Miracle-dz/UniFAR-FTUs huggingface dataset:
A Principled Taxonomy of Software Visualization

Abstract In the early 1980s researchers began building systems to visualize computer programs and algorithms using newly emerging graphical workstation technology. After more than a decade of advances in interface technology, a large variety of systems has been built and many different aspects of the visualization process have been investigated. As in any new branch of a science, a taxonomy is required so that researchers can use a common language to discuss the merits of existing systems, classify new ones (to see if they really are new) and identify gaps which suggest promising areas for further development. Several authors have suggested taxonomies for these visualization systems, but they have been ad hoc and have relied on only a handful of characteristics to describe a large and diverse area of work. Another major drawback of these taxonomies is their inability to accommodate expansion: there is no clear way to add new categories when the need arises. In this paper we present a detailed taxonomy of systems for the visualization of computer software. This taxonomy was derived from an established black-box model of software and is composed of a hierarchy with six broad categories at the top and over 30 leaf-level nodes at four hierarchical levels. We describe 12 important systems in detail and apply the taxonomy to them in order to illustrate its features. After discussing each system in this context, we analyse its coverage of the categories and present a research agenda for future work in the area.
Kineosphaera limosa gen. nov., sp. nov., a novel Gram-positive polyhydroxyalkanoate-accumulating coccus isolated from activated sludge.

A high-G+C gram-positive, motile, non-spore-forming coccus capable of accumulating significant amounts of polyhydroxyalkanoate (PHA) was isolated from an inefficient biological phosphorus removal activated sludge reactor. The cell wall of strain Lpha5T was characterized by the presence of meso-diaminopimelic acid, menaquinone MK-8(H4) and a complex fatty-acid pattern consisting of C16:0 and at least five other major straight-chain saturated and unsaturated fatty acids. Strain Lpha5T also had a high G+C content (71.3 mol%). The nearest phylogenetic relative of strain Lpha5T, based on 16S rDNA sequence analysis, was the high-G+C gram-positive bacterium Dermatophilus congolensis (similarity value of 94%), of the family Dermatophilaceae, class Actinobacteria. As strain Lpha5T was distinct from D. congolensis in its morphological, phenotypical (i.e. its PHA-accumulating ability and fatty-acid profile) and genetic traits (phylogeny and G+C content), it is proposed that strain Lpha5T be designated as the type species of a novel genus within the Dermatophilaceae. The name Kineosphaera limosa is proposed for strain Lpha5T (= JCM 11399T = DSM 14548T).
Kinect based calling gesture recognition for taking order service of elderly care robot

This paper proposes a Kinect-based calling gesture recognition scenario for taking order service of an elderly care robot. The proposed scenarios are designed mainly for helping non expert users like elderly to call service robot for their service request. In order to facilitate elderly service, natural calling gestures are designed to interact with the robot. Our challenge here is how to make the natural calling gesture recognition work in a cluttered and randomly moving objects. In this approach, there are two modes of our calling gesture recognition: Skeleton based gesture recognition and Octree based gesture recognition. Individual people is segmented out from 3D point cloud acquired by Microsoft Kinect, skeleton is generated for each segment, face detection is applied to identify whether the segment is human or not, specific natural calling gestures are designed based on skeleton joints. For the case that user is sitting on a chair or sofa, correct skeleton cannot be generated, Octree based gesture recognition procedure is used to recognize the gesture, in which human segments with head and hand are identified by face detection as well as specific geometrical constrains and skin color evidence. The proposed method has been implemented and tested on “HomeMate”, a service robot developed for elderly care. The performance and results are given.
Automation of an underground mining vehicle using reactive navigation and opportunistic localization

This paper describes the implementation of an autonomous navigation system onto a 30 tonne Load-Haul-Dump truck. The control architecture is based on a robust reactive wall-following behaviour. To make it purposeful we provide driving hints derived from an approximate nodal-map. For most of the time, the vehicle is driven with weak localization (odometry). This need only be improved at intersections where decisions must be made-a technique we refer to as opportunistic localization. The truck has achieved full-speed autonomous operation at an artificial test mine, and subsequently, at a operational underground mine.
A polynomial projection algorithm for linear programming

