Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface plasmon resonance: a useful technique for cell biologists to characterize biomolecular interactions

Surface plasmon resonance (SPR) is a powerful technique for monitoring the affinity and selectivity of biomolecular interactions. SPR allows for analysis of association and dissociation rate constants and modeling of biomolecular interaction kinetics, as well as for equilibrium binding analysis and ligand specificity studies. SPR has received much use and improved precision in classifying protein–protein interactions, as well as in studying small-molecule ligand binding to receptors; however, lipid–protein interactions have been underserved in this regard. With the field of lipids perhaps the next frontier in cellular research, SPR is a highly advantageous technique for cell biologists, as newly identified proteins that associate with cellular membranes can be screened rapidly and robustly for lipid specificity and membrane affinity. This technical perspective discusses the conditions needed to achieve success with lipid–protein interactions and highlights the unique lipid–protein interaction mechanisms that have been elucidated using SPR. It is intended to provide the reader a framework for quantitative and confident conclusions from SPR analysis of lipid–protein interactions.
The Space-to-Product Ratio Effect: How Interstitial Space Influences Product Aesthetic Appeal, Store Perceptions, and Product Preference

The authors identify and examine the effect of space-to-product ratio on consumer response; very generally, consumers perceive products as more valuable when more space is devoted to their display. In both lab and field studies, the authors find that this phenomenon influences total sales, purchase likelihood, and even perceived product experience (taste perceptions). More interstitial space increases perceptions of individual products as more aesthetically pleasing and the store as more prestigious. The authors find these effects across a variety of product categories and rule out a number of competing alternative explanations that are based on perceptions of product popularity, scarcity, assortment search difficulty, and messiness.
Robust Identification of Time-Scaled Audio

Automatic identification of audio titles on radio broadcasts is a first step towards automatic annotation of radio programmes. Systems designed for the purpose of identification have to deal with a variety of postprocessing potentially imposed on audio material at the radio stations. One of the more difficult techniques to be handled is time-scaling, i.e., the variation of playback speed. In this paper we propose a robust fingerprinting technique designed for the identification of time-scaled audio data. To allow for fast timescale invariant audio identification, the extracted fingerprints are used as an input to an algebraic indexing technique that has already been successfully applied to the task of audio identification.
Inherent Decorrelating and Least Perturbation Properties of the Normalized Subband Adaptive Filter

This correspondence describes and analyzes a class of subband adaptive filters (SAFs) that stems from various approaches of applying subband and multirate techniques in adaptive filtering. This class of SAFs, called the normalized SAF (NSAF), has a unique weight-control mechanism, whereby subband error signals are used to adapt a fullband tap-weight vector. In this correspondence, we elaborate on the inherent decorrelating properties of the NSAF, which manifest themselves in different forms as integral elements of the weight-control mechanism. We also show that the NSAF possesses some least perturbation properties that are also found in the normalized least-mean-square (NLMS) and affine projection (AP) algorithms
Improving Nominal SRL in Chinese Language with Verbal SRL Information and Automatic Predicate Recognition

This paper explores Chinese semantic role labeling (SRL) for nominal predicates. Besides those widely used features in verbal SRL, various nominal SRL-specific features are first included. Then, we improve the performance of nominal SRL by integrating useful features derived from a state-of-the-art verbal SRL system. Finally, we address the issue of automatic predicate recognition, which is essential for a nominal SRL system. Evaluation on Chinese NomBank shows that our research in integrating various features derived from verbal SRL significantly improves the performance. It also shows that our nominal SRL system much outperforms the state-of-the-art ones.
SIDAN: A tool dedicated to software instrumentation for detecting attacks on non-control-data

Anomaly based intrusion detection systems rely on the build of a normal behavior model. When a deviation from this normal behavior is detected, an alert is raised. This anomaly approach, unlike the misuse approach, is able to detect unknown attacks. A basic technique to build such a model for a program is to use the system call sequences of the process. To improve the accuracy and completeness of this detection model, we can add information related to the system call, such as its arguments or its execution context. But even then, attacks that target non-control-data may be missed and attacks on control-data may be adapted to bypass the detection mechanism using evasion techniques. We propose in this article an approach that focuses on the detection of non-control-data attacks. Our approach aims at exploiting the internal state of a program to detect a memory corruption on non-control-data that could lead to an illegal system call. To achieve this, we propose to build a data-oriented detection model by statically analyzing a program source code. This model is used to instrument the program by adding reasonableness checks that verify the consistent state of the data items the system calls depend on. We thus argue that it is possible to detect a program misuse issued by a non-control-data attack inside the program during its execution. While keeping a low overhead, this approach allows to detect non-control-data attacks.
Cosmological parameters from cluster abundances, cosmic microwave background and IRAS

