Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of CCR7 on Priming and Distribution of Antiviral Effector and Memory CTL

The chemokine receptor CCR7 is a key factor in the coordinate migration of T cells and dendritic cells (DC) into and their localization within secondary lymphoid organs. In this study we investigated the impact of CCR7 on CD8+ T cell responses by infecting CCR7−/− mice with lymphocytic choriomeningitis virus (LCMV). We found that the absence of CCR7 affects the magnitude of an antiviral CTL response during the acute phase, with reduced numbers of virus-specific CTL in all lymphoid and nonlymphoid organs tested. On the single cell level, CCR7-deficient CTL gained full effector function, such that antiviral protection in CCR7-deficient mice was complete, but delayed. Similarly, adoptive transfer experiments using DC from CCR7-deficient or competent mice for the priming of CCR7-positive or CCR7-negative CD8+ T cells, respectively, revealed that ectopic positioning of DC and CTL outside organized T cell zones results in reduced priming efficacy. In the memory phase, CCR7-deficient mice maintained a stable LCMV-specific CTL population, predominantly in nonlymphoid organs, and rapidly mounted protective CTL responses against a challenge infection with a vaccinia virus recombinant for the gp33 epitope of LCMV. Taken together, the CCR7-dependent organization of the T cell zone does not appear to be a prerequisite for antiviral effector CTL differentiation and the sustenance of antiviral memory responses in lymphoid or peripheral tissues.
Ieee Transactions on Mobile Computing 1 a Two-phase Dispatch Heuristic to Schedule the Movement of Multi-attribute Mobile Sensors in a Hybrid Wireless Sensor Network

—The paper considers a hybrid wireless sensor network with static and mobile sensors, where each static sensor can detect only one attribute of event while a mobile sensor can analyze multiple attributes of events. Static sensors monitor the environment and report where events appear. Mobile sensors then move to these event locations to conduct more in-depth analysis. A critical issue is how to schedule the traveling paths of mobile sensors so as to extend their lifetime. We formulate this issue as a multi-round multi-attribute sensor dispatch problem and prove it to be NP-complete. Then, we develop a two-phase dispatch heuristic that adopts the concepts of Pareto optimality and spanning-tree construction. Our heuristic allows arbitrary numbers of mobile sensors and event locations and tries to reduce and balance the energy consumption of mobile sensors in each round. Through simulations, we verify the effectiveness of our heuristic. The paper contributes in defining a new sensor dispatch problem and developing an energy-efficient solution to the problem.
ANALYSIS TOOLS FOR GRAY LEVEL HISTOGRAMS

This paper summarizes three algorithms used for the analysis of gray level histograms. Two of them are easily developed from standard techniques and the other is a completely new method. We will study the advantages of each and give examples of real-world use. Gray level histogram analysis (mainly threshold computation) is a known technique that allows easy and fast segmentation of the regions of interest in an image [1]. Many methods have been proposed for this problem [2], but almost all of them focus only on the problem of bimodal histograms. We will deal with multimodal histograms and, besides, we improve the time efficiency of the most widely used method (Otsu’s [3]). Finally, we investigate the potentials of these techniques for scalar quantifiers design (because Otsu method is a clustering technique).
A Latent Class Typology of Justice-Involved Youth Victims and Exploration of Trauma-Related Psychological Symptoms

Abstract Justice-involved youth witness and experience disproportionately high levels of violence and abuse, yet our understanding of trauma-related symptoms and exposure to violence (ETV) in this group remains largely underdeveloped. Using data from a sample of 1,354 youth, this study uses latent class analysis to construct a typology of justice-involved trauma victims based on ETV items. Second, we test whether membership in different ETV classes is associated with more extensive and earlier system involvement and psychological symptomology. We identified with four classes of justice-involved trauma victims: minimally exposed youth, youth with high levels of witnessed violence, youth with high levels of witnessed and experienced non-lethal violence and youth with high levels of witnessed and experienced non-lethal and lethal gun violence. Membership in the latter class was strongly associated with higher number of arrests and younger age at first arrests. Significant differences in trauma-related symptoms were found across the various ETV classes. Implications for policy and practitioners are discussed.
Local Population Synchrony and the Encoding of Eye Position in the Primate Neural Integrator

