Miracle-dz/UniFAR-FTUs huggingface dataset:
Strategy for Systematic Assembly of Large RNA and DNA Genomes: Transmissible Gastroenteritis Virus Model

ABSTRACT A systematic method was developed to assemble functional full-length genomes of large RNA and DNA viruses. Coronaviruses contain the largest single-stranded positive-polarity RNA genome in nature. The ∼30-kb genome, coupled with regions of genomic instability, has hindered the development of a full-length infectious cDNA construct. We have assembled a full-length infectious construct of transmissible gastroenteritis virus (TGEV), an important pathogen in swine. Using a novel approach, six adjoining cDNA subclones that span the entire TGEV genome were isolated. Each clone was engineered with unique flanking interconnecting junctions which determine a precise systematic assembly with only the adjacent cDNA subclones, resulting in an intact TGEV cDNA construct of ∼28.5 kb in length. Transcripts derived from the full-length TGEV construct were infectious, and progeny virions were serially passaged in permissive host cells. Viral antigen production and subgenomic mRNA synthesis were evident during infection and throughout passage. Plaque-purified virus derived from the infectious construct replicated efficiently and displayed similar plaque morphology in permissive host cells. Host range phenotypes of the molecularly cloned and wild-type viruses were similar in cells of swine and feline origin. The recombinant viruses were sequenced across the unique interconnecting junctions, conclusively demonstrating the marker mutations and restriction sites that were engineered into the component clones. Full-length infectious constructs of TGEV will permit the precise genetic modification of the coronavirus genome. The method that we have designed to generate an infectious cDNA construct of TGEV could theoretically be used to precisely reconstruct microbial or eukaryotic genomes approaching several million base pairs in length.
L1 Adaptive Control for a Vertical Rotor Orientation System

Bottom-fixed vertical rotating devices are widely used in industrial and civilian fields. The free upside of the rotor will cause vibration and lead to noise and damage during operation. Meanwhile, parameter uncertainties, nonlinearities and external disturbances will further deteriorate the performance of the rotor. Therefore, in this paper, we present a rotor orientation control system based on an active magnetic bearing with L 1 adaptive control to restrain the influence of the nonlinearity and uncertainty and reduce the vibration amplitude of the vertical rotor. The boundedness and stability of the adaptive system are analyzed via a theoretical derivation. The impact of the adaptive gain is discussed through simulation. An experimental rig based on dSPACE is designed to test the validity of the rotor orientation system. The experimental results show that the relative vibration amplitude of the rotor using the L 1 adaptive controller will be reduced to ∼50% of that in the initial state, which is a 10% greater reduction than can be achieved with the nonadaptive controller. The control approach in this paper is of some significance to solve the orientation control problem in a low-speed vertical rotor with uncertainties and nonlinearities.
Genomic and Functional Studies of Drosophila Sex Hierarchy Regulated Gene Expression in Adult Head and Nervous System Tissues

The Drosophila sex determination hierarchy controls all aspects of somatic sexual differentiation, including sex-specific differences in adult morphology and behavior. To gain insight into the molecular-genetic specification of reproductive behaviors and physiology, we identified genes expressed in the adult head and central nervous system that are regulated downstream of sex-specific transcription factors encoded by doublesex (dsx) and fruitless (fru). We used a microarray approach and identified 54 genes regulated downstream of dsx. Furthermore, based on these expression studies we identified new modes of DSX-regulated gene expression. We also identified 90 and 26 genes regulated in the adult head and central nervous system tissues, respectively, downstream of the sex-specific transcription factors encoded by fru. In addition, we present molecular-genetic analyses of two genes identified in our studies, calphotin (cpn) and defective proboscis extension response (dpr), and begin to describe their functional roles in male behaviors. We show that dpr and dpr-expressing cells are required for the proper timing of male courtship behaviors.
Achievements of COST 266 Action and further prospects in research of advanced infrastructure for photonic networks

In spite of continuing stagnation in the telecommunication industry in general and in building new optical networks in particular, research in this area continues unabated. There are still many issues to be resolved in order to create advanced infrastructures based on new photonic technologies. COST 266 Action results achieved in the research of advanced infrastructures for photonic networks are reviewed and further prospects of research in this area are discussed.
Accurate equation of state of the hard sphere fluid in stable and metastable regions

New accurate data on the compressibility factor of the hard sphere fluid are obtained by highly optimized molecular dynamics calculations in the range of reduced densities 0.20–1.03. The relative inaccuracy at the 95% confidence level is better than 0.00004 for all densities but the last deeply metastable point. This accuracy requires careful examination of finite size effects and other possible sources of errors and applying corrections. The data are fitted to a power series in y/(1 − y), where y is the packing fraction; the coefficients are determined so that virial coefficients B2 to B6 are reproduced. To do this, values of B5 and B6 are accurately recalculated. Virial coefficients up to B11 are then estimated from the equation of state.
APPLICATION OF KALMAN FILTER ALGORITHMS IN A GMC CONTROL STRATEGY FOR FED-BATCH CULTIVATION PROCESS

