Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly Sensitive Assay for Detection of Enterovirus in Clinical Specimens by Reverse Transcription-PCR with an Armored RNA Internal Control

ABSTRACT The objective of the present study was the development of a diagnostic reverse transcription (RT)-PCR for the specific detection of enterovirus (EV) RNA in clinical specimens controlled by an internal control (IC) RNA. The IC RNA contains the same primer binding sites as EV RNA but has a different probe region. The IC RNA was packaged into an MS2 phage core particle (armored) and was added to the clinical sample to allow monitoring of both extraction efficiency and RT-PCR efficiency. Serial dilutions of the IC RNA were made, and the detection limit of the RT-PCR was tested in a background of EV RNA-negative cerebrospinal fluid. The sensitivity and specificity of the RT-PCR assay were tested by using all 64 known EV serotypes, several non-EV serotypes, and two Quality Control for Molecular Diagnostics (QCMD) Program EV proficiency panels from 2001 and 2002. In total, 322 clinical specimens were tested by RT-PCR, and to establish the clinical utility of the RT-PCR, a comparison of the results of viral culture and RT-PCR was done with 87 clinical specimens. The lower limit of sensitivity was reached at about 150 copies of IC RNA/ml. All 64 EV serotypes were positive, while all non-EV serotypes were negative. All culture-positive samples of the 2001 QCMD proficiency panel (according to the 50% tissue culture infective doses per milliliter) were positive by RT-PCR. Invalid results, i.e., negativity for both EV RNA and IC RNA, due to inhibition of RT-PCR were observed for 33.3% of the members of the 2002 QCMD proficiency panel and 3.1% of the clinical specimens. Inhibition of RT-PCR could be relieved by the addition of 400 ng of bovine α-casein per μl to both the RT reaction mixture and the PCR mixture. With this optimized protocol, the results for all samples of the 2002 QCMD proficiency panel and all clinical specimens except one fecal sample (0.3%) were valid. Evaluation of the clinical samples demonstrated that EV infection could be detected in 12 of 87 samples (13.8%) by RT-PCR, while viral culture was negative. Our data show that the RT-PCR with armored IC RNA offers a very reliable and rapid diagnostic tool for the detection of EV in clinical specimens and that the addition of bovine α-casein relieved inhibition of the RT-PCR for 99.7% of clinical specimens.
FPGA accelerated video-compression for cloud-based vision sensors

Vision Sensors for Cloud Applications have to drastically reduce the amount of image data that is transferred and stored. Due to the fact that such sensors are mostly bulk products, they must be optimized according to their performance, price, size and energy consumption. We present an approach for video compression that fulfills these needs by using FPGAs and allows scalability with respect to compression factor and compression rate. The underlying new algorithm is designed to be generic for (a) compressing a sequence of images in the JPEG standard and (b) extending the base system to a full video encoder using reference frames and prediction frames. The main idea is not to calculate the differences between consecutive video-frames directly, but between their spectra to eliminate almost equal macroblocks using a smart thresholding method. The algorithm is implemented and evaluated as part of an embedded vision system for room surveillance.
Template-Independent News Extraction Based on Visual Consistency

Wrapper is a traditional method to extract useful information from Web pages. Most previous works rely on the similarity between HTML tag trees and induced template-dependent wrappers. When hundreds of information sources need to be extracted in a specific domain like news, it is costly to generate and maintain the wrappers. In this paper, we propose a novel template-independent news extraction approach to easily identify news articles based on visual consistency. We first represent a page as a visual block tree. Then, by extracting a series of visual features, we can derive a composite visual feature set that is stable in the news domain. Finally, we use a machine learning approach to generate a template-independent wrapper. Experimental results indicate that our approach is effective in extracting news across websites, even from unseen websites. The performance is as high as around 95% in terms of F1-value.
The Role of Self-Regulation in Corporate Governance : Evidence from the Netherlands

