Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced wavelet correlogram methods for image indexing and retrieval

In this paper, three new algorithms including optimal quantized wavelet correlogram (OQWC), wavelet CCV-correlogram (W3C), and color-W3C (CW3C) for content-based image indexing and retrieval are presented. In OQWC the threshold levels for wavelet coefficient quantization are optimized using an evolutionary process. W3C is an extension of OQWC that utilizes color coherence vectors (CCV) to include gray level and texture information in image index. Finally, CW3C is an extended version of W3C for effective color image indexing. The retrieval results obtained by the new methods on a 1000 image database demonstrate significant improvements in recall and rank compared to wavelet correlogram and SIMPLIcity methods.
The 3C Protein of Enterovirus 71 Inhibits Retinoid Acid-Inducible Gene I-Mediated Interferon Regulatory Factor 3 Activation and Type I Interferon Responses

ABSTRACT Enterovirus 71 (EV71) is a human pathogen that induces hand, foot, and mouth disease and fatal neurological diseases. Immature or impaired immunity is thought to associate with increased morbidity and mortality. In a murine model, EV71 does not facilitate the production of type I interferon (IFN) that plays a critical role in the first-line defense against viral infection. Administration of a neutralizing antibody to IFN-α/β exacerbates the virus-induced disease. However, the molecular events governing this process remain elusive. Here, we report that EV71 suppresses the induction of antiviral immunity by targeting the cytosolic receptor retinoid acid-inducible gene I (RIG-I). In infected cells, EV71 inhibits the expression of IFN-β, IFN-stimulated gene 54 (ISG54), ISG56, and tumor necrosis factor alpha. Among structural and nonstructural proteins encoded by EV71, the 3C protein is capable of inhibiting IFN-β activation by virus and RIG-I. Nevertheless, EV71 3C exhibits no inhibitory activity on MDA5. Remarkably, when expressed in mammalian cells, EV71 3C associates with RIG-I via the caspase recruitment domain. This precludes the recruitment of an adaptor IPS-1 by RIG-I and subsequent nuclear translocation of interferon regulatory factor 3. An R84Q or V154S substitution in the RNA binding motifs has no effect. An H40D substitution is detrimental, but the protease activity associated with 3C is dispensable. Together, these results suggest that inhibition of RIG-I-mediated type I IFN responses by the 3C protein may contribute to the pathogenesis of EV71 infection.
A systematic review of psychological treatments for mild traumatic brain injury: An update on the evidence

Mild traumatic brain injury (MTBI) is common and results in persisting disability for a minority of cases. Evidence guiding clinical management of this more complex group is lacking. This study systematically reviews psychological/neuropsychological treatments for adults with MTBI, with an emphasis on external validity. A total of 8 further studies were found adding to 10 from previous reviews. Although the methodological quality remains poor, mild supportive evidence was found for educational interventions provided early following injury. However, the routine provision of interventions for all MTBI cases may not be effective. Continuing and novel research efforts are needed to identify factors associated with poor outcomes to enable efficient targeting of healthcare resources.
Diagnostic Value of Lumbar Facet Joint Injection: A Prospective Triple Cross-Over Study

The diagnosis “lumbar facet syndrome” is common and often indicates severe lumbar spine surgery procedures. It is doubtful whether a painful facet joint (FJ) can be identified by a single FJ block. The aim of this study was to clarify the validity of a single and placebo controlled bilateral FJ blocks using local anesthetics. A prospective single blinded triple cross-over study was performed. 60 patients (31 f, 29 m, mean age 53.2 yrs (22–73)) with chronic low back pain (mean pain persistance 31 months, 6 months of conservative treatment without success) admitted to a local orthopaedic department for surgical or conservative therapy of chronic LBP, were included in the study. Effect on pain reduction (10 point rating scale) was measured. The 60 subjects were divided into six groups with three defined sequences of fluoroscopically guided bilateral monosegmental lumbar FJ test injections in “oblique needle” technique: verum-(local anaesthetic-), placebo-(sodium chloride-) and sham-injection. Carry-over and periodic effects were evaluated and a descriptive and statistical analysis regarding the effectiveness, difference and equality of the FJ injections and the different responses was performed. The results show a high rate of non-response, which documents the lack of reliable and valid predictors for a positive response towards FJ blocks. There was a high rate of placebo reactions noted, including subjects who previously or later reacted positively to verum injections. Equivalence was shown among verum vs. placebo and partly vs. sham also. With regard to test validity criteria, a single intraarticular FJ block with local anesthetics is not useful to detect the pain-responsible FJ and therefore is no valid and reliable diagostic tool to specify indication of lumbar spine surgery. Comparative FJ blocks with local anesthetics and placebo-controls have to be interpretated carefully also, because they solely give no proper diagnosis on FJ being main pain generator.
Signal recognition particle assembly in relation to the function of amplified nucleoli of Xenopus oocytes

