Miracle-dz/UniFAR-FTUs huggingface dataset:
Cleavage site mutations in the encephalomyocarditis virus P3 region lethally abrogate the normal processing cascade

Site-specific mutations within the proteinase 3C-dependent P3 region cleavage sequences of encephalomyocarditis virus have been constructed. The mutations altered the normal QG cleavage site dipeptide pairs of the 2C/3A, 3A/3B, 3B/3C, and 3C/3D junctions into QV, QC, QF, QY, and RG sequences. When translated in vitro in the context of full-length viral polyproteins, all mutations blocked endogenous 3C-mediated processing at their engineered sites and produced stable forms of the expected viral P3 precursors that were also resistant to cleavage by exogenously added recombinant 3C. Relative to wild-type viral sequences, each mutant form of P3 had a somewhat different ability to mediate overall polyprotein processing. Mutations at the 2C/3A, 3A/3B, and 3B/3C sites, for example, were generally less impaired than 3C/3D mutations, when the cleavage reactions were quantitated with cotranslated L-P1-2A precursors. A notable exception was mutant 3B3C(QG-->RG), which proved far less active than sibling mutants 3B3C(QG-->QF) and 3B3C(QG-->QV), a finding that possibly implicates this segment in the proper folding of an active 3C. When transfected into HeLa cells, all mutant sequences were lethal, presumably because of the reduced L-P1-2A processing levels or reduced RNA synthesis capacity. However, when specifically tested for the latter activity, all mutations except those at the 3C/3D cleavage site were indeed able to initiate and perpetuate viral RNA replication in transfected cells, albeit to RNA accumulation levels lower than those produced by wild-type sequences. The transfection effects could be mimicked with cell-free synthesized proteins, in that translation samples containing locked 3CD polymerase precursors were catalytically inactive in poly(A)-oligo(U)-dependent assays, while all other mutant processing samples initiated detectable RNA synthesis. Surprisingly, not only did the 3B/3C mutant sequences prove capable of directing RNA synthesis, but the viral RNA thus synthesized could be immunolabeled and precipitated with 3C-specific monoclonal antibody reagents, indicating an unexpected covalent attachment of the proteinase to the RNA product whenever this cleavage site was blocked.
Staphylococcus aureus-Induced Corneal Inflammation Is Dependent on Toll-Like Receptor 2 and Myeloid Differentiation Factor 88

ABSTRACT Toll-like receptors (TLRs) expressed by the corneal epithelium represent a first line of host defense to microbial keratitis. The current study examined the role of TLR2, TLR4, and TLR9 and the common adaptor molecule myeloid differentiation factor 88 (MyD88) in a Staphylococcus aureus model of corneal inflammation. The corneal epithelia of C57BL/6, TLR2−/−, TLR4−/−, TLR9−/−, and MyD88−/− mice were abraded using a trephine and epithelial brush and were exposed to heat- or UV-inactivated S. aureus clinical strain 8325-4 and other clinical isolates. Corneal thickness and haze were measured by in vivo confocal microscopy, neutrophil recruitment to the corneal stroma was quantified by immunohistochemistry, and cytokine production was measured by enzyme-linked immunosorbent assay. The exposure of corneal epithelium to S. aureus induced neutrophil recruitment to the corneal stroma and increased corneal thickness and haze in control C57BL/6 mice but not in TLR2−/− or MyD88−/− mice. The responses of TLR4−/− and TLR9−/− mice were similar to those of C57BL/6 mice. S. aureus-induced cytokine production by corneal epithelial cells and neutrophils was also significantly reduced in TLR2−/− mice compared with that in C57BL/6 mice. These findings indicate that S. aureus-induced corneal inflammation is mediated by TLR2 and MyD88 in resident epithelial cells and infiltrating neutrophils.
3D non-rigid reconstruction with prior shape constraints

