Miracle-dz/UniFAR-FTUs huggingface dataset:
Infection of human pericytes by HIV-1 disrupts the integrity of the blood–brain barrier

Human immunodeficiency virus type 1 (HIV‐1) infection of the central nervous system (CNS) affects cross‐talk between the individual cell types of the neurovascular unit, which then contributes to disruption of the blood–brain barrier (BBB) and the development of neurological dysfunctions. Although the toxicity of HIV‐1 on neurons, astrocytes and brain endothelial cells has been widely studied, there are no reports addressing the influence of HIV‐1 on pericytes. Therefore, the purpose of this study was to evaluate whether or not pericytes can be infected with HIV‐1 and how such an infection affects the barrier function of brain endothelial cells. Our results indicate that human brain pericytes express the major HIV‐1 receptor CD4 and co‐receptors CXCR4 and CCR5. We also determined that HIV‐1 can replicate, although at a low level, in human brain pericytes as detected by HIV‐1 p24 ELISA. Pericytes were susceptible to infection with both the X4‐tropic NL4‐3 and R5‐tropic JR‐CSF HIV‐1 strains. Moreover, HIV‐1 infection of pericytes resulted in compromised integrity of an in vitro model of the BBB. These findings indicate that human brain pericytes can be infected with HIV‐1 and suggest that infected pericytes are involved in the progression of HIV‐1‐induced CNS damage.
Sperm entry position provides a surface marker for the first cleavage plane of the mouse zygote

Summary: The sperm entry position (SEP) of the mouse egg, labelled by placing a bead at the fertilisation cone, tends to be associated with the first cleavage plane (Piotrowska and Zernicka‐Goetz: Nature 409:517–521, 2001). Nevertheless, in up to one‐fourth of embryos the cleavage furrow did not pass close to the bead, and following the division the bead marked the cleavage plane in only 60% of cases. This raised the question of whether such variability arose from the labelling itself or had a biological basis. The zona pellucida was not responsible for this effect because similar results were obtained in its presence or absence. However, this variability could be attributable to the large size of the fertilisation cone relative to the SEP. Therefore, we have developed a means of fluorescently labelling sperm that can record the exact site of its penetration when the label transfers to the egg surface. This approach indicates that the SEP marks the first cleavage in the great majority (88%) of embryos. In conclusion, direct sperm labelling shows precisely the correlation between the SEP and the first cleavage, although there is natural variability in this process. genesis 32:193–198, 2002. © 2002 Wiley‐Liss, Inc.
Functional magnetic resonance imaging of impaired sensory prediction in schizophrenia.

IMPORTANCE Forward models predict the sensory consequences of planned actions and permit discrimination of self- and non-self-elicited sensation; their impairment in schizophrenia is implied by an abnormality in behavioral force-matching and the flawed agency judgments characteristic of positive symptoms, including auditory hallucinations and delusions of control. OBJECTIVE To assess attenuation of sensory processing by self-action in individuals with schizophrenia and its relation to current symptom severity. DESIGN, SETTING, AND PARTICIPANTS Functional magnetic resonance imaging data were acquired while medicated individuals with schizophrenia (n = 19) and matched controls (n = 19) performed a factorially designed sensorimotor task in which the occurrence and relative timing of action and sensation were manipulated. The study took place at the neuroimaging research unit at the Institute of Cognitive Neuroscience, University College London, and the Maudsley Hospital. RESULTS In controls, a region of secondary somatosensory cortex exhibited attenuated activation when sensation and action were synchronous compared with when the former occurred after an unexpected delay or alone. By contrast, reduced attenuation was observed in the schizophrenia group, suggesting that these individuals were unable to predict the sensory consequences of their own actions. Furthermore, failure to attenuate secondary somatosensory cortex processing was predicted by current hallucinatory severity. CONCLUSIONS AND RELEVANCE Although comparably reduced attenuation has been reported in the verbal domain, this work implies that a more general physiologic deficit underlies positive symptoms of schizophrenia.
Affiliative Stimuli as Primers to Prosocial Predispositions

