Miracle-dz/UniFAR-FTUs huggingface dataset:
ITK: enabling reproducible research and open science

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.
Fighting Phishing the Information-Centric Way

Recent research efforts have highlighted the role of information as key target future network architectures. These so-called information centric networks base their operation on the information itself, rather than on other aspects or entities of the architecture, such as location, host, or user identity. In this paper we apply this approach at the application layer of the current Internet in order to mitigate a significant threat: phishing attacks. We designed a mechanism capable of detecting phishing Web pages based on the information that the user perceives while browsing, i.e, the mechanism detects attacks based on the browser's graphical output, rather than on the code of the Web page. We implemented this mechanism in the form of a browser extension and we evaluated it using real data from a publicly available database of phishing URLs. Our extension, which is not affected by the location, popularity, or implementation of a Web page, detected 81% of the phishing attempts.
Query Expansion using Association Matrix for Improved Information Retrieval Performance

We propose a novel query expansion technique that employs association matrix to solve the problem of false positives: retrieving irrelevant documents, while missing actually required documents in a typical search engine environment. We present underlying infrastructure of our design, together with comparisons with existing query expansion algorithms and University of North Texas (UNT) Google search engine. Our results yield 14.3% improved Information Retrieval (IR) performance with more effective and precise retrievals than a conventional (non-expanded) search engine.
Mechanism of action of factor D of the alternative complement pathway

Factor D (C3 proactivator convertase) of human serum has been shown to be absolutely necessary for alternative pathway function, for activation of the C3/C5 convertase of that pathway and not to be a subunit of this enzyme. Factor D was found to be present in human plasma in active form only, at a concentration of 2 microgram/ml, and not to be controlled by plasma protease inhibitors or by spontaneous decay. Unlike trypsin, factor D cleaves and activates factor B only when it is in Mg++-dependent complex with C3b, has no esterolytic activity, and is unable to cleave the B chain of insulin. The alleged functional and antigenic relationship of factor D to alpha-thrombin could not be verified. The results of this study led to the description of the mechanism of action of factor D in terms of the cryptic site hypothesis.
Deep H-Band Galaxy Counts and Half-Light Radii from Hubble Space Telescope/NICMOS Parallel Observations

We present deep galaxy counts and half-light radii from F160W (λc=1.6 μm) images obtained with the Near-Infrared Camera and Multiobject Spectrograph on the Hubble Space Telescope. Nearly 9 arcmin2 have been imaged with camera 3, with 3 σ depths ranging from H=24.3 to 25.5 in a 0. ″6 diameter aperture. The slope of the counts fainter than H=20 is 0.31, and the integrated surface density to H≤24.75 is 4×105 galaxies deg-2. The half-light radii of the galaxies decline steeply with apparent magnitude. At H=24, we are limited by both the delivered FWHM and the detection threshold of the images.
Pseudorandom generators, measure theory, and natural proofs

We prove that if strong pseudorandom number generators exist, then the class of languages that have polynomial-sized circuits (P/poly) is not measurable within exponential time, in terms of the resource-bounded measure theory of Lutz. We prove our result by showing that if P/poly has measure zero in exponential time, then there is a natural proof against P/poly, in the terminology of Razborov and Rudich (1994). We also provide a partial converse of this result.
On predicting visual popping in dynamic scenes

Popping is a major source of visual artifacts in dynamic scenes. To alleviate or avoid it, usually some temporal smoothing scheme is employed or levels of detail are chosen conservatively based on geometric deviation measures. In this paper, we consider the actual perceptibility of popping artifacts and its prediction. We first discuss several issues affecting popping perception, pointing out its complexity. Introducing some simplifying assumptions, we then present a practical perceptually-motivated predictor for popping. It makes heavy use of a spatio-velocity color vision model and aggregates the model output in a novel and useful way. We demonstrate the predictor's application to concrete examples, and discuss a conducted user study which indicates the validity of our approach.
Analysis of Core Housekeeping and Virulence Genes Reveals Cryptic Lineages of Clostridium perfringens That Are Associated With Distinct Disease Presentations