We combine information on cosmological parameters from cluster abundances, CMB primordial anisotropies and the IRAS 1.2 Jy galaxy redshift survey. We take as free parameters the present values of the total matter density of the universe, Ωm, the Hubble parameter, h, the linear theory rms fluctuations in the matter density within 8 h 1 Mpc spheres, σ8, and the IRAS biasing factor, bIRAS. We assume that the universe is spatially flat, with a cosmolo gical constant, and that structure formed from adiabatic initial fluc tuations with a Harrison-Zel’dovich power spectrum (i.e. the primordial spectral index n = 1). The nucleosynthesis value for the baryonic matter density Ωb = 0.019/h 2 is adopted. We use the full three- and four- dimensional likelihood functions for each data set and marginali se these to two- and one- dimensional distributions in a Bayesian way, integrating over th e other parameters. It is shown that the three data sets are in excellent agreement, with a best fit point of Ωm = 1 ΩΛ = 0.36, h = 0.54, σ8 = 0.74, and bIRAS = 1.08. This point is within one sigma of the minimum for each data set alone. Pairs of these data sets have their degen eracies in sufficiently different directions that using only two data sets at a time is suffic ient to place good constraints on the cosmological parameters. We show that the results from each of the three possible pairings of the data are also in good agreement. Finally, we combine all three data sets to obtain marginalised 68 per cent confidence intervals of 0 . 30 < Ωm < 0.43, 0.48 < h < 0.59, 0.69 < σ8 < 0.79, and 1.01 < bIRAS < 1.16. For the best fit parameters the CMB quadrupole is Qrms ps = 18. 0µK, the shape parameter of the mass power-spectrum is Γ = 0.15, the baryon density is Ωb = 0.066 and the age of the universe is 16.7 Gyr.
Strain effects on transport properties of Si nanowire devices

We study the effects of strains on the performances of (001) and (110) oriented gate-all-around silicon nanowire (Si NW) transistors within a Non-Equilibrium Green's Functions framework. In agreement with previous works, we show that uniaxial strains can significantly improve the carrier mobility in the channel. However, we find that besides the enhancement of the carrier mobility, the ballistic resistance must be simultaneously optimized to achieve good performances in short channel devices. The response of the ballistic resistance to strains is different in [001] and [110] strained devices. Our study shows that the ballistic resistance is improved more consistently with the mobility in [110] Si NWs, providing the best opportunities for strain engineering in ultimate short channel transistors.
Investigating Gender Bias in Depression Measure with Children's Depression Inventory

This study investigated items depression measure that affected by differential item functioning (DIF). Discrimination parameters DIF and item location parameter DIF is implemented. Children's Depression Inventory (CDI) Indonesian version was analyzed. Result of the investigation suggest several items were infected by DIF. Participants were adolescents who represents four school districts in Yogyakarta Special Region (N = 3183). Data were analyzed using DIF test item response theory modeling. Results showed that some items CDI were affected by DIF based on gender both on the discrimination parameters (10 points) and the items location parameter (7 items). Items which infected by the different DIF indicates that those item only distinguish symptoms of depression in certain gender, whereas item location parameters DIF indicates that certain sex tend to get a high score than other. These findings of this study can serve as guidelines to assess symptoms depression in adolescent based on gender specific.
The σ54‐dependent transcriptional activator SfnR regulates the expression of the Pseudomonas putida sfnFG operon responsible for dimethyl sulphone utilization

Pseudomonas putida DS1 is able to utilize dimethyl sulphide through dimethyl sulphoxide, dimethyl sulphone (DMSO2), methanesulphonate (MSA) and sulphite as a sulphur source. We previously demonstrated that sfnR encoding a σ54‐dependent transcriptional regulator is essential for DMSO2 utilization by P. putida DS1. To identify the target genes of SfnR, we carried out transposon mutagenesis on an sfnR disruptant (DMSO2‐utilization‐defective phenotype) using mini‐Tn5, which contains two outward‐facing constitutively active promoters; as a result, we obtained a mutant that restored the ability to utilize DMSO2. The DMSO2‐positive mutant carried a mini‐Tn5 insertion in the intergenic region between two opposite‐facing operons, sfnAB and sfnFG. Both sfnA and sfnB products were similar to acyl‐CoA dehydrogenase family proteins, whereas sfnF and sfnG encoded a putative NADH‐dependent FMN reductase (SfnF) and an FMNH2‐dependent monooxygenase (SfnG). Disruption and complementation of the sfn genes indicated that the sfnG product is essential for DMSO2 utilization by P. putida DS1. Furthermore, an enzyme assay demonstrated that SfnG is an FMNH2‐dependent DMSO2 monooxygenase that converts DMSO2 to MSA. It was revealed that the expression of the sfnFG operon is directly activated by the binding of SfnR at its upstream region. Site‐directed mutagenesis of the SfnR binding sequences allowed us to define a potential recognition sequence for SfnR. These results provided insight into regulation of sulphate starvation‐induced genes in bacteria.
Detail-Enhanced Medical Image Fusion in NSCT Domain

