Miracle-dz/UniFAR-FTUs huggingface dataset:
Stochastic reaction networks with input processes: Analysis and applications to reporter gene systems

Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and inference of these systems is addressed by parametric approaches, where the laws governing exogenous input processes, if present, are themselves fixed in advance. Motivated by reporter gene systems, widely utilized in biology to monitor gene activation at the individual cell level, we address the analysis of reaction networks with state-affine reaction rates and arbitrary input processes. We derive a generalization of the so-called moment equations where the dynamics of the network statistics are expressed as a function of the input process statistics. In stationary conditions, we provide a spectral analysis of the system and elaborate on connections with linear filtering. We then apply the theoretical results to develop a method for the reconstruction of input process statistics, namely the gene activation autocovariance function, from reporter gene population snapshot data, and demonstrate its performance on a simulated case study.
Defect oriented fault analysis for SRAM

Fault analysis is an important step in establishing detailed fault models or subsequent diagnostics and debugging of a semiconductor memory product. We have performed defect injection in the memory cell array of an industrial SRAM circuit and analyzed the faulty behavior with respect to each defect injected. We found that although some of the defects can be mapped to existing fault models, there are many defects that result in unmodeled faults. Moreover, a defect may exhibit a different faulty behavior at a different location in the cell array. The voltage and temperature parameters can also change the faulty behavior. The simulation results show that almost all open and short defects lead to stuck-at faults, transition faults, and data retention faults.
Pedestrian detection based on DCT of multi-channel feature

In order to improve the accuracy of pedestrian detection, we proposed an algorithm of multi-channel feature detection based on Discrete Cosine Transform (DCT). We use a two-layer convolution network for arranging the image information after DCT to build a new channel in the frequency domain. The channel can describe complex textures about pedestrian. Combined with the features of the histogram of gradient and the color space as well as the DCT frequency domain, a low cost multi-channel pedestrian detector has been trained based on the Adaboost algorithm. Experimental results on two datasets demonstrate that our model outperforms state-of-the-art methods and the effect is remarkable in low false positive per image.
Multi-Objective and Multi-Stage Reliability Growth Planning in Early Product-Development Stage

This paper proposes a multi-objective multi-stage reliability growth planning method in the early product-development stage. Multi-stage reliability growth planning is common in practice, and it aligns well with multiple developmental stages of a new product such as concept design, detail design, prototype design, and final production version design. The multi-objective formulation reflects the needs of product development's multiple objectives, such as program cost, schedule, and reliability. Pareto optimal solutions of the multi-objective multi-stage formulation for reliability growth planning are searched using a modified nondominated sorting genetic algorithm (NSGA-II). To reduce the large size of Pareto optimal solutions to a workable size of efficient solutions for plan implementation, both constant return-to-scale and variable return-to-scale data envelopment analysis (DEA) methods are used for determining the efficient solutions. Based on tradeoff and sensitivity analysis, insights and guidelines are presented for choosing appropriate reliability growth plans in terms of optimal allocation of testing time and testing units, and the timing for new technology introduction. The growth rate in each product-development stage and its impact on the development cost, schedule, and reliability are also discussed. An illustrative example is given to demonstrate the approach for planning the reliability growth for a next-generation engine development.
Proposition d'interface Science-Société pour la gestion intégrée de la ressource en eau dans un contexte de changements climatiques