The purpose of this paper is to gather evidence on the success of market forces in promoting investor interests through self-regulation.Corporate governance is a complex mechanism design problem that is both economic and legal/political based.As such there is great interest in whether (and when) market forces alone are sufficient to prompt change, and whether (and when) additional legal/political actions are required to write and enforce contracts between the owners and managers of capital.The Netherlands provides an excellent opportunity to gather such information.In 1996, a private sector Committee was formed to initiate debate and change in the balance of power between a company's management and investors.In 1997, the Committee issued its recommendations and one year later the Committee initiated a project to assess the impact of the report.We identify the corporate governance variables that are linked to firm value and assess the impact of the committee's recommendations on the identified variables.Finally, we use event study techniques to assess investors reactions to the various events associated with the evolution of corporate governance practices in the Netherlands during this period.
On the Fly Encoded Application Flows Recognition by Relying on Statistical Features of IP Traffic

The secure collaborative judicial workspace (SCJW) has to allow the actors to use a number of communication and scheduling instruments for managing and storing any kind of documentation, video and audio recordings, evidence, among different Judicial offices of different countries. In this scenario is very important to identify encoded application delivering those application services to guarantee secure communication, but at the same time it is important to not compromise privacy of information exchanged. In this paper we aim at identifying application flows encoded within SSH tunnels by relying on statistical feature of IP packets. This will enable SCJW network administrator to identify un:trusted applications without analyze traffic contents.
Accuracy of multiparametric magnetic resonance imaging in detecting recurrent prostate cancer after radiotherapy

To assess the role of multiparametric magnetic resonance imaging (mp‐MRI) of the prostate in evaluating local recurrence of prostate cancer, using transperineal template‐guided 5 mm‐spaced biopsies as a reference standard, in men treated with external beam radiotherapy (EBRT) for prostate cancer.
Generating Non-Projective Word Order in Statistical Linearization

We propose a technique to generate non-projective word orders in an efficient statistical linearization system. Our approach predicts liftings of edges in an unordered syntactic tree by means of a classifier, and uses a projective algorithm for tree linearization. We obtain statistically significant improvements on six typologically different languages: English, German, Dutch, Danish, Hungarian, and Czech.
Knowledge, Attitudes and Practices (KAP) about Rabies Prevention and Control: A Community Survey in Tanzania

Background Despite being entirely preventable, canine rabies still kills 55,000 people/year in developing countries. Information about local beliefs and practices can identify knowledge gaps that may affect prevention practices and lead to unnecessary deaths. Methodology/Principal Findings We investigated knowledge, attitudes and practices related to rabies and its prevention and control amongst a cross-section of households (n = 5,141) in urban and rural areas of central, southern and northern Tanzania. Over 17% of respondents owned domestic dogs (average of 2.3 dogs/household),>95% had heard about rabies, and>80% knew that rabies is transmitted through dog bites. People who (1) had greater education, (2) originated from areas with a history of rabies interventions, (3) had experienced exposure by a suspect rabid animal, (4) were male and (5) owned dogs were more likely to have greater knowledge about the disease. Around 80% of respondents would seek hospital treatment after a suspect bite, but only 5% were aware of the need for prompt wound cleansing after a bite. Although>65% of respondents knew of dog vaccination as a means to control rabies, only 51% vaccinated their dogs. Determinants of dog vaccination included (1) being a male-headed household, (2) presence of children, (3) low economic status, (4) residing in urban areas, (5) owning livestock, (6) originating from areas with rabies interventions and (7) having purchased a dog. The majority of dog-owning respondents were willing to contribute no more than US$0.31 towards veterinary services. Conclusions/Significance We identified important knowledge gaps related to, and factors influencing the prevention and control of rabies in Tanzania. Increasing knowledge regarding wound washing, seeking post-exposure prophylaxis and the need to vaccinate dogs are likely to result in more effective prevention of rabies; however, greater engagement of the veterinary and medical sectors is also needed to ensure the availability of preventative services.
Automated Bayesian segmentation of microvascular white-matter lesions in the ACCORD-MIND study.