We propose a polynomial algorithm for linear programming. The algorithm represents a linear optimization or decision problem in the form of a system of linear equations and non-negativity constraints. Then it uses a procedure that either finds a solution for the respective homogeneous system or provides the information based on which the algorithm rescales the homogeneous system so that its feasible solutions in the unit cube get closer to the vector of all ones. In a polynomial number of calls to the procedure the algorithm either proves that the original system is infeasible or finds a solution in the relative interior of the feasible set.
Study of the Electromagnetic Resonances of a Cavity with an Aperture Using Numerical Method and Equivalent Circuit Method

— The shielding ability of a shielding cavity with an aperture will be greatly degraded at resonance frequencies, and the resonance modes and frequencies are affected by aperture resonances and aperture-cavity coupling, which are closely related with aperture sizes. The equivalent circuit method and numerical method of Transmission Line Matrix (TLM) are used to analyze the effects of aperture resonances and aperture-cavity coupling on the electromagnetic resonances of a cavity with an aperture in this paper. Both analytical and numerical results show that the resonance modes of a shielding cavity with an aperture consist of cavity resonance modes and aperture resonance modes, and the resonance frequencies will shift with the change of the aperture sizes because of the aperture resonances and aperture-cavity coupling. Variation rules of electromagnetic resonances with aperture sizes for a cavity with an aperture are given, which will be useful for design of shielding cavities.
siRNA Selection Server: an automated siRNA oligonucleotide prediction server

The Whitehead siRNA (short interfering RNA) Selection Web Server (http://jura.wi.mit.edu/bioc/siRNA) automates the design of short oligonucleotides that can specifically 'knock down' expression of target genes. These short sequences are about 21 nt in length, and when synthesized as double stranded RNA and introduced into cell culture, can reduce or eliminate the function of the target gene. Depending on the length of a gene, there are potentially numerous combinations of possible 21mers. Some experimental evidence has already shown that not all 21mers in a gene have the same effectiveness at silencing gene function. Our tool incorporates published design rules and presents the scientist with information about uniqueness of the 21mers within the genome, thermodynamic stability of the double stranded RNA duplex, GC content, presence of SNPs and other features that may contribute to the effectiveness of a siRNA.
Amyloid-β Peptide Is Needed for cGMP-Induced Long-Term Potentiation and Memory

High levels of amyloid-β peptide (Aβ) have been related to Alzheimer's disease pathogenesis. However, in the healthy brain, low physiologically relevant concentrations of Aβ are necessary for long-term potentiation (LTP) and memory. Because cGMP plays a key role in these processes, here we investigated whether the cyclic nucleotide cGMP influences Aβ levels and function during LTP and memory. We demonstrate that the increase of cGMP levels by the phosphodiesterase-5 inhibitors sildenafil and vardenafil induces a parallel release of Aβ due to a change in the approximation of amyloid precursor protein (APP) and the β-site APP cleaving enzyme 1. Moreover, electrophysiological and behavioral studies performed on animals of both sexes showed that blocking Aβ function, by using anti-murine Aβ antibodies or APP knock-out mice, prevents the cGMP-dependent enhancement of LTP and memory. Our data suggest that cGMP positively regulates Aβ levels in the healthy brain which, in turn, boosts synaptic plasticity and memory. SIGNIFICANCE STATEMENT Amyloid-β (Aβ) is a key pathogenetic factor in Alzheimer's disease. However, low concentrations of endogenous Aβ, mimicking levels of the peptide in the healthy brain, enhance hippocampal long-term potentiation (LTP) and memory. Because the second messenger cGMP exerts a central role in LTP mechanisms, here we studied whether cGMP affects Aβ levels and function during LTP. We show that cGMP enhances Aβ production by increasing the APP/BACE-1 convergence in endolysosomal compartments. Moreover, the cGMP-induced enhancement of LTP and memory was disrupted by blockade of Aβ, suggesting that the physiological effect of the cyclic nucleotide on LTP and memory is dependent upon Aβ.
An Investigation of Improving Wear of 390 Die-cast Aluminum Through Hardcoat Anodizing

