Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive intervention in Probabilistic Boolean Networks

Probabilistic Boolean Networks (PBNs) have been recently introduced as a paradigm for modeling genetic regulatory networks. One of the objectives of PBN modeling is to use the network for the design and analysis of intervention strategies aimed at moving the network out of undesirable states, such as those associated with disease, and into desirable ones. To date, a number of intervention strategies have been proposed in the context of PBNs. However, most of these techniques assume perfect knowledge of the transition probability matrix of the PBN. Such an assumption cannot be satisfied in practice, and may lead to degraded, if not completely unacceptable, performance. To remedy the situation, one can adopt one of two main approaches:(i) design an intervention strategy that is “robust” or somewhat insensitive to the presence of a class of modeling errors, such as uncertainties in the transition probability matrix; or (ii) introduce on-line adaptation or learning into the intervention strategy to ensure satisfactory performance provided the modeling error belongs to a particular class. The first approach has already been developed in an earlier paper. The main goal of this paper is to demonstrate the feasibility of the second approach. Using simulation studies, it is shown that adaptive intervention works well in two different scenarios: first, when we have a family of PBNs whose individual transition probability matrices are reasonably well modeled and the predominant uncertainty is about which member of that family represents the underlying genetic regulatory network; and second, when we have a context sensitive PBN with a low probability of a context change so that there is sufficient time between context changes for the adaptive algorithm to learn the context and exploit it in the intervention design. These results agree quite well with intuitive expectations.
RPT2 Is a Signal Transducer Involved in Phototropic Response and Stomatal Opening by Association with Phototropin 1 in Arabidopsis thaliana

Phototropin 1 (phot1) and phot2, which are blue light receptor kinases, function in blue light–induced hypocotyl phototropism, chloroplast relocation, and stomatal opening in Arabidopsis (Arabidopsis thaliana). Previous studies have shown that the proteins RPT2 (for ROOT PHOTOTROPISM2) and NPH3 (for NONPHOTOTROPIC HYPOCOTYL3) transduce signals downstream of phototropins to induce the phototropic response. However, the involvement of RPT2 and NPH3 in stomatal opening and in chloroplast relocation mediated by phot1 and phot2 was unknown. Genetic analysis of the rpt2 mutant and of a series of double mutants indicates that RPT2 is involved in the phot1-induced phototropic response and stomatal opening but not in chloroplast relocation or phot2-induced movements. Biochemical analyses indicate that RPT2 is purified in the crude microsomal fraction, as well as phot1 and NPH3, and that RPT2 makes a complex with phot1 in vivo. On the other hand, NPH3 is not necessary for stomatal opening or chloroplast relocation. Thus, these results suggest that phot1 and phot2 choose different signal transducers to induce three responses: phototropic response of hypocotyl, stomatal opening, and chloroplast relocation.
Connecting OCL with the Rest of the World

The paper addresses the problems of making program specifications written in OCL easier to read and to maintain. The solution proposed is to use the grammar formalism GF to define a high-level abstract grammar of specifications with translations into OCL, logic, and natural languages. A prototype of the solution is illustrated by an example.
HCN2 and HCN4 Isoforms Self-assemble and Co-assemble with Equal Preference to Form Functional Pacemaker Channels*

Hyperpolarization-activated cyclic nucleotide-modulated (HCN) “pacemaker” channel subunits are integral membrane proteins that assemble as tetramers to form channels in cardiac conduction tissue and nerve cells. Previous studies have suggested that the HCN2 and HCN4 channel isoforms physically interact when overexpressed in mammalian cells, but whether they are able to co-assemble and form functional channels remains unclear. The extent to which co-assembly occurs over self-assembly and whether HCN2-HCN4 heteromeric channels are formed in native tissue are not known. In this study, we show co-assembly of HCN2 and HCN4 in live Chinese hamster ovary cells using bioluminescence resonance energy transfer (BRET2), a novel approach for studying tetramerization of ion channel subunits. Together with results from electrophysiological and imaging approaches, the BRET2 data show that HCN2 and HCN4 subunits self-assemble and co-assemble with equal preference. We also demonstrate colocalization of HCN2 and HCN4 and a positive correlation of their intensities in the embryonic mouse heart using immunohistochemistry, as well as physical interactions between these isoforms in the rat thalamus by coimmunoprecipitation. Together, these data support the formation of HCN2-HCN4 heteromeric channels in native tissue.
Laser in Situ Keratomileusis for Treatment of Fully or Partially Refractive Accommodative Esotropia