PURPOSE Automatic brain-lesion segmentation has the potential to greatly expand the analysis of the relationships between brain function and lesion locations in large-scale epidemiologic studies, such as the ACCORD-MIND study. In this manuscript we describe the design and evaluation of a Bayesian lesion-segmentation method, with the expectation that our approach would segment white-matter brain lesions in MR images without user intervention. MATERIALS AND METHODS Each ACCORD-MIND subject has T1-weighted, T2-weighted, spin-density-weighted, and FLAIR sequences. The training portion of our algorithm first registers training images to a standard coordinate space; then, it collects statistics that capture signal-intensity information, and residual spatial variability of normal structures and lesions. The classification portion of our algorithm then uses these statistics to segment lesions in images from new subjects, without the need for user intervention. We evaluated this algorithm using 42 subjects with primarily white-matter lesions from the ACCORD-MIND project. RESULTS Our experiments demonstrated high classification accuracy, using an expert neuroradiologist as a standard. CONCLUSIONS A Bayesian lesion-segmentation algorithm that collects multi-channel signal-intensity and spatial information from MR images of the brain shows potential for accurately segmenting brain lesions in images obtained from subjects not used in training.
Trichinella spiralis Paramyosin Binds Human Complement C1q and Inhibits Classical Complement Activation

Background Trichinella spiralis expresses paramyosin (Ts-Pmy) as a defense mechanism. Ts-Pmy is a functional protein with binding activity to human complement C8 and C9 and thus plays a role in evading the attack of the host’s immune system. In the present study, the binding activity of Ts-Pmy to human complement C1q and its ability to inhibit classical complement activation were investigated. Methods and Findings The binding of recombinant and natural Ts-Pmy to human C1q were determined by ELISA, Far Western blotting and immunoprecipitation, respectively. Binding of recombinant Ts-Pmy (rTs-Pmy) to C1q inhibited C1q binding to IgM and consequently inhibited C3 deposition. The lysis of antibody-sensitized erythrocytes (EAs) elicited by the classical complement pathway was also inhibited in the presence of rTs-Pmy. In addition to inhibiting classical complement activation, rTs-Pmy also suppressed C1q binding to THP-1-derived macrophages, thereby reducing C1q-induced macrophages migration. Conclusion Our results suggest that T. spiralis paramyosin plays an important role in immune evasion by interfering with complement activation through binding to C1q in addition to C8 and C9.
Evaluation of antimicrobial activity and efficacy of herbal oils and extracts in disinfection of gutta percha cones before obturation

Objectives Literature has shown that micro-organisms contaminate gutta percha (GP) during storage and manipulation. Till date herbal extracts are not explored as an alternative medicament for pre-operative chairside disinfection of GP cones. The purpose of our study was to evaluate the antimicrobial activity and efficacy of lemon grass oil (LG), basil oil (BO), and obicure tea extract (OT) in disinfecting GP cones before obturation. Materials and Methods Agar diffusion method was used to evaluate the antimicrobial efficacy of LG, BO, OT, and sodium hypochlorite (control) against common contaminants, namely, Enterococcus faecalis, Staphylococcus aureus, and Candida albicans. One hundred and twenty GP cones were contaminated and cut into 2. First half was placed in the broth and incubated; whereas the second was treated with herbal extracts for 1 minute and then incubated for 24 hours in the broth. Any inhibition in bacterial growth was noted with presence/absence of turbidity. Two-way analysis of variance and χ2 test were used to assess the effectiveness of herbal extracts to decontaminate GP. Results LG showed the highest inhibition zones (29.9 ± 6.9 mm) for all tested organisms, followed by OT extract (16.3 ± 1.8 mm), sodium hypochlorite (16.0 ± 1.6 mm), and BO (14.5 ± 5.3 mm). Statistically significant difference was observed between LG and other herbal extracts (p < 0.05). Conclusions All extracts proved to be potential rapid chairside disinfectants of GP cones with LG showing the highest antimicrobial activity.
Factor Analysis of the General Health Questionnaire

