Miracle-dz/UniFAR-FTUs huggingface dataset:
Tensile Bond Strength and SEM Evaluation of Caries-affected Dentin Using Dentin Adhesives

Tensile bond strength measurements are commonly used for the evaluation of dentin adhesive systems. Most tests are performed using extracted non-carious human or bovine dentin. However, the adhesion of resins to caries-affected dentin is still unclear. The objectives of this study were to test the hypothesis that bonding to caries-affected dentin is inferior to bonding to normal dentin, and that the quality of the hybrid layer plays a major role in creating good adhesion. We used a micro-tensile bond strength test to compare test bond strengths made to either caries-affected dentin or normal dentin, using three commercial adhesive systems (All Bond 2, Scotchbond Multi-Purpose, and Clearfil Liner Bond II). For scanning electron microscopy, the polished interfaces between the adhesive bond and dentin were subjected to brief exposure to 10% phosphoric acid solution and 5% sodium hypochlorite, so that the quality of the hybrid layers could be observed. Bonding to normal dentin with either All Bond 2 (26.9 ± 8.8 MPa) or Clearfil Liner Bond II (29.5 ± 10.9 MPa) showed tensile bond strengths higher than those to caries-affected dentin (13.0 ± 3.6 MPa and 14.0 ± 4.3 MPa, respectively). The tensile bond strengths obtained with Scotchbond Multi-Purpose were similar in normal and caries-affected dentin (20.3 ± 5.5 MPa and 18.5 ± 4.0 MPa, respectively). The hybrid layers created by All Bond 2 in normal dentin and by Clearfil Liner Bond II in normal or caries-affected dentin showed phosphoric acid and sodium hypochlorite resistance, whereas the hybrid layers created by All Bond 2 in caries-affected dentin and those created by Scotchbond Multi-Purpose to normal and caries-affected dentin showed partial susceptibility to the acid and sodium hypochlorite treatment. The results indicate that the strength of adhesion to dentin depends upon both the adhesive system used and the type of dentin. Moreover, the quality of the hybrid layer may not always contribute significantly to tensile bond strength.
Approximation of hard uncertain convex inequalities

Robust Optimization is a widespread approach to treat uncertainty in optimization problems. Finding a computationally tractable formulation of the robust counterpart of an uncertain optimization problem is a key step in applying this approach. Techniques for finding a computationally tractable robust counterpart are available for constraints concave in the uncertain parameters. In many problems, however, the uncertain parameters appear in a convex way, which is problematic as no general techniques exist for such problems. In this paper, we provide a systematic way to construct safe approximations to such constraints when the uncertainty set is polyhedral. Specifically, we reformulate the original problem as a linear adjustable robust optimization problem in which the nonlinearity of the original problem is captured by the new uncertainty set. Additionally, we prove that preprocessing a constraint with a concave transformation that preserves its convexity can tighten the safe approximation obtained. We subsequently apply our theory to quadratic constraints, constraints that are the sum of maxima and the sum of maxima squared, as well as constraints from geometric programming. We demonstrate the quality of the approximations with a study of geometric programming problems and numerical examples from radiotherapy optimization, which contain a constraint of the sum of maxima squared type. ∗Corresponding author: e.j.roos@tilburguniversity.edu
Novel compound heterozygous mutations in CERKL cause autosomal recessive retinitis pigmentosa in a nonconsanguineous Chinese family.

1. Arseculeratne SN. Recent advances in rhinosporidiosis and Rhinosporidium seeberi. Indian J Med Microbiol. 2002;20(3):119-131. 2. Reidy JJ, Sudesh S, Klafter AB, Olivia C. Infection of the conjunctiva by Rhinosporidium seeberi. Surv Ophthalmol. 1997;41(5):409-413. 3. De Doncker RML, De Keizer RJW, Oosterhuis JA, Maes A. Scleral melting in a patient with conjunctival rhinosporidiosis. Br J Ophthalmol. 1990;74(10): 635-637. 4. Job A, Venkateswaran S, Mathan M, Krishnaswami H, Raman R. Medical therapy of rhinosporidiosis with dapsone. J Laryngol Otol. 1993;107(9):809-812. 5. Fredricks DN, Jolley JA, Lepp PW, Kosek JC, Relman DA. Rhinosporidium seeberi: a human pathogen from a novel group of aquatic protistan parasites. Emerg Infect Dis. 2000;6(3):273-282. 6. Silva V, Pereira CN, Ajello L, Mendoza L. Molecular evidence for multiple host-specific strains in genus Rhinosporidium. J Clin Microbiol. 2005;43(4): 1865-1868.
Magnetic Resonance Imaging Patterns of Tumor Regression After Neoadjuvant Chemotherapy in Breast Cancer Patients: Correlation With Pathological Response Grading System Based on Tumor Cellularity