Purpose To evaluate the efficacy and safety of laser in situ keratomileusis (LASIK) in partially refractive accommodative esotropia (pRAE) and fully refractive accommodative esotropia (fRAE). Methods Forty-two eyes of 21 patients who had LASIK for correcting hyperopic refractive error were evaluated. Refractive errors, uncorrected visual acuity (UCVA) and best-corrected visual acuity (BCVA), ocular alignment, and stereopsis were recorded before and after LASIK. Results Sixteen patients with fRAE and 5 with pRAE were evaluated. Mean age at the time of surgery was 19.00±3.79 years. Mean follow-up time was 12.19±4.51 months. For the fRAE group, the mean preoperative angle of deviation without spectacle correction was +19.13±5.87 prism diopters (PD); all were orthophoric with spectacles. Postoperatively, all these patients achieved less than 10 PD of deviation without spectacles. For the pRAE group, the mean preoperative angle of deviation was +32.60±9.81 PD and +14.60±6.14 PD without and with spectacles, respectively. Postoperatively, the mean angle of deviation was +13.60±5.72 PD and +12.80±5.40 PD without and with spectacles, respectively. For all 21 patients, the preoperative mean spherical equivalent (SE) with cycloplegia was +4.94±1.43 diopters (D); it was +1.49D±0.70 D postoperatively. Three eyes lost 1 line of BCVA and 3 eyes gained 1 line. No intraoperative complication was recorded. Conclusions LASIK is a safe and effective method for treating refractive error and creating orthophoria in fRAE. In pRAE, it eliminates the refractive component of deviation safely and effectively. (Eur J Ophthalmol 2009; 19: 733–7)
New radiochromic gel for 3D dosimetry based on Turnbull blue: basic properties

The recently developed new radiochromic gel dosimeter based on Turnbull blue dye formed by irradiation (the TBG dosimeter) does not exhibit dose pattern degradation due to diffusion effects as observed in the Fricke-gel dosimeter with xylenol orange incorporated into the gel matrix (the FXG dosimeter). The TBG dosimeter can be easily prepared and its optical properties enable evaluation of the gel's response using the cone-beam optical computed tomography technique. The preparation procedure is described in the paper along with the basic characteristics of the gel, including dose response, dose sensitivity, ageing under different storage conditions, diffusion rates of Turnbull blue and gel density. The measurement of diffusion is described in more detail. The same method was applied to the FXG dosimeter for direct comparison. It was found that the diffusion coefficient of the TBG dosimeter stored at 24 °C is less than 4 × 10−3 mm2 h−1 (1σ confidence level), compared to the value of 7.3 × 10−1 mm2 h−1 (1σ) of the FXG dosimeter measured at the same temperature. Although the TBG dosimeter is less sensitive than the FXG dosimeter, its diffusion coefficient is practically negligible and, therefore, it offers large potential as a three-dimensional dosimeter for applications encompassing sharp dose gradients such as high-dose-rate brachytherapy.
The Hybrid Service Model of Electronic Resources Access in the Cloud-Based Learning Environment

Nowadays, the search for innovative technological solutions to the organization of access to electronic learning resources in the university and their configuration within the environment to fit the needs of users and to improve learning outcomes has become key issues. These solutions are based on the emerging tools among which cloud computing and ICT outsourcing have become very promising and important trends in research. The problems of providing access to electronic learning resources on the basis of cloud computing are the focus of the article. The article outlines the conceptual framework of the study by reviewing existing approaches and models for the cloud-based learning environment's architecture and design, including its advantages and disadvantages, and the features of its pedagogical application and the experience of it. The hybrid service model of access to learning resources within the university environment is described and proved. An empirical estimation of the proposed approach and current developments in its implementation are provided.
Development of a Hand-Launched Small UAV for Ground Reconnaissance

The engineering design of a hand-launched, small unmanned aerial vehicle (SUAV), including guidance strategy and control design, together with real data from practical flight tests, is presented. The main goal in this work is the implementation of a low cost, portable, and reliable aerial platform for ground reconnaissance. The vehicle was specially designed so that the number of necessary sensors and actuators was reduced, without precluding the feasibility of the assigned mission.
Genetic Variation in an Individual Human Exome

There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's ‘exome,’ which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the ∼12,500 variants that affect the protein coding portion of an individual's genome. We identified ∼10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which ∼15–20% are rare in the human population. We predict ∼1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the ∼700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of ∼12,500 nonsilent coding variants by ∼8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation.
Edema formation in the hyperacute phase of ischemic stroke. Laboratory investigation.