3D non-rigid shape recovery from a single uncalibrated camera is a challenging, under-constrained problem in computer vision. Although tremendous progress has been achieved towards solving the problem, two main limitations still exist in most previous solutions. First, current methods focus on non-incremental solutions, that is, the algorithms require collection of all the measurement data before the reconstruction takes place. This methodology is inherently unsuitable for applications requiring real-time solutions. At the same time, most of the existing approaches assume that 3D shapes can be accurately modelled in a linear subspace. These methods are simple and have been proven effective for reconstructions of objects with relatively small deformations, but have considerable limitations when the deformations are large or complex. The non-linear deformations are often observed in highly flexible objects for which the use of the linear model is impractical. Note that specific types of shape variation might be governed by only a small number of parameters and therefore can be well-represented in a low dimensional manifold. The methods proposed in this thesis aim to estimate the non-rigid shapes and the corresponding camera trajectories, based on both the observations and the prior learned manifold. Firstly, an incremental approach is proposed for estimating the deformable objects. An important advantage of this method is the ability to reconstruct the 3D shape from a newly observed image and update the parameters in 3D shape space. However, this recursive method assumes the deformable shapes only have small variations from a mean shape, thus is still not feasible for objects subject to large scale deformations. To address this problem, a series of approaches are proposed, all based on non-linear manifold learning techniques. Such manifold is used as a shape prior, with the reconstructed shapes constrained to lie within the manifold. Those non-linear manifold based approaches significantly improve the quality of reconstructed results and are well-adapted to different types of shapes undergoing significant and complex deformations. Throughout the thesis, methods are validated quantitatively on 2D points sequences projected from the 3D motion capture data for a ground truth comparison, and are qualitatively demonstrated on real example of 2D video sequences. Comparisons are made for the proposed methods against several state-of-the-art techniques, with results shown for a variety of challenging deformable objects. Extensive experiments also demonstrate the robustness of the proposed algorithms with respect to measurement noise and missing data.
Function of regulatory T-cells improved by dexamethasone in Graves' disease.

OBJECTIVE Intrathyroid injection of dexamethasone (DEX) has been used to treat Graves' disease (GD); however, the mechanism of this treatment remains poorly understood. The objective of this study was to investigate the effects of DEX on the function of regulatory T (Treg) cells (CD4(+)CD25(+)T cells) in patients with GD. METHODS Peripheral blood was obtained from 20 patients with GD, and peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density gradient separation. CD4(+)CD25(-)/CD4(+)CD25(+)T cells were isolated by immunomagnetic selection and DEX was co-cultured with PBMCs or isolated T-cells for 72 h. Treg cell function was analyzed using the proliferation rate of CD4(+)CD25(-)T cells. RESULTS The proportion of Treg cells and the transcription factor forkhead box P3 (FOXP3) mRNA expression in PBMCs decreased in GD patients compared with healthy subjects, and Treg cell function was impaired in patients with GD. Although the proportion of Treg cells and FOXP3 mRNA expression in PBMCs did not increase, the function of Treg cells improved after the treatment with DEX. Moreover, the proportion of T-helper 2 (Th2) cells was decreased by the DEX treatment. CONCLUSIONS DEX could effectively improve the function of Treg cells and set up a new balance of Th1/Th2 in GD patients. This study might help to further understand the immune mechanism of the intrathyroid injection of DEX in the treatment of GD and facilitate the potential use of this therapy.
Market Distortions in Flexibility Markets Caused by Renewable Subsidies – The Case for Side Payments

Strongly increasing costs of congestion management have provoked a discussion in Europe about new approaches to solve grid congestions in a more efficient way. One approach is to design flexibility markets. In this paper we focus on the effects of subsidies for renewable energy on the market outcome of a flexibility market. We show that subsidies can cause market distortions and lead to an inefficient selection of flexibility options to solve grid congestions. We propose the implementation of side payments together with price caps and uniform pricing to achieve an efficient market design. Ultimately choosing between flexibility markets with and without side payments involves a tradeoff between minimizing system costs and maximizing renewable infeed. Our analysis provides the framework for a conscious political choice on that subject.
Locally recurrent prostate cancer after high-dose-rate brachytherapy: the value of diffusion-weighted imaging, dynamic contrast-enhanced MRI, and T2-weighted imaging in localizing tumors.