L'eau est un besoin vital pour l'Homme et chaque societe se doit de la gerer au mieux pour subvenir a ce besoin elementaire aujourd'hui et dans l'avenir. Les changements climatiques en cours et en particulier le rechauffement climatique influencent fortement les hydrosystemes et les activites economiques de montagne forcant ces territoires a s'adapter a ces nouvelles conditions. Les choix de developpement socio-economiques ont egalement une importance preponderante dans l'emergence ou non de penuries d'eau.Au cours de cette these un modele couplant representations des ressources naturelles et des activites socio-economiques a ete construit. Il permet d'explorer a la fois les impacts sur la disponibilite des ressources en eau, des changements climatiques et des choix socio-economiques pour un territoire de montagne a differents horizons temporels. Toutes les combinaisons de scenarios climatiques et socio-economiques peuvent etre experimentees dans le modele.La station de ski de Megeve (France) a servi de terrain d'application pour le developpement du modele hydro-anthropique. Ce modele devant servir comme aide a la decision pour la mise en place de politiques d'adaptation, la delicate question du transfert de connaissances entre Science et Societe est interrogee. Via l'insertion du modele scientifique developpe dans des Serious-Games une proposition d'interface est realisee. A travers le projet C3-Alps qui a finance cette these, d'autres transferts de connaissances pour l'adaptation aux changements climatiques dans les Alpes ont egalement ete realises.
Self-electrophoresis is not the mechanism for motility in swimming cyanobacteria

Swimming cyanobacteria do not have flagella. In principle, they could be propelled by streams of ions flowing from head to tail, i.e., by a self-electrophoretic mechanism. We have ruled out this possibility by showing that cells of a swimming Synechococcus species fail to drift in an external electric field.
Cytoskeletal dysfunction dominates in DAP12-deficient osteoclasts

Despite evidence that DAP12 regulates osteoclasts, mice lacking the ITAM-bearing protein exhibit only mild osteopetrosis. Alternatively, Dap12−/− mice, also lacking FcRγ, are severely osteopetrotic, suggesting that FcRγ compensates for DAP12 deficiency in the bone-resorbing polykaryons. Controversy exists, however, as to whether these co-stimulatory molecules regulate differentiation of osteoclasts or the capacity of the mature cell to degrade bone. We find that Dap12−/− osteoclasts differentiate normally when generated on osteoblasts but have a dysfunctional cytoskeleton, impairing their ability to transmigrate through the osteoblast layer and resorb bone. To determine whether the FcRγ co-receptor, OSCAR mediates osteoclast function in the absence of DAP12, we overexpressed OSCAR fused to FLAG (OSCAR-FLAG), in Dap12−/− osteoclasts. OSCAR-FLAG partially rescues the abnormal cytoskeleton of Dap12−/− osteoclasts grown on bone, but not those grown on osteoblasts. Thus, cytoskeletal dysfunction, and not arrested differentiation, is the dominant consequence of DAP12 deficiency in osteoclasts. The failure of osteoblasts to normalize Dap12−/− osteoclasts indicates that functionally relevant quantities of OSCAR ligand do not reside in bone-forming cells.
Selective color correction for arbitrary hues

This paper proposes new selective color correction methods for digital color images, which do not require masking of the correction area. The most commonly employed method can only effectively correct pixels containing one of six specific hues (R.G.B.C.M.Y). In response to this situation, the authors have developed two new selective color correction methods, the HSV method and the RGB subtractive method, both of which can be applied to arbitrary hues within a adjustable hue range. In actual testing, the methods have produced excellent results, and may be expected to make it easier for users to retouch photograph images.
A low-power reconfigurable ADC for biomedical sensor interfaces

This paper presents a 12-bit low-voltage low-power reconfigurable Analog-to-Digital Converter (ADC). The design employs Switched Capacitor (SC) techniques and implements a Successive Approximation (SA) algorithm. The ADC can be tuned to handle a large variety of biopotential signals, with digitally selectable resolution and input signal amplitude. It achieves 10.4-bit of effective resolution sampling at 56 kS/s, with a power consumption below 3 ¿W from a 1 V voltage supply.
Impact of FD-SOI on Deep-Sub-100-nm CMOS LSIs -A View of Memory Designers-

A planar double-gate FD-SOI is compared with the bulk CMOS in terms of low-voltage operations. It turns out that due to the small VT variation the FD-SOI is suitable for deep-sub-1 V operations with improved voltage margin of RAM cells and sense amplifiers, and reduced speed variations of logic gates
Comparison of Different Methods for Detection of Biofilm Production in Multi-Drug Resistance Bacteria Causing