Encoding horizontal eye position in the oculomotor system occurs through temporal integration of eye velocity inputs to produce tonic outputs. The nucleus prepositus is commonly believed to be the “neural integrator” that accomplishes this function through the activity of its ensemble of predominantly burst-tonic neurons. Single-unit characterizations and labeling studies of these neurons have suggested that their collective output is achieved through local feedback loops produced by direct connections between them. If this is the case, then the ensemble of burst-tonic neurons should exhibit correlated activity. To obtain electrophysiological evidence of local interactions between neurons, we simultaneously recorded pairs (n = 29) of burst-tonic neurons in the nucleus prepositus of rhesus macaque monkeys using eight-channel linear microelectrode arrays. We computed the magnitude of synchrony between their spike trains as a function of eye position during ocular fixations and as a function of distance between neurons. Importantly, we found that neurons exhibit unexpected levels of positive synchrony, which is maximal during contralateral fixations and weakest when neurons are located far apart from one another (>300 μm). Together, our results support a role for shared inputs to ipsilateral pairs of burst-tonic neurons in the encoding of eye position in the primate nucleus prepositus.
Priority IO Scheduling in the Cloud

Current state of the art runtime systems, built for managing cloud environments, almost always assume resource sharing among multiple users and applications. In large part, these runtime systems rely on functionalities of the node-local operating systems to divide the local resources among the applications that share a node. While OSes usually achieve good resource sharing by creating distinct application-level domains across CPUs and DRAM, managing the IO bandwidth is a complex task due to lack of communication between the host and IO device. In our work we focus on controlling the hard disk drive (HDD) IO bandwidth available to user-level applications in a cloud environment. We introduce prioritybased (PBS) IO scheduling, where the ordering of IO commands is decided cooperatively by the host and IO device. We implemented our scheduling policies in the Linux storage stack and Hadoop Distributed File System. Initial results show that in a cloud environment, the realtime commands managed by PBS outperform the realtime IO scheduling of the Linux kernel by up to a factor of ∼ 5 for the worst case latency, and by more than 2x for average latency.
Modelling the Business Cycle in South Africa: A Non-Linear Approach

Abstract In this paper the South African business cycle is modeled, using a simple linear method and comparing it to non-linear methods. This is useful to address the debate between the Classical and Keynesian economists regarding their views on the business cycle. They believe in a stable economy with exogenous shocks and an unstable economy with an endogenous business cycle respectively. Linear models are usually associated with the Classical view and non-linear models with the Keynesian view. A detailed discussion on the non-linear model-building process, with particular emphasis on the family of STAR models is done. The South African GDP is used and AR, TAR, LSTAR and ESTAR models are fitted and compared. It finds that a parameterized nonlinear model (such as the family of STAR models) outperforms the simple regression model. This is due to asymmetric behaviour in the GDP data and the possibility of a threshold between a recession and an expansion. The results in this paper support the structural or institutional view of business cycles, which states that economic fluctuations are caused by various structural or institutional changes.
Acquiring qualitative and quantitative knowledge from verbal statements and dialogues in probabilistic domains

We describe an approach to acquire qualitative and quantitative knowledge from verbal statements and dialogues in complex, probabilistic domains. This work is part of the development of an intelligent environment, MEDICUS (Modelling, explanation, and diagnostic support for complex, uncertain subject matters), that supports modelling and diagnostic reasoning in the domains of environmental medicine and human genetics. The system is designed for professional as well as for further education purposes in these two medical domains. Support for other domains of rapidly changing and uncertain knowledge will be possible as well. In MEDICUS, uncertainty is handled by the Bayesian network approach. Thus modelling consists of creating a Bayesian network for the problem at hand. Since MEDICUS is designed for users interested in the domain but not necessarily in mathematical issues, it is possible to state propositions verbally and let the system generate a Bayesian network proposal. This differs from existing reasoning systems based on Bayesian networks, i.e. in medical domains, which contain a built-in knowledge base that may be used but not created or modified by the user. Diagnostic reasoning and deciding consists of using the network for stating and testing diagnostic hypotheses, and asking for recommendations.
Quantum Computation via Paraconsistent Computation

