Miracle-dz/UniFAR-FTUs huggingface dataset:
CD1d-unrestricted NKT cells are endowed with a hybrid function far superior than that of iNKT cells

Significance The Immunological Genome Project Consortium has recently identified a gene-expression program that links invariant natural killer T (iNKT) cells to NK cells. While this is true, our study provides molecular and functional evidence demonstrating that CD1d-independent NKT cells are uniquely programmed with a hybrid function far superior to that of iNKT cells. Such a unique feature enables this subset of NKT cells to contribute to adaptive immunity (like T cells) and at the same time act as a prominent player in innate defense (like NK cells). Invariant natural killer T (iNKT) cells to date represent the best example of cells known to have a hybrid function, representing both innate and adaptive immunity. Shared phenotypic similarities with NK cells together with a rapid response to a cytokine stimulus and a productive TCR engagement are the features that underline the hybrid nature of iNKT cells. Using these criteria, we provide molecular and functional evidence demonstrating that CD1d-independent (CD1dind) NKT cells, a population of CD1d-unrestricted NKT cells, are endowed with a hybrid function far superior to that of iNKT cells: (i) an extensive shared program with NK cells, (ii) a closer Euclidian distance with NK cells, and (iii) the ability to respond to innate stimuli (Poly:IC) with cytotoxic potential in the same manner as NK cells identify a hybrid feature in CD1dindNKT cells that truly fulfills the dual function of an NK and a T cell. Our finding that CD1dindNKT cells are programmed to act like NK cells in response to innate signals while being capable of adaptive responses is unprecedented, and thus might reemphasize CD1d-unrestricted NKT cells as a subset of lymphocytes that could affect biological processes of antimicrobial and tumor immunity in a unique way.
Vision-Based Differential GPS: Improving VSLAM / GPS Fusion in Urban Environment with 3D Building Models

We improve in this paper the localization accuracy of visual SLAM (VSLAM) / GPS fusion in dense urban area by using 3D building models provided by Geographic Information System (GIS). GPS inaccuracies are corrected by comparison of the reconstruction resulting from the VSLAM / GPS fusion with 3D building models. These corrected GPS data are thereafter re-injected in the fusion process. Experimental results demonstrate the accuracy improvements achieved through our proposed solution.
Multitarget selection of catalytic antibodies with β‐lactamase activity using phage display

β‐lactamase enzymes responsible for bacterial resistance to antibiotics are among the most important health threats to the human population today. Understanding the increasingly vast structural motifs responsible for the catalytic mechanism of β‐lactamases will help improve the future design of new generation antibiotics and mechanism‐based inhibitors of these enzymes. Here we report the construction of a large murine single chain fragment variable (scFv) phage display library of size 2.7 × 109 with extended diversity by combining different mouse models. We have used two molecularly different inhibitors of the R‐TEM β‐lactamase as targets for selection of catalytic antibodies with β‐lactamase activity. This novel methodology has led to the isolation of five antibody fragments, which are all capable of hydrolyzing the β‐lactam ring. Structural modeling of the selected scFv has revealed the presence of different motifs in each of the antibody fragments potentially responsible for their catalytic activity. Our results confirm (a) the validity of using our two target inhibitors for the in vitro selection of catalytic antibodies endowed with β‐lactamase activity, and (b) the plasticity of the β‐lactamase active site responsible for the wide resistance of these enzymes to clinically available inhibitors and antibiotics.
Curved PN triangles

To improve the visual quality of existing triangle-based art in realtime entertainment, such as computer games, we propose replacing flat triangles with curved patches and higher-order normal variation. At the hardware level, based only on the three vertices and three vertex normals of a given flat triangle, we substitute the geometry of a three-sided cubic Bezier patch for the triangle’s flat geometry, and a quadratically varying normal for Gouraud shading. These curved point-normal triangles, or PN triangles, require minimal or no change to existing authoring tools and hardware designs while providing a smoother, though not necessarily everywhere tangent continuous, silhouette and more organic shapes. CR Categories: I.3. 5 [surface representation, splines]: I.3. 6— graphics data structures
Prediction in Multilevel Logistic Regression