The signal recognition particle (SRP) is a ribonucleoprotein machine that controls the translation and intracellular sorting of membrane and secreted proteins. The SRP contains a core RNA subunit with which six proteins are assembled. Recent work in both yeast and mammalian cells has identified the nucleolus as a possible initial site of SRP assembly. In the present study, SRP RNA and protein components were identified in the extrachromosomal, amplified nucleoli of Xenopus laevis oocytes. Fluorescent SRP RNA microinjected into the oocyte nucleus became specifically localized in the nucleoli, and endogenous SRP RNA was also detected in oocyte nucleoli by RNA in situ hybridization. An initial step in the assembly of SRP involves the binding of the SRP19 protein to SRP RNA. When green fluorescent protein (GFP)-tagged SRP19 protein was injected into the oocyte cytoplasm it was imported into the nucleus and became concentrated in the amplified nucleoli. After visiting the amplified nucleoli, GFP-tagged SRP19 protein was detected in the cytoplasm in a ribonucleoprotein complex, having a sedimentation coefficient characteristic of the SRP. These results suggest that the amplified nucleoli of Xenopus oocytes produce maternal stores not only of ribosomes, the classical product of nucleoli, but also of SRP, presumably as a global developmental strategy for stockpiling translational machinery for early embryogenesis.
Burkitt Lymphoma: Pathogenesis and Immune Evasion

B-cell lymphomas arise at distinct stages of cellular development and maturation, potentially influencing antigen (Ag) presentation and T-cell recognition. Burkitt lymphoma (BL) is a highly malignant B-cell tumor associated with Epstein-Barr Virus (EBV) infection. Although BL can be effectively treated in adults and children, leading to high survival rates, its ability to mask itself from the immune system makes BL an intriguing disease to study. In this paper, we will provide an overview of BL and its association with EBV and the c-myc oncogene. The contributions of EBV and c-myc to B-cell transformation, proliferation, or attenuation of cellular network and immune recognition or evasion will be summarized. We will also discuss the various pathways by which BL escapes immune detection by inhibiting both HLA class I- and II-mediated Ag presentation to T cells. Finally, we will provide an overview of recent developments suggesting the existence of BL-associated inhibitory molecules that may block HLA class II-mediated Ag presentation to CD4+ T cells, facilitating immune escape of BL.
CFD Studies on Velocity Distribution of Air in a Swirling Fluidized Bed

This paper presents computational fluid dynamics (CFD) studies to characterize air velocity distribution for various bed configurations in a swirling fluidized bed (SFB). Unlike conventional fluidized beds, a SFB provides radial mixing which is desirable is fluidization. Three velocities components were observed, the tangential velocity, radial velocity and axial velocity. These velocities were created as a result of using annular blade type distributor which mimics the turbine blades. In actual industrial applications, the axial velocity will create fluidization while the tangential velocity provides swirling effect. The presence of radial velocity can be explained as a consequence of centrifugal force generated by the swirling gas. Understanding these velocity distributions will enable optimization of the annular blade distributor design towards a high efficient fluidized bed system.
University of Birmingham Identification of Novel Imidazo[1,2-a]pyridine Inhibitors Targeting M. tuberculosis QcrB

Mycobacterium tuberculosis is a major human pathogen and the causative agent for the pulmonary disease, tuberculosis (TB). Current treatment programs to combat TB are under threat due to the emergence of multi-drug and extensively-drug resistant TB. Through the use of high throughput whole cell screening of an extensive compound library a number of imidazo[1,2-a ]pyridine (IP) compounds were obtained as potent lead molecules active against M. tuberculosis and Mycobacterium bovis BCG. The IP inhibitors ( 1 – 4 ) demonstrated minimum inhibitory concentrations (MICs) in the range of 0.03 to 5 m M against a panel of M. tuberculosis strains. M. bovis BCG spontaneous resistant mutants were generated against IP 1 , 3 , and 4 at 5 6 MIC and subsequent whole genome sequencing identified a single nucleotide polymorphism 937 ACC . 937 GCC (T313A) in qcrB , which encodes the b subunit of the electron transport ubiquinol cytochrome C reductase. This mutation also conferred cross-resistance against IP 1 , 3 and 4 demonstrating a common target. Gene dosage experiments confirmed M. bovis BCG QcrB as the target where over-expression in M. bovis BCG led to an increase in MIC from 0.5 to . 8 m M for IP 3 . An acute murine model of TB infection established bacteriostatic activity of the IP series, which await further detailed characterization.
Latent Topic Embedding