OBJECTIVE The purpose of this article is to retrospectively evaluate the utility of prostate MRI for detecting locally recurrent prostate cancer after high-dose-rate (HDR) brachytherapy. MATERIALS AND METHODS Sixteen men with biochemical failure after HDR brachytherapy for prostate cancer underwent prostate MRI, including T2-weighted imaging, dynamic contrast-enhanced MRI (DCE-MRI), and diffusion-weighted imaging (DWI), using a 1.5-T MRI unit before 12-core-specimen biopsy. Two radiologists in consensus assessed the presence of tumor on each sequence within eight regions of the prostate (six from the peripheral zone [PZ] and two from the transition zone [TZ]) on the basis of biopsy. RESULTS Biopsy revealed locally recurrent prostate cancer in 22 (17 in PZ and five in TZ) of 128 regions (17.2%). The sensitivity, specificity, and accuracy of each MRI method in the detection of recurrent tumor were 27%, 99%, and 87%, respectively, for T2-weighted imaging; 50%, 98%, and 90%, respectively, for DCE-MRI; and 68%, 95%, and 91%, respectively, for DWI. The sensitivity of DWI in detecting recurrent tumor was significantly higher than that of T2-weighted imaging (p = 0.004). Multiparametric MRI achieved the highest sensitivity (77%) but with slightly decreased specificity (92%). CONCLUSION These results indicate that a multiparametric MRI protocol that includes DWI provides a sensitive method to detect local recurrence after HDR brachytherapy.
From smart destinations to smart tourism regions

There is growing interest in developing smart tourism beyond individual smart destinations, but research and practice currently do not supply the necessary conceptualizations that could inform smart tourism development at a regional level. This paper argues that this is the case because of smart tourism’s roots in smart city ideas and literature. It discusses the main pillars of smart tourism and smart destinations and then illustrates how pervasive urban biases are in the smart development arena. The paper then highlights the many ways in which these are problematic for reaching regional smart tourism understandings and designing appropriate regional-level strategies. It calls for smart tourism regions to be defined beyond clusters of individual smart destinations and across all domains of smartness.
The multiple mechanisms of Ca2+ signalling by listeriolysin O, the cholesterol‐dependent cytolysin of Listeria monocytogenes

Cholesterol‐dependent cytolysins (CDCs) represent a large family of conserved pore‐forming toxins produced by several Gram‐positive bacteria such as Listeria monocytogenes, Streptococcus pyrogenes and Bacillus anthracis. These toxins trigger a broad range of cellular responses that greatly influence pathogenesis. Using mast cells, we demonstrate that listeriolysin O (LLO), a prototype of CDCs produced by L. monocytogenes, triggers cellular responses such as degranulation and cytokine synthesis in a Ca2+‐dependent manner. Ca2+ signalling by LLO is due to Ca2+ influx from extracellular milieu and release of from intracellular stores. We show that LLO‐induced release of Ca2+ from intracellular stores occurs via at least two mechanisms: (i) activation of intracellular Ca2+ channels and (ii) a Ca2+ channels independent mechanism. The former involves PLC‐IP3R operated Ca2+ channels activated via G‐proteins and protein tyrosine kinases. For the latter, we propose a novel mechanism of intracellular Ca2+ release involving injury of intracellular Ca2+ stores such as the endoplasmic reticulum. In addition to Ca2+ signalling, the discovery that LLO causes damage to an intracellular organelle provides a new perspective in our understanding of how CDCs affect target cells during infection by the respective bacterial pathogens.
Perfectionism and personality