This paper addresses the study of a Generic Model Control (GMC) approach for regulation of the specific growth rate of for fed-batch cultivation process. This approach requires all the process states to be available on line. Since direct measurement of these states is not possible, a state estimator must be implemented. In this work, the estimator is a Kalman filter that uses the oxygen uptake rate (OUR) of the microorganisms as the measurable process output. Another practical issue constitutes the time delay present in the OUR measurements, a Smith predictor compensation is proposed to overcome this problem. Several simulations were carried out to test this scheme using an experimentally identified process model.
Proving Congruence of Bisimulation in Functional Programming Languages

We give a method for proving congruence of bisimulation-like equivalences in functional programming languages. The method applies to languages that can be presented as a set of expressions together with an evaluation relation. We use this method to show that some generalizations of Abramsky's applicative bisimulation are congruences whenever evaluation can be specified by a certain natural form of structured operational semantics. One of the generalizations handles nondeterminism and diverging computations.
Support vector machines with composite kernels for nonlinear systems identification

In this paper, a nonlinear system identification based on support vector machines (SVM) has been addressed. A family of SVM-ARMA models is presented in order to integrate the input and the output in the reproducing kernel Hilbert space (RKHS). The performances of the different SVM-ARMA formulations for system identification are illustrated with two systems and compared with the least square method.
A descriptive engineering approach for cyber-physical systems

Plug and produce (PnP) aims at reducing system engineering effort. Therefore several PnP aspects have to be solved. This paper gives an overview and classifies process types and PnP aspects. Furthermore it identifies coupled processes as the most challenging ones and provides a new engineering approach for such systems. A new two-step descriptive engineering approach is applied to automatically synthesise control code from a given product specification. The main idea of the approach is to use a descriptive view rather than a prescriptive. This means that the engineer specifies what he wants to produce and no longer how he wants to produce it. Thus, it reduces engineering effort and releases more resources to optimize the process.
Tactile Score , a language of describing thinking in our mind from computational aesthetics view !

Wireless sensor networks play an increasingly important role in our society. One early proposal to miniaturize them concerns the Smart Dust project [4] at the University of California in Berkeley, which envisioned a vast wireless sensor network consisting of millimeter-scale nodes. An important problem of wireless sensor networks with tiny nodes is their energy expenditure: since there is little space available in nodes, batteries should be extremely limited. Alternatively, there have been proposals to harvest energy from the environment [3]. Wireless sensor networks typically have nodes containing a primitive CPU to control sensing, communication, and data preprocessing. Energy consumption of nodes tends to be dominated by transmission of data and passive listening for data from other nodes, as well as data processing, but this may already be too much to support a useful model of sensor networks with tiny nodes. The complexity of computations and communications in wireless sensor networks should thus be decreased as much as possible, to the extent that a node is capable of conducting only the simplest of operations. Unfortunately, the existing wireless networking protocols do not support such a mode of operation [1], since their information encoding and routing is packetbased. Problems like these necessitate the rethinking of the model for wireless sensor networks. A node in such a network would not need addressing, and it would employ extremely simple signaling and operations. The much decreased complexity of nodes would result in lowered costs, and this would allow the use of nodes in huge numbers. This in turn will change the strategies used for sensing, information processing, and communication. This presentation explores wireless sensor networks in which the nodes employ a pulse-based protocol for signaling inside nodes, as well as for signaling between nodes. This mode of signaling, inspired by the brain’s use of spiking signals between neurons, has the potential for dramatically simpler hardware requirements of nodes, since all processing and communication takes place in the pulse domain, obviating the need for components like a A/D converter, CPU, etc. This in its turn will allow a drastically reduced power consumption of nodes to the extent that all energy can be harvested from the environment, and no pre-installed battery is necessary. We discuss how concepts from neuroscience can be useful in this endeavor, as well as the potential of new applications that rely on the availability of a huge number of (albeit simple) sensor nodes. Elements of this paper have been presented before in [2].
Optimal power allocation scheme under FSA constraint for OFDM based cognitive radio systems