Affiliative stimuli are pleasant and highly biologically relevant. Affiliative cues are thought to elicit a prosocial predisposition. Here affiliative and neutral pictures were exposed prior to a reaction time task which consisted in responding to a visual target. Half the participants responded with finger-flexion, a movement frequently involved in prosocial activities. The other half responded with finger extension, a less prosocially compatible movement. Results showed that under the exposure to affiliative pictures, as compared to neutral ones, participants who used finger flexion were faster, while those using finger extension were slower. Performance benefits to the task, when flexing the finger, together with performance costs, when extending it, indicate the relevance of movement compatibility to the context. These findings put forward a possible link between affiliative primers and motor preparation to facilitate a repertoire of movements related to prosocial predispositions including finger flexion. Los estímulos afiliativos son agradables y de gran relevancia biológica. Se cree que las señales afiliativas provocan una predisposición pro-social. En este estudio, fotos afiliativas y neutras fueron presentadas antes de una tarea de tiempo de reacción que consistía en responder a un objetivo/target visual. La mitad de los participantes respondieron utilizando dedo-flexión, un movimiento asociado con frecuencia a actividades pro-sociales. La otra mitad respondió con la extensión del dedo, un movimiento prosocialmente menos compatible. Los resultados mostraron que en la exposición a imágenes afiliativas, en comparación con las neutras, los participantes que usaron flexión del dedo eran más rápidos, mientras que aquellos que usaron extensión del dedo eran más lentos. El rendimiento superior en la tarea, en la flexion del dedo, junto con el perjuicio para el rendimiento en la extensión, son indicativos de la relevancia de la compatibilidad del movimiento con el contexto. Estos resultados presentan una posible relación entre primers afiliativos y la preparación motora que facilita un repertorio de movimientos relacionados con la predisposición prosocial, entre ellos, la flexión de los dedos.
Study on Process Model for IP Traffic Estimation

We present a process model for IP-traffic matrix estimation, in which the task to be modeled is separated into several processes. This model enables us to analyze the complicated IP-traffic matrix estimation in unit of processes and make the causal relationships among processes easy to understand. In the course of deriving the model, we arrange the possible techniques for estimation including the method of analyzing the broadband market structure
Extracting Components from Open Source: The Component Adaptation Environment (COPE) Approach

Open Source Software (OSS) represents an extremely valuable resource that is reused systematically almost in every software project. The reuse of OSS components however is restricted to ready-made components and developers who want to reuse code that exists in OSS projects but is not offered as a black-box component often resort to copying existing code and adapting it in their projects. OPEN-SME is a European research project which aims at providing ready-to-use OSS components that originate from existing OSS projects but are not necessarily provided as such. In this work we describe the Component Adaptation Environment (COPE) tool that was developed in the context of the OPEN-SME project and enables software experts, called reuse engineers, to extract components from OSS projects, test them and provide test documentation, validate them with Model-Based Testing techniques, package them and upload them in a component repository for reuse. The whole approach aims at creating an ever increasing repository of trustworthy reusable software components from different application domains.
Global estimation of nonlinear systems with unknown-input coefficients

This paper deals with simultaneous state and input-parameter estimation of a class of bounded-state nonlinear systems. By state augmentation, the unknown-input coefficient is seen as an extension of the system states and consequently, an input-gain observer can be conceived to steer the observation error to the origin for some bounded and non-null control input. The proposed design remains valid for nonlinear-input systems with linear parametrization.
Genomewide search for type 2 diabetes mellitus susceptibility loci in Finnish families: the Botnia study.