Multimodal medical image fusion technique plays an important role in clinical applications, such as pathologic diagnosis and surgical options. However, many traditional fusion methods cannot well preserve details of source images in the fused image. To address this problem, a detail-enhanced image fusion scheme based on nonsubsampled contourlet transform (NSCT) and gain control (i.e., NCGC) is developed in this paper, which can effectively combine the spectral information and the spatial features of source images. The proposed method applies power law transformation to tune coefficients of each decomposed subband, and adjusts the strength of subband signals by smooth gain control. Eventually, the fused image with more anatomical details and functional information is constructed by the inverse NSCT. Three pairs of medical images with different modalities and three fusion metrics are applied to validate the feasibility of this algorithm. Experimental results demonstrate that the proposed method can achieve superior performance in both visual perception and objective assessment.
Optical see-through calibration with vision-based trackers: propagation of projection matrices

Recently, M. Tuceryan and N. Navab (2000) introduced a method for calibrating an optical see-through system based on the alignment of a set of 2D markers on the display with a single point in the scene, while not restricting the user's head movements (the single point active alignment method or SPAAM). This method is applicable with any tracking system, provided that it gives the pose of the sensor attached to the see-through display. When cameras are used for tracking, one can avoid the computationally intensive and potentially unstable pose estimation process. A vision-based tracker usually consists of a camera attached to the optical see-through display, which observes a set of known features in the scene. From the observed locations of these features, the pose of the camera can be computed. Most pose computation methods are very involved and can be unstable at times. The authors propose to keep the projection matrix for the tracker camera without decomposing it into intrinsic and extrinsic parameters and use it within the SPAAM method directly. The propagation of the projection matrices from the tracker camera to the virtual camera, representing the eye and the optical see-through display combination as a pinhole camera model, allows us to skip the most time consuming and potentially unstable step of registration, namely, estimating the pose of the tracker camera.
Fine-Grained Image Classification via Low-Rank Sparse Coding With General and Class-Specific Codebooks

This paper tries to separate fine-grained images by jointly learning the encoding parameters and codebooks through low-rank sparse coding (LRSC) with general and class-specific codebook generation. Instead of treating each local feature independently, we encode the local features within a spatial region jointly by LRSC. This ensures that the spatially nearby local features with similar visual characters are encoded by correlated parameters. In this way, we can make the encoded parameters more consistent for fine-grained image representation. Besides, we also learn a general codebook and a number of class-specific codebooks in combination with the encoding scheme. Since images of fine-grained classes are visually similar, the difference is relatively small between the general codebook and each class-specific codebook. We impose sparsity constraints to model this relationship. Moreover, the incoherences with different codebooks and class-specific codebooks are jointly considered. We evaluate the proposed method on several public image data sets. The experimental results show that by learning general and class-specific codebooks with the joint encoding of local features, we are able to model the differences among different fine-grained classes than many other fine-grained image classification methods.
Normalization of metabolomics data with applications to correlation maps

MOTIVATION In metabolomics, the goal is to identify and measure the concentrations of different metabolites (small molecules) in a cell or a biological system. The metabolites form an important layer in the complex metabolic network, and the interactions between different metabolites are often of interest. It is crucial to perform proper normalization of metabolomics data, but current methods may not be applicable when estimating interactions in the form of correlations between metabolites. We propose a normalization approach based on a mixed model, with simultaneous estimation of a correlation matrix. We also investigate how the common use of a calibration standard in nuclear magnetic resonance (NMR) experiments affects the estimation of correlations. RESULTS We show with both real and simulated data that our proposed normalization method is robust and has good performance when discovering true correlations between metabolites. The standardization of NMR data is shown in simulation studies to affect our ability to discover true correlations to a small extent. However, comparing standardized and non-standardized real data does not result in any large differences in correlation estimates. AVAILABILITY AND IMPLEMENTATION Source code is freely available at https://sourceforge.net/projects/metabnorm/ CONTACT alexandra.jauhiainen@ki.se SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Host Specificity and Ectoparasite Load of Bat Flies in Utila, Honduras

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Outer Membrane Vesicles from Brucella abortus Promote Bacterial Internalization by Human Monocytes and Modulate Their Innate Immune Response