Clostridium perfringens is an important human and animal pathogen that causes a number of diseases that vary in their etiology and severity. Differences between strains regarding toxin gene composition and toxin production partly explain why some strains cause radically different diseases than others. However, they do not provide a complete explanation. The purpose of this study was to determine if there is a phylogenetic component that explains the variance in C. perfringens strain virulence by assessing patterns of genetic polymorphism in genes (colA gyrA, plc, pfoS, and rplL) that form part of the core genome in 248 type A strains. We found that purifying selection plays a central role in shaping the patterns of nucleotide substitution and polymorphism in both housekeeping and virulence genes. In contrast, recombination was found to be a significant factor only for the virulence genes plc and colA and the housekeeping gene gyrA. Finally, we found that the strains grouped into five distinct evolutionary lineages that show evidence of host adaptation and the early stages of speciation. The discovery of these previously unknown lineages and their association with distinct disease presentations carries important implications for human and veterinary clostridial disease epidemiology and provides important insights into the pathways through which virulence has evolved in C. perfringens.
Design and implementation of a non-proprietary campus energy management and control system (EMCS)

The energy management and control system (EMCS) used at the University of Nebraska-Lincoln (UNL) is unique in that system hardware and software has been developed primarily in-house. UNL has a successful track record with this approach stretching back more than twenty years. This paper presents an industry experience report describing the high-level design and development of the latest version of this EMCS. This system is now being deployed on campus. We discuss aspects of our EMCS that enhance usability, fault tolerance, and security. Our system is unique in that it was primarily developed using non-proprietary, open-source software building blocks and software construction tools. This approach provides a framework for potential collaboration with others who are interested in expanding this system beyond UNL
Human Papillomavirus Type 16 E6 Promotes Retinoblastoma Protein Phosphorylation and Cell Cycle Progression

ABSTRACT We show that E6 proteins from benign human papillomavirus type 1 (HPV1) and oncogenic HPV16 have the ability to alter the regulation of the G1/S transition of the cell cycle in primary human fibroblasts. Overexpression of both viral proteins induces cellular proliferation, retinoblastoma (pRb) phosphorylation, and accumulation of products of genes that are negatively regulated by pRb, such as p16INK4a, CDC2, E2F-1, and cyclin A. Hyperphosphorylated forms of pRb are present in E6-expressing cells even in the presence of ectopic levels of p16INK4a. The E6 proteins strongly increased the cyclin A/cyclin-dependent kinase 2 (CDK2) activity, which is involved in pRb phosphorylation. In addition, mRNA and protein levels of the CDK2 inhibitor p21WAF1/CIP1 were strongly down-regulated in cells expressing E6 proteins. The down-regulation of the p21WAF1/CIP1 gene appears to be independent of p53 inactivation, since HPV1 E6 and an HPV16 E6 mutant unable to target p53 were fully competent in decreasing p21WAF1/CIP1 levels. E6 from HPV1 and HPV16 also enabled cells to overcome the G1 arrest imposed by oncogenic ras. Immunofluorescence staining of cells coexpressing ras and E6 from either HPV16 or HPV1 revealed that antiproliferative (p16INK4a) and proliferative (Ki67) markers were coexpressed in the same cells. Together, these data underline a novel activity of E6 that is not mediated by inactivation of p53.
Digital Multi-Focusing From a Single Photograph Taken With an Uncalibrated Conventional Camera

The demand to restore all-in-focus images from defocused images and produce photographs focused at different depths is emerging in more and more cases, such as low-end hand-held cameras and surveillance cameras. In this paper, we manage to solve this challenging multi-focusing problem with a single image taken with an uncalibrated conventional camera. Different from all existing multi-focusing approaches, our method does not need to include a deconvolution process, which is quite time-consuming and will cause ringing artifacts in the focused region and low depth-of-field. This paper proposes a novel systematic approach to realize multi-focusing from a single photograph. First of all, with the optical explanation for the local smooth assumption, we present a new point-to-point defocus model. Next, the blur map of the input image, which reflects the amount of defocus blur at each pixel in the image, is estimated by two steps. 1) With the sharp edge prior, a rough blur map is obtained by estimating the blur amount at the edge regions. 2) The guided image filter is applied to propagate the blur value from the edge regions to the whole image by which a refined blur map is obtained. Thus far, we can restore the all-in-focus photograph from a defocused input. To further produce photographs focused at different depths, the depth map from the blur map must be derived. To eliminate the ambiguity over the focal plane, user interaction is introduced and a binary graph cut algorithm is used. So we introduce user interaction and use a binary graph cut algorithm to eliminate the ambiguity over the focal plane. Coupled with the camera parameters, this approach produces images focused at different depths. The performance of this new multi-focusing algorithm is evaluated both objectively and subjectively by various test images. Both results demonstrate that this algorithm produces high quality depth maps and multi-focusing results, outperforming the previous approaches.
What sound symbolism can and cannot do: Testing the iconicity of ideophones from five languages

