Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of point matching methods for wide-baseline stereo correspondence on mobile platforms

Wide-baseline stereo matching is a common problem of computer vision. By the explosion of smartphones equipped with camera modules, many classical computer vision solutions have been adapted to such platforms. Considering the widespread use of various networking options for mobile phones, one can consider a set of smart phones as an ad-hoc camera network, where each camera is equipped with a more and more powerful computing engine in addition to a limited bandwidth communication with other devices. Therefore the performance of classical vision algorithms in a collaborative mobile environment is of particular interest. In such a scenario we expect that the images are taken almost simultaneously but from different viewpoints, implying that the camera poses are significantly different but lighting conditions are the same. In this work, we provide quantitative comparison of the most important keypoint detectors and descriptors in the context of wide baseline stereo matching. We found that for resolution of 2 megapixels images the current mobile hardware is capable of providing results efficiently.
Code vectorization using Intel Array Notation

In this paper, we explain the steps we have taken to port a large, industry-grade computational fluid dynamics application to the Intel® Xeon Phi™coprocessor using the C/C++ Array Notation extensions of Intel® Cilk™Plus. An essential part of the performance refactoring process for the Xeon Phi coprocessor is to achieve high-quality SIMD-vectorization. Even though there are other ways to vectorize code, the Array Notation extensions has proven to work best for our application. We have encapsulated the Array Notation extension syntax in a C++ wrapper class to drastically reduce the refactoring effort. In addition the architecture independency of Array Notation extensions minimizes porting and tuning efforts further. In this paper, we study how our approach helps the compiler to generate vectorized code. Derived from that study, we summarize our key learnings and findings as well as current limitations. Finally, we present a performance evaluation of the ported computational fluid dynamics application by using the introduced C++ wrapper class and differentiate our solution to other related solutions.
A Procedure for Word Derivational Processes Concerning Lexicon Extension in Highly Inflected Languages

The aim of this paper is to describe an efficient tool (I_PAR) for a supervised and semi-automatic extension of a lexicon or morphological database and its easy updating. We will present the underlying algorithms and their implementation that are general enough to capture the main word-forming processes (both inflectional and derivational). They are designed for languages with a rich inflectional morphology, such as Slavonic languages, particularly Czech.
Trends and Efficacy of Interferon-Free Anti–hepatitis C Virus Therapy in the Region of High Prevalence of Elderly Patients, Cirrhosis, and Hepatocellular Carcinoma: A Real-World, Nationwide, Multicenter Study of 10 688 Patients in Japan

Abstract Background We investigated changes in patient characteristics, rate of sustained virologic response (SVR), and factors associated with SVR after anti-hepatitis C virus (HCV) therapy with direct-acting antiviral (DAA) regimens in real-world practice in Japan, where patients with HCV are characterized by older age and high prevalence of cirrhosis and hepatocellular carcinoma (HCC). Methods Changes in patient characteristics and SVR rates were evaluated from medical records among 10 688 patients who started interferon (IFN)-free DAA therapy between September 2014 and June 2018 in a nationwide, multicenter study. Factors associated with failure of SVR were analyzed. In particular, effects of cirrhosis or history of HCC on SVR were assessed by exact matching. Results Patient age was becoming younger and baseline liver fibrosis was becoming milder over time. Overall SVR rate was 95.4%. The SVR rates increased over time in patients without a history of IFN-free DAA therapy. Multivariate analysis revealed that cirrhosis was unfavorably associated with achievement of SVR in both patients with genotype 1 (odds ratio, 1.68; 95% confidence interval [CI], 1.27–2.21) and genotype 2 (odds ratio, 1.69; 95% CI, 1.01–2.78). Comparisons after exact matching showed that the SVR rate was significantly lower in patients with cirrhosis than without it, whereas patients with and without a history of HCC had similar SVR rates. Conclusions Background characteristics of patients who undergo IFN-free DAA therapy are changing in Japan. Patients without a history of IFN-free DAA therapy have high SVR rates. Exact matching confirmed that cirrhosis significantly influences the achievement of SVR in real-world settings.
INTERLEUKIN-1 RECEPTOR ANTAGONIST GENE POLYMORPHISM AND TRADITIONAL CLASSIFICATION IN OBESE WOMEN