OBJECT Brain edema formation is a serious complication of ischemic stroke and can lead to mechanical compression of adjacent brain structures, cerebral herniation, and death. Furthermore, the space-occupying effect of edema impairs regional cerebral blood flow (rCBF), which is particularly important in the penumbra phase of stroke. In the present study, the authors evaluated the natural course of edema formation in the hyperacute phase of focal cerebral ischemia. METHODS Middle cerebral artery occlusion (MCAO) or a sham procedure was performed in rats within an MR imaging unit (in-bore occlusion). Both pre- and postischemic images could be compared on a pixel-by-pixel basis. The T2 relaxation time (T2RT), a marker for brain water content, was measured in regions of interest. RESULTS A significant increase in the T2RT was detectable as early as 20-45 minutes after MCAO. At this early time point the midline shift (MLS) amounted to 0.214 +/- 0.092 cm in the MCAO group and 0.061 +/- 0.063 cm in the sham group (p < 0.007). The T2RT and MLS increased linearly thereafter. Evans blue dye was intravenously injected in additional animals 20 and 155 minutes after MCAO. Extravasation of the dye was visible in all animals, indicating increased permeability of the blood-brain barrier. CONCLUSIONS Vasogenic brain edema occurs much earlier than expected following permanent MCAO and leads to MLS and mechanical compression of adjacent brain structures. Since compression effects can impair rCBF, early edema formation can significantly contribute to infarct formation and thus represents a promising target for neuroprotection.
IMS-enabled interactive broadcasting network utilizing peer to peer constellations

This paper propose an overlay interoperability technology for introducing the concept of Peer to peer (P2P) communications in the context of IP Multimedia Subsystem (IMS) enabled interactive broadcasting networks (iDVB-T), bearing the following: a) user initiated conception of communication applications paradigms and deployment, b) access of users on P2P applications from any rural-access network, and c) creation of a new ecosystem of users, emerging different behaviour from the traditional consumers, gearing-up new business and revenue prospects. The overall assessment of the proposed P2P-IMS architecture is evaluated by Real transmission reception experiments justifying the interoperability and validity of the iDVB-T environment proposed.
Improving the ability of matching pursuit algorithm in detecting spikes

Detection of signal transients, or spikes, is a suitable application of time-frequency signal processing. One such time-frequency method for spike detection is matching pursuit, incorporating a redundant time-frequency dictionary. However, problems arise when using matching pursuit to detect repetitive rhythmical spiking, which is a common characteristic in an application such as newborn EEG seizure detection. In this paper we investigate the ability of matching pursuit to detect spikes both in synthetic signals and real newborn EEG seizure. It is shown that repetitive spikes may be recognised by matching pursuit as harmonic patterns rather than individual spikes. Consequently, these spikes cannot be located in the matching pursuit time-frequency domain representation. However, we have found that the relationship between the length of a repetitive spike sequence and interval between successive spikes in the sequence plays a pivotal role in the ability of matching pursuit to detect these spikes.
An exploratory study of patent litigation behavior: Evidence from the smartphone industry

This study aims at providing a framework to delineate the patent litigation behaviors based on the resource-based view, transaction cost economics, and the view of competitive dynamics. Empirical data were collected from the smartphone industry during the period from 2003 to 2011. Propositions are raised to illustrate how high-tech firms launch patent litigation attacks, including what focused patents are, whom firms are motivated to attack, when to initiate an attack, and where to file the lawsuit. We first conclude that a patent with higher value would be more likely to cause litigation. Second, the firm with a dominant design is more likely to be attacked by the incumbents through patent litigation while enjoying greater performance and the defendant usually initiates a countersuit against their competitors with their own patents. Third, the more important stake of the patents in dispute, the more likely the plaintiff will choose the courts skilled in dealing with the complexities of patent law and the technology at issue, and the more likely the patentee will file patent litigations in district court and International Trade Commission at the same time. The study not only contributes to the patent theory, but also benefits both firms from developing and developed countries in formulating offensive and/or defensive patent litigation strategies.
Approximation by approximate interpolation neural networks with single hidden layer