Topic modeling and word embedding are two important techniques for deriving latent semantics from data. General-purpose topic models typically work in coarse granularity by capturing word co-occurrence at the document/sentence level. In contrast, word embedding models usually work in much finer granularity by modeling word co-occurrence within small sliding windows. With the aim of deriving latent semantics by considering word co-occurrence at different levels of granularity, we propose a novel model named Latent Topic Embedding (LTE), which seamlessly integrates topic generation and embedding learning in one unified framework. We further propose an efficient Monte Carlo EM algorithm to estimate the parameters of interest. By retaining the individual advantages of topic modeling and word embedding, LTE results in better latent topics and word embedding. Extensive experiments verify the superiority of LTE over the state-of-the-arts.
Characteristics and requirements of basal autophagy in HEK 293 cells

Basal autophagy—here defined as macroautophagic activity during cellular growth in normal medium containing amino acids and serum—appears to be highly active in many cell types and in animal tissues. Here we characterized this pathway in mammalian HEK 293 cells. First, we examined, side by side, three compounds that are widely used to reveal basal autophagy by blocking maturation of autophagosomes: bafilomycin A1 (BafA1), chloroquine and vinblastine. Only BafA1 appeared to be without complicating side effects. Chloroquine partially inhibited mechanistic target of rapamycin (MTOR) activity, which would induce autophagy induction as well as block autophagosome maturation. Vinblastine caused the distribution of early omegasome components into punctate phagophore assembly sites, and therefore it would also induce autophagy, complicating interpretation. Basal autophagy was significantly sensitive to inhibition by wortmannin, and therefore required formation of phosphatidylinositol 3-phosphate (PtdIns3P), but it was twice as resistant to wortmannin as starvation-induced autophagy. We also determined that basal autophagy was significantly suppressed by MTOR activation brought about by overexpression of RHEB or activated RAGs. Finally we investigated the spatial relationship of nascent autophagosomes to the endoplasmic reticulum (ER) or to mitochondria by live imaging experiments under conditions that reveal basal autophagy (with BafA1 treatment), or upon MTOR inactivation (which would result in autophagy induction). Side-by-side comparison showed that under both basal and induced autophagy, 100% of autophagosomes first appeared in close proximity to ER strands. In parallel measurements, 40% were in close proximity to mitochondria under both conditions. We concluded that in HEK 293 cells, basal autophagy is mechanistically similar to that induced by MTOR inactivation in all aspects examined.
Stability interval for time-varying delay systems

We investigate the stability analysis of linear time-delay systems. The time-delay is assumed to be a time-varying continuous function belonging to an interval (possibly excluding zero) with a bound on its derivative. To this end, we propose to use the quadratic separation framework to assess the intervals on the delay that preserves the stability. Nevertheless, to take the time-varying nature of the delay into account, the quadratic separation principle has to be extended to cope with the general case of time-varying operators. The key idea lies in rewording the delay system as a feedback interconnection consisting of operators that characterize it. The original feature of this contribution is to design a set of additional auxiliary operators that enhance the system modelling and reduce the conservatism of the methodology. Then, separation conditions lead to linear matrix inequality conditions which can be efficiently solved with available semi-definite programming algorithms. The paper concludes with illustrative academic examples.
Contributions to large-scale learning for image classification. (Contributions à l'apprentissage grande échelle pour la classification d'images)

Building algorithms that classify images on a large scale is an essential task due to the difficulty in searching massive amount of unlabeled visual data available on the Internet. We aim at classifying images based on their content to simplify the manageability of such large-scale collections. Large-scale image classification is a difficult problem as datasets are large with respect to both the number of images and the number of classes. Some of these classes are fine grained and they may not contain any labeled representatives. In this thesis, we use state-of-the-art image representations and focus on efficient learning methods. Our contributions are (1) a benchmark of learning algorithms for large scale image classification, and (2) a novel learning algorithm based on label embedding for learning with scarce training data. Firstly, we propose a benchmark of learning algorithms for large scale image classification in the fully supervised setting. It compares several objective functions for learning linear classifiers such as one-vs-rest, multiclass, ranking and weighted average ranking using the stochastic gradient descent optimization. The output of this benchmark is a set of recommendations for large-scale learning. We experimentally show that, online learning is well suited for large-scale image classification. With simple data rebalancing, One-vs-Rest performs better than all other methods. Moreover, in online learning, using a small enough step size with respect to the learning rate is sufficient for state-of-the-art performance. Finally, regularization through early stopping results in fast training and a good generalization performance. Secondly, when dealing with thousands of classes, it is difficult to collect sufficient labeled training data for each class. For some classes we might not even have a single training example. We propose a novel algorithm for this zero-shot learning scenario. Our algorithm uses side information, such as attributes to embed classes in a Euclidean space. We also introduce a function to measure the compatibility between an image and a label. The parameters of this function are learned using a ranking objective. Our algorithm outperforms the state-of-the-art for zero-shot learning. It is flexible and can accommodate other sources of side information such as hierarchies. It also allows for a smooth transition from zero-shot to few-shots learning.
Cytokines and Biologics in non-infectious autoimmune uveitis: Bench to Bedside

