Miracle-dz/UniFAR-FTUs huggingface dataset:
Setting-up an In Vitro Model of Rat Blood-brain Barrier (BBB): A Focus on BBB Impermeability and Receptor-mediated Transport

The blood brain barrier (BBB) specifically regulates molecular and cellular flux between the blood and the nervous tissue. Our aim was to develop and characterize a highly reproducible rat syngeneic in vitro model of the BBB using co-cultures of primary rat brain endothelial cells (RBEC) and astrocytes to study receptors involved in transcytosis across the endothelial cell monolayer. Astrocytes were isolated by mechanical dissection following trypsin digestion and were frozen for later co-culture. RBEC were isolated from 5-week-old rat cortices. The brains were cleaned of meninges and white matter, and mechanically dissociated following enzymatic digestion. Thereafter, the tissue homogenate was centrifuged in bovine serum albumin to separate vessel fragments from nervous tissue. The vessel fragments underwent a second enzymatic digestion to free endothelial cells from their extracellular matrix. The remaining contaminating cells such as pericytes were further eliminated by plating the microvessel fragments in puromycin-containing medium. They were then passaged onto filters for co-culture with astrocytes grown on the bottom of the wells. RBEC expressed high levels of tight junction (TJ) proteins such as occludin, claudin-5 and ZO-1 with a typical localization at the cell borders. The transendothelial electrical resistance (TEER) of brain endothelial monolayers, indicating the tightness of TJs reached 300 ohm·cm2 on average. The endothelial permeability coefficients (Pe) for lucifer yellow (LY) was highly reproducible with an average of 0.26 ± 0.11 x 10-3 cm/min. Brain endothelial cells organized in monolayers expressed the efflux transporter P-glycoprotein (P-gp), showed a polarized transport of rhodamine 123, a ligand for P-gp, and showed specific transport of transferrin-Cy3 and DiILDL across the endothelial cell monolayer. In conclusion, we provide a protocol for setting up an in vitro BBB model that is highly reproducible due to the quality assurance methods, and that is suitable for research on BBB transporters and receptors.
Bounded Decomposition of Stochastic Models

In this extended abstract we discuss bounding techniques for a collection of interacting simple QN and SAN models that we have been developing. Each simple model pro- duces bounded output when presented with bounded inputs. A collection of bounded models can be used to construct larger models that have the same bounding properties. Additionally, the constructed model can be decomposed at the boundaries of the sub-structures, resulting in bounded submodels that can exchange bounded results. These bounds explicitly demonstrate the accuracy of the solution, and can be used to determine if the models need to be refined to increase the accuracy of the solution. This work is based on the observation that many simple Petri net structures can be compared to G/GI/1 queues either directly or indirectly. Bounds exist for total delay of customers through G/GI/1 queues, and for other quantities. We have developed new bounds for the departure process based upon existing bounds.
Constructing RBAC Based Security Model in u-Healthcare Service Platform

In today's era of aging society, people want to handle personal health care by themselves in everyday life. In particular, the evolution of medical and IT convergence technology and mobile smart devices has made it possible for people to gather information on their health status anytime and anywhere easily using biometric information acquisition devices. Healthcare information systems can contribute to the improvement of the nation's healthcare quality and the reduction of related cost. However, there are no perfect security models or mechanisms for healthcare service applications, and privacy information can therefore be leaked. In this paper, we examine security requirements related to privacy protection in u-healthcare service and propose an extended RBAC based security model. We propose and design u-healthcare service integration platform (u-HCSIP) applying RBAC security model. The proposed u-HCSIP performs four main functions: storing and exchanging personal health records (PHR), recommending meals and exercise, buying/selling private health information or experience, and managing personal health data using smart devices.
An NMR assignment module implemented in the Gifa NMR processing program

MOTIVATION Peptide and protein structures are determined daily using NMR spectroscopy. Assignment of the NMR spectra is an important step within the procedure and is usually the limiting one. Computer-aided assignment tools should be user friendly with open architecture to communicate with other programs involved in the structure determination. RESULTS Here we present an interactive NMR assignment module which provides numerous graphic tools for the user. The module is composed of a database management system-handling peaks, spins and spin-systems. The assignment information is maintained as a set of interrelated associative arrays, which serve as generic high-level data structures. The module is developed in the macro language embedded in the Gifa NMR processing program (Pons et al. , J. Biomol. NMR, 8 , 445-452, 1996). This provides the user with a consistent interface, a set of sophisticated tools, and an easily extendible and customizable environment. AVAILABILITY The program is available on request from the authors. The Gifa package can be accessed at: ((http://www.cbs. univ-montp1.fr/GIFA)) CONTACT: Marc-Andre.Delsuc@cbs.univ-montp1.fr
Dual-Engine Cross-ISA DBTO Technique Utilising MultiThreaded Support for Multicore Processor System