We present an original model of paraconsistent Turing machines (PTMs), a generalization of the classical Turing machines model of computation using a paraconsistent logic. Next, we briefl y describe the standard models of quantum computation: quantum Turing machines and quantum circuits, and revise quantum algorithms to solve the so-called Deutsch's problem and Deutsch-Jozsa problem. Then, we show the potentialities of the PTMs model of computation simulating the presented quantum algorithms via paraconsistent algorithms. This way, we show that PTMs can resolve some problems in exponentially less time than any classical deterministic Turing machine. Finally, We show that it is not possible to simulate all characteristics (in particular entangled states) of quantum computation by the particular model of PTMs here presented, therefore we open the possibility of constructing a new model of PTMs by which it is feasible to simulate such states.
Building a Coreference-Annotated Corpus from the Domain of Biochemistry

One of the reasons for which the resolution of coreferences has remained a challenging information extraction task, especially in the biomedical domain, is the lack of training data in the form of annotated corpora. In order to address this issue, we developed the HANAPIN corpus. It consists of full-text articles from biochemistry literature, covering entities of several semantic types: chemical compounds, drug targets (e.g., proteins, enzymes, cell lines, pathogens), diseases, organisms and drug effects. All of the co-referring expressions pertaining to these semantic types were annotated based on the annotation scheme that we developed. We observed four general types of coreferences in the corpus: sortal, pronominal, abbreviation and numerical. Using the MASI distance metric, we obtained 84% in computing the inter-annotator agreement in terms of Krippendorff's alpha. Consisting of 20 full-text, open-access articles, the corpus will enable other researchers to use it as a resource for their own coreference resolution methodologies.
Sliding mode control of ROV based on RBF neural networks adaptive learning

This paper deals with a variable structure sliding mode control of ROV (remotely operated vehicle), with which the adaptive learning of the RBF neural network is used to estimate and approach the upper bound of the uncertainty and disturbance induced by hydrodynamics so as to avoid the difficulties of establishment and resolving of precision dynamic model. According the description and setting up of the control model, a tracking simulation was carried out and a series of tests on the yaw of ROV were performed in static pool. It is proved that this control strategy is available for the ROV.
Tissue-Resident Exhausted Effector Memory CD8+ T Cells Accumulate in the Retina during Chronic Experimental Autoimmune Uveoretinitis

Experimental autoimmune uveoretinitis is a model for noninfectious posterior segment intraocular inflammation in humans. Although this disease is CD4+ T cell dependent, in the persistent phase of disease CD8+ T cells accumulate. We show that these are effector memory CD8+ T cells that differ from their splenic counterparts with respect to surface expression of CD69, CD103, and Ly6C. These retinal effector memory CD8+ T cells have limited cytotoxic effector function, are impaired in their ability to proliferate in response to Ag-specific stimulation, and upregulate programmed death 1 receptor. Treatment with fingolimod (FTY720) during the late phase of disease revealed that retinal CD8+ T cells were tissue resident. Despite signs of exhaustion, these cells were functional, as their depletion resulted in an expansion of retinal CD4+ T cells and CD11b+ macrophages. These results demonstrate that, during chronic autoimmune inflammation, exhausted CD8+ T cells become established in the local tissue. They are phenotypically distinct from peripheral CD8+ T cells and provide local signals within the tissue by expression of inhibitory receptors such as programmed death 1 that limit persistent inflammation.
Perceptions of a curriculum vitae clinic for conservation science students