AN INVESTIGATION OF IMPROVING WEAR OF 390 DIE-CAST ALUMINUM THROUGH HARDCOAT ANODIZING Michael J. Whiting Department of Mechanical Engineering Master of Science The objectives of this research were to investigate the wear that occurs on the surface of a Hardcoat anodized die-cast aluminum surface, which was sliding against a composite rubber belt. This research investigated known wear theories and the results for previous testing to understand the mechanisms that were likely occurring in this application. These theories indicated that the wear occurring may be reduced by changing the hardness of the materials involved. Archard’s equation gave tangible evidence of this fact, but related to the base material and not a surface coating. It was hypothesized that Hardcoat anodizing would follow the theory of Archard’s equation and increase the wear resistance of 390 die-cast aluminum when sliding against a composite rubber belt. Standardized wear tests were implemented in order to test this theory. The results of the wear tests indicated that the wear resistance of the Hardcoat anodized coating did not follow the wear theories and wore at a higher rate than the base material surfaces. This is likely due to the phenomenon seen by Jiang and Arnell where the surface roughness influenced the wear rate of DLC coatings. They found that there existed a transition point where the wear rate of the surface increased with an increase of surface roughness. The Hardcoat anodized surface was rougher than the surface of the base material due to alloy materials and the processing characteristics of 390 Aluminum die-casting material. Subsequently the Hardcoat anodized surface wore at a higher rate than did the base surface. A case study was conducted on an ATV to investigate the accuracy of the results from the laboratory testing. This case study showed a significant localized wear groove in the stock CVT drive sheave with little wear occurring elsewhere. The Hardcoat anodized CVT drive sheave did not show evidence of a significant localized wear groove as the stock sheave but indicates that wear occurred more evenly across the surface. This wear is evident due to visible aluminum through the Hardcoat layer. In addition, there was a ridge at the outer diameter of the sheave where the belt could not wear the surface. Both of these items indicated that significant wear occurred on the surface, but the presence of a localized wear groove is non-existent.
Asynchronous dynamic multi-group formation for swarm robots

This paper addresses the asynchronous dynamic formation problem for swarm robots based on multi-group shape transformation. Considering robot swarm as a whole will make achieving the adaptation to the environment very difficult. Decomposition of multi-robot system into smaller groups gives capability and flexibility in complex pattern transformation which remarkably increases environmental adjustability. Unlike existing methods in dynamic formation control of swarm robots which is limited to synchronous shape transformation of the whole system, and is causing unnecessary repositioning of some robots; the proposed method can deal with asynchronous shape transformation which leads to efficient dynamic formation control. The stability of the system is examined by introducing a Lyapunov-like function. Simulation results are presented to illustrate the performance of the proposed method.
Lane departure detection for improved road geometry estimation

An essential part of future collision avoidance systems is to be able to predict road curvature. This can be based on vision data, but the lateral movement of leading vehicles can also be used to support road geometry estimation. This paper presents a method for detecting lane departures, including lane changes, of leading vehicles. This information is used to adapt the dynamic models used in the estimation algorithm in order to accommodate for the fact that a lane departure is in progress. The goal is to improve the accuracy of the road geometry estimates, which is affected by the motion of leading vehicles. The significantly improved performance is demonstrated using sensor data from authentic traffic environments
A Kernel Based Neighborhood Discriminant Submanifold Learning for Pattern Classification