The emergence of new era of Internet of Things or IoT have encouraged intensive if not extensive usage of modern mobile apps, thus multi-ISA equipped multicore processor gain great potential to be used for more efficient instruction binary processing in near future. In order to support this ISA diversity of computing platforms, mix modes of statically and dynamically Binary Translation and Optimization system, popularly consists of QEMU and LLVM or similar system, is the default technique used. However this complex system exhibits heavy slowdown (60x slowdown as compare to generic QEMU) [21] which impede its performance especially for short running application codes, typically used in IoT based apps applications. This research introduce a dual binary code translation engines to support apps based and kernel based application codes, through utilising multithreaded supported apart of original single thread supported binary translation processing in run-time. The dual engine consists of TCG generator from QEMU, and LLVM which include rich optimisations library. The evaluation through PARSEC-3.0 Benchmark shows our Hybrid DBTO system achieved performance improvement approaching 2.0x for apps based programs and 1.25x for kernel based programs, for x86 to X86-64 emulation. This technique possess great potential and serve as research based platform for future binary translation technique development, including adaptive method.
De Novo Transcriptomic Analysis of Peripheral Blood Lymphocytes from the Chinese Goose: Gene Discovery and Immune System Pathway Description

Background The Chinese goose is one of the most economically important poultry birds and is a natural reservoir for many avian viruses. However, the nature and regulation of the innate and adaptive immune systems of this waterfowl species are not completely understood due to limited information on the goose genome. Recently, transcriptome sequencing technology was applied in the genomic studies focused on novel gene discovery. Thus, this study described the transcriptome of the goose peripheral blood lymphocytes to identify immunity relevant genes. Principal Findings De novo transcriptome assembly of the goose peripheral blood lymphocytes was sequenced by Illumina-Solexa technology. In total, 211,198 unigenes were assembled from the 69.36 million cleaned reads. The average length, N50 size and the maximum length of the assembled unigenes were 687 bp, 1,298 bp and 18,992 bp, respectively. A total of 36,854 unigenes showed similarity by BLAST search against the NCBI non-redundant (Nr) protein database. For functional classification, 163,161 unigenes were comprised of three Gene Ontology (Go) categories and 67 subcategories. A total of 15,334 unigenes were annotated into 25 eukaryotic orthologous groups (KOGs) categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) database annotated 39,585 unigenes into six biological functional groups and 308 pathways. Among the 2,757 unigenes that participated in the 15 immune system KEGG pathways, 125 of the most important immune relevant genes were summarized and analyzed by STRING analysis to identify gene interactions and relationships. Moreover, 10 genes were confirmed by PCR and analyzed. Of these 125 unigenes, 109 unigenes, approximately 87%, were not previously identified in the goose. Conclusion This de novo transcriptome analysis could provide important Chinese goose sequence information and highlights the value of new gene discovery, pathways investigation and immune system gene identification, and comparison with other avian species as useful tools to understand the goose immune system.
The Neural Correlates of Long-Term Carryover following Functional Electrical Stimulation for Stroke

Neurorehabilitation effective delivery for stroke is likely to be improved by establishing a mechanistic understanding of how to enhance adaptive plasticity. Functional electrical stimulation is effective at reducing poststroke foot drop; in some patients, the effect persists after therapy has finished with an unknown mechanism. We used fMRI to examine neural correlates of functional electrical stimulation key elements, volitional intent to move and concurrent stimulation, in a group of chronic stroke patients receiving functional electrical stimulation for foot-drop correction. Patients exhibited task-related activation in a complex network, sharing bilateral sensorimotor and supplementary motor activation with age-matched controls. We observed consistent separation of patients with and without carryover effect on the basis of brain responses. Patients who experienced the carryover effect had responses in supplementary motor area that correspond to healthy controls; the interaction between experimental factors in contralateral angular gyrus was seen only in those without carryover. We suggest that the functional electrical stimulation carryover mechanism of action is based on movement prediction and sense of agency/body ownership—the ability of a patient to plan the movement and to perceive the stimulation as a part of his/her own control loop is important for carryover effect to take place.
Modeling and simulating free/open source software processes

The focus of this article is on identifying what is known about the processes found in free and open source software development (F/OSSD) projects. The results and findings from a survey of empirical studies of F/OSSD give rise to an interesting variety of opportunities and challenges for modeling and simulating these processes, which are identified along the way. The article also presents a framework for organizing new studies according to their research focus, sampling strategy, data collection methods, modeling and simulation approach, and the strategy used to assure the quality of the modeling and simulation results. This framework thus serves to help guide research into F/OSSD processes in ways that maximize and bound their contribution.
Identification and characterization of AtSTP14, a novel galactose transporter from Arabidopsis.

