Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple procyclin isoforms are expressed differentially during the development of insect forms of Trypanosoma brucei.

Transmission of Trypanosoma brucei by the tsetse fly entails several rounds of differentiation as the parasite migrates through the digestive tract to the salivary glands of its vector. Differentiation of the bloodstream to the procyclic form in the fly midgut is accompanied by the synthesis of a new coat consisting of EP and GPEET procyclins. There are three closely related EP isoforms, two of which (EP1 and EP3) contain N-glycans. To identify the individual EP isoforms that are expressed early during synchronous differentiation in vitro, we exploited the selective extraction of GPI-anchored proteins and mass spectrometry. Unexpectedly, we found that GPEET and all isoforms of EP were coexpressed for a few hours at the onset of differentiation. At this time, the majority of EP1 and EP3 molecules were already glycosylated. Within 24 hours, GPEET became the major surface component, to be replaced in turn by glycosylated forms of EP, principally EP1, at a later phase of development. Transient transfection experiments using reporter genes revealed that each procyclin 3' untranslated region contributes to differential expression as the procyclic form develops. We postulate that programmed expression of other procyclin species will accompany further rounds of differentiation, enabling the parasite to progress through the fly.
LQG balancing: Intertwining balancing and sign iterations

In this paper an efficient new approach to LQG balancing is presented. We propose an algorithm which intertwines iterations of a matrix sign function computation with state space balancing iterations, giving directly the balancing transformation upon convergence. Our approach has the advantage that the balancing and sign iterations can be computed in parallel and therefore can yield a performance gain in a suitable parallel implementation. In particular, our approach does not require as a first step the solution of the control and filter Riccati equations followed by the second step of calculating the balancing transformation from the solutions.
Does dental agenesis have an impact on OHRQoL of children, adolescents and young adults? A systematic review

Abstract Dental agenesis (DA) is defined as the congenital absence of teeth and is considered as the most common dental anomaly. It may cause speech and masticatory dysfunctions as well as esthetic problems. Its impact on oral health-related quality of life (OHRQoL) is not fully understood. The aim of the study was to assess whether DA affects OHRQoL of children, adolescents and young adults. A broad search was done on databases (Pubmed, Scopus, Web of Science and Virtual Health Library) using Medical Subject Headings (MeSH) and free terms. Eligibility criteria for article selection were predetermined and were classified according to quality assessment and risk of bias. The electronic search produced 178 titles and abstracts. After excluding duplicate abstracts and applying the eligibility criteria, three articles were assessed for the final qualitative synthesis. The three articles were classified as moderate quality and present risk of bias. No articles were found that had evaluated children and young adults. From the three articles that were selected, only one was found to have a greater impact in the adolescent agenesis group with statistical differences in all domains. There is insufficient evidence available to conclude if DA affects OHRQoL of children, adolescents and young adults.
Clinical Immunology Review Series: An approach to the patient with recurrent superficial abscesses

Patients may be referred to the immunology clinic for investigation of recurrent superficial abscess formation. In the majority of adult patients this clinical presentation does not equate with an underlying primary immune deficiency. Nevertheless, recurrent mucocutaneous abscesses can be associated with significant morbidity and long‐term complications, including scarring and fistula formation, and may be associated with underlying immune‐mediated disease. This review sets out an approach to the patient with recurrent superficial abscesses, focusing on the differential diagnoses, investigation and management of both the common causes and those associated with specific immune deficiency.
On the Structure of Nonlinearities in Pose Graph SLAM

Pose graphs have become an attractive representation for solving Simultaneous Localization and Mapping (SLAM) problems. In this paper, we analyze the structure of the nonlinearities in the 2D SLAM problem formulated as the optimizing of a pose graph. First, we prove that finding the optimal configuration of a very basic pose graph with 3 nodes (poses) and 3 edges (relative pose constraints) with spherical covariance matrices, which can be formulated as a six dimensional least squares optimization problem, is equivalent to solving a one dimensional optimization problem. Then we show that the same result can be extended to the optimizing of a pose graph with “two anchor nodes” where every edge is connecting to one of the two anchor nodes. Furthermore, we prove that the global minimum of the resulting one dimensional optimization problem must belong to a certain interval and there are at most 3 minima in that interval. Thus the globally optimal pose configuration of the pose graph can be obtained very easily through the bisection method and closed-form formulas.
Phenotypic and Functional Profiling of CD4 T Cell Compartment in Distinct Populations of Healthy Adults with Different Antigenic Exposure