We present the factor structure of the General Health Questionnaire-60 as derived from a population of 2115 Army soldiers. An eight-factor principal components analysis provided the most clinically relevant solution and explained 58.0% of the variance. We distinguished two types of depressive symptomatology, suggesting the questionnaire may be useful in differentiating shame-ridden dysphoria from anergic disinterest.
Serial concatenation of block and convolutional codes

Parallel concatenated coding schemes employing convolutional codes as constituent codes linked by an interleaver have been proposed in the literature as ‘turbo codes’. They yield very good performance in connection with simple suboptimum decoding algorithms. The authors propose an alternative scheme consisting in the serial concatenation of block or convolutional codes and evaluate its average performance in terms of bit error probability.
Residual Stress Estimation with Identification of Stress Directionality Using Instrumented Indentation Technique

The instrumented indentation technique (IIT) has recently attracted significant research interest because it is nondestructive and easy to perform, and can characterize materials on local scales. Residual stress can be determined by analyzing the indentation load-depth curve from IIT. However, this technique using a symmetric indenter is limited to an equibiaxial residual stress state. In this study, we determine the directionality of the non-equibiaxial residual stress by using the Knoop indentation technique. Different indentation load-depth curves are obtained at nonequibiaxial residual stresses depending on the Knoop indentation direction. A model for Knoop indentation was developed through experiments and theoretical analysis.
Dynamic Mechanical Properties of EPDM Rubber Blends

The damping properties of ethylene-propylene-diene rubber (EPDM) with aliphatic hydrocarbon (C94) resin were investigated by dynamic mechanical analysis (DMA). It was found that the damping property of EPDM was improved after addition of aliphatic hydrocarbon resin. With increasing content of the resin, the main tan δ peak shifted to higher temperatures and the valid damping range in temperature was broadened. An addition of mica or NBR was found to widen the effective damping range. After addition of NBR into EPDM, the effective damping range of the blends was evidently extended in the applicable temperature region, especially when NBR content was 50 wt%. It was concluded that the NBR was incompatible with EPDM, and there existed two tan δ peaks in DMA spectra.
A Generalized Elastic Net Regularization with Smoothed l0 Penalty

This paper presents an accurate and efficient algorithm for solving the generalized elastic net regularization problem with smoothed l0 penalty for recovering sparse vector. Finding the optimal solution to the unconstrained l0 minimization problem in the recovery of compressive sensed signals is an NP-hard problem. We proposed an iterative algorithm to solve this problem. We then prove that the algorithm is convergent based on algebraic methods. The numerical result shows the efficiency and the accuracy of the algorithm.
Investigation of Adhesion and Mechanical Properties of Human Glioma Cells by Single Cell Force Spectroscopy and Atomic Force Microscopy

Active cell migration and invasion is a peculiar feature of glioma that makes this tumor able to rapidly infiltrate into the surrounding brain tissue. In our recent work, we identified a novel class of glioma-associated-stem cells (defined as GASC for high-grade glioma -HG- and Gasc for low-grade glioma -LG-) that, although not tumorigenic, act supporting the biological aggressiveness of glioma-initiating stem cells (defined as GSC for HG and Gsc for LG) favoring also their motility. Migrating cancer cells undergo considerable molecular and cellular changes by remodeling their cytoskeleton and cell interactions with surrounding environment. To get a better understanding about the role of the glioma-associated-stem cells in tumor progression, cell deformability and interactions between glioma-initiating stem cells and glioma-associated-stem cells were investigated. Adhesion of HG/LG-cancer cells on HG/LG-glioma-associated stem cells was studied by time-lapse microscopy, while cell deformability and cell-cell adhesion strengths were quantified by indentation measurements by atomic force microscopy and single cell force spectroscopy. Our results demonstrate that for both HG and LG glioma, cancer-initiating-stem cells are softer than glioma-associated-stem cells, in agreement with their neoplastic features. The adhesion strength of GSC on GASC appears to be significantly lower than that observed for Gsc on Gasc. Whereas, GSC spread and firmly adhere on Gasc with an adhesion strength increased as compared to that obtained on GASC. These findings highlight that the grade of glioma-associated-stem cells plays an important role in modulating cancer cell adhesion, which could affect glioma cell migration, invasion and thus cancer aggressiveness. Moreover this work provides evidence about the importance of investigating cell adhesion and elasticity for new developments in disease diagnostics and therapeutics.
Animated transitions between user interface views