We propose a novel method, called Kernel Neighborhood Discriminant Analysis (KNDA), which can be regarded as a supervised kernel extension of Locality Preserving Projection (LPP). KNDA nonlinearly maps the original data into a kernel space in which two graphs are constructed to depict the within-class submanifold and the between-class submanifold. Then a criterion function which minimizes the quotient between the within-class representation and the between-class representation of the submanifolds is designed to separate each submanifold constructed by each class. The real contribution of this paper is that we bring and extend the submanifold based algorithm to a general model and by some derivation a simple result is given by which we can classify a given object to a predefined class effectively. Experiments on the MNIST Handwritten Digits database, the Binary Alphadigits database, the ORL face database, the Extended Yale Face Database B, and a downloaded documents dataset demonstrate the effectiveness and robustness of the proposed method.
Robustness of Causal Claims

A causal claim is any assertion that invokes causal relationships between variables, for example that a drug has a certain effect on preventing a disease. Causal claims are established through a combination of data and a set of causal assumptions called a causal model. A claim is robust when it is insensitive to violations of some of the causal assumptions embodied in the model. This paper gives a formal definition of this notion of robustness and establishes a graphical condition for quantifying the degree of robustness of a given causal claim. Algorithms for computing the degree of robustness are also presented.
Novel synthesis of Ni-ferrite (NiFe2O4) electrode material for supercapacitor applications

Novel nanocrystalline NiFe2O4 has been synthesized through combustion route using citric acid as a fuel. Phase of the synthesized material was analyzed using powder X-ray diffraction. The XRD study revealed the formation of spinel phase cubic NiFe2O4 with high crystallinity. The average crystallite size of NiFe2O4 nanomaterial was calculated from scherrer equation. The electrochemical properties were realized by cyclic voltammetry, chronopotentiometry and electrochemical impedance spectroscopy. The electrode material shows a maximum specific capacitance of 454 F/g with pseudocapacitive behavior. High capacitance retention of electrode material over 1000 continuous charging-discharging cycles suggests its excellent electrochemical stability. The results revealed that the nickel ferrite electrode is a potential candidate for energy storage applications in supercapacitor.
Amino Acid Residues in the P2X7 Receptor that Mediate Differential Sensitivity to ATP and BzATP

Agonist properties of the P2X7 receptor (P2X7R) differ strikingly from other P2X receptors in two main ways: high concentrations of ATP (> 100 μM) are required to activate the receptor, and the ATP analog 2′,3′-O-(4-benzoyl-benzoyl)ATP (BzATP) is both more potent than ATP and evokes a higher maximum current. However, there are striking species differences in these properties. We sought to exploit the large differences in ATP and BzATP responses between rat and mouse P2X7R to delineate regions or specific residues that may be responsible for the unique actions of these agonists at the P2X7R. We measured membrane currents in response to ATP and BzATP at wild-type rat and mouse P2X7R, at chimeric P2X7Rs, and at mouse P2X7Rs bearing point mutations. Wild-type rat P2X7R was 10 times more sensitive to ATP and 100 times more sensitive to BzATP than wild-type mouse P2X7R. We found that agonist EC50 values were determined solely by the ectodomain of the P2X7R. Two segments (residues 115-136 and 282-288), when transposed together, converted mouse sensitivities to those of rat. Point mutations through these regions revealed a single residue, asparagine284, in the rat P2X7R that fully accounted for the 10-fold difference in ATP sensitivity, whereas the 100-fold difference in BzATP sensitivity required the transfer of both Lys127 and Asn284 from rat to mouse. Thus, single amino acid differences between species can account for large changes in agonist effectiveness and differentiate between the two widely used agonists at P2X7 receptors.
Local Reasoning about Mashups

Web mashups are complex programs that dynamically compose data and code from many sources. Whereas data is sometimes formally specified by XML schema, code never is. This makes it difficult to construct reliable software. Using local Hoare reasoning, introduced in separation logic to reason about e.g. C programs and extended in context logic to reason about e.g. the DOM library, we are able to reason about mashup programs, proving that they are fault-free and providing specifications for code that are analogous to XML schema for data.
Spectro-Temporal Filtering for Multichannel Speech Enhancement in Short-Time Fourier Transform Domain