Background Multiparameter flow cytometry has revealed extensive phenotypic and functional heterogeneity of CD4 T cell responses in mice and humans, emphasizing the importance of assessing multiple aspects of the immune response in correlation with infection or vaccination outcome. The aim of this study was to establish and validate reliable and feasible flow cytometry assays, which will allow us to characterize CD4 T cell population in humans in field studies more fully. Methodology/Principal Findings We developed polychromatic flow cytometry antibody panels for immunophenotyping the major CD4 T cell subsets as well as broadly characterizing the functional profiles of the CD4 T cells in peripheral blood. We then validated these assays by conducting a pilot study comparing CD4 T cell responses in distinct populations of healthy adults living in either rural or urban Kenya. This study revealed that the expression profile of CD4 T cell activation and memory markers differed significantly between African and European donors but was similar amongst African individuals from either rural or urban areas. Adults from rural Kenya had, however, higher frequencies and greater polyfunctionality among cytokine producing CD4 T cells compared to both urban populations, particularly for “Th1” type of response. Finally, endemic exposure to malaria in rural Kenya may have influenced the expansion of few discrete CD4 T cell populations with specific functional signatures. Conclusion/Significance These findings suggest that environmentally driven T cell activation does not drive the dysfunction of CD4 T cells but is rather associated with greater magnitude and quality of CD4 T cell response, indicating that the level or type of microbial exposure and antigenic experience may influence and shape the functionality of CD4 T cell compartment. Our data confirm that it is possible and mandatory to assess multiple functional attributes of CD4 T cell response in the context of infection.
Pain issues in disorders of consciousness

Abstract Background: The assessment of pain and nociception in non-communicative patients with disorders of consciousness (DOC) is a real challenge for clinicians. It is, therefore, important to develop sensitive standardized tools usable at the bedside. Objectives: This review aims to provide an overview of the current knowledge about pain processing and assessment in patients with DOC. Methods: A search was performed on PubMed using MeSH terms including vegetative state, unresponsive wakefulness syndrome, minimally conscious state, consciousness disorders, pain, nociception, neuroimaging and pain assessment. Results: Neuroimaging studies investigating pain processing in patients with DOC and their implication for clinicians are reviewed. Current works on the development of standardized and sensitive tools for assessing nociception are described. Conclusion: The suggested pain perception capacity highlighted by neuroimaging studies in patients in a MCS and in some patients in a VS/UWS supports the idea that these patients need analgesic treatment and monitoring. The first tool which has been developed to assess nociception and pain in patients with DOC is the NCS. Its revised version represents a rapid, standardized and sensitive scale which can be easily implemented in a clinical setting. Complementary pain assessments are also under validation in order to offer more options to clinicians.
Offline signature verification based on statistical features

Signature identification and verification is considered among the most popular biometric methods in the area of personal authentication. In proposed method, we deal with offline verification of signature by two different algorithms. Before extracting different features from the signature, some preprocessing of the signature is done. In preprocessing, the signature is colour normalized and scaled into a standard format. The algorithm is quite different and it deals with extraction of features based on mean, standard deviation and moment. The algorithm uses Euclidean distance classifier for comparing test signature with database. The algorithm have shown promising results while dealing with random forgeries and simple forgeries; also it gives good recognition rate.
Topoisomerase I-Mediated Inhibition of Hypoxia-Inducible Factor 1

We have shown previously that the camptothecin analogue topotecan (TPT), a topoisomerase I (Top 1) poison, inhibits hypoxia-inducible factor 1 (HIF-1) transcriptional activity and HIF-1α protein accumulation in hypoxia-treated U251 human glioma cells. In this article, we demonstrate that TPT does not affect HIF-1α protein half-life or mRNA accumulation but inhibits its translation. In addition, we demonstrate that Top 1 is required for the inhibition of HIF-1α protein accumulation by TPT as shown by experiments performed using camptothecin-resistant cell lines with known Top 1 alterations. Experiments performed with aphidicolin indicated that TPT inhibited HIF-1 protein accumulation in the absence of DNA replication. DNA-damaging agents, such as ionizing radiation and doxorubicin, did not affect HIF-1α protein accumulation. Ongoing transcription was essential for the inhibition of HIF-1α protein accumulation by TPT. Our results demonstrate the existence of a novel pathway connecting Top 1-dependent signaling events and the regulation of HIF-1α protein expression and function. In addition, our findings dissociate the cytotoxic activity of TPT from the inhibition of the HIF-1 pathway and raise the possibility of novel clinical applications of TPT aimed at targeting HIF-1-dependent responses.
Role of p75 Neurotrophin Receptor in the Neurotoxicity by β-amyloid Peptides and Synergistic Effect of Inflammatory Cytokines

