Miracle-dz/UniFAR-FTUs huggingface dataset:
Nasal airflow patterns during the velopharyngeal closing phase in speech in children with and without cleft palate.

OBJECTIVES (1) To study the nasal airflow patterns during the velopharyngeal closing phase in speech produced by children with and without cleft palate. (2) To compare the nasal airflow patterns in bilabial, dental, and velar articulation in these children. DESIGN Prospective, cross-sectional study of a consecutive series of children with cleft palate referred for routine speech evaluation and controls. SETTING Sahlgrenska University Hospital, Göteborg, Sweden. PARTICIPANTS Seventeen children with cleft lip and palate or cleft palate only and 22 controls aged 7 and 10 years. METHOD Nasal airflow was transduced with a pneumotachograph attached to a nose mask and registered together with the acoustic speech signal. Sentences containing nasal-to-stop combinations in bilabial, dental, and velar articulatory positions were used. MAIN OUTCOMES MEASURES The duration from peak to 5% nasal airflow, the maximum flow declination rate, and the nasal airflow at selected points in time during the transition from nasal-to-stop consonants. RESULTS In the cleft palate group, duration from peak to 5% nasal airflow was clearly longer than among the controls (p <.0001). The declination of airflow was slower (p <.006) and the rate of nasal airflow at the release of the stop consonant was higher (p <.004) in the cleft palate group. Differences between bilabial versus dental and velar articulation were found in the control group. CONCLUSION Studies of the temporal and dynamic characteristics of the nasal airflow variations during speech appear potentially useful for the assessment of velopharyngeal function.
Complement Receptor 3 and Toll-Like Receptor 4 Act Sequentially in Uptake and Intracellular Killing of Unopsonized Salmonella enterica Serovar Typhimurium by Human Neutrophils

ABSTRACT The uptake and subsequent killing of Salmonella enterica serovar Typhimurium by human neutrophils was studied. In particular, two pattern recognition receptors, complement receptor 3 (CR3) and Toll-like receptor 4 (TLR4), were found to be essential for the efficient uptake and activation, respectively, of the NADPH oxidase. The uptake of Salmonella was almost completely inhibited by various monoclonal antibodies against CR3, and neutrophils from a patient with leukocyte adhesion deficiency type 1, which lack CR3, showed almost no uptake of Salmonella. A lipopolysaccharide (LPS) mutant strain of Salmonella was used to show that the expression of full-length, wild-type, or so-called smooth LPS is important for the efficient killing of intracellular Salmonella. Infection with wild-type-LPS-expressing Salmonella resulted in the generation of reactive oxygen species (ROS) in TLR4-decorated, Salmonella-containing vacuoles, whereas ROS were not induced by an LPS mutant strain. In addition, the recognition of Salmonella by neutrophils, leading to ROS production, was shown to be intracellular, as determined by priming experiments with intact bacteria under conditions where the bacterium is not taken up. Finally, the generation of ROS in the wild-type-Salmonella-infected neutrophils was largely inhibited by the action of a TLR4-blocking, cell-permeable peptide, showing that signaling by this receptor from the Salmonella-containing vacuole is essential for the activation of the NADPH oxidase. In sum, our data identify the sequential recognition of unopsonized Salmonella strains by CR3 and TLR4 as essential events in the efficient uptake and killing of this intracellular pathogen.
Real-Time Tracking of Moving Persons by Exploiting Spatio-Temporal Image Slices

This paper addresses the problem of analyzing human motion in an image sequence. This is of particular importance for video-surveillance applications. We have developed an original and efficient approach to track the apparent contours of a moving articulated structure, avoiding the use of 3D models. This method exploits spatio-temporal XT-slices from the image sequence volume XYT, where typical trajectory patterns can be associated with articulated motion such as human walking. We reconstruct these trajectories online by introducing an appropriate predictive model while correctly handling occlusion periods. This paradigm can lead to a simple trajectory recognition scheme. Experiments with real-world images depicting human walk or gesture are reported, and obtained results validate the proposed approach.
Preserving Location-Based Service Protocol