Intraocular inflammatory eye disease is one of the important causes of ocular morbidity. Even though the prevalence of uveitis is less common in relation to diabetic retinopathy, glaucoma or age related macular degeneration, the complexity and heterogeneity of the disease makes it more unique. Putative uveitogenic retinal antigens incite innate immunity by the process of antigen mimicry and have been shown to be associated in patients with intraocular inflammatory disease by numerous experimental studies. Laboratory diagnostic tools to aid the etiologic association in intraocular inflammatory disease have evolved over the last two decades and we are entering into an era of molecular diagnostic tests. Sophisticated novel technologies such as multiplex bead assays to assess biological signatures have revolutionized the management of complex refractory uveitis. Nevertheless, there is still a long way to go to establish the causal relationship between these biomarkers and specific uveitic entities. Experimental studies have shown the supreme role of infliximab in the management of Behcet's disease. Despite significant experimental and case control studies, the deficiency of randomized clinical trials using these biologic agents has handicapped us in exploring them as a front line therapy in severe refractory uveitis. Studies still need to answer the safety of these potentially life threatening drugs in a selected group of patients and determine when to commence and for how long the treatment has to be given. This review article covers some basic concepts of cytokines in uveitis and their potential application for therapy in refractory uveitis.
The Biological Behaviors of Rat Dermal Fibroblasts Can Be Inhibited by High Levels of MMP9

Aims. To explore the effects of the high expression of MMP9 on biological behaviors of fibroblasts. Methods. High glucose and hyperhomocysteine were used to induce MMP9 expression in skin fibroblasts. Cell proliferation was detected by flow cytometry and cell viability by CCK-8. ELISA assay was used to detect collagen (hydroxyproline) secretion. Scratch test was employed to evaluate horizontal migration of cells and transwell method to evaluate vertical migration of cells. Results. The mRNA and protein expressions of MMP9 and its protease activity were significantly higher in cells treated with high glucose and hyperhomocysteine than those in control group. At the same time, the S-phase cell ratio, proliferation index, cell viability, collagen (hydroxyproline) secretion, horizontal migration rate, and the number of vertical migration cells decreased in high-glucose and hyperhomocysteine-treated group. Tissue inhibitor of metalloproteinase 1 (TIMP1), which inhibits the activity of MMP9, recovered the above biological behaviors. Conclusions. High expression of MMP9 in skin fibroblasts could be induced by cultureing in high glucose and hyperhomocysteine medium, which inhibited cell biological behaviors. Inhibitions could be reversed by TIMP1. The findings suggested that MMP9 deters the healing of diabetic foot ulcers by inhibiting the biological behaviors of fibroblasts.
Composition and antibacterial activity of the lipophilic fraction of honeybee pollen from native species of Montesinho Natural Park

The lipophilic composition of honeybee pollen from Cistus ladanifer, Castanea saliva and Rubus sp. was analysed by GC-MS. The extracts are mainly composed by saturated and llilsaturated fatty acids, sterols, long chain aliphat:ic alcohols, alkanes and alkenes. The profiles of chemical composition allow the chemical differentiation of pollen species. The biological activity of the lipophilic fractions against several Gram positive bacteria was demonstrated and related to the resistance of beehives to certain diseases when feed with such poll ens.
Ankyloglossia: a morphofunctional investigation in children.

OBJECTIVES To provide diagnostic criteria for ankyloglossia in children by anatomical measurements; to investigate the correlation between severity of ankyloglossia and a series of morphofunctional findings; to evaluate the potential mismatch between a clinical suspect of ankyloglossia and the authentic anatomical diagnosis. DESIGN Two different techniques of anatomical measurements and a clinical evaluation of a series of morphofunctional findings were performed. SUBJECTS AND METHODS In 200 children referred for evaluation and treatment of tongue-tie, the length of the frenulum and the interincisal distance were measured in maximum opening of the mouth and with the tip of the tongue touching the palatal papilla. Occlusion, type of bite, tongue resting position, swallowing mechanism, oral floor mobility, frenulum insertion modality and speech were investigated. Any correlation between these morphofunctional findings and anatomical measures was investigated. RESULTS Children with a frenulum length more than 2 cm and an interincisal distance of more than 2.3 cm were normal. In both measurements, significant correlations among mean values and other variables were observed. Moreover, three levels -- mild, moderate and severe -- of ankyloglossia were assessed. CONCLUSIONS Length of frenulum and interincisal distance allow an assessment of severity of ankyloglossia in children. Ankyloglossia was not associated with infantile swallowing.