AtSTP14, a new Arabidopsis sugar transporter, was identified and characterized on the molecular and physiological level. Reverse transcriptase-PCR analyses and reporter plants demonstrate high AtSTP14 expression levels in the seed endosperm and in cotyledons, as well as in green leaves. Thus, unlike previously characterized monosaccharide transporters, AtSTP14 is expressed in both source and sink tissues and represents the first monosaccharide transporter in the female gametophyte. Heterologous expression in yeast revealed that AtSTP14 does not transport glucose or fructose, but is the first plant transporter specific for galactose. Interestingly, AtSTP14 expression is regulated by factors which also induce cell wall degradation such as extended dark periods or changes in the sugar level, i.e. AtSTP14 is induced 3-fold by 24 h darkness and repressed 3-fold by 2% glucose and 2% sucrose. Two independent Atstp14 mutant lines were identified, but no effect on seed development or other differences during growth under normal conditions could be observed. A putative role for AtSTP14 in the recycling of cell wall-derived galactose during different developmental processes is discussed.
Experimental analysis of a protective wafer coating process for the die preparation

The application of coating process is a conventional part of the photolithography which is widely used in the IC fabrication and the manufacturing of micro-electro-mechanical systems (MEMS). The uniform experimental design method combined with regression analysis is applied to investigate the protective coating process aimed to protect the die from silicon contaminations in the die preparation phase of the IC assembly. Ten experimental runs based on the randomization principle and the uniform design tables are executed. The weight of the flux coated on the substitute coupon is measured and adopted as the quality target of the coating process and four control parameters, the scale of micrometer valve, the flux pressure, the dispenser velocity and the atomizing pressure are selected as experimental factors in this study. A significant regression model is obtained based on the experimental data and the scale of micrometer valve, the flux pressure and the dispenser velocity are found to be significant factors in the protective coating process. Such model could be used as the mathematical prediction of the flux weight and help to improve the coating velocity without violating the weight constraint required for its protection purpose.
Properties of axon terminals contacting intermediate zone excitatory and inhibitory premotor interneurons with monosynaptic input from group I and II muscle afferents

The intermediate zone of the spinal grey matter contains premotor interneurons mediating reflex actions of group I and II muscle afferents. However, limited information is available on how activity of inhibitory versus excitatory interneurons in this population are modulated and how they contribute to motor networks. There were three aims of this study: (1) to characterize excitatory axonal contacts on interneurons; (2) to determine if contact patterns on excitatory and inhibitory interneurons are different; (3) to determine if there are differences in presynaptic inhibitory control of excitatory and inhibitory interneurons. We used intracellular labelling of electrophysiologically identified cells along with immunochemistry to characterise contacts formed by axons that contain vesicular glutamate transporters (VGLUT1 and VGLUT2) and contacts formed by VGLUT1 terminals which in turn were contacted by GABAergic terminals on cells that were characterised according to their transmitter phenotype. All 17 cells investigated were associated with numerous VGLUT1 contacts originating from primary afferents, and similar contact densities were found on excitatory and inhibitory cells, but VGLUT2‐immunoreactive terminals originating from intraspinal neurons were less frequent, or were practically absent, especially on excitatory cells. Similar numbers of VGLUT1 contacts with associated GABAergic terminals were found on excitatory and inhibitory cells indicating a similar extent of presynaptic GABAergic control. However, scarce VGLUT2 terminals on intermediate zone excitatory premotor interneurons with input from muscle afferents suggest that they are not significantly excited by other spinal neurons but are under direct excitatory control of supraspinal neurons and, principally inhibitory, control of spinal neurons.
Dynamic spectrum allocation in adjacent regions with physical interference based geographic coupling parameter

This paper considers the problem of dynamic spectrum allocation (DSA) in the adjacent regions controlled by each spectrum broker (SB). In this scenario, the SB has a responsibility to allocate the spectrum to network service providers (NSPs) in region that SB controls. However, the SB cannot manage the interference arising between regions, and, therefore, the quality of allocated spectrum cannot be maintained. Thus, we introduce the spectrum broker coordinator (SBC) for managing the internal and external interference effects in the region. In this paper, we propose a physical interference based geographic coupling parameter to capture the impact of the internal and external interference of each NSP within each region. The proposed parameter is then used to derive the quality of spectrum applied to the spectrum allocation algorithm called as the simulated annealing (SA) to determine the optimal spectrum allocation. Simulation results demonstrate that our scheme can coordinate the DSA-enabled band size to maximize the spectrum utilization in accordance with changes of the density of BSs in NSPs.
Building a Large Thesaurus for Information Retrieval