The article deals with a theoretical and empirical analysis of the relationship between perfectionistic cognitions and personality factors of the Big Five. The presented research was made on a sample of 144 students of the Faculty of Education. The following methods were used in the research: the PCI – Perfectionism Cognitions Inventory (Flett, Hewitt, Blankstein, Gray, 1998) consisting of 25 items designed to identify the frequency of perfectionistic cognitions and the personality inventory NEO-FFI (Ruisel, Halama, 2007) consisting of five well-known factors created by P. T. Costa and R. R. McCare: extroversion, agreeableness, conscientiousness, neuroticism, openness. A correlation analysis of the variables confirmed statistically significant relationships between perfectionistic cognitions and neuroticism 0.467**, openness to experience 0.22** and agreeableness -0.251**. Klíčová slova perfectionism, perfectionist cognitions, personality traits, Big Five
What Happens After Discharge? Return Hospital Visits After Ambulatory Surgery

The purpose of this study was to examine the frequency of return hospital visits after ambulatory surgery discharge and to identify any predictor variables for its occurrence.A retrospective review of hospital records for all patients returning to the same hospital within 30 days after ambulatory surgery was conducted. Data on return hospital visits that resulted in rehospitalization (as an inpatient or to the ambulatory surgery unit [ASU]) or treatment as an outpatient in the emergency room were recorded. A total of 6243 patients underwent ambulatory surgery over 12 consecutive months and 187 returned to the same hospital of which 1.3% were for complications. Of all the returns, 54% returned to the emergency room (ER) and 46% were rehospitalized as inpatients or to ASU. To identify factors associated with an increased likelihood of return, two case controls for each return visit were obtained from medical records of ambulatory surgical patients operated on during the same time period. Results of the multivariate analysis on the matched case controls identified urology as the only significant surgical service that predicted returns. (Odds ratio 27.87; confidence interval [CI] 3.78-74.86; P = 0.0002). A separate analysis of the most common ASU procedures performed identified two surgical procedures that predicted hospital return as compared with overall ambulatory surgery population: patients undergoing varicocelectomy and hydrocelectomy procedures were 8.3 times more likely to return (CI 2.090-23.75; P = 0.0042); patients undergoing dilation and curettage were three times as likely to return (CI 1.78-5.55; P = 0.0002). Bleeding was the most common reason for all hospital returns (41.5%), with 76.5% of these patients treated and discharged through the ER. The increased likelihood of return visits after urology procedures warrants further evaluation. As patients with bleeding were most likely to return to the ER and discharged, more effective pre- and postprocedure patient education may further reduce this occurrence. Better informing patients regarding the prognosis of bleeding, and advising them of medical alternatives, could reduce inappropriate patient returns to the ER. (Anesth Analg 1997;84:319-24)
High frequency of genital human papillomavirus infections and related cervical dysplasia in adolescent girls in Belgium

Human papillomavirus (HPV) infections are causally related to cervical cancer and a range of other diseases, both in adults and in minors. Information on the frequency of genital HPV infections in adolescents is sparse. The aim of this study was to gain insight into the genotype-specific distribution of HPV genotypes in patients younger than 18 years of age. This observational retrospective study included 4807 samples of patients presenting for opportunistic screening in Belgium between June 2006 and January 2012. For statistical analysis, only the first visits of patients were withheld, reducing the sample to 4180. Samples were collected in liquid-based cytology medium and analyzed using a series of genotype-specific real-time PCR reactions. Cytology was read with previous knowledge of HPV infection and scored using the Bethesda classification. The mean age was 16.9 years. Most youngsters had no complaints (88.4%), were using hormonal contraception (79.5%), and clinical examination did not show any abnormalities (96.0%). The overall HPV frequency was 15.7%, with the most frequently found types being HPV16 (16.7%), HPV51 (14.6%), HPV66 (10.4%), HPV31 (9.9%), and HPV39 (9.1%). More than one-third (39.0%) of the infected girls harbored an infection with at least two HPV genotypes. Cytological abnormalities were found in 8.2% of samples. L-SIL (4.2%) was most frequently observed, followed by ASC-US (3.6%), HSIL (0.3%), and ASC-H (0.1%). The severity of lesions worsened with increasing age. Our findings indicate that an aberrant HPV genotype profile can be found in adolescent girls; moreover, this group shows a high rate of cervical abnormalities.
Renal denervation attenuates the sodium retention and hypertension associated with obesity.

