Miracle-dz/UniFAR-FTUs huggingface dataset:
Cholangiocarcinoma-associated genes identified by integrative analysis of gene expression data

Cholangiocarcinoma (CCA) is characterized by delayed diagnosis and poor survival rate. Research efforts have focused on novel diagnostic technologies for this type of cancer. Transcriptomic microarray technology is a useful research strategy for investigating the molecular properties of CCA. The objective of the present study was to identify candidate biomarkers with high potential for clinical application in CCA using a meta-analysis-based approach. Gene expression profiles of CCA were downloaded from the Gene Expression Omnibus database for integrated analysis. All differentially expressed genes (DEGs) were analyzed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Protein-protein interaction (PPI) networks were further constructed, hub proteins were identified and functional modules were extracted. Following integrated analysis of the seven eligible datasets (428 cases and 46 controls), a set of 1,080 DEGs was identified, including 710 upregulated and 370 downregulated genes. Functional enrichment analysis demonstrated that ‘chromosome organization’ was a significantly enriched GO term in the biological process category. ‘DNA replication’, ‘influenza A’, and ‘lysosome’ were the top three significantly enriched KEGG pathways. Furthermore, PPI network analysis indicated that the significant hub proteins were histone deacetylase 1, cullin-associated NEDD8-dissociated protein 1, ubiquitin D, early growth response protein 1 and glycogen synthase kinase 3β. The majority of these proteins are involved in CCA. These results provided a set of targets that may help researchers to clarify further the underlying mechanisms of CCA tumorigenesis.
Experimental evaluation and characterization of the magnets wireless backbone

High-speed wireless backbones have the potential to replace or complement wired connections. This paper provides a comprehensive network and transport layer performance evaluation of the Magnets WiFi backbone. The backbone, deployed in a metropolitan area of Berlin, consists of six 108 Mbps capable links using directional antennas and spans over 2.3 km. Built with off-the-shelf hardware, it features mixed 802.11a/g technology, link distances between 330 m and 930 m and support for two enhanced MAC/PHY layer modes at the access points (AP) to improve their performance. These unique characteristics provide a challenging environment to investigate the impact of a wide range of parameters. In particular, using CBR and VBR traffic profiles, we assess the influence of distance, 802.11 technology and AP modes on throughput, delay, packet loss and jitter between pairs of adjacent nodes. For example, our measurements show that the average UDP throughput of the 802.11g links varies between 15.9 and 18.7 Mbps, whereas the 802.11a link achieves 27.8 Mbps. Finally, the average UDP throughput can even be increased to 55.2 Mbps by concomitantly enabling the two enhanced AP modes.
Metrology and detonics: analysis of necking

The purpose of the experiment discussed in the present paper is to study the deformation of a structure (here a copper cylinder) induced by explosives. During its expansion, the (initially 3-mm thick) cylinder keeps on thinning until fracture appears. Some tens of microseconds before failure, strain localization occurs, which induces mechanical necking. In order to characterize the time for the onset of localization and the necking development, two diagnostic techniques are designed to provide images: one based on X ray observations (for total thickness variations) and a second consisting in 25 stereoscopic acquisitions at about 400,000 frames per second. The latter enables us to estimate the three dimensional shape changes of the cylinder with time. The 3D reconstructions from the single X radiograph and stereoscopic films are described. Both techniques require calibration as a first stage. For the X view, a self calibration is performed in order to convert X measurements (a radiographic stack with 12 detection levels) to total dose in rad using a flashlight on a steel mock-up with calibrated defects. For stereovision, a controlled calibration object is used. The second stage is the reconstruction. For X radiographs, the results of a 2D hydrodynamic computation of the expansion at radiographic time coupled with an X photon transport code provide us an estimate of the scatter field and allow us to perform attenuation evaluations of copper alone, and to estimate its thickness. In stereovision, the reconstruction is achieved by an image correlation software which exploits the random patterns marking on the object outer surface.
Felix: Scaling Inference for Markov Logic with an Operator-based Approach

