Miracle-dz/UniFAR-FTUs huggingface dataset:
dim‐2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora

To understand better the control of DNA methylation, we cloned and characterized the dim‐2 gene of Neurospora crassa, the only eukaryotic gene currently known in which mutations appear to eliminate DNA methylation. The dim‐2 gene is responsible for methylation in both symmetrical and asymmetrical sites. We mapped dim‐2 between wc‐1 and un‐10 on linkage group (LG) VIIR and identified the gene by RFLP mapping and genetic complementation. Dim‐2 encodes a 1454 amino acid protein including a C‐terminal domain homologous to known DNA methyltransferases (MTases) and a novel N‐terminal domain. Neither a deletion that removed the first 186 amino acids of the protein nor a mutation in a putative nucleotide binding site abolished function, but a single amino acid substitution in the predicted catalytic site did. Tests for repeat‐induced point mutation (RIP) indicated that dim‐2 does not play a role in this process, i.e. duplicated sequences are mutated in dim‐2 strains, as usual, but the mutated sequences are not methylated, unlike the situation in dim‐2+ strains. We conclude that dim‐2 encodes an MTase that is responsible for all DNA methylation in vegetative tissues of Neurospora.
Receding horizon quadratic optimal control: Performance bounds for a finite horizon strategy

Stability results for receding horizon control (RHC) have generally been restricted to two cases: a finite horizon formulation with end (terminal) constraints, and an infinite horizon formulation. In this paper, we prove that stability can be guaranteed for finite receding horizon control applied to linear systems with quadratic costs, without the imposition of end constraints. In addition, conditions which guarantee that the receding horizon control will perform within specified bounds of the optimal infinite horizon performance are derived. The unconstrained case is presented, with extensions to constrained and nonlinear systems being possible. In the unconstrained case, computations involve iterations of the Riccati difference equation, and are demonstrated on a simple example.
Effect of Trace Cerium on the As-Cast Microstructure of Ag-Cu-Ni Alloy

It is well known that the rare-earth elements (RE) have exhibited favorable microalloying effects on the microstructure and properties of silver alloys. In the present investigation, a detailed description of the microstructure of a Silver-4wt. %Copper-0.3wt. % Nickle as–cast alloy containing 0.2wt. % of a cerium element was presented. Particles types occurring and their distribution in the microstructure, as well as the distribution of elements in the phases were described. The result show that the second phase in Ag-Cu-Ni Alloy is Cu-Ni-rich solution phase, some of which forms interdendritic segregation in Ag matrix as eutectic colonies. Trace additions of cerium to the alloy decrease eutectic proportion and size of the Cu-Ni-rich phase, result in finer and more uniform secondary phases distributed in the α-Ag matrix. Besides Cu-Ni-rich phase, the Ni-Cu-Ce-rich and Ag-Cu-Ce-rich phases were found in the alloy. The Ni-Cu-Ce-rich should be the (NiCu)5Ce, which is distributed as dispersive particle in the Ag matrix, and Ag-Cu-Ce-rich phases should be (AgCu)4Ce, which is distributed as fibrous particle of eutectic colonies. Some of (AgCu)4Ce phases are located at the interface between α-Ag matrix and Cu-Ni-rich phases, which indicate that Ce could be segregated at the frontier of Cu-Ni-rich phases during the growth, causing Cu-Ni-rich phase refinement.
Outage probability for maximal ratio combining receivers in asynchronous CDMA channels

Direct sequence code division multiple access (DS-CDMA) receivers typically use maximal ratio combining (MRC) to favorably combine the energies of distinct multipath components from diversity branches. There have been a large number of studies on DS-CDMA and MRC receivers, respectively, but there have been a comparatively small number of papers analyzing MRC for DS-CDMA. Prior work does not accurately analyze the outage probability using the actual random characteristics of the cross correlations, instead, equality has been assumed. The contribution of this paper is to provide a general and accurate analysis of the outage probability of the diversity receiver in CDMA systems without compromising approximations. From the analytical and numerical results, it is shown that the analysis provides an accurate closed-form solution.
CXXC5 plays a role as a transcription activator for myelin genes on oligodendrocyte differentiation