Purpose The objectives of the study were to analyze the tumor shrinkage pattern on magnetic resonance imaging (MRI) after neoadjuvant chemotherapy and to evaluate whether there is any difference in shrinkage pattern between pathological responder and nonresponder groups. In addition, we wanted to compare tumor diameter obtained from MRI with histological diameter according to the tumor shrinkage pattern. Methods Between July 2008 and December 2010, 55 consecutive patients (56 lesions) with pathologically proven breast cancer who underwent neoadjuvant chemotherapy followed by surgery were retrospectively enrolled. The shrinkage pattern was classified into 4 categories: I (concentric shrinkage without surrounding lesion), II (concentric shrinkage with surrounding lesions), III (shrinkage with residual multinodular lesions, and IV (diffuse contrast enhancement in whole quadrants). Histological regression was scored on a 5-point scale regarding tumor cellularity reduction (Miller-Payne grading system). Patients with Miller-Payne grade 1 or 2 were classified into the nonresponder group, and patients with grade 3, 4, or 5 were in the responder group. Results Of 56 lesions, pattern I was seen in 29 lesions, pattern II in 13 lesions, pattern III in 5 lesions, and pattern IV in 4 lesions. Three lesions were not visualized on MRI after neoadjuvant chemotherapy, and 2 lesions were increased in size. There was a statistically significant difference in the tumor shrinkage pattern between responder and nonresponder groups (P = 0.017). All 5 lesions with type III shrinkage pattern were found in the responder group, and all 4 lesions with pattern IV were in the nonresponder group. Magnetic resonance imaging diameter of lesions with types I, II, and IV patterns showed significant correlation with the histological diameter. Among them, the correlation factor was highest in pattern IV (&rgr; = 0.94, P < 0.001) followed by pattern I (&rgr; = 0.67, P < 0.01) and pattern II (&rgr; = 0.502, P = 0.08). However, in type III shrinkage pattern, tumor size measured on MRI was not significantly correlated with histological size (P = 0.87). Conclusions Types III and I shrinkage patterns were more frequently observed in the pathological responder group, and type IV was more frequently noted in the nonresponder group. Tumor diameter measured on MRI showed strong correlation with histological diameter in lesions with types I and IV shrinkage patterns, whereas lesions with type III did not show significant correlation. Type II pattern showed similar frequencies between the 2 groups and moderate correlation between sizes obtained from MRI and histology.
PqsE Functions Independently of PqsR-Pseudomonas Quinolone Signal and Enhances the rhl Quorum-Sensing System

ABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that causes both acute and chronic infections in immunocompromised individuals. This gram-negative bacterium produces a battery of virulence factors that allow it to infect and survive in many different hostile environments. The control of many of these virulence factors falls under the influence of one of three P. aeruginosa cell-to-cell signaling systems. The focus of this study, the quinolone signaling system, functions through the Pseudomonas quinolone signal (PQS), previously identified as 2-heptyl-3-hydroxy-4-quinolone. This signal binds to and activates the LysR-type transcriptional regulator PqsR (also known as MvfR), which in turn induces the expression of the pqsABCDE operon. The first four genes of this operon are required for PQS synthesis, but the fifth gene, pqsE, is not. The function of the pqsE gene is not known, but it is required for the production of multiple PQS-controlled virulence factors and for virulence in multiple models of infection. In this report, we show that PqsE can activate PQS-controlled genes in the absence of PqsR and PQS. Our data also suggest that the regulatory activity of PqsE requires RhlR and indicate that a pqsE mutant can be complemented for pyocyanin production by a large excess of exogenous N-butyryl homoserine lactone (C4-HSL). Finally, we show that PqsE enhances the ability of Escherichia coli expressing RhlR to respond to C4-HSL. Overall, our data lead us to conclude that PqsE functions as a regulator that is independent of PqsR and PQS but dependent on the rhl quorum-sensing system.
Using phase linearity in frequency-domain ICA to tackle the permutation problem