We led a curriculum vitae (CV) clinic aimed at student participants attending the 28th International Congress for Conservation Biology (ICCB 2017) in Cartagena, Colombia. The CV Clinic was a pilot program consisting of resources to assist with developing an effective CV and involving preconference and at‐conference reviews of student attendees' CVs. Here, we explore our experiences in organizing the CV Clinic as well as nonparticipant and participant perceptions of the clinic. We used an online standardized interview form to gather qualitative data on nonparticipant and participant perceptions of the CV Clinic, and to explore how such a CV Clinic program could best align with student needs. Most respondents who submitted their CV for review ahead of ICCB 2017 (n = 9) found the template and guidance useful. Half of the respondents who did not participate in the CV Clinic perceived the clinic as duplicating services provided by their academic institutions. Both participant and nonparticipant respondents perceived value in such a CV Clinic, but also believed that adjustments could be made to make the CV review part of a broader professional development program lead by Society for Conservation Biology (SCB). Key lessons learned from the CV Clinic include the need to: (a) document and evaluate professional development initiatives within SCB; (b) better understand and account for the diversity of student needs before program creation; and (c) pilot and evaluate appropriateness of different locations, frequency, and duration of professional development programs.
Arabic handwriting recognition using Gabor wavelet transform and SVM

In this paper, we propose a segmentation based recognition approach for handwritten Arabic text. The approach starts by segmenting the word images into their constituent letter representatives through exploiting a set of structural features. For classification, Gabor transform-based features are extracted from each letter that passed to a SVM classifier for recognition. For training and testing, we used IESK-arDB database, which is an Arabic off-line handwritten database, that containing the most common Arabic words as well as security-related Arabic terms. The database is developed in the Institute for Electronics, Signal Processing and Communication (IESK) at Otto-von- Guericke University Magdeburg, Germany. And it is freely available at (http://www.iesk-ardb.ovgu.de/). The approach achieved an average of 70% segmentation accuracy on 600 word images. Recognition rate of 74%, on set of 5436 segmented letter images is reached, according to a Leave-one-out estimation method.
Obesity-Susceptibility Loci and Their Influence on Adiposity-Related Traits in Transition from Adolescence to Adulthood - The HUNT Study

Introduction Obesity-susceptibility loci have been related to adiposity traits in adults and may affect body fat estimates in adolescence. There are indications that different sets of obesity-susceptibility loci influence level of and change in obesity-related traits from adolescence to adulthood. Objectives To investigate whether previously reported obesity-susceptible loci in adults influence adiposity traits in adolescence and change in BMI and waist circumference (WC) from adolescence into young adulthood. We also examined whether physical activity modifies the effects of these genetic loci on adiposity-related traits. Methods Nine obesity-susceptibility variants were genotyped in 1 643 adolescents (13–19 years old) from the HUNT study, Norway, who were followed-up into young adulthood. Lifestyle was assessed using questionnaires and anthropometric measurements were taken. The effects of genetic variants individually and combined in a genetic predisposition score (GPS) on obesity-related traits were studied cross-sectionally and longitudinally. A modifying effect of physical activity was tested. Results The GPS was significantly associated to BMI (B: 0.046 SD/allele [0.020, 0.073], p = 0.001) in adolescence and in young adulthood (B: 0.041 SD/allele [0.015, 0.067], p = 0.002) as it was to waist circumference (WC). The GPS was not associated to change in BMI (p = 0.762) or WC (p = 0.726). We found no significant interaction effect between the GPS and physical activity. Conclusions Our observations suggest that obesity-susceptibility loci established in adults affect BMI and WC already in adolescence. However, an association with change in adiposity-related traits from adolescence to adulthood could not be verified for these loci. Neither could an attenuating effect of physical activity on the association between the obesity-susceptibility genes and body fat estimates be revealed.
Osteoclast-like Cells in Early Zebrafish Embryos