Location-based service (LBS) is booming up in recent years with the rapid growth of mobile devices and the emerging of cloud computing paradigm. Along with the challenges to establish LBS and the user privacy issue becomes the most important concern. So successful privacy-preserving LBS must be secure and provide accurate query results. In this paper we present a solution to one of the location-based query problems. This problems are defined as follows: (i) a user wants to query a database of location data, known as Points Of Interest (POI), and does not want to reveal his/her location to the server due to privacy concerns; (ii) the owner of the location data, that is, the location server, does not want to simply distribute its data to all users. The location server needs to have some control over its data, since the data is its asset. For this work, we propose a private circular query protocol (PCQP) to deal with the privacy and the accuracy issues of privacypreserving LBS. The protocol includes space filling curve and a public key homomorphic cryptosystem. As a result, the security level of the proposed protocol is close to perfect secrecy without the help of a trusted third party and simulation results show that the -NN query accuracy rate of the proposed protocol is higher than 90% even when is large.
The Wnt Receptor Ryk Plays a Role in Mammalian Planar Cell Polarity Signaling*

Background: Ryk acts as a Wnt receptor in several processes, including mouse neuronal development. Results: Ryk interacts with Wnt11 in zebrafish convergent extension and with Vangl2 in mouse cochlear development and neural tube closure. Conclusion: Ryk is required for Wnt/planar cell polarity signaling during mammalian development and signals via Vangl2 and RhoA. Significance: This study extends our knowledge of signaling downstream of Ryk. Wnts are essential for a wide range of developmental processes, including cell growth, division, and differentiation. Some of these processes signal via the planar cell polarity (PCP) pathway, which is a β-catenin-independent Wnt signaling pathway. Previous studies have shown that Ryk, a member of the receptor tyrosine kinase family, can bind to Wnts. Ryk is required for normal axon guidance and neuronal differentiation during development. Here, we demonstrate that mammalian Ryk interacts with the Wnt/PCP pathway. In vitro analysis showed that the Wnt inhibitory factor domain of Ryk was necessary for Wnt binding. Detailed analysis of two vertebrate model organisms showed Ryk phenotypes consistent with PCP signaling. In zebrafish, gene knockdown using morpholinos revealed a genetic interaction between Ryk and Wnt11 during the PCP pathway-regulated process of embryo convergent extension. Ryk-deficient mouse embryos displayed disrupted polarity of stereociliary hair cells in the cochlea, a characteristic of disturbed PCP signaling. This PCP defect was also observed in mouse embryos that were double heterozygotes for Ryk and Looptail (containing a mutation in the core Wnt/PCP pathway gene Vangl2) but not in either of the single heterozygotes, suggesting a genetic interaction between Ryk and Vangl2. Co-immunoprecipitation studies demonstrated that RYK and VANGL2 proteins form a complex, whereas RYK also activated RhoA, a downstream effector of PCP signaling. Overall, our data suggest an important role for Ryk in Wnt/planar cell polarity signaling during vertebrate development via the Vangl2 signaling pathway, as demonstrated in the mouse cochlea.
Frequency of close positioning of chromosomal loci detected by FRET correlates with their participation in carcinogenic rearrangements in human cells