Tonsillitis and Pharyngitis are an infection of the throat region poses one of the most common problems in the upper respiratory tract infection and are one of the main reasons leading the persons to seek advice from a physician. This study was carried out during the period (December, 2012 to August, 2013). A total of two hundred of throat sawbs were collected from patients with tonsillitis and pharyngitis infection at the age ranged between (1-70) years, who were attending the clinic outpatient unit in Rizgary and Raparin teaching hospitals in Erbil city. Throat swabs were collected and examined for microscopically using Gram stain examination and culture technique. Isolated microorganisms were identified using microscopical, morphological, biochemical tests and Vitek2 co mpact system. The results showed that 134 (67%) of throat swabs were culture positive the total number of isolated microorganism isolates obtained from patients were (185) isolates. According to antibiotic sensitivity test most of the Gram-positive bacteria isolates and Gram negative bacteria isolates showed high resistance to antibiotics that used. All Gram-positive and Gram-negative bacteria isolates (177) were screened for biofilm production as one of the virulence factors by using three different methods (Tissue culture plate method, Congo red agar method and Tube method) and the results showed that the tissue culture plate method was the most sensitive method for detection of biofilm production. The results by tissue culture plate method by using ELISA (Enzyme-Linked immune sorbent assay) system were 17 (9.61%) non or weak and 160 (90.39%) were strong and moderate biofilm producers, while by congo red agar method 26 (14.7%) non or weak and 151 (85.3%) were strong and moderate biofilm producers and by tube method 47 (26.5%) non or weak and 130 (73.5%) were strong and moderate biofilm producers. The highest percentage of bacterial biofilm producers were resistant to (7) antibiotics.
Simplified mathematical description of longitudinal recovery in multiple‐echo sequences

The intensity of multiple echoes separated by a time 2τ has been modeled using the closed form of a finite geometric series. This eliminates long exponential series, introduces the number of echoes as an independent parameter, and corrects for the net T1 relaxation during the echo train. Other sequences having echo trains can be modeled similarly. © 1987 Academic Press, Inc.
The effect of epidural injection speed on epidural pressure and distribution of solution in anesthetized dogs.

OBJECTIVE To determine the effect of injection speed on epidural pressure (EP), injection pressure (IP), epidural distribution (ED) of solution, and extent of sensory blockade (SB) during lumbosacral epidural anesthesia in dogs. STUDY DESIGN Prospective experimental trial. ANIMALS Ten healthy adult Beagle dogs weighing 8.7 ± 1.6 kg. METHODS General anesthesia was induced with propofol administered intravenously and maintained with isoflurane. Keeping the dogs in sternal recumbency, two spinal needles connected to electrical pressure transducers were inserted into the L6-L7 and the L7-S1 intervertebral epidural spaces for EP and IP measurements, respectively. Bupivacaine 0.5% diluted in iohexol was administered epidurally to each dog via spinal needle at L7-S1 intervertebral space, at two rates of injection (1 and 2 mL minute(-1) groups), with a 1-week washout period. Epidural distribution was verified with computed tomography, and SB was evaluated after arousal by pinching the skin with a mosquito hemostatic forceps over the vertebral dermatomes. The results were analyzed according to each injection speed, using paired t- and Wilcoxon signed-rank tests. RESULTS Mean ± SD of baseline EP and IP values were 2.1 ± 6.1 and 2.6 ± 7.1 mmHg, respectively. Significant differences were observed between 1 and 2 mL minute(-1) groups for peak EP (23.1 ± 8.5 and 35.0 ± 14.5 mmHg, p = 0.047) and peak IP (68.5 ± 10.7 and 144.7 ± 32.6 mmHg, p <0.001). However, the median (range) of the ED, 11.5 (4-22) and 12 (5-21) vertebrae, and SB, 3.5 (0-20) and 1 (0-20) dermatomes, values of the two groups were not related to injection speed. CONCLUSIONS AND CLINICAL RELEVANCE The EP profile during injection was measured by separating the injection and pressure monitoring lines. The increase in epidural injection speed increased the EP, but not the ED or the SB in dogs.
Sparse group testing codes for low-energy massive random access