Abstract:Sound symbolism is a phenomenon with broad relevance to the study of language and mind, but there has been a disconnect between its investigations in linguistics and psychology. This study tests the sound-symbolic potential of ideophones—words described as iconic—in an experimental task that improves over prior work in terms of ecological validity and experimental control. We presented 203 ideophones from five languages to eighty-two Dutch listeners in a binary-choice task, in four versions: original recording, full diphone resynthesis, segments-only resynthesis, and prosody-only resynthesis. Listeners guessed the meaning of all four versions above chance, confirming the iconicity of ideophones and showing the viability of speech synthesis as a way of controlling for segmental and suprasegmental properties in experimental studies of sound symbolism. The success rate was more modest than prior studies using pseudowords like bouba/kiki, implying that assumptions based on such words cannot simply be transferred to natural languages. Prosody and segments together drive the effect: neither alone is sufficient, showing that segments and prosody work together as cues supporting iconic interpretations. The findings cast doubt on attempts to ascribe iconic meanings to segments alone and support a view of ideophones as words that combine arbitrariness and iconicity. We discuss the implications for theory and methods in the empirical study of sound symbolism and iconicity.
Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons

The Drosophila non-long terminal repeat (non-LTR) retrotransposons TART and HeT-A specifically retrotranspose to chromosome ends to maintain Drosophila telomeric DNA. Relatively little is known, though, about the regulation of their expression and their retrotransposition to telomeres. We have used rapid amplification of cDNA ends (RACE) to identify multiple transcription initiation and polyadenylation sites for sense and antisense transcripts of three subfamilies of TART elements in Drosophila melanogaster. These results are consistent with the production of an array of TART transcripts. In contrast to other Drosophila non-LTR elements, a major initiation site for sense transcripts was mapped near the 3′ end of the TART 5′-untranslated region (5′-UTR), rather than at the start of the 5′-UTR. A sequence overlapping this sense start site contains a good match to an initiator consensus for the transcription start sites of Drosophila LTR retrotransposons. Interestingly, analysis of 5′ RACE products for antisense transcripts and the GenBank EST database revealed that TART antisense transcripts contain multiple introns. Our results highlight differences between transcription of TART and of other Drosophila non-LTR elements and they provide a foundation for testing the relationship between exceptional aspects of TART transcription and TART's specialized role at telomeres.
Ecology of Cognitive Radio Ad Hoc Networks

The success of cognitive radio networks lies on whether secondary users (SUs) follow the sharing rule that do not disturb the existing primary users (PUs). However, SUs may not behave in the desirable way as long as their own transmissions are successful. In this case, PUs may suffer heavy interference and system is deteriorated. Via evolutionary game modeling, this letter studies the dynamics of cognitive radio ad hoc networks against misbehaved SUs due to sensing errors or selfish nature. Our study suggests that cognitive radio network is fragile to the misbehaved SUs if incentives for the successful secondary transmissions are high. Consequently, all other SUs evolve to dishonest behaviors leading to network collapse.
Anomalous Price Behavior Following Earnings Surprises: Does Representativeness Cause Overreaction?

Behavioral Finance aims to explain empirical anomalies by introducing investor psychology as a determinant of asset pricing. Two kinds of anomalies, namely underreaction and overreaction, have been established by an impressive record of empirical work. While underreaction defines a slow adjustment of prices to corporate events or announcements, overreaction deals with extreme stock price reactions to previous information or past performance. This study investigates current and past earnings surprises for listed US companies over the period 1983-1999. It provides evidence that investors exhibit long-term overreaction to past, highly unexpected, earnings surprises. Investors tend to overestimate (underestimate) future earnings after extreme positive (negative) earnings surprises. As, on average, these extreme past surprises are not confirmed by subsequent earnings figures, they are followed by a correction of the initial overreaction at the date of the subsequent earnings announcement. Moreover, the longer the similar earnings surprise series, the higher the subsequent correction, suggesting that representativeness may cause this overreaction phenomenon.
Study and comparison of non linear and LPV control approaches for vehicle stability control