This paper describes a method for solving the permutation problem in the frequency-domain independent component analysis (FD-ICA) approach to blind source separation (BSS). FD-ICA is a well-known method for BSS of convolutive mixtures. However, FD-ICA has a source permutation problem, where estimated source components can become swapped at different frequencies. Many researchers have suggested methods to solve the source permutation problem including using correlation between adjacent frequencies and direction of arrival (DOA). We propose a modification to the DOA method, based on phase linearity of the FD-ICA de-mixing matrix, that can extend the range of frequencies over which the permutation problem can be resolved. Experiments indicate that our method can provide a better performance than the inter-frequency correlation method and the DOA method in real environments.
Hepatitis B surface antigen assembles in a post-ER, pre-Golgi compartment

Expression of hepatitis B surface antigen (HBsAg), the major envelope protein of the virus, in the absence of other viral proteins leads to its secretion as oligomers in the form of disk-like or tubular lipoprotein particles. The observation that these lipoprotein particles are heavily disulphide crosslinked is paradoxical since HBsAg assembly is classically believed to occur in the ER, and hence in the presence of high levels of protein disulphide isomerase (PDI) which should resolve these higher intermolecular crosslinks. Indeed, incubation of mature, highly disulphide crosslinked HBsAg with recombinant PDI causes the disassembly of HBsAg to dimers. We have used antibodies against resident ER proteins in double immunofluorescence studies to study the stages of the conversion of the HBsAg from individual protein subunits to the secreted, crosslinked, oligomer. We show that HBsAg is rapidly sorted to a post-ER, pre-Golgi compartment which excludes PDI and other major soluble resident ER proteins although it overlaps with the distribution of rab2, an established marker of an intermediate compartment. Kinetic studies showed that disulphide-linked HBsAg dimers began to form during a short (2 min) pulse, increased in concentration to peak at 60 min, and then decreased as the dimers were crosslinked to form higher oligomers. These higher oligomers are the latest identifiable intracellular form of HBsAg before its secretion (t 1/2 = 2 h). Brefeldin A treatment does not alter the localization of HBsAg in this PDI excluding compartment, however, it blocks the formation of new oligomers causing the accumulation of dimeric HBsAg. Hence this oligomerization must occur in a pre-Golgi compartment. These data support a model in which rapid dimer formation, catalyzed by PDI, occurs in the ER, and is followed by transport of dimers to a pre-Golgi compartment where the absence of PDI and a different lumenal environment allow the assembly process to be completed.
Genetic variations in nitric oxide synthase and arginase influence exhaled nitric oxide levels in children

To cite this article: Salam MT, Bastain TM, Rappaport EB, Islam T, Berhane K, Gauderman WJ, Gilliland FD. Genetic variations in nitric oxide synthase and arginase influence exhaled nitric oxide levels in children. Allergy 2011; 66: 412–419.
Diffusion of Credit in Markovian Models

This paper studies the problem of diffusion in Markovian models, such as hidden Markov models (HMMs) and how it makes very difficult the task of learning of long-term dependencies in sequences. Using results from Markov chain theory, we show that the problem of diffusion is reduced if the transition probabilities approach 0 or 1. Under this condition, standard HMMs have very limited modeling capabilities, but input/output HMMs can still perform interesting computations.
Interference and error probability evaluation in multiservice interference limited wireless ad hoc networks