Myelination in corpus callosum plays important role for normal brain functions by transferring neurological information between various brain regions. However, the factors controlling expression of myelin genes in myelination are poorly understood. Here, CXXC5, a recently identified protein with CXXC‐type zinc finger DNA binding motif, was characterized as a transcriptional activator of major myelin genes. We identified expression of CXXC5 expression was increased by Wnt/β‐catenin signaling. CXXC5 specifically expressed in the white matter induced expression of myelin genes through the direct binding of CXXC DNA‐binding motif of CXXC5 on the MBP promoter. During the differentiation of neural stem cells (NSCs) of CXXC5−/− mice, the expressions of myelin genes were simultaneously reduced. The CXXC5−/− mice exhibited severely reduction of myelin genes expression in corpus callosum as well as abnormalities in myelin structure. The disrupted structural integrity of myelin in the CXXC5−/− mice resulted in reduced electrical conduction amplitudes at corpus callosum. These findings indicate that the regulation of myelin genes expression by CXXC5 is important for forming myelin structure involved with axonal electrical signal transfer in the corpus callosum. GLIA 2016;64:350–362
Dispensable role of the NF-kappa B sites in the UV-induction of the HIV- 1 LTR in transgenic mice

We have previously reported the epidermis-specific expression of the HIV-1 LTR in transgenic mice and its induction by UV-B rays. To dissect the underlying mechanism of the UV induction of the LTR in mice, we developed two approaches. We first demonstrated by gel mobility shift analysis, using mice epidermal extracts, that the NF-kappa B sites of the HIV-1 LTR were one of the targets of the UV induction. The Sp-1 sites and the potential AP-1 sites of the LTR were not involved in this phenomenon. The transient transfection assays of modified LTR in HeLa cells also demonstrated the involvement of the NF-kappa B sites in the UV induction and were consistent with previously published data. Secondly, to study the regulation acting on an integrated gene, we generated transgenic mice carrying the lacZ gene under the control of the partially deleted LTR. All the transgenic lines and unexpectedly those carrying the LTR deleted for the kappa B sites displayed a UV-inducible epidermal expression. This suggests that, in mice, the UV induction might be mediated through other sites than the kappa B sites and may also depend on changes of the chromatin state.
A novel approach for interference suppression in multi-subband convolutional coded OFDM system

This paper proposes a novel approach of suppressing narrowband interference from a multi-subband convolutional coded orthogonal frequency division multiplexing (OFDM) system. In this system, the convolutional coded data symbols using different coding generators are transmitted in different subbands. By identifying and discarding the interfered subband(s), the interference level can be greatly reduced and the system performance of the OFDM system can be improved. The interference thresholds for discarding the interfered subband(s) are determined through simulations over additive white Gaussian noise (AWGN) channel for demonstration purpose. The principle can also be applied to multipath fading channel.
An open source C++ implementation of multi-threaded Gaussian mixture models, k-means and expectation maximisation

Modelling of multivariate densities is a core component in many signal processing, pattern recognition and machine learning applications. The modelling is often done via Gaussian mixture models (GMMs), which use computationally expensive and potentially unstable training algorithms. We provide an overview of a fast and robust implementation of GMMs in the C++ language, employing multi-threaded versions of the Expectation Maximisation (EM) and k-means training algorithms. Multi-threading is achieved through reformulation of the EM and k-means algorithms into a MapReduce-like framework. Furthermore, the implementation uses several techniques to improve numerical stability and modelling accuracy. We demonstrate that the multi-threaded implementation achieves a speedup of an order of magnitude on a recent 16 core machine, and that it can achieve higher modelling accuracy than a previously well-established publically accessible implementation. The multi-threaded implementation is included as a user-friendly class in recent releases of the open source Armadillo C++ linear algebra library. The library is provided under the permissive Apache 2.0 license, allowing unencumbered use in commercial products.
A radial cumulative similarity transform for robust image correspondence

We develop a local image-correspondence algorithm which performs well near occluding boundaries. Unlike traditional robust methods, our method can find correspondences when the only contrast present is the occluding boundary itself an when the sign of contrast along the boundary is possibly reversed. We define a new image transform which characterizes local image homogeneity, defined as an attribute value in a central region and most generally a function describing the surrounding local similarity structure. In this paper we use radial similarity functions and color attributes; within each window we compute the central color and an image with the cumulative probability color is unchanged along a ray from the center to given point in the window: this representation is insensitive to structure outside an occluding boundary, but can model the boundary itself. We show comparative results tracking finger, mouth, and eye features.
THEORETICAL EQUATIONS TO EVALUATE THE STRESS OF PILES ON PILED RAFT FOUNDATION DURING EARTHQUAKE