The purpose of this article is to present a new method to predict the response variable of an observation in a new cluster for a multilevel logistic regression. The central idea is based on the empirical best estimator for the random effect. Two estimation methods for multilevel model are compared: penalized quasi-likelihood and Gauss–Hermite quadrature. The performance measures for the prediction of the probability for a new cluster observation of the multilevel logistic model in comparison with the usual logistic model are examined through simulations and an application.
Scalable Exploration of Relevance Prospects to Support Decision Making

© 2016, CEUR-WS. All rights reserved. Recent efforts in recommender systems research focus increasingly on human factors that affect acceptance of recommendations, such as user satisfaction, trust, transparency, and user control. In this paper, we present a scalable visualisation to interleave the output of several recommender engines with human-generated data, such as user bookmarks and tags. Such a visualisation enables users to explore which recommendations have been bookmarked by like-minded members of the community or marked with a specific relevant tag. Results of a preliminary user study (N =20) indicate that effectiveness and probability of item selection increase when users can explore relations between multiple recommendations and human feedback. In addition, perceived effectiveness and actual effectiveness of the recommendations as well as user trust into the recommendations are higher than a traditional list representation of recommendations.
Methods for discovering novel motifs in nucleic acid sequences

We describe a computer tool to aid the discovery of new motifs in nucleic acid sequences. A typical use would be to analyse a set of upstream regions from a family of related genes in order to find possible control sequences. The heart of the method is the creation of dictionaries of related subsequences. These dictionaries can then be analysed to look for the commonest or best-defined subsequences, those that occur in the highest number of different sequences, or for those in equivalent positions within the family. We show the application of the method to a set of E. coli promoter sequences.
Human periodontal ligament fibroblast responses to compression in chronic periodontitis.

AIM Test whether human periodontal ligament fibroblasts (PDLFs) retain homeostatic responses to a physiological compressive force during chronic periodontitis. MATERIAL AND METHODS Six cell lines were established from periodontally healthy individuals (H-PDLFs) and another six were cultured from patients diagnosed with chronic periodontitis (D-PDLFs). Compressive force at 150 psi was applied to H-and D-PDLFs for 3 h on 2 consecutive days. After compression, comparisons between H-and D-PDLFs were performed by gene expression analysis of IL-6, proteases and 84 inflammation-related targets using real-time PCR. RESULTS Compression of H-PDLFs resulted in a significant increase only in MMP-1 mRNA. In contrast, the same compressive force on D-PDLFs produced significant increases in the expression of MMPs-1,-7,-9 and -16. Moreover, compression of H-PDLFs resulted in down-regulation of IL-6, while IL-6 was significantly up-regulated in compressed D-PDLFs. Compression of H-PDLFs slightly up-regulated 3 and significantly down-regulated 15 inflammation-related genes, while the same treatment strongly up-regulated 21 inflammation-related genes in D-PDLFs. CONCLUSION These results suggest a fundamental difference in the inflammatory response of healthy versus diseased PDLFs under physiological compression. Maintenance of these characteristics in vitro suggests that these cells may be at least partly responsible for the persistence of inflammation and localized susceptibility in chronic periodontitis.
Falcon: a Matlab Interactive Restructuring Compiler Falcon: a Matlab Interactive Restructuring Compiler

The development of e cient numerical programs and library routines for high-performance parallel computers is a complex task requiring not only an understanding of the algorithms to be implemented, but also detailed knowledge of the target machine and the software environment. In this paper, we describe a programming environment that can utilize such knowledge for the development of high-performance numerical programs and libraries. This environment uses an existing highlevel array language (MATLAB) as source language and performs static, dynamic, and interactive analysis to generate Fortran 90 programs with directives for parallelism. It includes capabilities for interactive and automatic transformations at both the operation-level and the functionalor algorithm-level. Preliminary experiments, comparing interpreted MATLAB programs with their compiled versions, show that compiled programs can perform up to 48 times faster on a serial machine, and up to 140 times faster on a vector machine.
Robust Trajectory Tracking for a Class of Hybrid Systems: An Internal Model Principle Approach