In this letter, we propose a spectro-temporal filtering algorithm for multichannel speech enhancement in the short-time Fourier transform (STFT) domain. Compared with the traditional multiplicative filtering technique, the proposed method takes account of interdependencies between components in adjacent frames and frequency bins. For spectro-temporal filtering, speech and noise power spectral density (PSD) matrices are estimated based on an extended formulation utilizing temporal and spectral correlations, and the parametric noise reduction filter based on these PSD matrices is applied to the input microphone array signal. Moreover, multichannel speech presence probabilities are also estimated within a unified framework. A number of experimental results show that the proposed spectro-temporal filtering method improves the performance of multichannel speech enhancement.
Context-based Cell Search in Millimeter Wave 5G Networks

The exploitation of the mm-wave bands is one of the most promising solutions for 5G mobile radio networks. However, the use of mm-wave technologies in cellular networks is not straightforward due to mm-wave severe propagation conditions that limit access availability. In order to overcome this obstacle, hybrid network architectures are being considered where mmwave small cells can exploit an overlay coverage layer based on legacy technology. The additional mm-wave layer can also take advantage of a functional split between control and user plane, that allows to delegate most of the signaling functions to legacy base stations and to gather context information from users for resource optimization. However, mm-wave technology requires multiple antennas and highly directional transmissions to compensate for high path loss and limited power. Directional transmissions must be also used for the cell discovery and synchronization process, and this can lead to a non negligible delay due to need to scan the cell area with multiple transmissions in different angles. In this paper, we propose to exploit the context information related to user position, provided by the separated control plane, to improve the cell search procedure and minimize delay. We investigate the fundamental trade-offs of the cell discovery process with directional antennas and the effects of the context information accuracy on its performance. Numerical results are provided to validate our observations.
Mitochondrial potassium ATP channels and retinal ischemic preconditioning.

PURPOSE To examine the mechanisms of ischemic preconditioning (IPC) related to the opening of mitochondrial KATP (mKATP) channels in the retina. METHODS Rats were subjected to retinal ischemia after IPC, or retinas were rendered ischemic after pharmacological opening of mKATP channels. The effects of blocking mKATP channel opening, nitric oxide synthase (NOS) subtypes, or protein kinase C (PKC) on the protective effect of IPC or on the opening of mKATP channels were studied. Electroretinography assessed functional recovery after ischemia. Immunohistochemistry and image analysis were used to measure changes in levels of reactive oxygen species (ROS) and NOS subtypes and to determine their cellular localization. RESULTS IPC was effectively mimicked by injection of the mKATP channel opener diazoxide. Both IPC and its mimicking by diazoxide were completely attenuated by the mKATP channel blocker 5-hydroxydecanoic acid (5-HD). Nonspecific blockade of NOS by N(omega)-nitro-L-arginine (L-NNA), but not by specific inducible (i)NOS or neuronal (n)NOS inhibitors, blunted IPC and IPC-mimicking, as did blockade of PKC. IPC and diazoxide IPC-mimicking significantly enhanced mitochondrial ROS production in the inner retina, an effect blocked by 5-HD. Mitochondrial ROS colocalized with e- and nNOS in retinal cells after stimulation with diazoxide. CONCLUSIONS The results showed that IPC in the retina requires opening of the mKATP channel, and that IPC could be effectively mimicked using the mKATP channel opener diazoxide. eNOS-generated nitric oxide, PKC, and ROS are activated by opening of the mKATP channel.
Screen-space perceptual rendering of human skin

We propose a novel skin shader which translates the simulation of subsurface scattering from texture space to a screen-space diffusion approximation. It naturally scales well while maintaining a perceptually plausible result. This technique allows us to ensure real-time performance even when several characters may appear on screen at the same time. The visual realism of the resulting images is validated using a subjective psychophysical preference experiment. Our results show that, independent of distance and light position, the images rendered using our novel shader have as high visual realism as a previously developed physically-based shader.