We present random access protocols for machinetype communication where a massive number of low-energy wireless devices want to occasionally transmit short information packets. We focus on the device discovery problem, with extensions to joint discovery and data transmission as well as data transmission without communicating the device identities. We formulate this problem as a combinatorial group testing problem, where the goal is to exactly identify the set of at most d defective items from a pool of n items. We translate the energy constraint at the wireless physical layer to a constraint on the number of tests each item can participate in, and study the resulting “sparse” combinatorial group testing problem. The celebrated result for the combinatorial group testing problem is that the number of tests t can be made logarithmic in n when d = O (log n). However, state-of-the-art group testing codes require the items to be tested w = Ω(d log n/ log d + log log n) times. In our sparse setting, we restrict the number of tests each item can participate in by w<inf>max</inf>. We show that t decreases suddenly from n to (d + 1)√n when w<inf>max</inf> is increased from d to d + 1. If w<inf>max</inf> = ld + 1 for any positive integer l such that ld + 1 ≤ l+1√n we can achieve t = (ld + 1)n<sup>1/(i+1)</sup>. We also prove a nearly matching lower bound. These results reveal a favorable trade-off between energy and spectral efficiency for random access.
Measuring Dynamics of Risk and Performance of Sector Indices on Zagreb Stock Exchange

Abstract Investors are interested in sector diversification on stock markets among other important portfolio topics. This paper looks at five sector indices on Croatian capital market as an example of a small, relatively illiquid market. Sector indices have been constructed at the beginning of 2013 and since then there is a lack of studies, which focus on sector diversification on Zagreb Stock Exchange (ZSE). Thus, the purpose of this paper is to evaluate the recent dynamics of risk and performance of five sector indices on ZSE by employing MGARCH (Multivariate Generalized Autoregressive Conditional Heteroskedasticity) models empirically. Output from the analysis is used to form guidance for investors on Croatian capital market. The results indicate that in the observed period from February 4th 2013 to October 13th 2015 portfolios based on MGARCH methodology outperform other portfolios in terms return and risk. Thus, it is advisable to use this methodology when making portfolio selection.
Prise en charge des personnes vivant avec le virus de l'immunodéficience humaine en zone décentralisée au Cameroun

L'infection par le VIH represente toujours un probleme de sante publique majeur, en particulier en Afrique sub-saharienne. Le passage a l'echelle des traitements antiretroviraux est un enjeu majeur, et implique une veritable cascade de soins, c'est a dire un continuum entre l'infection, son depistage, sa prise en charge, son suivi clinique et biologique au long cours et l'obtention d'une charge virale indetectable – marqueur du controle de l'infection –. Seule la decentralisation des programmes de prise en charge permet d'elargir l'acces a ce continuum de soins. Dans cette these, nous explorerons certains des ecueils rencontres dans le cadre de la decentralisation de l'acces aux antiretroviraux, en nous appuyant sur des etudes menees de 2006 a 2013 dans la region du Centre du Cameroun. Dans un premier article, l'impact de la delegation des tâches des medecins vers les infirmiers est evalue au travers de la cohorte de patients suivis dans les 9 hopitaux de District ruraux de l'essai clinique Stratall. Notre analyse montre que cette solution pour pallier le deficit de medecins preserve les resultats cliniques et biologiques des patients sur les deux premieres annees de traitement. Dans un deuxieme article, la pertinence de differents criteres definissant l'echec therapeutique est evaluee pour predire l'apparition de resistance du VIH aux antiretroviraux. Nonobstant les difficultes de deploiement des outils du suivi biologique, nos resultats soulignent l'importance de l'evaluation de la charge virale pour predire l'apparition de cette resistance, et en particulier d'une deuxieme mesure rapide apres la premiere notion de detectabilite pour effectuer un changement pour une seconde ligne de traitement dans les meilleurs delais. Le troisieme volet de la these s'interesse aux difficultes liees aux individus, en particulier liees au sexe. Nos resultats montrent que les hommes sont plus vulnerables a l'echec therapeutique que les femmes malgre une observance similaire. Enfin le quatrieme volet fait le bilan d'une prise en charge de routine, a l'hopital de District de Mfou au Cameroun. Nos resultats s'ajoutent a ceux deja publies pour permettre de formuler des recommandations de sante publique sur la delegation des tâches et la definition de l'echec. Ils soulevent egalement des perspectives de recherche en mettant a mal le paradigme de l'observance pour expliquer une difference d'efficacite therapeutique entre hommes et femmes en zone decentralisee.
Localized 1H NMR spectroscopy in different regions of human brain in vivo at 7 T: T2 relaxation times and concentrations of cerebral metabolites