User interface development life cycle often involve several different views of the user interface over time either at the same level of abstraction or at different levels of abstraction. The relationship between these different views is often supported by tiling coordinated windows containing these related views simultaneously, thus leaving the developer with the responsibility to effectively and efficiently link the corresponding elements of these different views. This paper attempts to overcome the shortcomings posed by the coordinated visualization of multiple views by providing UsiView, a user interface rendering engine in which one single window ensures an animated transition between these different user interface views dynamically an internal view, an external view, and a conceptual view. Examples include the following cases: an authoring environment ensures an animated transition between an internal view (e.g., HTML5) and its external view (e. g., a web page), an Integrated Development Environment ensures an animated transition between its conceptual view and its external view; a model-driven engineering environment ensures an animated transition between the conceptual view at different levels of abstraction, e.g., from task to abstract user interface to concrete user interface until final user interface. The paper discusses the potential advantages of using animated transitions between user interface views during the development life cycle.
Identification of an ER Fluid in Unsteady Flow with Random Electric Field and Solidification

An identification procedure to simultaneously determine electrorheological (ER) and viscous characteristics of an ER fluid is presented. The analysis is performed under unsteady flow conditions with randomly varying electric field and intermittent solidification of the fluid. Tests conducted using a standard viscometer and cylindrical couette geometry indicate that there is some interaction between viscous and ER effects and that some residual structuring persists in the fluid after removal of the electric field.
A Highly Sensitive Diagnostic System for Detecting Dengue Viruses Using the Interaction between a Sulfated Sugar Chain and a Virion

We propose a novel method of detecting trace amounts of dengue virus (DENVs) from serum. Our method is based on the interaction between a sulfated sugar chain and a DENV surface glycoprotein. After capturing DENV with the sulfated sugar chain-immobilized gold nanoparticles (SGNPs), the resulting complex is precipitated and viral RNA content is measured using the reverse-transcription quantitative polymerase chain reaction SYBR Green I (RT-qPCR-Syb) method. Sugar chains that bind to DENVs were identified using the array-type sugar chain immobilized chip (Sugar Chip) and surface plasmon resonance (SPR) imaging. Heparin and low-molecular-weight dextran sulfate were identified as binding partners, and immobilized on gold nanoparticles to prepare 3 types of SGNPs. The capacity of these SGNPs to capture and concentrate trace amounts of DENVs was evaluated in vitro. The SGNP with greatest sensitivity was tested using clinical samples in Indonesia in 2013–2014. As a result, the novel method was able to detect low concentrations of DENVs using only 6 μL of serum, with similar sensitivity to that of a Qiagen RNA extraction kit using 140 μL of serum. In addition, this method allows for multiplex-like identification of serotypes of DENVs. This feature is important for good healthcare management of DENV infection in order to safely diagnose the dangerous, highly contagious disease quickly, with high sensitivity.
Cloning and sequencing of a full-length cDNA of mouse N-acetylglucosamine (beta 1-4)galactosyltransferase.

A full-length cDNA clone for mouse N-acetylglucosamine (beta 1-4)galactosyltransferase (beta 1-4GT) [EC 2.4. 1.90] and several clones diverged from the beta 1-4GT cDNA were isolated from a mouse F9 cDNA library and then sequenced. The beta 1-4GT cDNA has an open reading frame consisting of 399 amino acids. The homology at the amino acid level is 80 and 91% as to the partial sequences of bovine and human milk beta 1-4GT, respectively. The general enzyme structure of the beta 1-4GT seems to be similar to that of a rat beta-galactoside (alpha 2-6) sialyltransferase. Junctions of the common and divergent regions of cDNA have dinucleotides, AG, suggesting that the variety of cDNA clones is generated through alternative splicing.