Miracle-dz/UniFAR-FTUs huggingface dataset:
The WEBFIND tool for finding scientific papers over the worldwide web

Information retrieval in the worldwide web environment poses unique challenges. The worldwide web is a distributed, always changing, and ever expanding collection of documents. These features of the web make it difficult to find information about a specific topic. The most common approaches involve indexing, but indexes introduce centralization and can never be up-to-date. Available information retrieval software has been designed for very different environments with typical tools [Salton and McGill, 1983; Salton and Buckley, 1988] working on an unchanging corpus, with the entire corpus available for direct access. This paper describes WEBFIND, an application that discovers scientific papers made available by their authors on the web. WEBFIND uses a novel approach to performing information retrieval on the worldwide web. The approach is to use a combination of external information sources as a guide for locating where to look for information on the web. The external information sources used by WEBFIND are MELVYL and NETFIND. MELVYL is a University of California library service that includes comprehensive databases of bibliographic records, including a science and engineering database called INSPEC [University of California, 1996]. NETFIND is a white pages service that gives internet host addresses and people’s email addresses [Schwartz and Pu, 1994]. Separately, these services do not provide enough information to locate papers on the web. WEBFIND integrates the information provided by each in order to find a path for discovering on the web the information actually wanted by a user.
Genomic and Proteomic Analysis of Schizaphis graminum Reveals Cyclophilin Proteins Are Involved in the Transmission of Cereal Yellow Dwarf Virus

Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Two cyclophilin B proteins, S28 and S29, were identified previously in populations of Schizaphisgraminum that differed in their ability to transmit the RPV strain of Cereal yellow dwarf virus (CYDV-RPV). The presence of S29 was correlated with F2 genotypes that were efficient virus transmitters. The present study revealed the two proteins were isoforms, and a single amino acid change distinguished S28 and S29. The distribution of the two alleles was determined in 12 F2 genotypes segregating for CYDV-RPV transmission capacity and in 11 genetically independent, field-collected S . graminum biotypes. Transmission efficiency for CYDV-RPV was determined in all genotypes and biotypes. The S29 isoform was present in all genotypes or biotypes that efficiently transmit CYDV-RPV and more specifically in genotypes that efficiently transport virus across the hindgut. We confirmed a direct interaction between CYDV-RPV and both S28 and S29 using purified virus and bacterially expressed, his-tagged S28 and S29 proteins. Importantly, S29 failed to interact with a closely related virus that is transported across the aphid midgut. We tested for in vivo interactions using an aphid-virus co-immunoprecipitation strategy coupled with a bottom-up LC-MS/MS analysis using a Q Exactive mass spectrometer. This analysis enabled us to identify a third cyclophilin protein, cyclophilin A, interacting directly or in complex with purified CYDV-RPV. Taken together, these data provide evidence that both cyclophilin A and B interact with CYDV-RPV, and these interactions may be important but not sufficient to mediate virus transport from the hindgut lumen into the hemocoel.
Portable mapping of openMP to multicore embedded systems using MCA APIs

Multicore embedded systems are being widely used in telecommunication systems, robotics, medical applications and more.While they offer a high-performance with low-power solution, programming in an efficient way is still a challenge. In order to exploit the capabilities that the hardware offers, software developers are expected to handle many of the low-level details of programming including utilizing DMA, ensuring cache coherency, and inserting synchronization primitives explicitly. The state-of-the-art involves solutions where the software toolchain is too vendor-specific thus tying the software to a particular hardware leaving no room-for portability. In this paper we present a runtime system to explore mapping a high-level programming model, OpenMP, on to multicore embedded systems. A key feature of our scheme is that unlike the existing approaches that largely rely on POSIX threads, our approach leverages the Multicore Association (MCA) APIs as an OpenMP translation layer. The MCA APIs is a set of low-level APIs handling resource management, inter-process communications and task scheduling for multicore embedded systems. By deploying the MCA APIs, our runtime is able to effectively capture the characteristics of multicore embedded systems compared with the POSIX threads. Furthermore, the MCA layer enables our runtime implementation to be portable across various architectures. Thus programmers only need to maintain a single OpenMP code base which is compatible by various compilers, while on the other hand, the code is portable across different possible types of platforms. We have evaluated our runtime system using several embedded benchmarks. The experiments demonstrate promising and competitive performance compared to the native approach for the platform.
Towards Open-Universe Image Parsing with Broad Coverage