The neurodegenerative changes in Alzheimer's disease (AD) are elicited by the accumulation of β-amyloid peptides (Aβ), which damage neurons either directly by interacting with components of the cell surface to trigger cell death signaling or indirectly by activating astrocytes and microglia to produce inflammatory mediators. It has been recently proposed that the p75 neurotrophin receptor (p75NTR) is responsible for neuronal damage by interacting with Aβ. By using neuroblastoma cell clones lacking the expression of all neurotrophin receptors or engineered to express full-length or various truncated forms of p75NTR, we could show that p75NTR is involved in the direct signaling of cell death by Aβ via the function of its death domain. This signaling leads to the activation of caspases-8 and -3, the production of reactive oxygen intermediates and the induction of an oxidative stress. We also found that the direct and indirect (inflammatory) mechanisms of neuronal damage by Aβ could act synergistically. In fact, TNF-α and IL-1β, cytokines produced by Aβ-activated microglia, could potentiate the neurotoxic action of Aβ mediated by p75NTR signaling. Together, our results indicate that neurons expressing p75NTR, mostly if expressing also proinflammatory cytokine receptors, might be preferential targets of the cytotoxic action of Aβ in AD.
Saccharomyces cerevisiae Donor Preference During Mating-Type Switching Is Dependent on Chromosome Architecture and Organization

Saccharomyces mating-type (MAT) switching occurs by gene conversion using one of two donors, HMLα and HMRa, located near the ends of the same chromosome. MATa cells preferentially choose HMLα, a decision that depends on the recombination enhancer (RE) that controls recombination along the left arm of chromosome III (III-L). When RE is inactive, the two chromosome arms constitute separate domains inaccessible to each other; thus HMRa, located on the same arm as MAT, becomes the default donor. Activation of RE increases HMLα usage, even when RE is moved 50 kb closer to the centromere. If MAT is inserted into the same domain as HML, RE plays little or no role in activating HML, thus ruling out any role for RE in remodeling the silent chromatin of HML in regulating donor preference. When the donors MAT and RE are moved to chromosome V, RE increases HML usage, but the inaccessibility of HML without RE apparently depends on other chromosome III-specific sequences. Similar conclusions were reached when RE was placed adjacent to leu2 or arg4 sequences engaged in spontaneous recombination. We propose that RE's targets are anchor sites that tether chromosome III-L in MATα cells thus reducing its mobility in the nucleus.
Effect of instillation method on absorption of phenol red as a model from liver and small intestinal serosal surface in rats

The aim of this study is to examine the effect of the instillation method on absorption of a drug from the liver and small intestinal serosal surface in rats. We performed continuous microinstillation via an infusion pump and bolus instillation via a syringe. Phenol red as a model was absorbed after continuous microinstillation of 2.35 mg in 235 μL for 5 min on the liver and small intestinal serosal surface in rats with a significantly higher AUC of the plasma concentration profile until 60 min, compared with that after bolus instillation. A similar trend was observed after continuous microinstillation of 2.35 mg in 117.5 μL for 2.5 min. The calculated absorption rate constants Ka after continuous microinstillation of phenol red based on a two-compartment model with first-order absorption were higher than those after bolus instillation on the liver and small intestinal serosal surface at either instillation concentration. Moreover, Ka was increased after continuous microinstillation of 2.35 mg in 117.5 μL on either instillation site. In the comparison between instillation sites, instillation of phenol red on the liver surface resulted in 1.2 to 2.3-fold higher Ka, compared to small intestinal serosal surface. This tendency was marked after continuous microinstillation of 2.35 mg in 117.5 μL. In conclusion, absorption could be enhanced by instilling a small amount of drug solution on the liver surface gradually and continuously, suggesting a promising approach for instillation site-selective drug delivery in the peritoneal cavity.
Visualisation System Based on Image Warping and Delaunay Triangulation of the Space

In this article we present a visualisation algorithm based on image warping. A source data for the algorithm is a set of images with colour and depth information rendered for the observer located in a number of reference positions. For each position there are 6 images rendered for the directions of axes forming the “image cube”. The algorithm computes a 3D Delaunay triangulation on these positions and divides the space inside the convex hull into tetrahedra. During the visualisation process the observer situated in one tetrahedron sees warped images from the vertices of this tetrahedron. We also describe the automatic algorithm for selection of new reference positions to improve the quality and remove “holes”. For both algorithms we utilize 3D hardware acceleration.
Learning and Interactive Tangible User Interfaces (Smart Toys)

Smart Toys allow an interaction with the user that goes beyond what a normal toy can provide. They possess the ability to learn from teachings by their owner, and it is by this learning process that an intimate bond is forged between the owner and their toy. This research looks at the the forces behind the learning process and the development of a physical device that can function as a Smart Toy. The Sulley Smart Toy is adapted from a plush doll. This introduces some interesting challenges, but also allows an interaction of a kind that is different to most existing smart toys. Sulley can be hugged and squeezed, and from this interaction he can perform actions. The action itself is determined by an interactive reinforcement learning model. Part of this research was to determine how best to apply existing reinforcement learning methods to the quirks of this model.
Fractionally spaced non-linear equalization of faster than Nyquist signals