Type 2 diabetes mellitus is a heterogeneous inherited disorder characterized by chronic hyperglycemia resulting from pancreatic beta-cell dysfunction and insulin resistance. Although the pathogenic mechanisms are not fully understood, manifestation of the disease most likely requires interaction between both environmental and genetic factors. In the search for such susceptibility genes, we have performed a genomewide scan in 58 multiplex families (comprising 440 individuals, 229 of whom were affected) from the Botnia region in Finland. Initially, linkage between chromosome 12q24 and impaired insulin secretion had been reported, by Mahtani et al., in a subsample of 26 families. In the present study, we extend the initial genomewide scan to include 32 additional families, update the affectation status, and fine map regions of interest, and we try to replicate the initial stratification analysis. In our analysis of all 58 families, we identified suggestive linkage to one region, chromosome 9p13-q21 (nonparametric linkage [NPL] score 3.9; P<.0002). Regions with nominal P values <. 05 include chromosomes 2p11 (NPL score 2.0 [P<.03]), 3p24-p22 (NPL score 2.2 [P<.02]), 4q32-q33 (NPL score 2.5 [P<.01]), 12q24 (NPL score 2.1 [P<.03]), 16p12-11 (NPL score 1.7 [P<.05]), and 17p12-p11 (NPL score 1.9 [P<.03]). When chromosome 12q24 was analyzed in only the 32 additional families, a nominal P value <. 04 was observed. Together with data from other published genomewide scans, these findings lend support to the hypothesis that regions on chromosome 9p13-q21 and 12q24 may harbor susceptibility genes for type 2 diabetes.
Brain Bases for Auditory Stimulus-Driven Figure–Ground Segregation

Auditory figure–ground segregation, listeners' ability to selectively hear out a sound of interest from a background of competing sounds, is a fundamental aspect of scene analysis. In contrast to the disordered acoustic environment we experience during everyday listening, most studies of auditory segregation have used relatively simple, temporally regular signals. We developed a new figure–ground stimulus that incorporates stochastic variation of the figure and background that captures the rich spectrotemporal complexity of natural acoustic scenes. Figure and background signals overlap in spectrotemporal space, but vary in the statistics of fluctuation, such that the only way to extract the figure is by integrating the patterns over time and frequency. Our behavioral results demonstrate that human listeners are remarkably sensitive to the appearance of such figures. In a functional magnetic resonance imaging experiment, aimed at investigating preattentive, stimulus-driven, auditory segregation mechanisms, naive subjects listened to these stimuli while performing an irrelevant task. Results demonstrate significant activations in the intraparietal sulcus (IPS) and the superior temporal sulcus related to bottom-up, stimulus-driven figure–ground decomposition. We did not observe any significant activation in the primary auditory cortex. Our results support a role for automatic, bottom-up mechanisms in the IPS in mediating stimulus-driven, auditory figure–ground segregation, which is consistent with accumulating evidence implicating the IPS in structuring sensory input and perceptual organization.
Have a say over what you see: evaluating interactive compression techniques

We all encounter many documents on a daily basis that we do not have time to process in their entirety. Nevertheless, we lack good tools to rapidly skim and identify key information from within such documents. This paper develops and evaluates Interactive Compression (IC) techniques that allow users to dynamically configure the amount of information they view in a document, e.g. by automatically removing unimportant information from view (Excision) or by making important information more salient (Highlighting). We explore IC techniques in the context of meeting transcripts that are typically unstructured - making it difficult to isolate relevant regions and extract key information. We demonstrate the superiority of IC compared with an unmodified text control. In contrast to traditional summaries, our results show extensive use of interactive, as opposed to fixed compression level, summarization. They also show the value of word- as opposed to utterance-based compression. There are also trade-offs between different IC designs. Excision allows users to scan documents faster than Highlighting but at the expense of overlooking relevant sections of the document.
Premature mortality in active convulsive epilepsy in rural Kenya

An increased risk of premature death associated with epilepsy is well known. Recent reports have documented an even higher risk of premature mortality among people with epilepsy living in low- and middle-income countries (LAMICs). 1 The epidemiology of epilepsy-associated mortality in LAMICs is of great relevance, as more than 85% of those with epilepsy live in resource-limited countries.2 Not only is the risk of premature mortality higher in LAMICs, but a greater proportion of deaths in these regions are epilepsy-related (e.g., falls, burns, drowning, and status epilepticus). 1
Spatial and Temporal Attention Modulate the Early Stages of Face Processing: Behavioural Evidence from a Reaching Paradigm

