Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Improved Adenosine Deaminase Retroviral Vectors

ABSTRACT A series of adenosine deaminase (ADA) retroviral vectors were designed and constructed with the goal of improved performance over the PA317/LASN vector currently used in clinical trials. First, the bacterial selectable-marker neomycin phosphotransferase (neo) gene was removed to create a “simplified” vector. Second, the Moloney murine leukemia virus long terminal repeat (LTR) promoter used for ADA expression was replaced with either the myeloproliferative sarcoma virus (MPSV) or SL3-3 LTR. Supernatant from each ADA vector was used to transduce ADA-deficient (ADA−) B- and T-cell lines as well as primary peripheral blood mononuclear cells (PBMC) from an ADA− severe combined immunodeficiency patient. Total ADA enzyme activity and ADA activity per integrant in the transduced cells demonstrated that the MPSV LTR splicing vector design provided the highest level of ADA expression per cell. This ADA(MPSV) vector was then tested in packaging cell lines containing either the gibbon ape leukemia virus envelope (PG13 cells), the murine amphotropic envelope (FLYA13 cells), or the feline endogenous virus RD114 envelope (FLYRD18 cells). The results indicate that FLYRD18/ADA(MPSV), a simplified ADA retroviral vector with the MPSV LTR, provides a 17-fold-higher level of ADA expression in human lymphohematopoietic cells than the PA317/LASN vector currently in use.
Subjective comparison of brightness preservation methods for local backlight dimming displays

Local backlight dimming is a popular technology in high quality Liquid Crystal Displays (LCDs). In those displays, the backlight is composed of contributions from several individually adjustable backlight segments, set at different backlight luminance levels in different parts of the screen, according to the luma of the target image displayed on LCD. Typically, transmittance of the liquid crystal cells (pixels) located in the regions with dimmed backlight is increased in order to preserve their relative brightness with respect to the pixels located in the regions with bright backlight. There are different methods for brightness preservation for local backlight dimming displays, producing images with different visual characteristics. In this study, we have implemented, analyzed and evaluated several different approaches for brightness preservation, and conducted a subjective study based on rank ordering to compare the relevant methods on a real-life LCD with a local backlight dimming capability. In general, our results show that locally adapted brightness preservation methods produce more preferred visual outcome than global methods, but dependency on the content is also observed. Based on the results, guidelines for selecting the perceptually preferred brightness preservation method for local backlight dimming displays are outlined.
Internet X.509 Public Key Infrastructure Certificate and Certificate Revocation List (CRL) Profile

This memo profiles the X.509 v3 certificate and X.509 v2 Certificate Revocation List (CRL) for use in the Internet. An overview of this approach and model are provided as an introduction. The X.509 v3 certificate format is described in detail, with additional information regarding the format and semantics of Internet name forms. Standard certificate extensions are described and two Internet-specific extensions are defined. A set of required certificate extensions is specified. The X.509 v2 CRL format is described in detail, and required extensions are defined. An algorithm for X.509 certification path validation is described. An ASN.1 module and examples are provided in the appendices.
Advanced Methylome Analysis after Bisulfite Deep Sequencing: An Example in Arabidopsis

Deep sequencing after bisulfite conversion (BS-Seq) is the method of choice to generate whole genome maps of cytosine methylation at single base-pair resolution. Its application to genomic DNA of Arabidopsis flower bud tissue resulted in the first complete methylome, determining a methylation rate of 6.7% in this tissue. BS-Seq reads were mapped onto an in silico converted reference genome, applying the so-called 3-letter genome method. Here, we present BiSS (Bisufite Sequencing Scorer), a new method applying Smith-Waterman alignment to map bisulfite-converted reads to a reference genome. In addition, we introduce a comprehensive adaptive error estimate that accounts for sequencing errors, erroneous bisulfite conversion and also wrongly mapped reads. The re-analysis of the Arabidopsis methylome data with BiSS mapped substantially more reads to the genome. As a result, it determines the methylation status of an extra 10% of cytosines and estimates the methylation rate to be 7.7%. We validated the results by individual traditional bisulfite sequencing for selected genomic regions. In addition to predicting the methylation status of each cytosine, BiSS also provides an estimate of the methylation degree at each genomic site. Thus, BiSS explores BS-Seq data more extensively and provides more information for downstream analysis.
Digital circuit verification using partially-ordered state models

Many aspects of digital circuit operation can be efficiently verified by simulating circuit operation over "weakened" state values. This technique has long been practiced with logic simulators, using the value X to indicate a signal that could be either 0 or 1. This concept can be formally extended to a wider class of circuit models and signal values, yielding lattice-structured state domains. For more precise modeling of circuit operation, these values can be encoded in binary and hence represented symbolically as ordered binary decision diagrams. The net result is a tool for formal verification that can apply a hybrid of symbolic and partially-ordered evaluation. <<ETX>>
Exploiting Staleness for Approximating Loads on CMPs