Objective Genes involved in bone and tissue remodelling in the vertebrates include matrix metalloproteinase-9 (mmp-9), receptor activator of necrosis factor κ-β (rank), cathepsin-k (Ctsk) and tartrate-resistant acid phosphatase (TRAcP). We examine whether these markers are expressed in cells of zebrafish embryos of 1-5 days post fertilization. We also examine adult scales, which are known to contain mature osteoclasts, for comparison. Materials and Methods In this experimental study, in situ hybrdisation, histochemistry and serial plastic and paraffin sectioning were used to analyse marker expression. Results We found that mmp-9 mRNA, TRAcP enzyme and Ctsk YFP protein were expressed in haematopoietic tissues and in the cells scattered sparsely in the embryo. Ctsk and rank mRNA were both expressed in the branchial skeleton and in the developing pectoral fin. In these skeletal structures, histology showed that the expressing cells were located around the developing cartilage elements, in the parachondral tissue. In a transgenic zebrafish line with YFP coupled to Ctsk promoter, Ctsk expressing cells were found around pharyngeal skeletal elements. To see whether we could activate osteoclasts, we exposed prim-6 zebrafish embryos to a mixture of 1 µM dexamethasone and 1 µM vitaminutes D3. These compounds, which are known to trigger osteoclastogenensis in cell cultures, lead to an increase in intensity of Ctsk YFP expression around the skeletal elements. Conclusion Our findings show that cells expressing a range of osteoclast markers are present in early larvae and can be activated by the addition of osteoclastogenic compounds.
H-infinity Takagi-Sugeno fuzzy control of a lower limbs rehabilitation device

This paper deals with the nonlinear control of a lower limbs isokinetic rehabilitation device based on a Takagi-Sugeno modeling. A parallel distributed compensation control law is used to stabilize the closed-loop system in the whole operational space. The human force applied to the device's arm is considered as an external disturbance to the system dynamics. To attenuate this disturbance, an Hinfin criterion is considered and classical stability conditions were adapted for a class of external perturbed TS model. The voluntary control of the movement by the patient is finally proposed with the use of a discrete state machine
Characterization of Clinical and Environmental Mycobacterium avium Spp. Isolates and Their Interaction with Human Macrophages

Members of the Mycobacterium avium complex (MAC) are naturally occurring bacteria in the environment. A link has been suggested between M. avium strains in drinking water and clinical isolates from infected individuals. There is a need to develop new screening methodologies that can identify specific virulence properties of M. avium isolates found in water that predict a level of risk to exposed individuals. In this work we have characterized 15 clinical and environmental M. avium spp. isolates provided by the US Environmental Protection Agency (EPA) to improve our understanding of the key processes involved in the binding, uptake and survival of these isolates in primary human macrophages. M. avium serovar 8 was predominant among the isolates studied. Different amounts and exposure of mannose-capped lipoarabinomannan (ManLAM) and glycopeptidolipids (GPLs), both major mycobacterial virulence factors, were found among the isolates studied. Reference clinical isolate 104 serovar 1 and clinical isolates 11 and 14 serovar 8 showed an increased association with macrophages. Serum opsonization increased the cell association and survival at 2 h post infection for all isolates. However, only the clinical isolates 104 and 3 among those tested showed an increased growth in primary human macrophages. The other isolates varied in their survival in these cells. Thus we conclude that the amounts of cell envelope ManLAM and GPL, as well as GPL serovar specificity are not the only important bacterial factors for dictating the early interactions of M. avium with human macrophages.
Text Extraction from Web Images Based on Human Perception and Fuzzy Inference

There is a significant need to extract and recognise the semantically-important text contained in images on Web pages. This paper proposes a new approach to text extraction from this special class of images. The method attempts to emulate closer than before the way humans perceive colour differences in order to differentiate between text and background regions. Pixels of similar colour (as humans see it) are merged into components and a fuzzy inference mechanism (using connectivity and colour distance features) is devised to group components into larger character-like regions.