We examine how to scale up text-processing applications that are expressed in a language, Markov Logic, that allows one to express both logical and statistical rules. Our idea is to exploit the observation that to build text-processing applications one must solve a host of common subtasks, e.g., named-entity extraction, relationship discovery, coreference resolution. For some subtasks, there are specialized algorithms that achieve both high quality and high performance. But current general-purpose statistical inference approaches are oblivious to these subtasks and so use a single algorithm independent of the subtasks that they are performing. The result is that general purpose approaches have either lower quality, performance, or both compared to the specialized approaches. To combat this, we present Felix. In Felix programs are expressed in Markov Logic but are executed using a handful of predened
User Model Evolution Algorithm: Forgetting and Reenergizing User Preference

User model is one of the fundamentals to support personalized services. Not only the model has to represent user preferences precisely, but it must reflect the changes of user preferences over time as well. Existing user modeling approaches have several deficiencies such as lack of dynamics and adaptation, so the evolution of these models is much de-pendent on user's explicit feedbacks. Particularly, the existing approaches cannot update user models automatically to adapt the drift of user preferences over time. Aiming at solving these problems, the Forgetting and Reenergizing User Preference (FRUP) algorithm based on forgetting and reenergizing mechanism of memory in psychology is presented in this paper. Firstly, the characteristics of memory are analyzed through ZGrapher. Then, FRUP algorithm which can trace the user preference through Ebbinghaus forgetting curve is presented. Finally, the preferences in FRUP algorithm are divided into long-term, medium-term and short-term for describing different memory patterns accurately in different cases. The forget-ting mechanism of memory in FRUP algorithm shows proper adaptivity to evolve the user model. The reenergizing mechanism can trace the changes of user preference in time.
MLBoost Revisited: A Faster Metric Learning Algorithm for Identity-Based Face Retrieval

This paper addresses the question of metric learning, i.e. the learning of a dissimilar-ity function from a set of similar/dissimilar example pairs. This domain plays an important role in many machine learning applications such as those related to face recognition or face retrieval. More specifically, this paper builds on the recent MLBoost method proposed by Negrel et al. [25]. MLBoost has been shown to perform very well for face retrieval tasks, but this algorithm relies on the computation of a weak metric which is very time consuming. This paper demonstrates how, by introducing sparsity into the weak projectors, the convergence time can be reduced up to a factor of 10× compared to MLBoost, without any performance loss. The paper also introduces an explicit way to control the rank of the so-obtained metrics, allowing to fix in advance the dimension of the (projected) feature space. The proposed ideas are experimentally validated on a face retrieval task with three different signatures.
Do American Goldfinches See Their World Like Passive Prey Foragers? A Study on Visual Fields, Retinal Topography, and Sensitivity of Photoreceptors

Several species of the most diverse avian order, Passeriformes, specialize in foraging on passive prey, although relatively little is known about their visual systems. We tested whether some components of the visual system of the American goldfinch (Spinus tristis), a granivorous bird, followed the profile of species seeking passive food items (small eye size relative to body mass, narrow binocular fields and blind areas, centrally located retinal specialization projecting laterally, ultraviolet-sensitive vision). We measured eye size, visual field configuration, the degree of eye movement, variations in the density of ganglion cells and cone photoreceptors, and the sensitivity of photoreceptor visual pigments and oil droplets. Goldfinches had relatively large binocular (46°) and lateral (134°) visual fields with a high degree of eye movement (66° at the plane of the bill). They had a single centrotemporally located fovea that projects laterally, but can be moved closer to the edge of the binocular field by converging the eyes. Goldfinches could also increase their panoramic vision by diverging their eyes while handling food items in head-up positions. The distribution of photoreceptors indicated that the highest density of single and double cones was surrounding the fovea, making it the center of chromatic and achromatic vision and motion detection. Goldfinches possessed a tetrachromatic ultraviolet visual system with visual pigment peak sensitivities of 399 nm (ultraviolet-sensitive cone), 442 nm (short-wavelength-sensitive cone), 512 nm (medium-wavelength-sensitive cone), and 580 nm (long-wavelength-sensitive cone). Overall, the visual system of American goldfinches showed characteristics of passive as well as active prey foragers, with a single-fovea configuration and a large degree of eye movement that would enhance food searching and handling with their relatively wide binocular fields.
Mostly-digital design of sinusoidal signal generators for mixed-signal BIST applications using harmonic cancellation