This paper deals with the asymptotic tracking of periodic trajectories for hybrid systems having linear dynamics in each operating mode and isolated discrete switching events (switching systems). Parametric uncertainties are considered and the dimension of the state vector is allowed to vary among modes. To deal with the hybrid nature of the system, and the possible discontinuities of its solutions at switching times, a properly amended tracking control problem is defined and a feedback control law based on a discontinuous version of the classical internal model principle is proposed. The innovative design of the discrete-time dynamics of the compensator guarantees the robust existence of a steady-state response giving zero tracking error in the controlled output, and local convergence to it.
Over-the-internet: efficient remote content management for secure elements in mobile devices

We propose Over-the-Internet (OTI), a novel system that manages secure element based applications. We demonstrate our solution in the context of NFC ecosystem and show that it can be effectively used for transmitting big applications to the secure element. Our system leverages the GlobalPlatform card specification as well as the GlobalPlatform user-centric ownership model. Our solution integrates the different actors of the NFC ecosystem in its architecture. We propose to leverage the concept of security domain, so that service providers can manage their applications independently from the SE issuer. We implement our solution within available platforms and show that it is secure, fast, reliable and easily deployable.
Transcatheter left atrial appendage closure for stroke prevention among atrial fibrillation patients

Stroke is the most feared complication of atrial fibrillation (AF) and remains a major cause of serious disability and death in these patients. Therefore, strategies to prevent stroke among AF patients are essential and can effectively improve prognosis [1,2]. The standard stroke prevention among AF patients consists of life-long oral anticoagulation mainly using vitamin K antagonists. Having, at a maximum, a 67% relative risk reduction compared with placebo [3], in addition to various intrinsic limitations and adverse effects (e.g., narrow therapeutic range, variability in pharmacokinetics, food dependency of efficacy or 0.5% annual risk of cerebral hemorrhage), vitamin K antagonists represented for many decades a suboptimal ‘best medical therapy’ for AF patients. Novel oral anticoagulants (e.g., factor Xa antagonists and direct thrombin inhibitors) with better safety, efficacy and compliance than warfarin are therefore much welcomed [4,5]. Yet the long-term outcomes of these products are unknown, and bleeding, although reduced, will not be fully eliminated. This excludes certain patients even from novel oral anticoagulants. Transesophageal echocardiographic, surgical and autoptic studies have shown that the left atrial appendage (LAA) is the site for thrombus formation in 90% of patients with thrombosis owing to nonvalvular AF [6–8]. This finding formed the rationale for LAA closure procedures as a stroke prevention therapy among AF patients. This was initially done by excision or ligation as part of open-heart surgeries [9], later thoracoscopically [10], and since 2001 via a transcatheter approach [11].
Statistical timing driven partitioning for VLSI circuits

Presents statistical-timing driven partitioning for performance optimization. We show that by using the concept of node criticality we can enhance the Fiduccia-Mattheyses (FM) partitioning algorithm to achieve, on average, around 20% improvements in terms of timing, among partitions with the same cut size. By incorporating mechanisms for timing optimization at the partitioning level, we facilitate wire-planning at high levels of the design process.
Primary structure and cellular localization of chicken brain myosin-V (p190), an unconventional myosin with calmodulin light chains

