Miracle-dz/UniFAR-FTUs huggingface dataset:
The C-Type Lectin OCILRP2 Costimulates EL4 T Cell Activation via the DAP12-Raf-MAP Kinase Pathway

OCILRP2 is a typical Type-II transmembrane protein that is selectively expressed in activated T lymphocytes, dendritic cells, and B cells and functions as a novel co-stimulator of T cell activation. However, the signaling pathways underlying OCILRP2 in T cell activation are still not completely understood. In this study, we found that the knockdown of OCILRP2 expression with shRNA or the blockage of its activity by an anti-OCILRP2 antagonist antibody reduced CD3/CD28-costimulated EL4 T cell viability and IL-2 production, inhibit Raf1, MAPK3, and MAPK8 activation, and impair NFAT and NF-κB transcriptional activities. Furthermore, immunoprecipitation results indicated that OCILRP2 could interact with the DAP12 protein, an adaptor containing an intracellular ITAM motif that can transduce signals to induce MAP kinase activation for T cell activation. Our data reveal that after binding with DAP12, OCILRP2 activates the Raf-MAP kinase pathways, resulting in T cell activation.
A mechanistic modelling and data assimilation approach to estimate the carbon/chlorophyll and carbon/nitrogen ratios in a coupled hydrodynamical-biological model

The principal objective of hydrodynamical-biological models is to provide estimates of the main carbon fluxes such as total and export oceanic production. These models are nitrogen based, that is to say that the variables are expressed in terms of their nitrogen content. Moreover models are calibrated using chlorophyll data sets. Therefore carbon to chlorophyll (C:Chl) and carbon to nitrogen (C:N) ratios have to be assumed. This paper addresses the problem of the representation of these ratios. In a 1D framework at the DYFAMED station (NW Mediterranean Sea) we propose a model which enables the estimation of the basic biogeochemical fluxes and in which the spatio-temporal variability of the C:Chl and C:N ratios is fully represented in a mechanical way. This is achieved through the introduction of new state variables coming from the embedding of a phytoplankton growth model in a more classical Redfieldian NNPZD-DOM model (in which the C:N ratio is assumed to be a constant). Following this modelling step, the parameters of the model are estimated using the adjoint data assimilation method which enables the assimilation of chlorophyll and nitrate data sets collected at DYFAMED in 1997.Comparing the predictions of the new Mechanistic model with those of the classical Redfieldian NNPZD-DOM model which was calibrated with the same data sets, we find that both models reproduce the reference data in a comparable manner. Both fluxes and stocks can be equally well predicted by either model. However if the models are coinciding on an average basis, they are diverging from a variability prediction point of view. In the Mechanistic model biology adapts much faster to its environment giving rise to higher short term variations. Moreover the seasonal variability in total production differs from the Redfieldian NNPZD-DOM model to the Mechanistic model. In summer the Mechanistic model predicts higher production values in carbon unit than the Redfieldian NNPZD-DOM model. In winter the contrary holds.
Schedulability analysis of flows scheduled with FIFO: application to the expedited forwarding class

In this paper, we are interested in real-time flows requiring quantitative and deterministic QoS (quality of service) guarantees. We focus more particularly on two QoS parameters: the worst case end-to-end response time and jitter. We consider a FIFO (first in first out) scheduling of flows. The FIFO scheduling is the simplest one to implement and very used. We first establish a bound on the worst case end-to-end response time of any flow in the network, using the trajectory approach. We present an example illustrating our results. Finally, we show how to apply these results to the EF (expedited forwarding) class in a DiffServ (differentiated services) architecture
A two-stage technique to improve intrusion detection systems based on data mining algorithms

An intrusion detection system (IDS) is the fundamental part of the security infrastructure, since it ensures the detection of any suspicious action. Although the detection of intrusions and attacks is the ultimate goal, the huge amount of generated alerts cannot be properly managed by the administrator. In order to improve the accuracy of sensors, we adopt a two-stage technique. The first one aims to generate meta-alerts through clustering and the second one aims to reduce the rate of false alarms using a binary classification of the generated meta-alerts. For the first stage we use two alternatives, self-organizing map (SOM) with k-means algorithm and neural GAS with fuzzy c-means algorithm. For the second stage we use three approaches, SOM with K-means algorithm, support vector machine and decision trees. Based on a public data set and several evaluation criteria, our proposed procedures are evaluated. Results show that our procedures outperform other competitor methods by reducing the rate of false positives.
Transcriptomic characterization of two major Fusarium resistance quantitative trait loci (QTLs), Fhb1 and Qfhs.ifa‐5A, identifies novel candidate genes