Information retrieval systems that support searching of large textual databases are typically accessed by trained search intermediaries who provide assistance to end users in bridging the gap between the languages of authors and inquirers. We are building a thesaurus in the form of a large semantic network to support interactive query expansion and search by end users. Our lexicon is being built by analyzing and merging data from several large English dictionaries; testing of its value for retrieval is with the SMART and CODER systems.
The Effect of Ground Tilt on the Lower Extremity Muscle Activity of Stroke Patients Performing Squat Exercises

[Purpose] The purpose of this study was to determine the effect of ground tilt on the lower extremity muscle activity of stroke patients performing squat exercises. [Subjects] Fifteen hemiparetic patients volunteered to participate in this study. [Methods] The subjects performed squat exercises at three different ground tilt angles: 15° plantar flexion, a neutral position, and 15° dorsiflexion. A surface electromyogram (sEMG) was used to record the electromyographic activities of the leg extensor muscle in the vastus lateralis (VL), vastus medialis (VM), gastrocnemius lateralis (GL), and gastrocnemius medialis (GM). The sEMG activity was analyzed using a one-way repeated measures ANOVA and a post hoc Bonferroni correction. [Results] The results of this study are summarized as follows. Significant differences were noted for the VL and the GL when the angle of the ankle joint was between the 15° plantar flexion and neutral positions during squat exercises involving the VL and when the angle of the ankle joint was between the neutral position and 15° dorsiflexion during squat exercises involving the VM. [Conclusion] In this study, sEMG showed that the VL and GL changed significantly during squat exercises according to the ground tilt angle of hemiparetic patients. Therefore, squat exercises with different ground tilt angles can be used to improve VL and GL strength.
The Development of a Revised Canadian Myalgic Encephalomyelitis Chronic Fatigue Syndrome Case Definition

Problem statement: Several investigators have indicated that case defi nitions for Chronic Fatigue Syndrome (CFS) are characterized by vaguely worded criteria that lack operational definitions and guidelines. The most widely used CFS case definition is the Fukuda et al. criteria, which uses polythetic criteria (i.e., patients are only requir ed to have four out of a possible eight symptoms). Yet two of these eight symptoms (post-exertional malais e and memory/concentration problems) are an essential feature of this illness and the Fukuda et al. criteria do not require that these symptoms be present among all patients. Significant methodologi cal problems could occur if investigators in different settings recruit samples with different p ercentages of these core symptoms. In contrast, the Canadian clinical case definition does require spec ific ME/CFS symptoms such as post-exertional malaise and memory/concentration problems. The provision of operationally explicit, objective criteria on specific key symptoms might reduce criterion var iance as a source of unreliability. In addition, th e use of structured interview schedules will ensure t hat symptoms are assessed in a consistent way across settings. Conclusion/Recommendations: In this article, we specified explicit rules for determining whether critical symptoms meet ME/CFS criteria using a revised Canadian case definition and a questionnaire has been developed to assess co re symptoms. It is hoped that these developments will lead to increased reliability of this revised Canadian case definition as well as more frequent u se of these criteria by investigators.
Optimal joint source and relay beamforming for MIMO relays with direct link

In this letter, we investigate the optimal structure of the source precoding matrix and the relay amplifying matrix for non-regenerative multiple-input multiple-output (MIMO) relay communication systems with the direct source-destination link. We show that both the optimal source precoding matrix and the optimal relay amplifying matrix have a beamforming structure. Based on this structure, an iterative joint source and relay beamforming algorithm is developed to minimize the mean-squared error (MSE) of the signal waveform estimation. Numerical example demonstrates an improved performance of the proposed algorithm.
Continuous-time subspace identification in closed-loop using Laguerre filters

This paper deals with the problem of continuous-time model identification and presents a subspace-based algorithm capable of dealing with data generated by systems operating in closed-loop. The algorithm is developed by reformulating the identification problem from the time-domain to the so-called all-pass domain by using a bank of Laguerre filters applied to the input-output data. In this framework, the PBSID subspace identification algorithm, originally developed in the case of discrete-time systems, can be reformulated for the continuous-time case. Simulation results are presented to illustrate the performance of the algorithm.