One of the main goals of computer vision is to develop algorithms that allow the computer to interpret an image not as a pattern of colors but as the semantic relationships that make up a real world three-dimensional scene. In this dissertation, I present a system for image parsing, or labeling the regions of an image with their semantic categories, as a means of scene understanding. Most existing image parsing systems use a fixed set of a few hundred hand-labeled images as examples from which they learn how to label image regions, but our world cannot be adequately described with only a few hundred images. A new breed of "open universe" datasets have recently started to emerge. These datasets not only have more images but are constantly expanding, with new images and labels assigned by users on the web. Here I present a system that is able to both learn from these larger datasets of labeled images and scale as the dataset expands, thus greatly broadening the number of class labels that can correctly be identified in an image. Throughout this work I employ a retrieval-based methodology: I first retrieve images similar to the query and then match image regions from this set of retrieved images. My system can assign to each image region multiple forms of meaning: for example, it can simultaneously label the wing of a crow as an animal, crow, wing, and feather. I also broaden the label coverage by using both region and detector based similarity measures to effectively match a broad range to label types. This work shows the power of retrieval-based systems and the importance of having a diverse set of image cues and interpretations.
The contribution of real-time mirror reflections of motor actions on virtual body ownership in an immersive virtual environment

This paper reports an experiment that investigated people's body ownership of an avatar that was observed in a virtual mirror. Twenty subjects were recruited in a within-groups study where 10 first experienced a virtual character that synchronously reflected their upper-body movements as seen in a virtual mirror, and then an asynchronous condition where the mirror avatar displayed prerecorded actions, unrelated to those of the participant. The other 10 subjects experienced the conditions in the opposite order. In both conditions the participant could carry out actions that led to elevation above ground level, as seen from their first person perspective and correspondingly in the mirror. A rotating virtual fan eventually descended to 2 m above the ground. The hypothesis was that synchronous mirror reflection would result in higher subjective sense of ownership. A questionnaire analysis showed that the body ownership illusion was significantly greater for the synchronous than asynchronous condition. Additionally participants in the synchronous condition avoided collision with the descending fan significantly more often than those in the asynchronous condition. The results of this experiment are put into context within similar experiments on multisensory correlation and body ownership within cognitive neuroscience.
Concurrency patterns for easier robotic coordination

Software design patterns are reusable solutions to commonly occurring problems in software development. Growing complexity of robotics software increases the importance of applying proper software engineering principles and methods such as design patterns to robotics. Concurrency design patterns are particularly interesting to robotics because robots often have many components that can operate in parallel. However, there has not yet been any established set of reusable concurrency design patterns for robotics. For this purpose, we choose six known concurrency patterns - Future, Periodic timer, Invoke later, Active object, Cooperative cancellation, and Guarded suspension. We demonstrate how these patterns could be used for solving common robotic coordination tasks. We also discuss advantages and disadvantages of the patterns and how existing robotics programming frameworks can support them.
Fault-Tolerance Through Scheduling of Aperiodic Tasks in Hard Real-Time Multiprocessor Systems

Real time systems are being increasingly used in several applications which are time critical in nature. Fault tolerance is an important requirement of such systems, due to the catastrophic consequences of not tolerating faults. We study a scheme that provides fault tolerance through scheduling in real time multiprocessor systems. We schedule multiple copies of dynamic, aperiodic, nonpreemptive tasks in the system, and use two techniques that we call deallocation and overloading to achieve high acceptance ratio (percentage of arriving tasks scheduled by the system). The paper compares the performance of our scheme with that of other fault tolerant scheduling schemes, and determines how much each of deallocation and overloading affects the acceptance ratio of tasks. The paper also provides a technique that can help real time system designers determine the number of processors required to provide fault tolerance in dynamic systems. Lastly, a formal model is developed for the analysis of systems with uniform tasks.
Transient Replication of Hepatitis C Virus Sub-Genomic RNA in Murine Cell Lines Is Enabled by miR-122 and Varies with Cell Passage

Hepatitis C Virus (HCV) is a serious global health problem, infecting almost 3% of the world’s population. The lack of model systems for studying this virus limit research options in vaccine and therapeutic development, as well as for studying the pathogenesis of chronic HCV infection. Herein we make use of the liver-specific microRNA miR-122 to render mouse cell lines permissive to HCV replication in an attempt to develop additional model systems for the identification of new features of the virus and its life cycle. We have determined that some wild-type and knockout mouse cell lines – NCoA6 and PKR knockout embryonic fibroblasts – can be rendered permissive to transient HCV sub-genomic RNA replication upon addition of miR-122, but we did not observe replication of full-length HCV RNA in these cells. However, other wild-type and knockout cell lines cannot be rendered permissive to HCV replication by addition of miR-122, and in fact, different NCoA6 and PKR knockout cell line passages and isolates from the same mice demonstrated varying permissiveness phenotypes and eventually complete loss of permissiveness. When we tested knockdown of NCoA6 and PKR in Huh7.5 cells, we saw no substantial impact in sub-genomic HCV replication, which we would expect if these genes were inhibitory to the virus’ life cycle. This leads us to conclude that along with the influence of specific gene knockouts there are additional factors within the cell lines that affect their permissiveness for HCV replication; we suggest that these may be epigenetically regulated, or modulated by cell line immortalization and transformation.
Spectropolarimetry of 3CR 68.1: A Highly Inclined Quasar