Coherence misses are an important factor in limiting the scalability of multi-threaded shared memory applications on chip multiprocessors (CMPs) that are envisaged to contain dozens of cores in the imminent future. This paper proposes a novel approach to tackling this problem by leveraging the growingly important paradigm of approximate computing. Many applications are either tolerant to slight errors in the output or if stringent, have in-built resiliency to tolerate some errors in the execution. The approximate computing paradigm suggests breaking conventional barriers of mandating stringent correctness on the hardware, allowing more flexibility in the performance-power-reliability design space. Taking the multi-threaded applications in the SPLASH-2 benchmark suite, we note that nearly all these applications have such inherent resiliency and/or tolerance to slight errors in the output. Based on this observation, we propose to approximate coherence-related load misses by returning stale values, i.e., the version at the time of the invalidation. We show that returning such values from the invalidated lines already present in d-L1 offers only limited scope for improvement since those lines get evicted fairly soon due to the high pressure on d-L1. Instead, we propose a very small (8 lines) Stale Victim Cache (SVC), to hold such lines upon d-L1 eviction. While this does offer significant improvement, there is the possibility of data getting very stale in such a structure, making it highly sensitive to the choice of what data to keep, and for how long. To address these concerns, we propose to time-out these lines from the SVC to limit their staleness in a mechanism called SVC+TB. We show that SVC+TB provides as much as 28.6% speedup in some SPLASH-2 applications, with an average speedup between 10-15% across the entire suite, becoming comparable to an ideal execution that does not incur coherence misses. Further, the consequent approximations have little impact on the correctness, allowing all of them to complete. There were no errors, because of inherent application resilience, in eleven applications, and the maximum error was at most 0.08% across the entire suite.
Vacuum-Arc Systems for Depositing 'Drop-Free' Coatings onto Inner Surfaces

Two variants of vacuum-arc sources with a consumable cathode, where the axial-to-radial plasma flow transformation is effected by the magnetoelectric system with plasma leaving through an annular magnetic slit (region with a minimum longitudinal magnetic field), are considered. Experimental diagrams of deposition rate distribution for these devices are given. It is shown that the proposed plasma transformation systems can be used for solving the problem of depositing drop-free coatings by the cathodic-arc method onto inner surfaces of hollow items (tube pieces, rings, etc.).
Ductility of Zircaloy Canning Tubes in Relation to Stress Ratio in Biaxial Testing

A biaxial-burst testing machine has been designed in which biaxial plane stress tests can be carried out on tubular material with any stress ratio in the range σ θ :σ z 4:5 to 2:1, where 2:1 implies the closed-end burst test. Unirradiated Zircaloy tubes cold worked 80 percent, recrystallized at 575°C, and characterized by a texture having a basal pole tilt angle of 33 deg were tested at room temperature with various stress ratios, namely, 4:5, 1:1, 5:4, 3:2, and 2:1. In addition, tension and open-end burst tests were carried out in conventional machines. The uniform ductility measured as uniform effective strain displays a minimum at the stress ratio 3:2. It has been found experimentally that the stress ratio for minimum uniform ductility corresponds to deformation under a plane strain loading condition, that is, the stress ratio which gives no change in the tube length. The fracture ductility defined as the effective strain at fracture exhibits a minimum at the stress ratio 5:4. When bulging begins, the applied stress ratio cannot be kept constant, but the stress ratio decreases due to an increased axial stress. This behavior probably explains the observed shift in minimum ductility from the uniform value 3:2 to the fracture value 5:4.
Time-compressing natural and synthetic speech

Phoneme detection is a useful tool to compare the perception of perfectly intelligible speech types. As previous research suggests that perception of fast speech is helped by segmental redundancy, we expected the hyperarticulation of synthetic speech to turn into an advantage at a fast rate. Consequently, the processing advantage of natural over synthetic speech was expected to decrease after time-compression. Secondly, detection times were expected to be slower after moderate time-compression because of the higher processing difficulty of fast speech. However, detection times tended to become shorter in the time-compressed condition. This was attributed to shorter durations of syllables and words. Furthermore, the processing advantage of natural over synthetic speech did not decrease, but rather tended to increase. This may be explained by the lack of a speaking effort pattern in synthetic diphone speech, which makes it rather blurred at faster playback rates.
Intestine-Specific Mttp Deletion Increases the Severity of Experimental Colitis and Leads to Greater Tumor Burden in a Model of Colitis Associated Cancer