This work proposes a novel approach for the design of high-quality on-chip sinusoidal signal generators using digital circuitry. The proposed generation technique is based on a simple digital shift-register that provides a set of phase-shifted versions of a digital square-wave signal. These square-wave signals are conveniently combined using a harmonic cancellation strategy to yield a spectrally pure sinusoidal output signal. The proposed strategy allows cancelling low-frequency harmonics close to the fundamental component of the generated sinusoidal signal, while a simple first order low-pass filter is used to attenuate higher order harmonic components. A simple one-shot calibration strategy is also presented in order to compensate the effects of the main non-idealities affecting the dynamic linearity of the generator. Statistical behavioral simulations are provided to demonstrate the feasibility of the proposed generator.
Learning computationally efficient dictionaries and their implementation as fast transforms

Dictionary learning is a branch of signal processing and machine learning that aims at finding a frame (called dictionary) in which some training data admits a sparse representation. The sparser the representation, the better the dictionary. The resulting dictionary is in general a dense matrix, and its manipulation can be computationally costly both at the learning stage and later in the usage of this dictionary, for tasks such as sparse coding. Dictionary learning is thus limited to relatively small-scale problems. In this paper, inspired by usual fast transforms, we consider a general dictionary structure that allows cheaper manipulation, and propose an algorithm to learn such dictionaries --and their fast implementation-- over training data. The approach is demonstrated experimentally with the factorization of the Hadamard matrix and with synthetic dictionary learning experiments.
Compiling finite domain constraints to SAT with BEE*

Abstract We present BEE, a compiler which enables to encode finite domain constraint problems to CNF. Using BEE both eases the encoding process for the user and also performs transformations to simplify constraints and optimize their encoding to CNF. These optimizations are based primarily on equi-propagation and on partial evaluation, and also on the idea that a given constraint may have various possible CNF encodings. Often, the better encoding choice is made after constraint simplification. BEE is written in Prolog and integrates directly with a SAT solver through a suitable Prolog interface. We demonstrate that constraint simplification is often highly beneficial when solving hard finite domain constraint problems. A BEE implementation is available with this paper.
A bioceramic with enhanced osteogenic properties to regulate the function of osteoblastic and osteocalastic cells for bone tissue regeneration

Bioceramics for regenerative medicine applications should have the ability to promote adhesion, proliferation and differentiation of osteoblast and osteoclast cells. Osteogenic properties of the material are essential for rapid bone regeneration and new bone formation. The aim of this study was to develop a silicate-based ceramic, gehlenite (GLN, Ca2Al2SiO7), and characterise its physiochemical, biocompatibility and osteogenic properties. A pure GLN powder was synthesised by a facile reactive sintering method and compacted to disc-shaped specimens. The sintering behaviour and degradation of the GLN discs in various buffer solutions were fully characterised. The cytotoxicity of GLN was evaluated by direct and indirect methods. In the indirect method, primary human osteoblast cells (HOBs) were exposed to diluted extracts (100, 50, 25, 12.5 and 6.25 mg ml−1) of fine GLN particles in culture medium. The results showed that the extracts did not cause any cytotoxic effect on the HOBs with the number of cells increasing significantly from day 1 to day 7. GLN-supported HOB attachment and proliferation, and significantly enhanced osteogenic gene expression levels (Runx2, osteocalcin, osteopontin and bone sialoprotein) were compared with biphasic calcium phosphate groups (BCP, a mixture of hydroxyapatite (60wt.%) and β-tricalcium phosphate(40wt.%)). We also demonstrated that in addition to supporting HOB attachment and proliferation, GLN promoted the formation of tartrate-acid resistance phosphatase (TRAP) positive multinucleated osteoclastic cells (OCs) derived from mouse bone marrow cells. Results also demonstrated the ability of GLN to support the polarisation of OCs, a prerequisite for their functional resorptive activity which is mainly influenced by the composition and degradability of biomaterials. Overall, the developed GLN is a prospective candidate to be used in bone regeneration applications due its effective osteogenic properties and biocompatibility.
TIKHONOV REGULARIZATION WITH NONNEGATIVITY CONSTRAINT