Summary Fusarium head blight, caused by Fusarium graminearum, is a devastating disease of wheat. We developed near‐isogenic lines (NILs) differing in the two strongest known F. graminearum resistance quantitative trait loci (QTLs), Qfhs.ndsu‐3BS (also known as resistance gene Fhb1) and Qfhs.ifa‐5A, which are located on the short arm of chromosome 3B and on chromosome 5A, respectively. These NILs showing different levels of resistance were used to identify transcripts that are changed significantly in a QTL‐specific manner in response to the pathogen and between mock‐inoculated samples. After inoculation with F. graminearum spores, 16 transcripts showed a significantly different response for Fhb1 and 352 for Qfhs.ifa‐5A. Notably, we identified a lipid transfer protein which is constitutively at least 50‐fold more abundant in plants carrying the resistant allele of Qfhs.ifa‐5A. In addition to this candidate gene associated with Qfhs.ifa‐5A, we identified a uridine diphosphate (UDP)‐glycosyltransferase gene, designated TaUGT12887, exhibiting a positive difference in response to the pathogen in lines harbouring both QTLs relative to lines carrying only the Qfhs.ifa‐5A resistance allele, suggesting Fhb1 dependence of this transcript. Yet, this dependence was observed only in the NIL with already higher basal resistance. The complete cDNA of TaUGT12887 was reconstituted from available wheat genomic sequences, and a synthetic recoded gene was expressed in a toxin‐sensitive strain of Saccharomyces cerevisiae. This gene conferred deoxynivalenol resistance, albeit much weaker than that observed with the previously characterized barley HvUGT13248.
Practical MCMC for Missing Data Treatmentin DegradedVideo

Thispaperpresentsa simplifiedframework for thesimultaneoustreatmentof missingdata and motion in degradedvideosequences.Using simple, translationalmodelsof motion, a joint solution for the detection,and reconstructionof missingdata is proposed.Theframework alsoincorporatesthenotionof dealing with occlusionand uncovering as it pertainsto picture building. The idea is to useMCMC to solvethe resultingproblemarticulatedundera Bayesianframework, but to deploypurely deterministic mechanismsfor dealing with the solution. This results in a relativelyfast implementationthat unifiesmanyof thepixelby-pixelschemespreviouslydescribedin theliterature. Thenovel contributionsof thispaperare i) A new framework for incorporating occlusionjointly with missingdataandmotionii) A practical approach to thedeployment of MCMC for videomanipulation
An Integer Linear Programming Based Routing Algorithm for Flip-Chip Design

The flip-chip package provides a high chip-density solution to the demand for more I/O pads of VLSI designs. In this paper, we present the first routing algorithm in the literature for the pre-assignment flip-chip routing problem with a pre-defined netlist among pads and wire-width and signal-skew considerations. Our algorithm is based on integer linear programming (ILP) and guarantees to find an optimal solution for the addressed problem. It adopts a two-stage technique of global routing followed by detailed routing. In global routing, it first uses two reduction techniques to prune redundant solutions and create a global-routing path for each net. Without loss of the solution optimality, our reduction techniques can further prune the ILP variables (constraints) by 85.5% (98.0%) on average over a recent reduction technique. The detailed routing applies X-based grid- less routing to complete the routing. Experimental results based on five real industry designs show that our router can achieve 100% routability and the optimal global-routing wirelength and satisfy all signal-skew constraints, under reasonable CPU times, while recent related work results in much inferior solution quality.
Roles of Retinoids and Retinoic Acid Receptors in the Regulation of Hematopoietic Stem Cell Self-Renewal and Differentiation

Multipotent hematopoietic stem cells (HSCs) sustain blood cell production throughout an individual's lifespan through complex processes ultimately leading to fates of self-renewal, differentiation or cell death decisions. A fine balance between these decisions in vivo allows for the size of the HSC pool to be maintained. While many key factors involved in regulating HSC/progenitor cell differentiation and cell death are known, the critical regulators of HSC self-renewal are largely unknown. In recent years, however, a number of studies describing methods of increasing or decreasing the numbers of HSCs in a given population have emerged. Of major interest here are the emerging roles of retinoids in the regulation of HSCs.
Spatial and seasonal analysis on leptospirosis in the municipality of São Paulo, Southeastern Brazil, 1998 to 2006.