It has been well established that genes participating in oncogenic rearrangements are non‐randomly positioned and frequently close to each other in human cell nuclei. However, the actual distance between these fusion partners has never been determined. The phenomenon of fluorescence resonance energy transfer (FRET) is observed when a donor fluorophore is close (<10 nm) to transfer some of it energy to an acceptor fluorophore. The aim of this study was to validate the use of FRET on directly labeled DNA molecules to assess the frequency of positioning at <10 nm distances between genes known to be involved in rearrangement and to correlate it with their probability to undergo rearrangement. In the validation experiments, the frequency of FRET‐sensitized emission (SE) was found to be 93–96% between probes for the immediately adjacent chromosomal regions as compared to 0.1–0.2% between probes for the random loci located on large linear separation. Further, we found that the frequency of FRET‐SE between four pairs of genes that form rearrangements in thyroid cancer was 5% for RET and CCDC6, 4% for RET and NCOA4, 2% for BRAF and AKAP9, and 2% for NTRK1 and TPR. Moreover, the frequency with which FRET was observed showed strong correlation (r = 0.9871) with the prevalence of respective rearrangements in thyroid cancer. Our findings demonstrate that FRET can be used as a technique to analyze proximity between specific DNA regions and that the frequency of gene positioning at distances allowing FRET correlates with their probability to undergo chromosomal rearrangements. © 2012 Wiley Periodicals, Inc.
THE INTERACTION OF SELECTION AND LINKAGE. II. OPTIMUM MODELS.

I N the first paper in this series (LEWONTIN 1964) I discussed the consequences of linkage in populations subject to natural selection when there is heterosis (higher fitness of heterozygote than of homozygotes). There is a great deal of theoretical and experimental evidence concerning the existence of heterosis at the level of single loci (so-called ouerdominance) , but it seems to be as yet undetermined whether such overdominance is widespread or only of academic interest . On the other hand, there can be no doubt at all that “optimizing selection” must be an extremely common and important biological phenomenon. By “optimizing selection” I mean that in a continuum of possible phenotypes, there is some intermediate value which has the greatest selective advantage and that deviations on either side of this intermediate phenotype are less fit on the average. It is a commonplace that there is a relatively narrow range of optimal size for an animal and although there is considerable genetic variation for size in both directions in a population of say, Drosophila, the population tends to remain at an intermediate phenotypic level. Even a component of fitness like fecundity can be increased over its normal value by artificial selection (KOJIMA and KELLEHER 1963) so that correlation with other fitness components somehow holds fecundity at an intermediate value in natural populations. Even though the widespread existence of “optimizing selection” cannot be questioned, what is still not thoroughly understood is the extent to which such selection can maintain genetic variation in a population. FISHER (1 930) first alluded to an optimum selection scheme later more fully developed by MATHER (1941 ) . FISHER’S scheme was that there were two factors A , a and €3, b such that “ A is advantageous in the presence of B but disadvantageous in the presence of b, and that B is advantageous in the presence of A but disadvantageous in the presence of a. ” Couched, as this description is, in terms of gene advantages rather than diploid genotypic fitnesses, it is not unambiguous in its interpretation and as it stands is neither a sufficient nor necessary description of the kind of two factor interaction necessary for stable equilibrium of gene frequencies and for linkage effects of a permanent sort. In the first careful treatment of a two factor polymorphism, KIMURA (1956) showed, in fact, that in order for the system
Design, Democracy and Agonistic Pluralism Design, Democracy and Agonistic Pluralism

In this paper, the author presents an alternative approach to ‘design for democracy,’ drawing on the notion of agonistic pluralism. Specifically, the author highlights the differences between politics and the political within agonistic pluralism, and employing examples of contemporary design projects, discusses how these differences can been seen in the objects and practices of design. Through this critical examination, the author contributes a new perspective to the discourses of ‘design for democracy’ and expands the possibilities for democratic action and critique available to both practicing designers and design scholars.
Draft Genome Sequence of Lactobacillus reuteri 121, a Source of α-Glucan and β-Fructan Exopolysaccharides

ABSTRACT The probiotic bacterium Lactobacillus reuteri 121 is a well-known producer of diverse homoexopolysaccharides (α-glucans and β-fructans) from sucrose and maltodextrins/starches of interest for food applications. Here, we report the draft genome sequence of this strain, with a focus on carbohydrate-active enzymes.
Molecular Cloning and Functional Expression of Soybean Allene Oxide Synthases