Simple theoretical equations in order to estimate the stress of pile and to evaluate the lateral load sharing ratio between piles and raft were derived for seismic design. First, this paper shows how to estimate the ground displacement caused by raft friction, second, shows how to do the differential equation of deflection of pile considering its ground displacement. Some approximations and assumptions are employed. First, soil deposit is homogeneous. In this case, a ground displacement is derived theoretically. Second, about interaction among piles-subsoil-raft, the influences from pile to pile and from pile to raft are ignored. This assumption is valid from the analytical results. Third, the ground displacement caused by raft friction is expressed as an exponential function or polynomial function. This approximation is effective to do the differential equation of deflection of pile considering ground displacement. These equations were compared with the lateral loading tests and numerical analysis on piled raft foundation subjected to lateral loading.
Unaddressed participants’ gaze in multi-person interaction: optimizing recipiency

One of the most intriguing aspects of human communication is its turn-taking system. It requires the ability to process on-going turns at talk while planning the next, and to launch this next turn without considerable overlap or delay. Recent research has investigated the eye movements of observers of dialogs to gain insight into how we process turns at talk. More specifically, this research has focused on the extent to which we are able to anticipate the end of current and the beginning of next turns. At the same time, there has been a call for shifting experimental paradigms exploring social-cognitive processes away from passive observation toward on-line processing. Here, we present research that responds to this call by situating state-of-the-art technology for tracking interlocutors’ eye movements within spontaneous, face-to-face conversation. Each conversation involved three native speakers of English. The analysis focused on question–response sequences involving just two of those participants, thus rendering the third momentarily unaddressed. Temporal analyses of the unaddressed participants’ gaze shifts from current to next speaker revealed that unaddressed participants are able to anticipate next turns, and moreover, that they often shift their gaze toward the next speaker before the current turn ends. However, an analysis of the complex structure of turns at talk revealed that the planning of these gaze shifts virtually coincides with the points at which the turns first become recognizable as possibly complete. We argue that the timing of these eye movements is governed by an organizational principle whereby unaddressed participants shift their gaze at a point that appears interactionally most optimal: It provides unaddressed participants with access to much of the visual, bodily behavior that accompanies both the current speaker’s and the next speaker’s turn, and it allows them to display recipiency with regard to both speakers’ turns.
All-genus calculation of Wilson loops using D-branes

The standard prescription for calculating a Wilson loop in the AdS/CFT correspondence is by a string world-sheet ending along the loop at the boundary of AdS. For a multiply wrapped Wilson loop this leads to many coincident strings, which may interact among themselves. In such cases a better description of the system is in terms of a D3-brane carrying electric flux. We find such solutions for the single straight line and the circular loop. The action agrees with the string calculation at small coupling and in addition captures all the higher genus corrections at leading order in α'. The resulting expression is in remarkable agreement with that found from a zero dimensional gaussian matrix model.
In vivo Bioluminescent Imaging of Mammary Tumors Using IVIS Spectrum

4T1 mouse mammary tumor cells can be implanted sub-cutaneously in nu/nu mice to form palpable tumors in 15 to 20 days. This xenograft tumor model system is valuable for the pre-clinical in vivo evaluation of putative antitumor compounds. The 4T1 cell line has been engineered to constitutively express the firefly luciferase gene (luc2). When mice carrying 4T1-luc2 tumors are injected with Luciferin the tumors emit a visual light signal that can be monitored using a sensitive optical imaging system like the IVIS Spectrum. The photon flux from the tumor is proportional to the number of light emitting cells and the signal can be measured to monitor tumor growth and development. IVIS is calibrated to enable absolute quantitation of the bioluminescent signal and longitudinal studies can be performed over many months and over several orders of signal magnitude without compromising the quantitative result. Tumor growth can be monitored for several days by bioluminescence before the tumor size becomes palpable or measurable by traditional physical means. This rapid monitoring can provide insight into early events in tumor development or lead to shorter experimental procedures. Tumor cell death and necrosis due to hypoxia or drug treatment is indicated early by a reduction in the bioluminescent signal. This cell death might not be accompanied by a reduction in tumor size as measured by physical means. The ability to see early events in tumor necrosis has significant impact on the selection and development of therapeutic agents. Quantitative imaging of tumor growth using IVIS provides precise quantitation and accelerates the experimental process to generate results.
Transmission Electron Microscopy of Substructures Developed during High-Temperature Creep in Alpha-Iron

degree of the substructure formation was not uniform over a specimen in the transient stage so that the substructures were different from grain to grain, while it was unifom in the secondary stage. The subgrain size, the dislocation density within subgrains, and the dislocation spacing in sub-boundaries were dependent not on creep temperature but on creep strain and stress. The dislocation spacing in sub-boundaries determined in the present work showed the stress dependence similar to that of the elementary jog spacing expected from a super-jog model which has recently been proposed by two of the present authors for high-temperature creep of alpha-iron. Many dislocation loops, the density of which depended on the creep condition, were observed within subgrains. The dislocation loops of large size were analysed to be of the vacancy-type. (Received April 19, 1971)
Adverse Drug Event classification of health records using dictionary based pre-processing and machine learning