Cytokines appear to be the major regulators of adipose tissue metabolism. Interleukin- 1 receptor antagonist (IL-1ra) serum levels are increased in human obesity, and are under strong genetic control. The hypothesis was tested that the IL-1ra gene might be a candidate for obesity. Furthermore, the relationship was investigated between Sasang constitution and IL-1ra polymorphism. The frequency of a penta-allelic 86-bp tandem repeat (VNTR) in the intron 2 of IL-1ra gene in 67 lean (BMI < 25 kg/m2), 133 overweight (BMI 25-29.9 kg/m2) and 61 obese (BMI ≥ 30 kg/m2) otherwise healthy Korean subjects was investigated. Total fat mass and percentage body fat were determined by dual-energy X-ray absorptiometry. Subjects were discriminated into four types by QSCC II program as well as clinical data (weight, height, blood pressure, etc.); Teaeumin, Taeyangin, Soyangin, and Soeumin. Genomic DNA was extracted and used for polymerase chain reaction-based genotyping of IL-1ra. The genotypic, or allelic distribution did not differ markedly between the three groups. The relative risk of being obese in comparison with lean was twofold increased in allele 2 carriers, although it was not statistically significant. Carriers of the allele 2 did not show a significant difference in physical and clinical characteristics. However, the relative risk of being obese in comparison with lean was increased in Taeumin subjects (p = .050), and so was in IL-1ra A2- carriers (p = .047). No relationship was found between the IL-1ra polymorphism and BMI in Korean women, but the authors first attempted to find an association among IL-1ra polymorphism, obesity, and Sasang constitution.
Preservation and contrast without osmication or section staining

Conventional treatment of tissues for sectioning and transmission electron microscopy uses aldehyde fixation and osmium tetroxide postfixation. Although the result is aesthetically pleasing, osmication destroys some cell components and reduces the chemical activity of others, such as reactions with antibodies and lectins. We have found that aldehyde fixation followed by uranyl acetate preserves and contrasts most structures and visualizes some that are not easily seen after osmication. Aldehyde/UA treated tissues have enough contrast to be observed without section staining while retaining some of the chemical activity that is lost through osmication. Sections of tissues with good preservation and contrast can be used for immunogold and lectin‐gold labelling of at least some molecules. © 1994 Wiley‐Liss, Inc.
High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations

High throughput DNA sequencing technologies have undergone tremendous development over the past decade. Although optical detection-based sequencing has constituted the majority of data output, it requires a large capital investment and aggregation of samples to achieve optimal cost per sample. We have developed a novel electronic detection-based platform capable of accurately detecting single base incorporations. The GenapSys technology with its electronic detection modality allows the system to be compact, accessible, and affordable. We demonstrate the performance of the system by sequencing several different microbial genomes with varying GC content. The platform is capable of generating up to 2 Gb of high-quality nucleic acid sequence in a single run. We routinely generate sequence data that exceeds 99% raw accuracy with read lengths of up to 175 bp. Average quality scores remain above Q30 (99.9% raw sequencing accuracy) beyond 150 bp, with more than 85% of total bases at or above Q30. The utility of the platform is highlighted by targeted sequencing of the human genome. We show high concordance of SNP detection on the human NA12878 HapMap cell line with data generated on the Illumina sequencing platform. In addition, we sequenced a targeted panel of cancer-associated genes in a well characterized reference standard. With multiple library preparation approaches on this sample, we were able to identify low frequency mutations at expected allele frequencies.
Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells

Large-scale codon re-encoding represents a powerful method of attenuating viruses to generate safe and cost-effective vaccines. In contrast to specific approaches of codon re-encoding which modify genome-scale properties, we evaluated the effects of random codon re-encoding on the re-emerging human pathogen Chikungunya virus (CHIKV), and assessed the stability of the resultant viruses during serial in cellulo passage. Using different combinations of three 1.4 kb randomly re-encoded regions located throughout the CHIKV genome six codon re-encoded viruses were obtained. Introducing a large number of slightly deleterious synonymous mutations reduced the replicative fitness of CHIKV in both primate and arthropod cells, demonstrating the impact of synonymous mutations on fitness. Decrease of replicative fitness correlated with the extent of re-encoding, an observation that may assist in the modulation of viral attenuation. The wild-type and two re-encoded viruses were passaged 50 times either in primate or insect cells, or in each cell line alternately. These viruses were analyzed using detailed fitness assays, complete genome sequences and the analysis of intra-population genetic diversity. The response to codon re-encoding and adaptation to culture conditions occurred simultaneously, resulting in significant replicative fitness increases for both re-encoded and wild type viruses. Importantly, however, the most re-encoded virus failed to recover its replicative fitness. Evolution of these viruses in response to codon re-encoding was largely characterized by the emergence of both synonymous and non-synonymous mutations, sometimes located in genomic regions other than those involving re-encoding, and multiple convergent and compensatory mutations. However, there was a striking absence of codon reversion (<0.4%). Finally, multiple mutations were rapidly fixed in primate cells, whereas mosquito cells acted as a brake on evolution. In conclusion, random codon re-encoding provides important information on the evolution and genetic stability of CHIKV viruses and could be exploited to develop a safe, live attenuated CHIKV vaccine.
Robust Doppler Spread Estimation in the Presence of a Residual Carrier Frequency Offset

In high data-rate transmission systems, accurate Doppler spread estimation is a critical task for not only mobile velocity estimation, but also for optimal adaptive processing. It is known that the residual carrier frequency offset (CFO) which is inherent to the asynchrony between the communicating ends in a wireless link has a detrimental effect on the Doppler spread estimation. In this correspondence, we propose a new simple and accurate approach that copes with this issue by explicitly taking the CFO into account when estimating the Doppler spread. This new approach stems from the fact that the cross-correlation of the channel is a weighted summation of monochromatic plane waves (or an inverse Fourier transform of its power spectral density). It turns out that these plane waves are locally (as compared to the sampling rate) distributed around a main frequency which is nothing but the CFO. Using this property, we base our analysis on Taylor series expansions in addition to an observation temporal aperture to develop a two-ray spectrum approximate model for the Doppler spread estimation. We find that the Doppler spread is half of the frequency spacing between both rays which are located symmetrically around the CFO. Finally, we deduce new closed-form estimators for the Doppler spread and also for the CFO. These estimators are accurate and practical in environments with isotropic scattering where the channel power spectrum density (PSD) is symmetric. Simulations are provided to illustrate the advantages of the proposed method and its robustness to the CFO.
Globular Cluster Photometry with the Hubble Space Telescope. VII. Color Gradients and Blue Stragglers in the Central Region of M30 from Wide Field Planetary Camera 2 Observations

We present F555W (V), F439W (B), and F336W (U) photometry of 9507 stars in the central 2′ of the dense, post–core-collapse cluster M30 (NGC 7099) derived from Hubble Space Telescope Wide Field Planetary Camera 2 images. These data are used to study the mix of stellar populations in the central region of the cluster. Forty-eight blue straggler stars are identified; they are found to be strongly concentrated toward the cluster center. The specific frequency of blue stragglers, FBSS ≡ N(BSS)/N(V < VHB + 2), is 0.25 ± 0.05 in the inner region of M30 (r < 20″), significantly higher than the frequency found in other clusters: FBSS = 0.05–0.15. The shape of M30's blue straggler luminosity function resembles the prediction of the collisional formation model, and is inconsistent with the binary merger model of Bailyn & Pinsonneault. An unusually blue star (B = 18.6, B-V = -0.97), possibly a cataclysmic variable based on its color, is found about 1. ″2 from the crowded cluster center; the photometric uncertainty for this star is large, however, because of the presence of a very close neighbor. Bright red giant stars (B < 16.6) appear to be depleted by a factor of 2–3 in the inner r < 10″ relative to fainter giants, subgiants, and main-sequence turnoff stars (95% significance). We confirm that there is a radial gradient in the color of the overall cluster light, going from B-V ∼ 0.82 at r ∼ 1′ to B-V ∼ 0.45 in the central 10″. The central depletion of the bright red giants is responsible for about half of the observed color gradient; the rest of the gradient is caused by the relative underabundance of faint red main-sequence stars near the cluster center (presumably a result of mass segregation). The luminosity function of M30's evolved stars does not match the luminosity function shape derived from standard stellar evolutionary models: the ratio of the number of bright giants to the number of turnoff stars in the cluster is 30% higher than predicted by the model (3.8 σ effect), roughly independent of red giant brightness over the range MV = -2 to +2.
A rooted-trees q-series lifting a one-parameter family of Lie idempotents