A bounded function φ defined on (−∞, +∞) is called general sigmoidal function if it satisfies lim<inf>x→+∞</inf>φ(x) = M, lim<inf>x→−∞</inf>φ(x) = m. Using the general sigmoidal function as the activation function, a type of neural networks with single hidden layer and n + 1 hidden neurons is constructed. These networks are called approximate interpolation networks, which can approximately interpolate, with arbitrary precision, any set of distinct data in one dimension. By using the modulus of continuity of function as metric, the errors of approximation by the constructed networks is estimated.
Scalable distributed visualization using off-the-shelf components

This paper describes a visualization architecture for scalable computer systems. The architecture is currently being prototyped for use in Beowulf-class clustered systems. A set of OpenGL frame buffers are driven in parallel by a set of CPUs. The visualization architecture merges the contents of these frame buffers by user programmable associative and commutative combining operations. The system hardware is built from off-the-shelf components including OpenGL accelerators, field programmable gate arrays (FPGAs), and gigabit network interfaces and switches. A second generation prototype supports 60 Hz operation at 1024/spl times/1024 pixel resolution with interactive latency up to 1000 nodes.
Role of Adipose Tissue for Cardiovascular-Renal Regulation in Health and Disease

Obesity is associated with profound alterations of the cardiovascular system including an increase in systemic blood pressure. Several vasoactive factors, including non-esterified fatty acids, angiotensin II, prostaglandins, and nitric oxide are known to be produced by adipose tissue, and are therefore of particular interest regarding their potential role for the regulation of vascular tone and structure. In addition, central nervous system actions of the adipose tissue-derived hormone leptin may contribute to increased sympathetic nervous system activity that is typically found in obesity. Enhanced leptin-driven renal sympathetic out-flow, in combination with low atrial natriuretic peptide plasma levels possibly due to over-expression of the natriuretic peptide clearance receptor in adipocytes, may enhance sodium retention and volume expansion, both key features in the pathophysiology of obesity-associated hypertension. In this review, we discuss these and other possible contributions of adipose tissue to the regulation of cardiovascular-renal function and speculate on the role of adipose tissue for the development of obesity-associated hypertension.
Dynamic bitstream switching using progressive S-frames for scalable video transmission

In this paper, a new dynamic bitstream switching method using progressive S-frames is presented. The progressive S-frames method can effectively switch two pre-encoded streams by reducing progressively the quantization mismatch. Progressive S-frames can provide better coding efficiency than an S-frame. Moreover, the proposed method can avoid the buffer overflow at the encoder and decoder sides while providing a soft transition between the quality levels of two bitstreams. The simulation results show that the proposed method is useful for the bit rate adaptation in heterogeneous networks.
Une autre sociologie des usages ? Pistes et postures pour l'étude des chaînes sociotechniques

Cet article dessine le cadre d'une sociologie des usages elargie. Il souligne les limites de la sociologie des usages traditionnelle : l'absence d'enquete sur les technologies elles-memes et la superficialite de l'analyse des pratiques quotidiennes. Et montre que la theorie de l'acteur reseau et les differents courants de recherche partageant une approche ecologique de l'activite offrent des pistes d'enrichissement particulierement utiles.
Switch Port Allocation in WDM Networks with Hybrid Optical-Electronic Switching Nodes

We investigate the problem of switch port allocation in WDM networks that use the hybrid optical-electronic switching node architecture. The objective is to support given traffic demands while minimizing the number of electronic switch ports used, or equivalently minimizing the number of established lightpaths. We first formulate the problem as a mixed integer linear programming (MILP) problem. However, due to the high computational complexity of exact optimization, we develop a simulated annealing (SA) algorithm to get an approximate solution. Results from the SA algorithm demonstrate that, compared to the optical-electrical-optical (O-E-O) node architecture, a WDM network that employs the hybrid switching node architecture requires many fewer lightpaths. We also develop a lightpath assignment heuristic which requires much less computation time than the SA algorithm while maintaining close objective values. The lightpath assignment heuristic is used to investigate the switch port allocation behaviors. Simulation results show that nodes with high degrees or with small average node distances require large numbers of optical switch ports. Moreover, nodes with large amounts of terminate (originated/destined) traffic require large numbers of electronic switch ports. Since the lightpath assignment heuristic requires small computation time, it can be used in the network design process in which a large number of network scenarios must be considered.