Background Gut derived lipid factors have been implicated in systemic injury and inflammation but the precise pathways involved are unknown. In addition, dietary fat intake and obesity are independent risk factors for the development of colorectal cancer. Here we studied the severity of experimental colitis and the development of colitis associated cancer (CAC) in mice with an inducible block in chylomicron secretion and fat malabsorption, following intestine-specific deletion of microsomal triglyceride transfer protein (Mttp-IKO). Methodology/Principal Findings Mttp-IKO mice exhibited more severe injury with ∼90% mortality following dextran sodium sulfate (DSS) induced colitis, compared to <20% in controls. Intestinal permeability was increased in Mttp-IKO mice compared to controls, both at baseline and after DSS administration, in association with increased circulating levels of TNFα. DSS treatment increased colonic mRNA expression of IL-1β and IL-17A as well as inflammasome expression in both genotypes, but the abundance of TNFα was selectively increased in DSS treated Mttp-IKO mice. There was a 2-fold increase in colonic tumor burden in Mttp-IKO mice following azoxymethane/DSS treatment, which was associated with increased colonic inflammation as well as alterations in cytokine expression. To examine the pathways by which alterations in fatty acid abundance might interact with cytokine signaling to regulate colonic epithelial growth, we used primary murine myofibroblasts to demonstrate that palmitate induced expression of amphiregulin and epiregulin and augmented the increase in both of these growth mediators when added to IL-1βor to TNFα. Conclusions These studies demonstrate that Mttp-IKO mice, despite absorbing virtually no dietary fat, exhibit augmented fatty acid dependent signaling that in turn exacerbates colonic injury and increases tumor formation.
Study on the Weld Strength of Fiber Reinforced Polyamide Injection Moldings

Weld lines markedly reduce the strength of FRTP injection moldings, which are often used for structural parts. The effects of weld lines on strength are closely related to molding conditions such as resin temperature, injection rate, injection pressure, etc. They are also related to fiber orientation in FRTP, which results in difficulties in the proper design of moldings. This study aims to clarify the effects of weld lines on the strength of short fiber reinforced Polyamide. Dumbbell type tensile specimens with a weld line were molded under several molding conditions. Furthermore, SEM observations of the fracture surface were carried out and the distributions of fiber orientation were measured. The results were obtained as follows. (1) A “back flow” occurred in the weld region when using the multi-cavity mold and led to the re-orientation of fibers in the flow direction. (2) The specimens did not break at the weld lines on the surface because of the back flow. (3) The distribution of fiber orientation on the fracture surface were influenced by molding conditions. The number of fibers oriented in the flow direction increased and the distribution became more uniform by increasing holding pressure. (4) The weld strength was improved by the back flow up to a maximum of about 140% with efficient holding times.
Individual Investors ’ Behavior : Are Small Investors Different ?

Individual investors’ stock trading has increased over time, thus attracting the attention of academics. The greater availability of information and the development of e-trading platforms are among the main determinants of this phenomenon. The behavioral finance literature has pointed out the dangers related to individual trading, mainly regarding overconfidence. This leads to excessive trading and consequent underperformance due to the effect of commissions on net returns. Since it has be shown that individual characteristics are important in determining the degree of overconfidence of a person, in this paper, we investigate the relationship between age, gender, job type, and income with the number of stock trades made by the clients of a small Italian cooperative bank. The aim of the analysis is to verify if being the client of such a bank affects somehow the trading behavior. In particular, given the emphasis that these cooperative banks put on trust and transparency with their client we could expect different trading attitudes. Alternatively, it could be that the trading behavior is mainly affected by individual characteristics irrespectively of being client of a small or big bank. Using a unique dataset for the three-year period 20052007, we propose bivariate and multivariate analysis using the Negative Binomial model. Our results show that the number of trades depends on individual characteristics, in line with previous research focusing on big banks. It seems therefore that neither the bank size, nor the cooperative nature of the bank is relevant when it comes to the determinants of trading behavior. JEL Classification: D03, G11, C25
mSWI/SNF (BAF) Complexes Are Indispensable for the Neurogenesis and Development of Embryonic Olfactory Epithelium