A plant allene oxide synthase (AOS) reacting with 13S-hydroperoxy-9Z,11E,15Z-octadecatrienoic acid (13-HPOT), a lipoxygenase product of α-linolenic acid, provides an allene oxide which functions as an intermediate for jasmonic acid (JA) synthesis, making AOS a key enzyme regulating the JA level in plants. Although AOSs in various plants have been investigated, there is only limited information about AOSs in soybean (Glycine max). In this study, we cloned and characterized two soybean AOSs, GmAOS1 and GmAOS2, sharing 95% homology in the predicted amino acid sequences. GmAOS1 and GmAOS2 were composed of 564 and 559 amino acids respectively, with predicted N-terminal chloroplast-targeting signal peptides. Both AOSs expressed in Escherichia coli were selective for 13S-hydroperoxides of α-linolenic and linoleic acids, suggesting the potential of GmAOS1 and GmAOS2 to contribute to JA synthesis. GmAOS1 and GmAOS2 were expressed in leaves, stems, and roots, suggesting broad distribution in a soybean plant.
Dynamic Modification of Sphingomyelin in Lipid Microdomains Controls Development of Obesity, Fatty Liver, and Type 2 Diabetes*

Lipid microdomains or caveolae, small invaginations of plasma membrane, have emerged as important elements for lipid uptake and glucose homeostasis. Sphingomyelin (SM) is one of the major phospholipids of the lipid microdomains. In this study, we investigated the physiological function of sphingomyelin synthase 2 (SMS2) using SMS2 knock-out mice, and we found that SMS2 deficiency prevents high fat diet-induced obesity and insulin resistance. Interestingly, in the liver of SMS2 knock-out mice, large and mature lipid droplets were scarcely observed. Treatment with siRNA for SMS2 also decreased the large lipid droplets in HepG2 cells. Additionally, the siRNA of SMS2 decreased the accumulation of triglyceride in liver of leptin-deficient (ob/ob) mice, strongly suggesting that SMS2 is involved in lipid droplet formation. Furthermore, we found that SMS2 exists in lipid microdomains and partially associates with the fatty acid transporter CD36/FAT and with caveolin 1, a scaffolding protein of caveolae. Because CD36/FAT and caveolin 1 exist in lipid microdomains and are coordinately involved in lipid droplet formation, SMS2 is implicated in the modulation of the SM in lipid microdomains, resulting in the regulation of CD36/FAT and caveolae. Here, we established new cell lines, in which we can completely distinguish SMS2 activity from SMS1 activity, and we demonstrated that SMS2 could convert ceramide produced in the outer leaflet of the plasma membrane into SM. Our findings demonstrate the novel and dynamic regulation of lipid microdomains via conformational changes in lipids on the plasma membrane by SMS2, which is responsible for obesity and type 2 diabetes.
A modified Polak–Ribi‘ere–Polyak descent method for unconstrained optimization

In this paper, a modified Polak–Ribi‘ere–Polyak (MPRP) conjugate gradient method for smooth unconstrained optimization is proposed. This method produces at each iteration a descent direction, and this property is independent of the line search adopted. Under standard assumptions, we prove that the MPRP method using strong Wolfe conditions is globally convergent. The results of computational experiments are reported and show the effectiveness of the proposed method.
Policy enforcement upon software based on microservice architecture

Microservice is an architectural style that has recently started gaining popularity to become a new architectural phenomenon. Microservice architecture provides new opportunities to deploy scalable, language free and dynamically adjustable applications. This type of applications consist of hundreds or more of service instances. So that, management, monitoring, refactoring and testing of applications are more complex than monolithic applications. Therefore, some metrics and policies for measuring the quality of an application which is based on microservice architecture is needed. Moreover, automated tools are needed to carry out those tasks and enforce those policies. This work represents such metrics and policies. Additionally, an automated tool is implemented for automatic analysis of those metrics and policies upon software.
Cryopreservation of human testicular diploid germ cell suspensions

