temperature field induced within an Alloy 690 butt weld fabricated using the two-pass GTA welding and the laser beam welding (LBW) methods, respectively. The welding thermal cycles of the two welding methods are simulated using ANSYS software based upon a moving heat source model and the high-temperature thermal physical property data are derived in the JMatPro database. The validity of the numerical model is confirmed by comparing the simulation results with the corresponding experimental findings. Agreement is found between the numerical results for the temperature field and the experimental temperature measurements. In addition, the FEM models we use can help us estimate the range and size of the sensitization zone and the time duration of the sensitization temperature. Overall, the results provide useful insight into the sensitization tendencies of Alloy 690 weldments.
Immunoglobulin concentrations in sera of normal children: quantitation against an international reference preparation.

Immunoglobulins G, A, and M were quantitated in sera from healthy children of various ages by using a standard related to the international reference preparation for human serum immunoglobulins. The results, expressed in International Units per milliliter, provide a basis for the establishment of normal immunoglobulin values in different laboratories.
Coupling of localised plasmon resonances

Plasmon resonances have attracted a lot of recent research interest for their potential applications, including bio-sensing, sub-wavelength optics, negative refractive index metamaterials and their ability to produce massively enhanced electromagnetic fields. Localised surface plasmon resonances (LSPR) in metallic nanostructures can offer large electromagnetic field enhancements, and nanometre-scale localisation of electric fields. Their resonance wavelengths and properties can be tuned by variation of the nanostructure geometry and are sensitive to environmental refractive index. Coupling of localised plasmon resonances can: Create new hybrid modes that cannot be supported by individual nanostructures, overcome some of the limitations of individual LSPR, and open up possibilities for new applications and active control of plasmon resonances. This thesis contains results from samples exploiting near-field, far-field and resistive coupling of localised plasmon resonances to create novel resonance modes that may make them suitable for important applications. Firstly results are presented from samples exhibiting strong collective plasmon resonances at normal incidence, which could be used to improve the spatial resolution of, miniaturise and add new functionality to highly sensitive surface plasmon resonance based approaches to bio-sensing. A very high bio-sensing figure of merit is calculated for the nanostructure arrays fabricated.Results are also presented from samples designed to produce the highest quality factor resonances possible when excited with light at grazing incidence. The highest resonance quality factors measured were conservatively estimated to be >210, which to our knowledge are the highest values of quality factor measured in diffraction coupled arrays at the resonance wavelengths around 1.5 ? m. Evidence for the existence of a presently largely unrecognised resistive coupling mechanism is also presented from an array of gold nanostripes covered with a graphene layer. If further work is successful, this could allow extremely rapid modulation of theoptical properties of a plasmonic array by application of gate voltage to the graphenelayer.Finally an improvement to the fabrication procedure for established near-field coupled composite plasmonic nanostructures that create a cascaded electromagnetic field enhancement effect is presented.
Equivalence of Reconstruction From the Absolute Value of the Frame Coefficients to a Sparse Representation Problem

The purpose of this letter is to prove, for real frames, that signal reconstruction from the absolute value of the frame coefficients is equivalent to solution of a sparse signal optimization problem, namely a minimum lscrp (quasi)norm over a linear constraint. This linear constraint reflects the coefficients relationship within the range of the analysis operator
Dynamic Processing of Dominating Queries with Performance Guarantees

The top-k dominating query returns the k database objects with the highest score with respect to their dominance score. The dominance score of an object p is simply the number of objects dominated by p, based on minimization or maximization preferences on the attribute values. Each object (tuple) is represented as a point in a multidimensional space, and therefore, the number of attributes equals the number of dimensions. The top-k dominating query combines the dominance concept of skyline queries with the ranking function of top-k queries and can be used as an important tool in multi-criteria decision making systems. In this work, we focus on the 2-dimensional space and present, for the first time, novel algorithms for top-k dominating query processing in main memory with non-trivial asymptotic guarantees. In particular, we focus on both the semi-dynamic case (only insertions are allowed) and the fully-dynamic case (insertions and deletions are supported). We perform a detailed cost analysis regarding the worst-case complexity of preprocessing, the worst-case complexity for the query cost and the worst-case and amortized complexity for updates (insertions and deletions) focusing on the RAM computation model. Our solutions require space linear with the number of points, which is very important especially for modern applications which manipulate massive datasets. In addition, we discuss the case of the word-RAM computation model, where slightly better results are obtained.
Probabilistic Message Passing in Peer Data Management Systems

Until recently, most data integration techniques involved central components, e.g., global schemas, to enable transparent access to heterogeneous databases. Today, however, with the democratization of tools facilitating knowledge elicitation in machine-processable formats, one cannot rely on global, centralized schemas anymore as knowledge creation and consumption are getting more and more dynamic and decentralized. Peer Data Management Systems (PDMS) provide an answer to this problem by eliminating the central semantic component and considering instead compositions of local, pair-wise mappings to propagate queries from one database to the others. PDMS approaches proposed so far make the implicit assumption that all mappings used in this way are correct. This obviously cannot be taken as granted in typical PDMS settings where mappings can be created (semi) automatically by independent parties. In this work, we propose a totally decentralized, efficient message passing scheme to automatically detect erroneous mappings in PDMS. Our scheme is based on a probabilistic model where we take advantage of transitive closures of mapping operations to confront local belief on the correctness of a mapping against evidences gathered around the network. We show that our scheme can be efficiently embedded in any PDMS and provide a preliminary evaluation of our techniques on sets of both automatically-generated and real-world schemas.
A tale of two directories: implementing distributed shared objects in Java

We consider two alternative directory protocols. A directory service keep tracks of the location and status of mobile objects in a distributed system. This paper describes our experience implementing two distributed directory protocols as part of the Aleph tool& a distributed shared object system implement.ed in Java. One protocol is a conventional home-based protocol, in which a fixed node keeps track of the object’s location and status. The ot.her is a novel orrout protocol, based on a simple path-reversal algorithm. We were surprised to discover that the arrow protocol outperformed the home protocol, sometimes substantially, across a range of system sizes. This paper describes a series of experiments testing whether the discrepancy is due to an artifact of the Java run-time system (such as differences in thread management or object serialization costs), or whether it is something inherent in the protocols themselves. In the end, we use insights gained from these experimental results to design a new directory protocol that usually outperforms both.