We present Keck spectropolarimetry of the highly polarized radio-loud quasar 3CR 68.1 (z = 1.228, V = 19). The polarization increases from 5% in the red (4000 Å rest frame) to greater than 10% in the blue (1900 Å rest frame). The broad emission lines are polarized the same as the continuum, which shows that 3CR 68.1 is not a blazar, as it has sometimes been regarded in the past. We also present measurements of the emission lines and a strong, blueshifted, associated absorption line system as well as a detection at the emission-line redshift of Ca II K absorption, presumably from stars in the host galaxy. Neither a blazar nor a partially obscured radio-quiet QSO, 3CR 68.1 belongs to an observationally rare class of highly polarized quasars. Taking into account the other unusual properties of 3CR 68.1, such as its extremely red spectral energy distribution and its extreme lobe dominance, we explain our spectropolarimetric results in terms of unified models. We argue that we have a dusty, highly inclined view of 3CR 68.1, with reddened scattered (polarized) quasar light diluted by even more dust-reddened quasar light reaching us directly from the nucleus.
Sensitivity of human pleural mesothelioma to oncolytic measles virus depends on defects of the type I interferon response

Attenuated measles virus (MV) is currently being evaluated as an oncolytic virus in clinical trials and could represent a new therapeutic approach for malignant pleural mesothelioma (MPM). Herein, we screened the sensitivity to MV infection and replication of twenty-two human MPM cell lines and some healthy primary cells. We show that MV replicates in fifteen of the twenty-two MPM cell lines. Despite overexpression of CD46 by a majority of MPM cell lines compared to healthy cells, we found that the sensitivity to MV replication did not correlate with this overexpression. We then evaluated the antiviral type I interferon (IFN) responses of MPM cell lines and healthy cells. We found that healthy cells and the seven insensitive MPM cell lines developed a type I IFN response in presence of the virus, thereby inhibiting replication. In contrast, eleven of the fifteen sensitive MPM cell lines were unable to develop a complete type I IFN response in presence of MV. Finally, we show that addition of type I IFN onto MV sensitive tumor cell lines inhibits replication. These results demonstrate that defects in type I IFN response are frequent in MPM and that MV takes advantage of these defects to exert oncolytic activity.
The Way Art Works : Insights for Community Development

How can we articulate what art does in rural community development? Drawing on a one-year experimental study combining ethnography and artistic fieldwork on the Holy Island of Lindisfarne in the north east of England (referred to hereafter as Holy Island), we explore the ways art works in the context of neo-endogenous forms of community development. We propose that the art experience is catalytic to processes of community engagement, personal and collective reflection, revealing relationships (or even disconnects) between the community as well as between the community and the natural environment. Such reflexive processes are characteristic within ideal frames of rural development that place the community at the heart of the development decision making. We argue therefore that art as a process within a community development strategy reveals the complexity of rural community or in other words ‘reads’ the community where development initiatives are being established. Community-led or ‘bottom-up’ perspectives are commonplace in rural development processes, well discussed within ideal models such as neo-endogenous or networked rural development (Lowe et al. 1998; Shucksmith 2000). Similarly, the role of arts is increasingly now promoted as a vehicle to rural development (Balfour and Alter 2015; Markusen 2006; Bell and Jayne 2010). However, this usually refers to understanding arts in positive or economic terms (Gibson 2010a, 2010b; Arts Council England 2005). This literature does not account for art as a practice on its own terms (an example from arts practice: Crawshaw and Bowman, 2007). Surprisingly perhaps, while these debates draw on theoretical discussions within economic and social geography, planning and rural studies, there is very little intersection with the field of art studies. This chapter aims to fill this gap, evidenced by our interdisciplinary collaboration across art and rural studies backgrounds.We draw inspiration on the relational perspectives of art practice from art studies. As proposed by Hennion and Grenier (2000: 351) instead of looking at works of art, we rather shape our study to trace the way artworks work. To contribute a nuanced articulation of the effects mobilised by art in rural development processes, through exploratory ethnographic research, we trace associations at the micro level: we are concerned with what art does in practice. To discuss the relational nature of communities, we draw on rural studies and in particular the framework for ‘reading communities’ suggested by Ruth Liepins (2000a, 2000b). In tracing associations, we notice how art impacts on community meanings, practices, and spaces and structures amidst complex relational networks. As such we make a specific contribution to the understanding of art in community development: through tracing the micro relationships of art in rural development, we propose art as a ‘relational reading’ of the community.
Amplified voltammetric detection of glycoproteins using 4-mercaptophenylboronic acid/biotin-modified multifunctional gold nanoparticles as labels