For patients with threatened fertility, preservation of it is a major concern. Although promising results have been obtained in animal models using testicular germ cell suspensions, in humans, it is crucial to first develop an efficient method of cryopreservation to be able to apply to transplantation. Thus, four reliable and available cryopreservation techniques in any fertility centre were tested to cryopreserve an enriched fraction of diploid germ cells isolated from human testicular biopsies. The protocols were evaluated based on cell viability, and the results showed significant differences between the four methods. The semen and tissue cryopreservation methods appeared to be inadequate for diploid germ cell suspensions, and programmed slow freezing gave significantly lower results than open pulled straw vitrification; the latter was found to be the protocol that best preserved cell viability. The vitrification of isolated human diploid germ cells is innovative and constitutes valuable information for cryopreservation in cases of transplants or in vitro maturation.
Statistical analysis of experimental designs applied to biological assays

Bioassays are methods employed to estimate the effect of a given substance in living matter, and therefore they are frequently used in the pharmaceutical industry. The experimental design of bioassays has to take into account the intrinsic variability in the biological test units and other factors as operators, day variation, batch variation, etc. Thus, statistical models employed to analyse bioassays include both fixed and random effects. The sample size estimation in mixed models is a complicated issue and no general formulas can be applied. An alternative approach to estimate the sample size to obtain a certain estimate with a confidence interval of a specific width is to perform computer simulations. In this thesis, simulations are performed to calculate the confidence interval of the logarithm of the effect of the test relative to the standard as a function of the number of replicates. The simulated data is compared with experimental data. The results obtained with the simulations agree well with the experimental ones. Furthermore, the method discussed here can also be used to analyse other experimental designs in which the size of the main sources of data variability are known.
An Unsupervised Classification Approach for Polarimetric SAR Data Based on the Chernoff Distance for Complex Wishart Distribution

A new unsupervised classification approach for polarimetric synthetic aperture radar (POLSAR) data is proposed in this paper. The Wishart-Chernoff distance is calculated and used in an agglomerative hierarchical clustering approach. Initial segmentation of POLSAR data into clusters is obtained based on the total backscattering power (SPAN) combined with the entropy, alpha angle, and anisotropy. The complex Wishart clustering is performed to optimize the initialization. Optimized clusters with minimum Wishart-Chernoff distance are merged hierarchically into an appropriate number of classes. The appropriate number of classes is estimated based on the data log-likelihood algorithm. Classification results show that the use of Wishart-Chernoff distance is superior to that of the Wishart test statistic distance. The effectiveness of the proposed Wishart-Chernoff distance is demonstrated using Advanced Land Observing Satellite POLSAR data.
Amitrole Absorption by Bean (Phaseolus vulgaris L. cv ;Red Kidney') Roots : Mechanism of Absorption.

The mechanism of transport of the herbicide 3-amino-1,2,4-triazole (amitrole) into Phaseolus vulgaris roots appears to be passive, as judged by the effect of temperature (Q(10) = 1.3 between 15 and 25 degrees C) and the lack of sensitivity to metabolic inhibition afforded by 2,4-dinitrophenol and NaN(3). Amitrole absorption is a linear function of external concentration over several orders of magnitude and, thus, is not facilitated by a carrier mechanism. The absorption of amitrole is sensitive to external pH, being stimulated under acid conditions. This stimulation of amitrole absorption is seen at low (</=1 millimolar) amitrole concentrations, but not at high (50 millimolar) amitrole levels. While the apparent octanol-water partition coefficient varies with the pH of the aqueous phase, there is no clear correspondence between absorption and the apparent partition coefficient. Roots do not accumulate amitrole above concentration equilibrium; however, at a time when the net amitrole content of the root tissue begins to saturate, amitrole can be detected in the xylem stream. On a fresh-weight basis, amitrole absorption by roots is equal to that accomplished by trifoliate-leaf tissue. An estimate of the permeability coefficient (according to the analysis of Tyree et al. 1979 Plant Physiol 63: 367-374) suggests that amitrole possesses near-optimal permeability for an ambimobile solute, on the order of 2.12 (+/- 0.47) x 10(-9) meters per second.