Recent studies have indicated that obesity is associated with hypertension, sodium retention, and increased sympathetic nervous system activity. The purpose of this study was to determine the role of renal nerves in mediating the sodium retention and hypertension associated with obesity. We determined the hemodynamic and renal excretory responses to a high-fat diet in control (n = 6) and bilaterally renal-denervated (n = 7) chronically instrumented dogs. After a control period of 8 days, dogs were placed on a high-fat diet for 5 weeks. In response to a high-fat diet, body weight increased from 19.9 +/- 2.2 to 29.9 +/- 2.4 kg in the control group and from 21.1 +/- 2.0 to 32.4 +/- 1.9 kg in the bilaterally renal-denervated group. Heart rate increased from 81 +/- 8 to 113 +/- 7 beats per minute in the control group and from 79 +/- 7 to 103 +/- 8 beats per minute in the bilaterally renal-denervated group. Arterial pressure increased significantly from 95 +/- 2 to 109 +/- 4 mm Hg in the control group. In contrast, 5 weeks of a high-fat diet in the bilaterally renal-denervated group did not significantly increase arterial pressure (which went from 87 +/- 3 to 90 +/- 4 mm Hg). Furthermore, the decrease in sodium excretion in response to the high-fat diet was significantly greater in the control group than in the bilaterally renal-denervated group. (ABSTRACT TRUNCATED AT 250 WORDS)
Immunohistochemistry and electron microscopy of early-onset fuchs corneal dystrophy in three cases with the same L450W COL8A2 mutation.

PURPOSE A rare, familial early-onset form of Fuchs corneal dystrophy (FCD) is caused by mutation in the COL8A2 gene. This study describes the aberrant pattern of distribution of collagen type VIII and basement membrane components in Descemet's membrane (DM) and endothelium of three individuals with the same L450W mutation that represent different stages of early-onset FCD. METHODS Immunohistochemical studies with bright field, fluorescence, and confocal microscopy characterized the pathology of sectioned corneal buttons with antibodies against COL8A1, COL8A2, COL4, laminin, and fibronectin. A portion of each was processed for electron microscopy. RESULTS Histologic examination of pathologic changes in case 1 demonstrated relative preservation of the endothelium, whereas in case 2 much of this layer was atrophic and in case 3 there was complete loss of the endothelium. DM also increased in thickness to 25 mum for case 1, to 31 mum for case 2, and to 38 mum for case 3. Case 1 was the only specimen to reveal shallow warts along the posterior surface of DM, whereas the most advanced specimen, case 3, showed evidence of earlier nodularity that had been buried by the accretion of further extracellular matrix material. The posterior aspect of DM in this specimen had the unusual property of lighter staining relative to the anterior region of DM, laid down earlier in life. Immunocytochemistry revealed increased expression and complex, sharply defined patterns of deposition of collagen VIII, collagen IV, laminin, and fibronectin. Ultrastructurally, the posterior nonbanded layer of DM was intermixed with banded collagen, and the posterior region of DM showed a high density of foci of spindle-shaped structures with intense-staining bands, spaced at approximately 120 nm. Finally, ultrastructural studies of the endothelium in case 1 revealed unusual accumulation of swelling mitochondria. The endothelial cells also had large amounts of abnormal prominent rough endoplasmic reticulum. Type VIII collagen alpha 2 immunogold signal was associated with the highly granular ribosomes of the rough endoplasmic reticulum of these patients. CONCLUSIONS Microscopic and electron microscopic examination revealed pathological changes in DM of L450W COL8A2 mutants that were consistent with several-fold increased growth of the extracellular matrix and progressive deposition and synthesis of extracellular material by endothelial cells. As with late-onset FCD, this is accompanied by attenuation and eventual loss of the endothelium itself. Whether the abnormal deposition of collagen, laminin, and fibronectin contributes to the dysfunction and death of the endothelium remains to be determined.