Ultrasensitive detection of protein biomarkers is essential for early diagnosis and therapy of many diseases. Glycoproteins, differing from other types of proteins, contain carbohydrate moieties in the oligosaccharide chains. Boronic acid can form boronate ester covalent bonds with diol-containing species. Herein, we present a sensitive and cost-effective electrochemical method for glycoprotein detection using 4-mercaptophenylboronic acid (MBA)/biotin-modified gold nanoparticles (AuNPs) (MBA-biotin-AuNPs) as labels. To demonstrate the feasibility and sensitivity of this method, recombinant human erythropoietin (rHuEPO) was tested as a model analyte. Specifically, rHuEPO was captured by the anti-rHuEPO aptamer-covered electrode and then derivatized with MBA-biotin-AuNPs through the boronic acid–carbohydrate interaction. The MBA-biotin-AuNPs facilitated the attachment of streptavidin-conjugated alkaline phosphatase for the production of electroactive p-aminophenol from p-aminophenyl phosphate substrate. A detection limit of 8 fmol L−1 for rHuEPO detection was achieved. Other glycosylated and non-glycosylated proteins, such as horseradish peroxidase, prostate specific antigen, metallothionein, streptavidin, and thrombin showed no interference in the detection assay.
Network infrastructure at the crossroads the emergence of smart cities

Although leading mobile network operators (MNOs) enjoy a healthy profit margin, revenues are stagnating while the size of the investment requirements keeps increasing at a rapid pace. In response to the current situation, operators take different directions towards the future. Enter the up-and-coming R&D area of “smart cities” which aims at fostering sustainable urban development through the ubiquitous interweaving of real-world infrastructure with online and city services. This emergence of smart cities coincides with the search for new directions by leading MNOs. This paper adds to the discussion on new directions for operators and argues that the emergence of smart cities can create a synergistic environment for network infrastructure providers in which they can have a competitive advantage.
The Neural Substrates and Timing of Top–Down Processes during Coarse-to-Fine Categorization of Visual Scenes: A Combined fMRI and ERP Study

Abstract Spatial frequencies in an image influence visual analysis across a distributed, hierarchically organized brain network. Low spatial frequency (LSF) information may rapidly reach high-order areas to allow an initial coarse parsing of the visual scene, which could then be “retroinjected” through feedback into lower level visual areas to guide finer analysis on the basis of high spatial frequency (HSF). To test this “coarse-to-fine” processing scheme and to identify its neural substrates in the human brain, we presented sequences of two spatial-frequency-filtered scenes in rapid succession (LSF followed by HSF or vice versa) during fMRI and ERPs in the same participants. We show that for low-to-high sequences (but not for high-to-low sequences), LSF produces a first increase of activity in prefrontal and temporo-parietal areas, followed by enhanced responses to HSF in primary visual cortex. This pattern is consistent with retroactive influences on low-level areas that process HSF after initial activation of higher order areas by LSF.
Rotation Compensated Human Iris Matching

By introducing rotation compensation into a human iris matching system, improved matching is demonstrated while reducing both the computational complexity and storage requirements. This is achieved by using Fourier domain cross correlation to estimate the relative rotation of two iris images. This eliminates the need to store and compare codes from multiple orientations of the same image. Instead, only one code is stored, plus the Discrete Fourier Transform of an annular segment derived from the iris. In addition, the cross correlation function can be used as a biometric either on its own or in combination with other iris codes. A Peak to Sidelobe Ratio metric is used to discriminate matching and non-matching correlation functions. Used to preselect irises for matching, the method greatly reduces feature-vector comparisons. Alternatively a cascaded classifier approach can be used, with the correlation stage tuned to make no false rejections, followed by a Hamming distance metric on a standard iris code. The performance and robustness of the new technique are tested on the CASIA iris image database synthetically altered to generate rotated, noisy and randomly occluded normalized iris images. Improved matching performance is achieved with a 21 times reduction in matching time.