OBJECTIVE To analyze the spatial and seasonal distribution of leptospirosis and identify possible ecological and social components of its transmission. METHODS A total of 2,490 cases registered in each district of the municipality of São Paulo, Southeastern Brazil, between 1998 and 2006, were georeferenced. The data were obtained from the Notifiable Diseases Information System. Thematic maps were made, showing the variables of incidence rate, lethality rate, literacy rate, average monthly income, number of residents per household, water supply and sewage system. To identify spatial patterns (dispersed, clustered or random), these variables were analyzed using the global and local Moran indices. Spearman's correlation coefficient was used to test associations between variables with clustered spatial patterns. RESULTS Clustered spatial patterns were observed for the variables of leptospirosis incidence, literacy rate, average monthly income, number of residents per household, water supply and sewage system. There were 773 notified cases in the dry season and 1,717 cases in the rainy season. The incidence and lethality rates correlated with the population's socioeconomic conditions, independently of the period. CONCLUSIONS Leptospirosis is spread throughout the municipality of São Paulo, and its incidence increases during the rainy season. In the dry season, the localities where cases appear coincide with the areas of poorest housing conditions. In the rainy season, it also increases in other districts, probably due to the proximity of rivers and streams.
PI-E: An Empathy Skills Training Package to Enhance Therapeutic Skills of IAPT and Other Therapists

This paper describes a condensed version of psychodynamic interpersonal therapy (PIT), Psychodynamic Interpersonal-Empathy (PI-E), which consists of the first level of competencies of the PIT model. The intention is to use basic psychodynamic principles and skills to enhance delivery of manualised, cognitive therapy based treatments. The intervention is designed to improve two common factors of therapy: the bond between client and therapist, and the ability of the therapist to create positive expectations through an explanation and understanding of the person’s problems. Both of these so-called common factors are consistently associated with clinical outcomes. Training has been developed specifically for low-intensity therapists who are employed in the Improving Access to Psychological Treatment programme. Training focuses upon 5 basic components of PI: negotiation; picking up cues;using statements rather than questions; focusing on feelings and understanding hypotheses. When used skilfully together, these simple components, offer a powerful way of empathizing with and deepening the collaborative work with the client. They all help the therapist to focus upon how the client is feeling ‘here and now’ in the session. Training in the model has the potential to improve outcomes and reduce drop-out rates by enabling therapists to manage problem scenarios in an empathic way.
New material of Gumardee pascuali Flannery et al., 1983 (Marsupialia: Macropodiformes) and two new species from the Riversleigh World Heritage Area, Queensland, Australia

New specimens of the late Oligocene macropodiform, Gumardee pascuali, are described, as well as two new late Oligocene to early Miocene species, G. springae sp. nov. and G. richi sp. nov. Species of Gumardee exhibit a unique combination of features, including very long upper and lower third premolars, partially lophodont molars and, in dorsoventral plane, concave lower molar row and convex upper molar row. We combined two morphological matrices to assess the phylogenetic relationships of these species. Our analysis recovered species of Gumardee as a well-supported monophyletic group, nested within Potoroinae. Gumardee richi and G. pascuali appear to be more derived than G. springae in having a more strongly developed posthypocristid that is almost hypolophid-like.
Iris: Mitigating Phase Noise in Millimeter Wave OFDM Systems

Next-generation wireless networks are widely expected to operate over millimeter-wave (mmW) frequencies of over 28GHz. These bands mitigate the acute spectrum shortage in the conventional microwave bands of less than 6GHz. The shorter wavelengths in these bands also allow for building dense antenna arrays on a single chip, thereby enabling various MIMO configurations and highly directional links that can increase the spatial reuse of spectrum. While attempting to build a practical over-the-air (OTA) link over mmW, we realized that the traditional baseband processing techniques used in the microwave bands simply could not cope with the exacerbated frequency offsets (or phase noise) observed in the RF oscillators at these mmW bands. While the frequency offsets are large, the real difficulty arose from the fact that they varied significantly over very short time-scales. Traditional feedback loop techniques still left significant residual offsets, which in turn led to inter-carrier-interference (ICI). The result was high symbol error rates (SER). This thesis presents Iris, a time-domain baseband processing block that compensates for these large and time-varying frequency offsets. Iris first measures the frequency offset on a per-symbol basis using the cyclic prefix. It then corrects a buffered version of the same symbol using a digital numerically controlled oscillator (NCO), and then sends it to the rest of the baseband processing chain. Over real mmW hardware, Iris reduces the SER by one to two orders of magnitude, as compared to competing techniques.
An architecture for social ad-hoc networks