This paper proposes a study and a comparison between two efficient and relatively recent vehicle control dynamics strategies, namely, the non linear Flatness control strategy and the LPV/H∞ control strategy. The first one concerns a controller based on the differential algebraic flatness of non linear systems and an algebraic non linear estimation applied to commercial vehicles. The second one is a LPV/H∞ (Linear Varying Parameter with the H∞ norm) control using a stability monitoring system to achieve the vehicle dynamics control objective. These two strategies use Active Steering and Electro-Mechanical Braking actuators and aim at improving the vehicle stability and steerability by designing a multivariable controller that acts simultaneously on the lateral and longitudinal dynamics of the car. Simulations are performed on a complex nonlinear full vehicle model, the same driving scenario is applied for the two control strategies. The model parameters are those of a Renault Mégane Coupé, obtained by identification with real data. Promising simulations results are obtained. Comparison between the two proposed strategies and the uncontrolled vehicle show the reliability and the robustness of the proposed solutions, even if one is developed within the linear control framework while the other one is a non linear control approach.
DESIGN OF NORMALIZED SUBBAND ADAPTIVE FILTER FOR ACOUSTIC ECHO CANCELLATION

In hands-free telephones and teleconferencing systems, acoustic echo cancellers are required, which are often implemented by adaptive filters. In these applications, the speech input signal of the adaptive filter is highly correlated and the impulse response of the echo path is very long. These characteristics will slow down the convergence rate of the adaptive filter if the well-known normalized leastmeansquare (NLMS) algorithm is used. The normalized subband adaptive filter (NSAF) offers a good solution to this problem because of its decorrelating property. This paper proposes a VHDL implementation of normalized subband adaptive filter structure(NSAF) adaptive algorithm.the experiment result shows that the power consumed by subband is lower than that of full band. Index Terms — Acoustic echo canceller, adaptive combination, normalized subband adaptive filter (NSAF), hands-free telephone, teleconferencing system Cascade intergrator-comb filter (CIC).
A Secure and Efficient Data Sharing Framework with Delegated Capabilities in Hybrid Cloud

Hybrid cloud is a widely used cloud architecture in large companies that can outsource data to the public cloud, while still supporting various clients like mobile devices. However, such public cloud data outsourcing raises serious security concerns, such as how to preserve data confidentiality and how to regulate access policies to the data stored in public cloud. To address this issue, we design a hybrid cloud architecture that supports data sharing securely and efficiently, even with resource-limited devices, where private cloud serves as a gateway between the public cloud and the data user. Under such architecture, we propose an improved construction of attribute-based encryption that has the capability of delegating encryption/decryption computation, which achieves flexible access control in the cloud and privacy-preserving in datautilization even with mobile devices. Extensive experiments show the scheme can further decrease the computational cost and space overhead at the user side, which is quite efficient for the user with limited mobile devices. In the process of delegating most of the encryption/decryption computation to private cloud, the user can not disclose any information to the private cloud. We also consider the communication securitythat once frequent attribute revocation happens, our scheme is able to resist some attacks between private cloud and data user by employing anonymous key agreement.
First approaches towards modelling glacial hazards in the Mount Cook region of New Zealand's Southern Alps

Abstract. Flood and mass movements originating from glacial environments are particularly devastating in populated mountain regions of the world, but in the remote Mount Cook region of New Zealand's Southern Alps minimal attention has been given to these processes. Glacial environments are characterized by high mass turnover and combined with changing climatic conditions, potential problems and process interactions can evolve rapidly. Remote sensing based terrain mapping, geographic information systems and flow path modelling are integrated here to explore the extent of ice avalanche, debris flow and lake flood hazard potential in the Mount Cook region. Numerous proglacial lakes have formed during recent decades, but well vegetated, low gradient outlet areas suggest catastrophic dam failure and flooding is unlikely. However, potential impacts from incoming mass movements of ice, debris or rock could lead to dam overtopping, particularly where lakes are forming directly beneath steep slopes. Physically based numerical modeling with RAMMS was introduced for local scale analyses of rock avalanche events, and was shown to be a useful tool for establishing accurate flow path dynamics and estimating potential event magnitudes. Potential debris flows originating from steep moraine and talus slopes can reach road and built infrastructure when worst-case runout distances are considered, while potential effects from ice avalanches are limited to walking tracks and alpine huts located in close proximity to initiation zones of steep ice. Further local scale studies of these processes are required, leading towards a full hazard assessment, and changing glacial conditions over coming decades will necessitate ongoing monitoring and reassessment of initiation zones and potential impacts.