Outer membrane vesicles (OMVs) released by some Gram-negative bacteria have been shown to exert immunomodulatory effects that favor the establishment of the infection. The aim of the present study was to assess the interaction of OMVs from Brucella abortus with human epithelial cells (HeLa) and monocytes (THP-1), and the potential immunomodulatory effects they may exert. Using confocal microscopy and flow cytometry, FITC-labeled OMVs were shown to be internalized by both cell types. Internalization was shown to be partially mediated by clathrin-mediated endocytosis. Pretreatment of THP-1 cells with Brucella OMVs inhibited some cytokine responses (TNF-α and IL-8) to E. coli LPS, Pam3Cys or flagellin (TLR4, TLR2 and TLR5 agonists, respectively). Similarly, pretreatment with Brucella OMVs inhibited the cytokine response of THP-1 cells to B. abortus infection. Treatment of THP-1 cells with OMVs during IFN-γ stimulation reduced significantly the inducing effect of this cytokine on MHC-II expression. OMVs induced a dose-dependent increase of ICAM-1 expression on THP-1 cells and an increased adhesion of these cells to human endothelial cells. The addition of OMVs to THP-1 cultures before the incubation with live B. abortus resulted in increased numbers of adhered and internalized bacteria as compared to cells not treated with OMVs. Overall, these results suggest that OMVs from B. abortus exert cellular effects that promote the internalization of these bacteria by human monocytes, but also downregulate the innate immune response of these cells to Brucella infection. These effects may favor the persistence of Brucella within host cells.
Assessing the needs of training on inclusive education for public school administrators

This study assessed the needs of urban school leaders for special education preparation in a large public school district in the USA in order to assist the school administrators with improving their knowledge and skills for providing appropriate services to students with disabilities and their families to support inclusive education. The needs survey was created based on the Council for Exceptional Children (CEC 2009) standards for school administrators in the USA and the literature in special education. The validity and reliability of the instrument were verified. The needs assessment measures 10 aspects regarding special education knowledge and skills as indicated by 10 factors in the exploratory factor analysis. Quantitative data analyses on a sample of 289 participants revealed that there were significant differences in the needs of training in special education knowledge based on the school administrators’ backgrounds. The current research supports the call for the professional development and inclusive education for school leaders. The findings of the current study indicated that school leaders wanted the knowledge to make them more successful in serving students with disabilities to answer the call for inclusive education.
RpoS-Dependent Transcriptional Control ofsprE: Regulatory Feedback Loop

ABSTRACT The stationary-phase response exhibited by Escherichia coli upon nutrient starvation is mainly induced by a decrease of the ClpXP-dependent degradation of the alternate primary ς factor RpoS. Although it is known that the specific regulation of this proteolysis is exercised by the orphan response regulator SprE, it remains unclear how SprE's activity is regulated in vivo. Previous studies have demonstrated that the cellular content of SprE itself is paradoxically increased in stationary-phase cells in an RpoS-dependent fashion. We show here that this RpoS-dependent upregulation of SprE levels is due to increased transcription. Furthermore, we demonstrate that sprE is part of the two-generssA-sprE operon, but it can also be transcribed from an additional RpoS-dependent promoter located in therssA-sprE intergenic region. In addition, by using an in-frame deletion in rssA we found that RssA does not regulate either SprE or RpoS under the conditions tested.
Praziquantel-loaded PLGA nanoparticles: preparation and characterization

Nanoparticles containing praziquantel made of poly (D,L-lactide-co-glycolide) were designed by an emulsion-solvent evaporation method. Two organic solvents were separately utilized as disperse phase: methylene chloride and ethyl acetate. The size of the particles prepared with the former solvent was bigger than the particles prepared with the latter. The entrapment efficiency was bigger when methylene chloride was used, 79.82% in comparison with 29.27% by using ethyl acetate. DSC and infrared studies showed that no strong chemical interaction between drug and polymer occurred. Release kinetics of praziquantel, used as a model drug, was governed not only by actual drug loading but also by particles size. The higher the drug content and the smaller the particle size resulted in faster drug release.
Formal analysis of Facebook Connect Single Sign-On authentication protocol

We present a formal analysis of the authentication protocol of Facebook Connect, the Single Sign-On service offered by the Facebook Platform which allows Facebook users to login to affiliated sites. Formal specification and verification have been carried out using the specification language HLPSL and AVISPA, a state-of-the-art verification tool for security protocols. AVISPA has revealed two security flaws, one of which (previously unheard of, up to our knowledge) allows an intruder to impersonate a user at a service provider affiliated with Facebook. To address this problem, we propose a modification of the protocol, by adding a message authentication mechanism; this protocol has been verified with AVISPA to be safe from the masquerade attack. Finally, we sketch a JavaScript implementation of the modified protocol.