Recent biochemical studies of p190, a calmodulin (CM)-binding protein purified from vertebrate brain, have demonstrated that this protein, purified as a complex with bound CM, shares a number of properties with myosins (Espindola, F. S., E. M. Espreafico, M. V. Coelho, A. R. Martins, F. R. C. Costa, M. S. Mooseker, and R. E. Larson. 1992. J. Cell Biol. 118:359-368). To determine whether or not p190 was a member of the myosin family of proteins, a set of overlapping cDNAs encoding the full-length protein sequence of chicken brain p190 was isolated and sequenced. Verification that the deduced primary structure was that of p190 was demonstrated through microsequence analysis of a cyanogen bromide peptide generated from chick brain p190. The deduced primary structure of chicken brain p190 revealed that this 1,830-amino acid (aa) 212,509-D) protein is a member of a novel structural class of unconventional myosins that includes the gene products encoded by the dilute locus of mouse and the MYO2 gene of Saccharomyces cerevisiae. We have named the p190-CM complex "myosin-V" based on the results of a detailed sequence comparison of the head domains of 29 myosin heavy chains (hc), which has revealed that this myosin, based on head structure, is the fifth of six distinct structural classes of myosin to be described thus far. Like the presumed products of the mouse dilute and yeast MYO2 genes, the head domain of chicken myosin-V hc (aa 1-764) is linked to a "neck" domain (aa 765-909) consisting of six tandem repeats of an approximately 23-aa "IQ-motif. " All known myosins contain at least one such motif at their head-tail junctions; these IQ-motifs may function as calmodulin or light chain binding sites. The tail domain of chicken myosin-V consists of an initial 511 aa predicted to form several segments of coiled-coil alpha helix followed by a terminal 410-aa globular domain (aa, 1,421-1,830). Interestingly, a portion of the tail domain (aa, 1,094-1,830) shares 58% amino acid sequence identity with a 723-aa protein from mouse brain reported to be a glutamic acid decarboxylase. The neck region of chicken myosin-V, which contains the IQ-motifs, was demonstrated to contain the binding sites for CM by analyzing CM binding to bacterially expressed fusion proteins containing the head, neck, and tail domains. Immunolocalization of myosin-V in brain and in cultured cells revealed an unusual distribution for this myosin in both neurons and nonneuronal cells. (ABSTRACT TRUNCATED AT 400 WORDS)
Nab-paclitaxel: potential for the treatment of advanced pancreatic cancer

Advanced pancreatic adenocarcinoma is a deadly disease and is considered incurable. For the past two decades, gemcitabine remained the major chemotherapeutic drug with modest clinical benefit. Many chemotherapy and targeted agents were combined with gemcitabine but failed to demonstrate improvement in pancreatic cancer (PC) survival. Taxanes (paclitaxel, docetaxel) were introduced in the clinic as anti-microtubule agents and showed activity against PC cells in vitro; however, clinical efficacy was limited. Nab-paclitaxel (Abraxane) is an albumin-bound paclitaxel that has shown clinical activity in advanced breast and lung cancer. Recently, nab-paclitaxel was tested in a large Phase III clinical trial in combination with gemcitabine for the treatment of advanced PC. The data showed that the addition of nab-paclitaxel improved the response rate (7% in gemcitabine alone versus 23% in combination), progression-free survival (from 3.7 months to 5.5 months), and overall survival from 6.7 months to 8.5 months, compared to single agent gemcitabine. Through this review, we provide the preclinical and clinical progress in the development of nab-paclitaxel for the treatment of metastatic PC.
Observer dependent deformations in illustration

Illustration has some visual characteristics that are very interesting yet also very difficult to obtain with a computer. Whilst the simulation of the tools used for painting and drawing is successful enough, expressive capabilities have not been developed to the same extent. The deformations of objects and space is a major element in the expressiveness of illustration. The use of Hierarchical Extended Non-Linear Transformations is presented as a powerful tool for obtaining such kind of expressivity.
A New Automated Classification Technique of Galaxy Spectra with Z<1.2 Based on PCA-ODP