Many numerical methods for the solution of ill-posed problems are based on Tikhonov regulariza- tion. Recently, Rojas and Steihaug (15) described a barrier method for computing nonnegative Tikhonov-regularized approximate solutions of linear discrete ill-posed problems. Their method is based on solving a sequence of param- eterized eigenvalue problems. This paper describes how the solution of parametrized eigenvalue problems can be avoided by computing bounds that follow from the connection between the Lanczos process, orthogonal polynomials and Gauss quadrature.
Neural networks for oil spill detection using ERS-SAR data

A neural network approach for semi-automatic detection of oil spills in European remote sensing satellite-synthetic aperture radar (ERS-SAR) imagery is presented. The network input is a vector containing the values of a set of features characterizing an oil spill candidate. The classification performance of the algorithm has been evaluated on a data set containing verified examples of oil spill and look-alike. A direct analysis of the information content of the calculated features has been also carried out through an extended pruning procedure of the net.
Acute toll‐like receptor 4 activation impairs rat renal microvascular autoregulatory behaviour

Little is known about how toll‐like receptor 4 (TLR4) influences the renal microvasculature. We hypothesized that acute TLR4 stimulation with lipopolysaccharide (LPS) impairs afferent arteriole autoregulatory behaviour, partially through reactive oxygen species (ROS).
Performance Evaluation of Locator/Identifier Separation Protocol through RIPE Atlas

The \emph{Locator/Identifier Separation Protocol} (LISP) introduces several benefits to the Internet architecture, yet, since it is just in the initial deployment stage, comprehensive understanding of its integration performance with legacy Internet becomes essential. We leverage on RIPE Atlas, the largest Internet measurement infrastructure, to conduct large scale measurements analysis to provide the feedback to improve LISP technology. The preliminary evaluations show that LISP generally has a reliable performance, compared with the existing Internet. From our vantage point, we observe that LISP introduces a non-negligible latency for the European and North American destinations, occasionally some extremely large delay, however, it shows a faster connection for the Asian intercontinental transmission.
Testing of fatigue and deformation properties in uniaxial tension tests

The swelling tensile test is used for examining the resistance against fatigue of surface asphalt. The swelling load simulates the superposition of the sinusoidal mechanical traffic loads and the cryogenic stress, which occurs, when the asphalt road cools down. The primary result of the test is the number of endured load impulses. In two research projects the fatigue characteristics of five surface course asphalts, two binder- and two base-layer asphalts were tested by variation of the test temperature, the load frequency and the applied stress. The results enable fatigue curves to be derived for estimating the fatigue characteristics for further test parameters with high precision. A specimen which is loaded with a high frequency can endure more load impulses and develops less strain then a specimen which is tested with a lower frequency. But if both quantities are charted against the testing time, the effect of the frequency is negligible. The strain curves can be compared with the results of tensile creep tests. For the covering abstract see ITRD E157233
The Research of Worms in P2P Networks

With the rapid development of the Internet, P2P technology has changed the traditional concept of Internet; this technology has become the dominant flow and greatly satisfied the needs of the users. At the same time, P2P worm has become one of the serious threats. This article include characteristics of P2P worms, classification, propagation model, detection and defense mechanism, also analyze some advantages and disadvantages of simulation software. At last this article discusses the direction for future research.
Reaching for objects in VR displays: lag and frame rate