We define and study a series indexed by rooted trees and with coefficients in Q(q). We show that it is related to a family of Lie idempotents. We prove that this series is a q-deformation of a more classical series and that some of its coefficients are Carlitz q-Bernoulli numbers.
A capacity estimation technique for JPEG-to-JPEG image watermarking

In JPEG-to-JPEG image watermarking (J2J), the input is a JPEG image file. After watermark embedding, the image is JPEG-compressed such that the output file is also a JPEG file. We use the human visual system (HVS) model to estimate the J2J data hiding capacity of JPEG images, or the maximum number of bits that can be embedded in JPEG-compressed images. A.B. Watson's HVS model (Proc. SPIE Human Vision, Visual Process., and Digital Display IV, p.202-16, 1993) is modified to estimate the just noticeable difference (JND) for DCT coefficients. The number of modifications to DCT coefficients is limited by JND in order to guarantee the invisibility of the watermark. Our capacity estimation method does not assume any specific watermarking method and thus would apply to any watermarking method in the J2J framework.
Analysis of an Immune Algorithm for Protein Structure Prediction

Andrew J. Bennett, Roy L. Johnston, and Eleanor TurpinUniversity of Birmingham, Birmingham, United KingdomE-mail: ajb@tc.bham. ac.ukJun Q. HeAberystwyth University, Aberystwyth, United KingdomKeywords: HP lattice bead model, immune algorithm, population diversity tracking, protein modellingReceived: June 23, 2008The aim of a protein folding simulation is to determine the native state of a protein from its amino acidsequence. In this paper we describe the development and application of an Immune Algorithm (IA) tond the lowest energy conformations for the 2D (square) HP lattice bead protein model. Here we intro-duce a modied chain growth constructor to produce the initial population, where intermediate infeasiblestructures are recorded, thereby reducing the risk of attempting to perform wasteful point mutations duringthe mutation phase. We also investigate various approaches for population diversity tracking, ultimatelyallowing a greater understanding of the progress of the optimization.Povzetek: V clanku je opisan razvoj in izvedba imunskega algoritma (IA) za iskanje najnije energijskestrukture za 2D (kvadratne) HP mreno nanizanega modela proteina.
A Study of Fixed-Length Subset Recombination

While bit based order based and real valued genetic algorithms have been well studied in the literature the xed length subset representation has received rela tively little attention We discuss various crossover operators for this representation and the pitfalls associated with each In particular we explore the ratio of the sub set size to the set size This important ratio is a major contributor to the rate of convergence
Parallel Auxiliary Space AMG Solver for H(div) Problems

In this paper we present a family of scalable preconditioners for matrices arising in the discretization of $H(div)$ problems using the lowest order Raviart--Thomas finite elements. Our approach belongs to the class of “auxiliary space''--based methods and requires only the finite element stiffness matrix plus some minimal additional discretization information about the topology and orientation of mesh entities. We provide a detailed algebraic description of the theory, parallel implementation, and different variants of this parallel auxiliary space divergence solver (ADS) and discuss its relations to the Hiptmair--Xu (HX) auxiliary space decomposition of $H(div)$ [SIAM J. Numer. Anal. , 45 (2007), pp. 2483--2509] and to the auxiliary space Maxwell solver AMS [J. Comput. Math., 27 (2009), pp. 604--623]. An extensive set of numerical experiments demonstrates the robustness and scalability of our implementation on large-scale $H(div)$ problems with large jumps in the material coefficients.
Rapid Fabrication Technique for Interpenetrated ZnO Nanotetrapod Networks for Fast UV Sensors