Many applications have emerged as social networking applications such as Facebook, YouTube, and Twitter. They allow users to share ideas, experiences, and files. However, to be able to gain access to the advantages and services of social networks, users have to have Internet connectivity. Unfortunately, Internet connectivity is not always available for all users in certain places such as; bus and train stations, disaster areas, wars, university campus, and conferences. In such places, the needs for social services are indeed required. Therefore, it is vital to provide the social service with the absence of regular communication technology. In this paper, we proposed a social ad-hoc network. It is based on mobile ad-hoc networks as a solution for the lack of communication means.
Joint resource allocation and interference avoidance with fairness consideration for multi-cell cognitive radio networks

This paper presents a joint resource allocation and interference avoidance algorithm for uplink transmissions in a multi-cell cognitive radio network (CRN), which overlays with a multi-cell primary network (PN). We consider a primary willingness based coexistent architecture. Primary base stations will broadcast pilot signals and interference margins to the CRN for interference channel evaluation and power control. The objective of the algorithm is to maximize the sum rate of cognitive radio cells without causing unacceptable interference to primary receivers, where Lagrangian duality based technique has been utilized to solve the maximization problem and jointly allocate the subchannels and power for each user. The fairness among users is considered within the joint resource allocation to guarantee that the instantaneous rate for each user is larger than a given minimum rate. Simulation results show the efficiency of our algorithm, which has good convergent performance. Moreover, compared to the conventional schemes, the proposed algorithm can satisfy the fairness well, and also obtain a large gain on cell-edge user throughput only with a small reduction in cell sum rate.
Book Review: Cognitive Grammar in Contemporary Fiction by Chloe Harrison, 2017. ‘Linguistic Approaches to Literature’ series

(a kind of ‘personality interview’). She examines how voice semiotics (such as volume and tone) and multimodality (such as the use of music) can add additional layers of meaning to the basic text of the interview. Part Three, ‘Playfulness and narrative functions of dialogue’, considers the ludic qualities of dialogue and its contributions in supporting narrativity in texts. Two chapters focus on games: Domsch examines game-playing dialogue in terms of the fictional world of the game (‘diegetic communication’) and in terms of player-directed dialogue (‘ludic communication’), suggesting we might reasonably expect future improvements in terms of Non-Player Characters’ communication, while Mäyrä highlights the diversity of dialogue in different Role-Playing Games (table-top, pen-and-paper, and single and multiplayer online computer), analysing both different levels of dialogue and different levels of player engagement. Mikkonen argues for a medium-specific understanding of the role of dialogue in comics (using examples such as speech balloons as a visual metaphor within this genre), and Bernaerts looks at the affordances and functions of radiophonic dialogue in two radio plays adapted from Harry Mulisch novels, discussing how this form of dialogue can add not only to the story as a whole but also to audience interpretations of conversations. In short, this book can be viewed as making three main contributions to the existing literature. Firstly, by focusing on contextualised dialogue, it gives priority to an underdeveloped, yet extremely relevant, area of research. In doing so, it lays the groundwork for future studies in this field. Secondly, it brings together an impressive range of original case studies from diverse scholars and practitioners working across different disciplinary boundaries and languages. Thirdly, the clarity and accessibility of the chapters, both in terms of how the authors explain their theoretical frameworks and how they guide the reader through their analysis and discussion, mean that this volume has the potential to engage a variety of readers at different levels and from multiple backgrounds. As this book aptly demonstrates, the study of dialogue is, in essence, a study of the richness and complexity of human interaction.
On the doggedness of self-enhancement and self-protection: How constraining are reality constraints?

ABSTRACT Self-enhancement and self-protection are constrained by reality. But to what extent? Broader constraints, often considered powerful, such as East-Asian culture, religion, mind-body practices, and prison environments are not particularly effective deterrents. Narrower constraints, also considered powerful, such as self-reflection and mnemic neglect, are not very helpful either. Deliberate and systematic laboratory efforts, both at the intrapersonal level (e.g., explanatory introspection, salience of one’s faults) and the interpersonal level (e.g., accountability, relationship closeness), can boast success in constraining self-enhancement and self-protection strivings, but the success is mixed, difficult to implement, and probably short-lived. The doggedness (potency and prevalence) of self-enhancement and self-protection are due to the functions or social benefits with which they are associated or confer: psychological health, goal pursuit and attainment, leadership election, and sexual selection. These functions are traceable to our species’ evolutionary past.
Speed control of electrical drives using classical control methods

A classical-control approach to the design and analysis of proportional-integral (PI) speed controllers for electrical drives is presented. After vindicating the fact that traditional one-degree-of-freedom PI control generally gives unsatisfactory performance, a well-performing two-degrees-of-freedom PI controller is designed, with analytic parameter selection. The robustness of the obtained closed-loop system is analyzed, and is found to be satisfactory.