In this work, we provide a mathematical framework for estimating the expected value of the carrier to interference ratio and evaluating the probability of error in a wireless ad hoc network. Our approach differs from the earlier studies in that previous valuable work has been mostly based on simulations, on simplified regular patterns for node distribution, has been limited to single service networks, or has not integrated the medium access model in the network. In our analysis, we consider a multiservice interference limited wireless ad hoc network using a multiple access scheme with carrier sensing at the data link layer. The population of nodes in the network is considered as a number governed by a two-dimensional Poisson process. We derive explicit formulas for the carrier to interference ratio and probability of error experienced by nodes in the network. Numerical results are provided for the case of two service classes, where carrier to interference ratios and probabilities of packet loss experienced by nodes in the network are presented as functions of the node densities.
Learning Graphs to Match

Many tasks in computer vision are formulated as graph matching problems. Despite the NP-hard nature of the problem, fast and accurate approximations have led to significant progress in a wide range of applications. Learning graph models from observed data, however, still remains a challenging issue. This paper presents an effective scheme to parameterize a graph model, and learn its structural attributes for visual object matching. For this, we propose a graph representation with histogram-based attributes, and optimize them to increase the matching accuracy. Experimental evaluations on synthetic and real image datasets demonstrate the effectiveness of our approach, and show significant improvement in matching accuracy over graphs with pre-defined structures.
Dynamical systems analysis applied to working memory data

In the present paper we investigate weekly fluctuations in the working memory capacity (WMC) assessed over a period of 2 years. We use dynamical system analysis, specifically a second order linear differential equation, to model weekly variability in WMC in a sample of 112 9th graders. In our longitudinal data we use a B-spline imputation method to deal with missing data. The results show a significant negative frequency parameter in the data, indicating a cyclical pattern in weekly memory updating performance across time. We use a multilevel modeling approach to capture individual differences in model parameters and find that a higher initial performance level and a slower improvement at the MU task is associated with a slower frequency of oscillation. Additionally, we conduct a simulation study examining the analysis procedure's performance using different numbers of B-spline knots and values of time delay embedding dimensions. Results show that the number of knots in the B-spline imputation influence accuracy more than the number of embedding dimensions.
Maximum Entropy Based Phrase Reordering Model for Statistical Machine Translation

We propose a novel reordering model for phrase-based statistical machine translation (SMT) that uses a maximum entropy (MaxEnt) model to predicate reorderings of neighbor blocks (phrase pairs). The model provides content-dependent, hierarchical phrasal reordering with generalization based on features automatically learned from a real-world bitext. We present an algorithm to extract all reordering events of neighbor blocks from bilingual data. In our experiments on Chinese-to-English translation, this MaxEnt-based reordering model obtains significant improvements in BLEU score on the NIST MT-05 and IWSLT-04 tasks.
Programming of Hypertension: Associations of Plasma Aldosterone in Adult Men and Women With Birthweight, Cortisol, and Blood Pressure

Abstract—Animal models suggest that explanations for the association of low birthweight with adult hypertension may include chronic activation of the hypothalamic-pituitary-adrenal or renin-angiotensin-aldosterone axes. In humans, low birthweight predicts elevated plasma cortisol, but associations with aldosterone have not been reported. We measured aldosterone in serum samples from 205 men and 106 women from 67 to 78 years of age, from Hertfordshire, UK, for whom birthweight was recorded. Participants underwent an overnight low-dose (0.25 mg) dexamethasone suppression test and a low-dose (1 &mgr;g) ACTH (corticotropin) stimulation test and were genotyped for the -344 C/T polymorphism of the CYP11B2 gene encoding aldosterone synthase. Median aldosterone was 6.22 ng/dL (range 0.15 to 38.74) and was higher in men than women (P<0.0001). Higher aldosterone levels after both dexamethasone and ACTH stimulation were associated with higher blood pressure (r=0.20, P=0.001; r=0.33, P<0.0001, respectively) and with lower birthweight (r=−0.16, P=0.008; r=−0.21, P=0.001, respectively). These associations remained significant after adjusting for age, gender, obesity, and genotype. Our findings supplement previous evidence that aldosterone is an important regulator of blood pressure and suggest that factors in early life that retard fetal growth and program activation of the hypothalamic-pituitary-adrenal axis in humans result not only in higher glucocorticoid activity but also in increased mineralocorticoid activity.
Preparation of PVA-GO composite hydrogel and effect of ionic coordination on its properties