Faster than Nyquist transmissions provide the opportunity of increasing data rate at the expenses of additional inter-symbol interference. The optimum receiver requires a maximum likelihood sequence detector, whose complexity grows exponentially with the number of filter taps and with the number of bits per symbol. In this paper we consider two suboptimal approaches based on non-linear equalization of the received signal. In order to further reduce the receiver complexity we consider an implementation of equalization filters in the frequency domain. The contributions of the paper are a) a receiver architecture for fractionally spaced non-linear equalizers, and b) efficient design methods of the equalization filters in the frequency domain. In particular, the derived optimal (in the mean square error sense) filters overcome approaches proposed in the literature.
Towards a practical silent speech recognition system

Our recent efforts towards developing a practical surface electromyography (sEMG) based silent speech recognition interface have resulted in significant advances in the hardware, software and algorithmic components of the system. In this paper, we report our algorithmic progress, specifically: sEMG feature extraction parameter optimization, advances in sEMG acoustic modeling, and sEMG sensor set reduction. The key findings are: 1) the gold-standard parameters for acoustic speech feature extraction are far from optimum for sEMG parameterization, 2) advances in state-of-the-art speech modelling can be leveraged to significantly enhance the continuous sEMG silent speech recognition accuracy, and 3) the number of sEMG sensors can be reduced by half with little impact on the final recognition accuracy, and the optimum sensor subset can be selected efficiently based on basic mono-phone HMM modeling.
Computational bodybuilding

We propose a method to create a wide range of human body shapes from a single input 3D anatomy template. Our approach is inspired by biological processes responsible for human body growth. In particular, we simulate growth of skeletal muscles and subcutaneous fat using physics-based models which combine growth and elasticity. Together with a tool to edit proportions of the bones, our method allows us to achieve a desired shape of the human body by directly controlling hypertrophy (or atrophy) of every muscle and enlargement of fat tissues. We achieve near-interactive run times by utilizing a special quasi-statics solver (Projective Dynamics) and by crafting a volumetric discretization which results in accurate deformations without an excessive number of degrees of freedom. Our system is intuitive to use and the resulting human body models are ready for simulation using existing physics-based animation methods, because we deform not only the surface, but also the entire volumetric model.
Wnt ligands from the embryonic surface ectoderm regulate ‘bimetallic strip’ optic cup morphogenesis in mouse

The Wnt/β-catenin response pathway is central to many developmental processes. Here, we assessed the role of Wnt signaling in early eye development using the mouse as a model system. We showed that the surface ectoderm region that includes the lens placode expressed 12 out of 19 possible Wnt ligands. When these activities were suppressed by conditional deletion of wntless (Le-cre; Wlsfl/fl) there were dramatic consequences that included a saucer-shaped optic cup, ventral coloboma, and a deficiency of periocular mesenchyme. This phenotype shared features with that produced when the Wnt/β-catenin pathway co-receptor Lrp6 is mutated or when retinoic acid (RA) signaling in the eye is compromised. Consistent with this, microarray and cell fate marker analysis identified a series of expression changes in genes known to be regulated by RA or by the Wnt/β-catenin pathway. Using pathway reporters, we showed that Wnt ligands from the surface ectoderm directly or indirectly elicit a Wnt/β-catenin response in retinal pigment epithelium (RPE) progenitors near the optic cup rim. In Le-cre; Wlsfl/fl mice, the numbers of RPE cells are reduced and this can explain, using the principle of the bimetallic strip, the curvature of the optic cup. These data thus establish a novel hypothesis to explain how differential cell numbers in a bilayered epithelium can lead to shape change. Summary: During optic cup morphogenesis, Wnt ligands expressed in the surface ectoderm control cell proliferation in the retinal pigmented epithelium, and thus influence bending of the neural retina.
Retrieval Algorithms for Road Surface Modelling Using Laser-Based Mobile Mapping

Automated processing of the data provided by a laser-based mobile mapping system will be a necessity due to the huge amount of data produced. In the future, vehicle-based laser scanning, here called mobile mapping, should see considerable use for road environment modelling. Since the geometry of the scanning and point density is different from airborne laser scanning, new algorithms are needed for information extraction. In this paper, we propose automatic methods for classifying the road marking and kerbstone points and modelling the road surface as a triangulated irregular network. On the basis of experimental tests, the mean classification accuracies obtained using automatic method for lines, zebra crossings and kerbstones were 80.6%, 92.3% and 79.7%, respectively.