At the high field strength of 7 T, in vivo spectra of the human brain with exceptional spectral quality sufficient to quantify 16 metabolites have been obtained previously only in the occipital lobe. However, neurochemical abnormalities associated with many brain disorders are expected to occur in brain structures other than the occipital lobe. The purpose of the present study was to obtain high‐quality spectra from various brain regions at 7 T and to quantify the concentrations of different metabolites. To obtain concentrations of metabolites within four different regions of the brain, such as the occipital lobe, motor cortex, basal ganglia and cerebellum, the T2 relaxation times of the singlets and J‐coupled metabolites in these regions were measured for the first time at 7 T. Our results demonstrate that high‐quality, quantifiable spectra can be obtained in regions other than the occipital lobe at 7 T utilizing a 16‐channel transceiver coil and B1+ shimming. Copyright © 2011 John Wiley & Sons, Ltd.
Lyapunov Function and Local Feedback Boundary Stabilization of the Navier--Stokes Equations

We study the local exponential stabilization, near a given steady-state flow, of solutions of the Navier-Stokes equations in a bounded domain. The control is performed through a Dirichlet boundary condition. We apply a linear feedback controller, provided by a well-posed infinite-dimensional Riccati equation. We give a characterization of the domain of the closed-loop operator which is obtained from the closed-loop linearized Navier-Stokes system. We give a class of initial data for which a Lyapunov function is obtained. For all $s\in[0,1/2[$, the stabilization of the two-dimensional Navier-Stokes equations is proved for initial data in $\mathbf{H}^s(\Omega)\cap V_n^0(\Omega)$, where $V_n^0(\Omega)$ is the space in which the Stokes operator is defined. We also obtain a three-dimensional stabilization result but only for a very specific set of initial data.
Distribution and phenotype of dendritic cells and resident tissue macrophages in the dura mater, leptomeninges, and choroid plexus of the rat brain as demonstrated in wholemount preparations

Dendritic cells (DC) are regarded as the 'sentinels' of the immune system. They play a crucial role in surveillance of peripheral tissues, trapping antigens encountered there, and migrating via the lymphatics to lymphoid organs where they interact with naive T cells thus generating antigen‐specific primary immune responses. Until now it has been assumed DC are largely absent from the brain, meninges, and the choroid plexus within the ventricles. Such a situation was thought to partly explain the 'immune privileged' nature of the central nervous system (CNS). The present study of normal rat tissues using single and double immunohistochemistry reveals for the first time that extensive networks of major histocompatability (MHC) class II+/OX62+ DC are widely distributed in sites which may potentially encounter CNS antigens. These sites included the dura mater, leptomeninges, and the choroid plexus. These putative DC were negative when stained with the anti‐resident tissue macrophage monoclonal antibody ED2. In addition to the rich networks of DC, dense populations of resident tissue macrophages (ED2+ and ED1+) were also demonstrated in the dura mater, leptomeninges and to a lesser extent in the choroid plexus. The presence of rich networks of DC and macrophages in the vascular and supporting tissues of the brain may play an important role in inflammatory and immune‐mediated disorders affecting the CNS, including auto‐immune demyelinating diseases such as multiple sclerosis. J. Comp. Neurol. 405:553–562, 1999. © 1999 Wiley‐Liss, Inc.