A presently unresolved question within the face perception literature is whether attending to the location of a face modulates face processing (i.e. spatial attention). Opinions on this matter diverge along methodological lines – where neuroimaging studies have observed that the allocation of spatial attention serves to enhance the neural response to a face, findings from behavioural paradigms suggest face processing is carried out independently of spatial attention. In the present study, we reconcile this divide by using a continuous behavioural response measure that indexes face processing at a temporal resolution not available in discrete behavioural measures (e.g. button press). Using reaching trajectories as our response measure, we observed that although participants were able to process faces both when attended and unattended (as others have found), face processing was not impervious to attentional modulation. Attending to the face conferred clear benefits on sex-classification processes at less than 350ms of stimulus processing time. These findings constitute the first reliable demonstration of the modulatory effects of both spatial and temporal attention on face processing within a behavioural paradigm.
A Fault Diagnosis and Prognosis Service for TeraGrid Clusters

In this paper, we present an ongoing research effort on developing an automatic fault diagnosis and prognosis service for large-scale computing systems, such as TeraGrid clusters. By leveraging the research on system health monitoring, the proposed service aims at automati- cally revealing fault patterns from historical data by applying data mining and machine learning techniques. To address key challenges posted by fault diagnosis and prognosis, two integrated techniques are developed: a knowledge base to accumulate empirical and inferred fault patterns from historical data and a meta-learning mechanism to optimally combine separately learned classifiers for improved detection and prediction accuracy. We also present preliminary studies on failure logs from the BlueGene/L systems at SDSC and ANL.
Signalling C‐Type lectin receptors, microbial recognition and immunity

Signalling C‐type lectin receptors (CLRs) are crucial in shaping the immune response to fungal pathogens, but comparably little is known about the role of these receptors in bacterial, viral and parasitic infections. CLRs have many diverse functions depending on the signalling motifs in their cytoplasmic domains, and can induce endocytic, phagocytic, antimicrobial, pro‐inflammatory or anti‐inflammatory responses which are either protective or not during an infection. Understanding the role of CLRs in shaping anti‐microbial immunity offers great potential for the future development of therapeutics for disease intervention. In this review we will focus on the recognition of bacterial, viral and parasitic pathogens by CLRs, and how these receptors influence the outcome of infection. We will also provide a brief update on the role of CLRs in antifungal immunity.
A distributed information repository for autonomic context-aware MANETs

Due to the emergence of multimedia context-rich applications and services over wireless networks, networking protocols and services are becoming more and more integrated, thus relying on context and application information to support their operation. Further, wireless protocols and services now employ information from several network layers and the environment, breaking the layering paradigm. In order to cope with this increasing reliance on information, we have proposed MANIP, a middleware for MANETs that instantiates a new networking plane. The Information Plane (InP) is a distributed entity to store and disseminate information concerning the network, its services and the environment, orchestrating the collaboration among cross-layer protocols, autonomic management solutions and context-aware services. We use MANIP to support the autonomic reconfiguration of a P2P network over MANETs. Simulation results show that the MANIP-enabled solutions reduce the response time and increase the number of solved P2P queries when compared to classic, cross-layer implementations of the same protocols.
A Framework for Webcam-based Hand Rehabilitation Exercises

Applications for home-based care are rapidly increasing in importance due to spiraling health and elderly care costs. An important aspect of home-based care is exercises for rehabilitation and improving general health. In this paper we present a framework for demonstrating and monitoring hand exercises. The three main components are a 3D hand model, a high-level animation framework which facilitates the task of specifying hand exercises via skeletal animation, and a hand tracking program to monitor and evaluate users’ performance. Our hand tracking solution has no calibration stage and is easily set-up. Segmentation is performed using a perception-based colour space, and hand tracking and motion estimate are obtained using novel variations to a CAMSHIFT and contour analysis algorithms. The results indicate that the robust tracking along with the demonstration and reconstruction of hand exercises provide an effective platform for hand rehabilitation.
Journal of Intercultural Ethnopharmacology I Ntroduction Antibacterial Synergy between Rosmarinic Acid and Antibiotics against Methicillin-resistant Staphylococcus Aureus