In this paper, we investigate the Principal Component Analysis-Optimal Discrimination Plane (PCA-ODP) approach on a data set of galaxy spectra including eleven standard subtypes with the redshift value ranging from 0 to 1.2 and a span of 0.001. These eleven subtypes are E, S0, Sa, Sb, Sc, SB1, SB2, SB3, SB4, SB5, SB6, respectively, according to the Hubble sequence. Among them, the first four subtypes belong to the class of normal galaxies (NGs); the remaining seven belong to active galaxies (AGs). We apply the PCA approach to extract the features of galaxy spectra, project the samples onto the PCs, and investigate the ODP method on the data of feature space to find the optimal discrimination plane of the two main classes. ODP approach was developed from Fisher's linear discriminant method. The difference between them is that Fisher's method uses only one Fisher's vector and ODP uses two orthogonal vectors including Fisher's vector and another. Besides the data set above, we also use the Sloan Digital Sky Survey (SDSS) galaxy spectra and Kennicutt (1992) galaxy data to test the ODP classifier. The experiment results show that our proposed technique is both robust and efficient. The correct rate can reach as high as 99.95% for the first group data, 96% for SDSS data and 98% for Kennicutt data.
A cellular model for the investigation of depot specific human adipocyte biology

ABSTRACT Upper-body adiposity is associated with increased metabolic disease risk, while lower-body adiposity is paradoxically protective. Efforts to understand the underlying mechanisms require appropriate and reproducible in vitro culture models. We have therefore generated immortalised (im) human preadipocyte (PAD) cell lines derived from paired subcutaneous abdominal and gluteal adipose tissue. These cell lines, denoted imAPAD and imGPAD display enhanced proliferation and robust adipogenic capacities. Differentiated imAPAD and imGPAD adipocytes synthesize triglycerides de novo and respond lipolytically to catecholamine-stimulation. Importantly the cells retain their depot-of-origin ‘memory’ as reflected by inherent differences in fatty acid metabolism and expression of depot-specific developmental genes. These features make these cell lines an invaluable tool for the in vitro investigation of depot-specific human adipocyte biology.
Phenotypic plasticity and constraint along the upper and lower limb diaphyses of Homo sapiens.

OBJECTIVES Morphological variation along the human limb reflects complex structural trade-offs between bone strength and mass. Here we assess how varying levels of plasticity and constraint affect this structure and influence the response to habitual loading along the diaphysis. MATERIALS AND METHODS Cross-sectional geometric properties including total area, cortical area, and rigidity were compared from the upper (humerus: 50% of length, radius: 66%, 50%, 4%) and lower (tibia: 50%, 38%, 4%) limbs of male varsity-level athletes and matched controls with distinct habitual loading histories. RESULTS Geometric properties among cricketers and swimmers were significantly greater at the humeral midshaft, mid-proximal radius, and radial midshaft compared to controls. By contrast, no significant differences were found among athletes or controls at the distal radius. The tibial midshafts of hockey players and runners also displayed greater area and rigidity compared to controls. Differences in geometry among the three groups became less pronounced distally, where structure was comparable among athletes and controls at 4% of tibial length. Additionally, coefficients of variation revealed that variation among athletes of the same sport was highest distally in both the upper and lower limb and lowest at midshaft, where structure most closely reflected the activity pattern of each loading group. DISCUSSION These results support previous research suggesting that distal limb sections are more tightly constrained by safety factors compared to midshafts and proximal sections. Overall, it appears that plasticity and constraint vary not only between limb segments in correspondence to known activity patterns, but also along specific sections of the diaphysis.
Clinical applications of magnetoencephalography in epilepsy

Magnetoencehalography (MEG) is being used with increased frequency in the pre-surgical evaluation of patients with epilepsy. One of the major advantages of this technique over the EEG is the lack of distortion of MEG signals by the skull and intervening soft tissue. In addition, the MEG preferentially records activity from tangential sources thus recording activity predominantly from sulci, which is not contaminated by activity from apical gyral (radial) sources. While the MEG is probably more sensitive than the EEG in detecting interictal spikes, especially in the some locations such as the superficial frontal cortex and the lateral temporal neocortex, both techniques are usually complementary to each other. The diagnostic accuracy of MEG source localization is usually better as compared to scalp EEG localization. Functional localization of eloquent cortex is another major application of the MEG. The combination of high spatial and temporal resolution of this technique makes it an extremely helpful tool for accurate localization of visual, somatosensory and auditory cortices as well as complex cognitive functions like language. Potential future applications include lateralization of memory function.