Neurogenesis is a key developmental event through which neurons are generated from neural stem/progenitor cells. Chromatin remodeling BAF (mSWI/SNF) complexes have been reported to play essential roles in the neurogenesis of the central nervous system. However, whether BAF complexes are required for neuron generation in the olfactory system is unknown. Here, we identified onscBAF and ornBAF complexes, which are specifically present in olfactory neural stem cells (oNSCs) and olfactory receptor neurons (ORNs), respectively. We demonstrated that BAF155 subunit is highly expressed in both oNSCs and ORNs, whereas high expression of BAF170 subunit is observed only in ORNs. We report that conditional deletion of BAF155, a core subunit in both onscBAF and ornBAF complexes, causes impaired proliferation of oNSCs as well as defective maturation and axonogenesis of ORNs in the developing olfactory epithelium (OE), while the high expression of BAF170 is important for maturation of ORNs. Interestingly, in the absence of BAF complexes in BAF155/BAF170 double-conditional knockout mice (dcKO), OE is not specified. Mechanistically, BAF complex is required for normal activation of Pax6-dependent transcriptional activity in stem cells/progenitors of the OE. Our findings unveil a novel mechanism mediated by the mSWI/SNF complex in OE neurogenesis and development.
Functional Connectome of the Striatal Medium Spiny Neuron

Dopamine system disorders ranging from movement disorders to addiction and schizophrenia involve striatal medium spiny neurons (MSNs), yet their functional connectivity has been difficult to determine comprehensively. We generated a mouse with conditional channelrhodopsin-2 expression restricted to medium spiny neurons and assessed the specificity and strength of their intrinsic connections in the striatum and their projections to the globus pallidus and the substantia nigra. In the striatum, medium spiny neurons connected with other MSNs and tonically active cholinergic interneurons, but not with fast-spiking GABA interneurons. In the globus pallidus, medium spiny neurons connected strongly with one class of electrophysiologically identified neurons, but weakly with the other. In the substantia nigra, medium spiny neurons connected strongly with GABA, but not with dopamine neurons. Projections to the globus pallidus showed solely D2-mediated presynaptic inhibition, whereas projections to the substantia nigra showed solely D1-mediated presynaptic facilitation. This optogenetic approach defines the functional connectome of the striatal medium spiny neuron.
Secure Sharing of Partially Homomorphic Encrypted IoT Data

IoT applications often utilize the cloud to store and provide ubiquitous access to collected data. This naturally facilitates data sharing with third-party services and other users, but bears privacy risks, due to data breaches or unauthorized trades with user data. To address these concerns, we present Pilatus, a data protection platform where the cloud stores only encrypted data, yet is still able to process certain queries (e.g., range, sum). More importantly, Pilatus features a novel encrypted data sharing scheme based on re-encryption, with revocation capabilities and in situ key-update. Our solution includes a suite of novel techniques that enable efficient partially homomorphic encryption, decryption, and sharing. We present performance optimizations that render these cryptographic tools practical for mobile platforms. We implement a prototype of Pilatus and evaluate it thoroughly. Our optimizations achieve a performance gain within one order of magnitude compared to state-of-the-art realizations; mobile devices can decrypt hundreds of data points in a few hundred milliseconds. Moreover, we discuss practical considerations through two example mobile applications (Fitbit and Ava) that run Pilatus on real-world data.
Collaborative Recommendation Vulnerability To Focused Bias Injection Attacks

Significant vulnerabilities have recently been identified in collaborative recommender systems. Attackers who cannot be readily distinguished from ordinary users may inject biased data in an attempt to force the system to “adapt” in a manner advantageous to them. Researchers have studied simple attack models and their impact on a system’s population of users. In this paper, we examine attacks that concentrate on a targeted set of users with similar tastes, biasing the system’s responses to these users. Not only are such attacks more pragmatically beneficial for the attacker (since a particular item can be pushed to those most likely to buy it), but as we show, such attacks are also highly effective against both user-based and item-based algorithms. As a result, an attacker can mount such a “segmented” attack with little knowledge of the specific system being targeted and with strong likelihood of success.
Low-Cost Bluetooth Mobile Positioning for Location-based Application

Bluetooth is a promising short-range radio network technology. We present a low cost and easily deployed, scalable infrastructure for indoor location-based computing of mobile devices based on the Bluetooth technology. The system consists of 2 main components, namely the Bluetooth (BT) Sensor System and the Central Navigation System which have been developed using the JDK 1.6. The Bluetooth Sensor System allows mobile devices whose Bluetooth mode is set to discoverable, to be scanned and detected, and they receive customizable text message and other relevant files (maps, sound files, video clips) of their positioning information, e.g. room identity. The positioning information is also sent to the Central Navigation System which in turn displays and updates the navigation map. The system is also used to track the movement of different BT mobile devices within the implemented environment.
A highly parameterizable parallel processor array architecture

In this paper a new class of highly parameterizable coarse-grained reconfigurable architectures called weakly programmable processor arrays is discussed. The main advantages of the proposed architecture template are the possibility of partial and differential reconfiguration and the systematical classification of different architectural parameters which allow to trade-off flexibility and hardware cost. The applicability of our approach is tested in a case study with different interconnect topologies on an FPGA platform. The results show substantial flexibility gains with only marginal additional hardware cost