Antibiotic resistance of microorganisms is a major challenge confronted by all scientists who are involved in antibiotic drug discovery. Bacteria widen its resistance to antibiotics by mutating existing genes (vertical evolution) or by acquiring new genes from other strains or species (horizontal gene transfer). The sharing of genes between bacteria by horizontal gene transfer occurs by many different mechanisms [1]. Methicillin-resistant Staphylococcus aureus (MRSA) is a nosocomial and community-acquired pathogen that has developed resistance to various antibiotics such as β-lactams, quinolones, aminoglycosides, vancomycin, oxazolidinone, and streptogramin type antibiotics [2-4]. Newly emerging community-associated MRSA (CA-MRSA) is transmissible from healthcare acquired MRSA (HA-MRSA). Some CA-MRSA strains display enhanced virulence, spreading more rapidly and causing illness much more severe than HA-MRSA infections, affecting vital organs which lead to sepsis, toxic shock syndrome, and necrotizing pneumonia [5]. One of the strategies employed to triumph over the bacterial resistance is the use of a combination of drugs. The secondary metabolites of the plants are the good sources for combination of drugs to act as multidrug resistant modifiers with varied mechanisms of action [6]. Polyphenols is a prominent class of plant metabolites possesses ABSTRACT Aim/Background: Medicinal plants have ability to resist microorganisms by synthesizing secondary metabolites such as phenols. Rosmarinic acid (RA) is a phenylpropanoid widely distributed in plants and well known as therapeutic and cosmetic agent. Methicillin-resistant Staphylococcus aureus (MRSA) which is resistant to all kinds of β-lactams, threatens even most potent antibiotics. To improve the efficiency of antibiotics against multi-drug resistant bacteria and to reduce the antibiotic dose, the antibacterial activity and the synergistic effect of RA with standard antibiotics against S. aureus and MRSA was investigated. Materials and Methods: Antibacterial activity of RA against S. aureus and a clinical isolate of MRSA was evaluated by agar well diffusion method. Minimum inhibitory concentration (MIC) of RA was determined by broth dilution method. Synergism of RA with various antibiotics against S. aureus and MRSA was studied by broth checkerboard method and time-kill kinetic assay. Effect of RA on microbial surface components recognizing adhesive matrix molecules (MSCRAMM's) of S. aureus and MRSA was studied using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Results: MIC of RA was found to be 0.8 and 10 mg/ml against S. aureus and MRSA, respectively. RA was synergistic with vancomycin, ofloxacin, and amoxicillin against S. aureus and only with vancomycin against MRSA. The time-kill analysis revealed that synergistic combinations were a more effective …
Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona

The CRISPR/Cas9 system has emerged as an important tool for various genome engineering applications. A current obstacle to high throughput applications of CRISPR/Cas9 is the imprecise prediction of highly active single guide. RNAs (sgRNAs). We previously implemented the CRISPR/Cas9 system to induce tissue-specific mutations in the tunicate Ciona. In the present study, we designed and tested 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues of Ciona embryo. Using high-throughput sequencing of mutagenized alleles, we identified guide sequences that correlate with sgRNA mutagenesis activity and used this information for the rational design of all possible sgRNAs targeting the Ciona transcriptome. We also describe a one-step cloning-free protocol for the assembly of sgRNA expression cassettes. These cassettes can be directly electroporated as unpurified PCR products into Ciona embryos for sgRNA expression in vivo, resulting in high frequency of CRISPR/Cas9-mediated mutagenesis in somatic cells of electroporated embryos. We found a strong correlation between the frequency of an Ebf loss-of-function phenotype and the mutagenesis efficacies of individual Ebf-targeting sgRNAs tested using this method. We anticipate that our approach can be scaled up to systematically design and deliver highly efficient sgRNAs for the tissue-specific investigation of gene functions in Ciona.