This paper adopts a method combining hybrid self-assembly, cyclic freezing-thawing and annealing treatment to prepare polyvinyl alcohol (PVA) and graphene oxide (GO) composite hydrogel. Then, the PVA-GO composite hydrogels are re-swelled in different ionic solutions (NaCl, MgCl2, CaCl2 and AlCl3) to improve mechanical strength, toughness and wear resistance by the ionic coordination bonds. The microstructure and morphology are characterized by Fourier transforms infrared spectroscopy (FTIR), x-ray diffraction (XRD) and Scanning electron microscopy (SEM), finding that the internal structure is porous three-dimensional network. Mechanical experiments indicate that the composite hydrogel with GO content of 0.05 wt% immersed in MgCl2 solution displays the best mechanical properties overall. Its tensile strength can reach 11.10 MPa and the elastic modulus reaches 1.72 MPa, which is 175% and 85% higher than the pure PVA, respectively. Sliding friction experiments illustrate that the composite hydrogel immersed in AlCl3 solution exhibits the lowest friction coefficient, and the higher the valence state of metal cation is, the better the wear reduction effect is. We expect to enrich the development of PVA-GO hydrogels in tissue engineering through synergy of hydrogen bonds and ionic coordination bonds.
Mind The Gap : Inductive Biases In Phonological Feature Learning

Although extensive research has been done into the acquisition of non-linguistic feature combinations, empirical evidence about phonological feature learning is scarce. I present results from learning experiments in which participants learnt a data set with the internal structure of a plosive segment inventory. The outcomes suggest that learning biases may indeed play a role in phonological typology, and that learners reduce the cumulative complexity in the data set considerably. These results support the hypothesis that the reduction of complexity is a driving force in the evolution of language.
Do visualizations foster experience sharing and retention in groups? Towards an experimental validation

In recent years the visualization of knowledge has been gaining wider attention: visualization is said to enhance human capabilities for knowledge intense activities such as decision making and strategic thinking. However, this is a recent field and still widely unexplored. Thus far, the advantages of knowledge visualization have been investigated mainly through anecdotal evidence and qualitative studies. In this paper, we propose an experimental approach to further comprehend the role of visualization in fostering knowledge sharing. We plan to compare the elicitation and evaluation processes of groups who are provided (1) with an optimal visual support, (2) with a sub-optimal visual support, and (3) without any visualization. The goal of our research is to apply the experimental approach – widely used in studying GSS (Group Support System) but seldom used in knowledge management – to shed light on the role of visualization for knowledge-intensive tasks in groups. We report first preliminary results of an experiment with 56 MBA students and also outline the limitations of our approach.
Parallel Sparse Matrix by Vector Multiplication using a Shared Virtual Memory Environment

Many iterative schemes in scientific applications require the multiplication of a sparse matrix by a vector. This kernel has been mainly studied on vector processors and shared-memory parallel computers. In this paper, we address the implementation issues when using a shared virtual memory system on a distributed memory parallel computer. We study in details the impact of loop distribution schemes in order to design an efficient algorithm.
Recent advances toward a molecular mechanism of efflux pump inhibition

Multidrug resistance (MDR) in Gram-negative pathogens, such as the Enterobacteriaceae and Pseudomonas aeruginosa, poses a significant threat to our ability to effectively treat infections caused by these organisms. A major component in the development of the MDR phenotype in Gram-negative bacteria is overexpression of Resistance-Nodulation-Division (RND)-type efflux pumps, which actively pump antibacterial agents and biocides from the periplasm to the outside of the cell. Consequently, bacterial efflux pumps are an important target for developing novel antibacterial treatments. Potent efflux pump inhibitors (EPIs) could be used as adjunctive therapies that would increase the potency of existing antibiotics and decrease the emergence of MDR bacteria. Several potent inhibitors of RND-type efflux pump have been reported in the literature, and at least three of these EPI series were optimized in a pre-clinical development program. However, none of these compounds have been tested in the clinic. One of the major hurdles to the development of EPIs has been the lack of biochemical, computational, and structural methods that could be used to guide rational drug design. Here, we review recent reports that have advanced our understanding of the mechanism of action of several potent EPIs against RND-type pumps.