In the literature, researchers have evaluated optimal power loading algorithms under the Zero Mean Circularly Symmetric Complex Gaussian (ZMCSCG) constraint in OFDM based CR systems. The capacity of the Secondary User (SU) is maximized while keeping the interference introduced to the Primary User (PU) band remains within tolerable range. However the drawback of such an approach is that channel capacity increases with increasing Signal to Noise Ratio (SNR), which is not applicable to a practical scenario. Therefore, we propose an optimal power loading scheme under the Finite Symbol Alphabet (FSA) constraint, (i.e., QPSK, 8-PSK, 16-QAM and 64-QAM, etc.) to achieve realistic system performance especially under the high SNR region. Subsequently, Mutual Information (MI) is derived and compared against channel capacity which reveals that in the low SNR region, they are closely related. Conversely, MI saturates in the high SNR region which indicates maximum achievable data rates for practical systems. We further evaluate channel capacity and MI by varying the interference threshold and our observation is that the saturation value of the achievable SU data rate indicated by MI changes accordingly, but total achievable data rate remains constant. On the other hand, capacity increases with increasing interference threshold.
Notice of RetractionEvaluation on small enterprise's competitiveness in Jilin province

Small enterprises are playing more and more important role in the development of China's economy, and the evaluation on small enterprises competitiveness is also more and more important. The small enterprise's competitiveness can be evaluated by the ability of influencing region, the ability of management, the ability of growing and the ability of regional support. Based on the analysis, this paper sets an indicator system. According to statistical data, the paper uses the principal component analysis to evaluate the small enterprise's competitiveness. It shows that the small enterprise's competitiveness in Jilin province is at moderate level in China and in Northeast China.
Unleashing the power of Schrijver's permanental inequality with the help of the Bethe Approximation

Let $A \in \Omega_n$ be doubly-stochastic $n \times n$ matrix. Alexander Schrijver proved in 1998 the following remarkable inequality per(\widetilde{A}) \geq \prod_{1 \leq i,j \leq n} (1- A(i,j)); \widetilde{A}(i,j) =: A(i,j)(1-A(i,j)), 1 \leq i,j \leq n. We use the above Shrijver's inequality to prove the following lower bound: \frac{per(A)}{F(A)} \geq 1; F(A) =: \prod_{1 \leq i,j \leq n} (1- A(i,j))^{1- A(i,j)}. We use this new lower bound to prove S.Friedland's Asymptotic Lower Matching Conjecture(LAMC) on monomer-dimer problem. We use some ideas of our proof of (LAMC) to disprove [Lu,Mohr,Szekely] positive correlation conjecture. We present explicit doubly-stochastic $n \times n$ matrices $A$ with the ratio $\frac{per(A)}{F(A)} = \sqrt{2}^{n}$; conjecture that \max_{A \in \Omega_n}\frac{per(A)}{F(A)} \approx (\sqrt{2})^{n} and give some examples supporting the conjecture. If true, the conjecture (and other ones stated in the paper) would imply a deterministic poly-time algorithm to approximate the permanent of $n \times n$ nonnegative matrices within the relative factor $(\sqrt{2})^{n}$. The best current such factor is $e^n$.
Poverty, Gender and Primary Education: Experiences of Learners in Elandskop, KwaZulu Natal

This article discusses the interconnectedness of poverty and gender and learning at primary school level in KwaZulu Natal Province of South Africa. A qualitative study was conducted in two schools in the poverty stricken Elandskop area where data were collected using in-depth face-to-face interviews from purposely selected participants comprising of learners, educators and the headmasters. The aim was to analyse how male and female learners experience poverty, gender role socialisation and the effect on children’ bio-psychosocial health of both sexes. While the findings of the study revealed that poverty and gender socialisation of boys and girls have bio-psychosocial negative influences on them, the gender dimension of poverty had the most negative influence on girls. It was found that primary school learners grapple with coping mechanisms when confronted with poverty coupled with limited family and professional support. Gendered family roles and oppressive religious beliefs have been found to have influence on early marriages and teenage pregnancies resulting in school dropouts. The findings of the study imply that school social work is vehemently lacking yet necessary in schools in the area to assist educators in addressing the psychosocial ill-health of learners which educators are less equipped to professionally handle. The study recommends appropriate bio-psychosocial interventions early in the lives of learners to curtail lifelong developmental predicaments.
Spatial Decision Forests for Glioma Segmentation in Multi-Channel MR Images

A fully automatic algorithm is presented for the automatic segmentation of gliomas in 3D MR images. It builds on the discriminative random decision forest framework to provide a voxel-wise probabilistic classi cation of the volume. Our method uses multi-channel MR intensi- ties (T1, T1C, T2, Flair), spatial prior and long-range comparisons with 3D regions to discriminate lesions. A symmetry feature is introduced ac- counting for the fact that gliomas tend to develop in an asymmetric way. Quantitative evaluation of the data is carried out on publicly available labeled cases from the BRATS Segmentation Challenge 2012 dataset and demonstrates improved results over the state of the art.
Image acquisition and automated inspection of wine bottlenecks by tracking in multiple views