Two flame-based synthesis methods are presented for fabricating ZnO-nanostructure-based UV photodetectors: burner flame transport synthesis (B-FTS)and crucible flame transport synthesis (C-FTS). B-FTS allows rapid growth of ZnO nanotetrapods and in situ bridging of them into electrical contacts. The photo detector made from interconnected ZnO nanotetrapod networks exhibits fast response/recovery times and a high current ratio under UV illumination.
Exploiting emergent technologies to create systems that meet shifting expectations

Properly combined, today's emerging technologies can potentially lead to systems that adapt quickly and smoothly to ongoing shifts in user requirements and expectations through improving sensing and analytics and utilizing advanced software innovations and service orientation to support dynamic reconfigurations. To produce a system flexible enough to continually meet evolving expectations, various emergent technologies need to be assembled in a coherent fashion based on the capabilities and flexibilities they afford. We outline a framework in which the many activities and choices involved from design to execution and usage of a system can be re-positioned in relation to each other in order to achieve different kinds of flexibility and adaptiveness, taking advantage of data available from sensing mechanisms. An example from the transportation domain is used as an illustration.
Localization Microscopy (SPDM) Reveals Clustered Formations of P-Glycoprotein in a Human Blood-Brain Barrier Model

P-glycoprotein (Pgp; also known as MDR1, ABCB1) is the most important and best studied efflux transporter at the blood-brain barrier (BBB); however, the organization of Pgp is unknown. The aim of this study was to employ the recently developed super-resolution fluorescence microscopy method spectral precision distance microscopy/spectral position determination microscopy (SPDM) to investigate the spatial distribution of Pgp in the luminal plasma membrane of brain capillary endothelial cells. Potential disturbing effects of cell membrane curvatures on the distribution analysis are addressed with computer simulations. Immortalized human cerebral microvascular endothelial cells (hCMEC/D3) served as a model of human BBB. hCMEC/D3 cells were transduced with a Pgp-green fluorescent protein (GFP) fusion protein incorporated in a lentivirus-derived vector. The expression and localization of the Pgp-GFP fusion protein was visualized by SPDM. The limited resolution of SPDM in the z-direction leads to a projection during the imaging process affecting the appeared spatial distribution of fluorescence molecules in the super-resolution images. Therefore, simulations of molecule distributions on differently curved cell membranes were performed and their projected spatial distribution was investigated. Function of the fusion protein was confirmed by FACS analysis after incubation of cells with the fluorescent probe eFluxx-ID Gold in absence and presence of verapamil. More than 112,000 single Pgp-GFP molecules (corresponding to approximately 5,600 Pgp-GFP molecules per cell) were detected by SPDM with an averaged spatial resolution of approximately 40 nm in hCMEC/D3 cells. We found that Pgp-GFP is distributed in clustered formations in hCMEC/D3 cells while the influence of present random cell membrane curvatures can be excluded based on the simulation results. Individual formations are distributed randomly over the cell membrane.
Discrete Fourier transform and cepstrum analysis of vibration events on semi-trailer truck

The aim of this paper is to present a novel techniqe to analyse the vibration signals during transportation in order to give new information to engineers to better understand these physical events. One of the primary sources of damages during transportation is the permanent vibration transmitted from the platform of semi-trailer to the cargo. The nature of this vibration depends on the road conditions and the features of the vehicle. In this study, a 2-axle-truck with a 3-axle-semi-trailer equipped with air spring suspension was observed to analyse the vibration circumstances. The affecting factors during the transportation were the type of the road (motorway, primary road, secondary road, tertiary road), and different vehicle speed levels. The vibration events were measured and registered on the platform of the trailer, then these values were evaluated in MATLAB environment. The presence of the harmonic vibrational components, the stationarity of the mode shapes, the characteristic frequency narrow-bands of the RMS and PSD values were primarily studied. The applied methods that were used are: discrete Fourier transformation, autocorrelation-, cross-correlation functions and cepstrum analysis.