A method to find adverse drug reactions in electronic health records written in Swedish is presented. A total of 14,751 health records were manually classified into four groups. The records are normalised by pre-processing using both dic- tionaries and manually created word lists. Three different supervised machine learning algorithm were used to find the best results; decision tree, random forest and LibSVM. The best performance on a test dataset was with LibSVM obtaining a pre- cision of 0.69 and a recall of 0.66, and a F-score of 0.67. Our method found 865 of 981 true positives (88.2%) in a 3-class dataset which is an improvement of 49.5% over previous approaches.
Syndecan-2 induces filopodia and dendritic spine formation via the neurofibromin–PKA–Ena/VASP pathway

Syndecan-2 induced filopodia before spinogenesis; therefore, filopodia formation was used here as a model to study the early downstream signaling of syndecan-2 that leads to spinogenesis. Screening using kinase inhibitors indicated that protein kinase A (PKA) is required for syndecan-2–induced filopodia formation in both human embryonic kidney cells and hippocampal neurons. Because neurofibromin, a syndecan-2–binding partner, activates the cyclic adenosine monophosphate pathway, the role of neurofibromin in syndecan-2–induced filopodia formation was investigated by deletion mutant analysis, RNA interference, and dominant-negative mutant. The results showed that neurofibromin mediates the syndecan-2 signal to PKA. Among actin-associated proteins, Enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) were predicted as PKA effectors downstream of syndecan-2, as Ena/VASP, which is activated by PKA, induces actin polymerization. Indeed, when the activities of Ena/VASP were blocked, syndecan-2 no longer induced filopodia formation. Finally, in addition to filopodia formation, neurofibromin and Ena/VASP contributed to spinogenesis. This study reveals a novel signaling pathway in which syndecan-2 activates PKA via neurofibromin and PKA consequently phosphorylates Ena/VASP, promoting filopodia and spine formation.
Thermomechanical properties of polyurethane shape memory polymer–experiment and modelling

In this paper extensive research on the polyurethane shape memory polymer (PU-SMP) is reported, including its structure analysis, our experimental investigation of its thermomechanical properties and its modelling. The influence of the effects of thermomechanical couplings on the SMP behaviour during tension at room temperature is studied using a fast and sensitive infrared camera. It is shown that the thermomechanical behaviour of the SMP significantly depends on the strain rate: at a higher strain rate higher stress and temperature values are obtained. This indicates that an increase of the strain rate leads to activation of different deformation mechanisms at the micro-scale, along with reorientation and alignment of the molecular chains. Furthermore, influence of temperature on the SMP’s mechanical behaviour is studied. It is observed during the loading in a thermal chamber that at the temperature 20 °C below the glass transition temperature (Tg) the PU-SMP strengthens about six times compared to the material above Tg but does not exhibit the shape recovery. A finite-strain constitutive model is formulated, where the SMP is described as a two-phase material composed of a hyperelastic rubbery phase and elastic-viscoplastic glassy phase. The volume content of phases is governed by the current temperature. Finally, model predictions are compared with the experimental results.
Eliminate bottlenecks with integrated analysis tools in eM-Plant

To build a realistic simulation model is all very well; to add real value you must identify the major difficulties and generate better alternatives. Tecnomatix Technologies, developers of eM-Plant, the object oriented simulation tool for discrete event simulation, planning and optimization of production and logistics, are the world leaders of the e-manufacturing market. EM-Plant is used across many industries from manufacturers like BMW and Daimler-Chrysler through shipyards to international finance. Experience from all these areas inspired the development of analysis and optimization tools as an integral part of the simulation objects that continuously monitor and evaluate the operation of each simulation object and its interactions at a local and global level. Thus, for example, bottlenecks in a material flow are automatically detected and Sankey diagrams generated. This object based approach fits closely with the object oriented nature of eM-Plant that allows unprecedented accuracy and reusability in simulation modeling. These analysis tools work with global evaluation wizards which, for example, make it simple to create specific Gantt-charts etc., and using genetic algorithm modules, the simulation system can even propose better layouts or operating strategies.