In this paper we propose a prototype for image sequence acquisition of glass wine bottlenecks, whose main novelty is the use of an inner lighting source for better capturing of potential defects. A novel approach for automatic inspection of the bottlenecks based on tracking potential flaws along the acquired sequence is also presented. Our inspection system achieves performance rates of 87% true positives and 0% false positives.
Towards Responsible Research and Innovation in the Information and Communication Technologies and Security Technologies Fields

This publication, introduced and edited by Rene von Schomberg, consists of a series of research articles reflecting on how to proceed towards Responsible Research and Innovation in the Information and Communication Technologies and Security Technology fields. The authors who contributed to this publication are coordinators or participants to major FP7 projects funded under the Science in Society Programme. A total of 10 projects have inspired the authors to reflect and address various governance and ethics issues underlying the responsible development of these new technologies.A deliberative approach to the responsible development of these technologies implies inclusive governance, based on broad stakeholder involvement, public debate and early societal intervention in research and innovation,among other, by means of ethics assessments and various technology and privacy impact assessments.
X-Ray and Optical Filaments in M87

We compare a very deep X-ray image of M87, at the center of the Virgo Cluster, to high-quality optical images of the low-excitation emission-line gas in the same region. There are striking coincidences of detail between the two. We explore the possibility that this represents a thermal interaction between hot gas at 107 K and warm gas at 104 K. We find that two temperatures are present in the X-ray gas, with the lower more prevalent in the vicinity of the optical filaments. Electron conduction from the hot phase to the cooler one provides a quantitatively acceptable energy source for the optical filaments, and we show additionally that it can do so for the brightest X-ray cluster, Perseus. If operative, conduction in the presence of gas-rich galaxy mergers may explain the presence of "cool cores" in clusters of galaxies.
A Multilocus Technique for Risk Evaluation of Patients with Neuroblastoma

Purpose: Precise and comprehensive analysis of neuroblastoma genetics is essential for accurate risk evaluation and only pangenomic/multilocus approaches fulfill the present-day requirements. We present the establishment and validation of the PCR-based multiplex ligation-dependent probe amplification (MLPA) technique for neuroblastoma. Experimental Design: A neuroblastoma-specific MLPA kit was designed by the SIOP Europe Neuroblastoma Biology Committee in cooperation with MRC-Holland. The contained target sequences cover 19 chromosomal arms and reference loci. Validation was performed by single locus and pangenomic techniques (n = 174). Dilution experiments for determination of minimal tumor cell percentage were performed and testing of reproducibility was checked by interlaboratory testing (n = 15). Further 156 neuroblastomas were used for establishing the amplification cutoff level. Results: The MLPA technique was tested in 310 neuroblastomas and 8 neuroblastoma cell lines (including validation and amplification cutoff level testing). Intertechnique validation showed a high concordance rate (99.5%). Interlaboratory MLPA testing (κ = 0.95, P < 0.01) revealed 7 discrepant of 1,490 results (0.5%). Validation by pangenomic techniques showed a single discordance of 190 consensus results (0.5%). The test results led to formulation of interpretation standards and to a kit revision. The minimal tumor cell percentage was fixed at 60%. Conclusions: The recently designed neuroblastoma-specific MLPA kit covers all chromosomal regions demanded by the International Neuroblastoma Risk Group for therapy stratification and includes all hitherto described genetic loci of prognostic interest for future studies and can be modified or extended at any time. Moreover, the technique is cost effective, reliable, and robust with a high interlaboratory and intertechnique concordance. Clin Cancer Res; 17(4); 792–804. ©2011 AACR.
Optimal Quadrati Spline Collo ation Methods for theShallow Water Equations on the

In this study, we present numerical methods, based on the opt imal quadratic spline collocation (OQSC) methods, for solving the shallow water equa tions (SWEs) in spherical coordinates. A quadratic spline collocation method approxim ates the solution of a differential problem by a quadratic spline. In the standard formulation, the quadratic spline is computed by making the residual of the differential equations zero at a set of collocation points; the resulting error is second order, while the error associated with quadratic spline interpolation is fourth order locally at certain points and third order glo bally. The OQSC methods generate approximations of the same order as quadratic spline int erpolation. In the one-step OQSC method, the discrete differential operators are perturbed to eliminate low-order error terms, and a high-order approximation is computed using the perturbed operators. In the two-step OQSC method, a second-order approximation is generated first, us ing the standard formulation, and then a high-order approximation is computed in a second phas e by perturbing the right sides of the equations appropriately. In this implementation, the SWEs are discretized in time usi ng the semi-Lagrangian semiimplicit scheme, which allows large timesteps while mainta ining numerical stability, and in space using the OQSC methods. The resulting methods are effic i nt and yield stable and accurate representation of the meteorologically important R ossby waves. Moreover, by adopting Part of this work was done while the author was at the Departme n of Computer Science, University of Toronto. yPartly supported by Natural Sciences and Engineering Resea rch Council (NSERC) of Canada.