This article reports the results from three experimental studies of reaching behavior in a head-coupled stereo display system with a hand-tracking subsystem for object selection. It is found that lag in the head-tracking system is relatively unimportant in predicting performance, whereas lag in the hand-tracking system is critical. The effect of hand lag can be modeled by means of a variation on Fitts' Law with the measured system lag introduced as a multiplicative variable to the Fitts' Law index of difficulty. This means that relatively small lags can cause considerable degradation in performance if the targets are small. Another finding is that errors are higher for movement in and out of the screen, as compared to movements in the plane of the screen, and there is a small (10%) time penalty for movement in the Z direction in all three experiments. Low frame rates cause a degradation in performance; however, this can be attributed to the lag which is caused by low frame rates, particularly if double buffering is used combined with early sampling of the hand-tracking device.
Cab45, a novel (Ca2+)-binding protein localized to the Golgi lumen

We have identified and characterized Cab45, a novel 45-kD protein from mouse 3T3-L1 adipocytes. Cab45 is ubiquitously expressed, contains an NH2-terminal signal sequence but no membrane-anchor sequences, and binds Ca2+ due to the presence of six EF-hand motifs. Within the superfamily of calcium-binding proteins, it belongs to a recently identified group of proteins consisting of Reticulocalbin (Ozawa, M., and T. Muramatsu. 1993. J. Biol. Chem. 268:699-705) and ERC 55 (Weis, K., G. Griffiths, and A.I. Lamond. 1994. J. Biol Chem. 269:19142- 19150), both of which share significant sequence homology with Cab45 outside the EF-hand motifs. In contrast to reticulocalbin and ERC-55 which are soluble components of the endoplasmic reticulum, Cab45 is a soluble protein localized to the Golgi. Cab45 is the first calcium- binding protein localized to the lumenal portion of a post-ER compartment; Cab45 is also the first known soluble protein resident in the Golgi lumen. Cab45 can serve as a model protein to determine the mechanism of retention of soluble proteins in the Golgi compartment.
Lysophosphatidic Acid Activates Peroxisome Proliferator Activated Receptor-γ in CHO Cells That Over-Express Glycerol 3-Phosphate Acyltransferase-1

Lysophosphatidic acid (LPA) is an agonist for peroxisome proliferator activated receptor-γ (PPARγ). Although glycerol-3-phosphate acyltransferase-1 (GPAT1) esterifies glycerol-3-phosphate to form LPA, an intermediate in the de novo synthesis of glycerolipids, it has been assumed that LPA synthesized by this route does not have a signaling role. The availability of Chinese Hamster Ovary (CHO) cells that stably overexpress GPAT1, allowed us to analyze PPARγ activation in the presence of LPA produced as an intracellular intermediate. LPA levels in CHO-GPAT1 cells were 6-fold higher than in wild-type CHO cells, and the mRNA abundance of CD36, a PPARγ target, was 2-fold higher. Transactivation assays showed that PPARγ activity was higher in the cells that overexpressed GPAT1. PPARγ activity was enhanced further in CHO-GPAT1 cells treated with the PPARγ ligand troglitazone. Extracellular LPA, phosphatidic acid (PA) or a membrane-permeable diacylglycerol had no effect, showing that PPARγ had been activated by LPA generated intracellularly. Transient transfection of a vector expressing 1-acylglycerol-3-phosphate acyltransferase-2, which converts endogenous LPA to PA, markedly reduced PPARγ activity, as did over-expressing diacylglycerol kinase, which converts DAG to PA, indicating that PA could be a potent inhibitor of PPARγ. These data suggest that LPA synthesized via the glycerol-3-phosphate pathway can activate PPARγ and that intermediates of de novo glycerolipid synthesis regulate gene expression.
Design analysis of lattice-matched AlInGaN-GaN QW for optimized intersubband absorption in the Mid-IR regime

Design analysis of III-Nitride based intersubband quantum well absorption in the mid-IR regime (&lgr; ~ 3-5 &mgr;m) is presented. The use of lattice-matched AlInGaN materials is advantageous because of its extremely fast intersubband relaxation time &tgr;rel ~ 150-fs. The ability to engineer lattice-matched AlInGaN layer with GaN should allow realization of multiple pairs of AlInGaN / GaN quantum well structures, which would otherwise be challenging due to the cracking issues that might develop in conventional multiple pairs AlGaN / GaN heterostructures. The large conduction band offset in III-Nitride heterostructures is also beneficial for minimizing dark current and thermal noise.