Miracle-dz/UniFAR-FTUs huggingface dataset:
Dilution of samples collected and transported for Gen-Probe PACE 2 processing facilitates detection of Chlamydia trachomatis by Roche Amplicor PCR

Chlamydia trachomatis is a common human pathogen transmitted through sexual contacts. Rapid, sensitive, and specific detection of C. trachomatis is essential for the effective treatment of the infection. The recent development of nucleic acid-based detection techniques for C. trachomatis has enabled more rapid and more accurate diagnosis than that offered by traditional culture or antigen detection methods (1, 2). As the first commercial nucleic acid test for Chlamydia, the Gen-Probe PACE 2 System (Gen-Probe, San Diego, Calif.) is a direct hybridization assay targeting the rRNA of C. trachomatis. The Roche Amplicor PCR (Roche Diagnostic Systems, Branchburg, N.J.) and the Abbott LCx Probe System (Abbott Laboratories, Abbott Park, Ill.) represent new-generation technology involving amplification of specific sequences in C. trachomatis’s cryptic plasmid. Hence, these assays are inherently more sensitive than those without amplification, such as the Gen-Probe PACE 2 System. Unfortunately, due to the requirement of specific transport media for sample handling, a direct, same-sample comparison of the amplification-based and non-amplification-based assays for C. trachomatis has proven difficult. To overcome this problem, we recently used swab samples collected for testing by the Gen-Probe PACE 2 System for direct detection of C. trachomatis by the Roche Amplicor PCR assay. Ten positive and 5 negative samples, as determined by the Gen-Probe PACE 2 System, collected by either cervical or urethral swabs were examined. Initially, these samples were processed as recommended in the instructions provided with the Roche Cobas Amplicor kit; this resulted in a 1/4 dilution of the samples. However, all 10 Gen-Probe-positive and 5 negative samples, as well as internal controls included, were negative by the Roche Cobas Amplicor assay, indicating the presence of substances inhibiting DNA polymerase in the Gen-Probe samples. In light of this finding, we modified the recommended sample preparation procedure and futher diluted the Gen-Probe samples to 1/10. To do this, 50 ml of Gen-Probe sample was mixed with 200 ml of CT/NG Lysis Buffer and later 250 ml of CT/NG Specimen Diluent was added. When 50 ml of the diluted sample was tested as described above, all 10 Gen-Probepositive and 5 negative swab samples were correctly identified by the Roche Cobas Amplicor assay. As a single copy of C. trachomatis plasmid DNA is amplified to one billion-fold within 30 cycles, a 1/10 (instead of 1/4) dilution of the specimen should have minimal negative impact on the sensitivity of the Amplicor assay. This procedure may therefore enable direct comparison of the Gen-Probe PACE 2 System and the Roche Amplicor PCR assay with the same sample. Future selection of an alternative, universal medium for sample collection may further simplify the direct comparison of performances of these assays without sample dilution.
[Development of an animal model of blood stasis syndrome and thrombosis].

OBJECTIVE To develop an animal model of thrombosis and blood stasis syndrome in rats by using lipopolysaccharide (LPS) in combination with carrageenan (Ca). METHOD SD rats in control group were randomly divided into control group and model group (LPS/Ca treatment). The rats in model group were firstly treated with Ca ip, and followed by LPS iv sixteen hours later. The rats in control group were given normal saline (NS). The moment of LPS iv was served as 0 h for the observation. The ear microcirculation, blood rheology parameters (whole blood viscosity etab, plasma viscosity etap and platelet aggregation PA), cruor parameters (thrombin time TT, prothrombin time PT, and partial thromboplastin time APIT) and inflammation factors (TNFalpha, IL-6) were observed at different time after treatment. RESULT LPS/Ca combinatory treatment can induce a stable and repeatable thrombosis animal model. The thrombus can be observed on the tails of rats by naked eyes, and can be quantitatively measured without necessary of autopsy. Obstacle in microcirculation, increase in whole blood viscosity (etab) and a change of platelets aggregation (PA) rate were observed after LPS/Ca treatment. Cruor parameters were significantly prolonged due to large consumption of cruor factors and platelets. The concentration of inflammation factors TNFalpha and IL-6 in blood was obviously increased at the early stage of the model. The results indicate that this animal model has the characteristics of blood stasis syndrome caused by pyrogen and toxin accompanied by thrombosis. CONCLUSION LPS/Ca combinatory treatment can induce a easily practicable and repeatable animal model characterized as thrombosis and blood stasis syndrome
A replicated experiment of usage-based and checklist-based reading

Software inspection is an effective method to detect faults in software artefacts. Several empirical studies have been performed on reading techniques, which are used in the individual preparation phase of software inspections. Besides new experiments, replications are needed to increase the body of knowledge in software inspections. We present a replication of an experiment, which compares usage-based and checklist-based reading. The results of the original experiment show that reviewers applying usage-based reading are more efficient and effective in detecting the most critical faults from a user's point of view than reviewers using checklist-based reading. We present the data of the replication together with the original experiment and compares the experiments. The main result of the replication is that it confirms the result of the original experiment. This replication strengthens the evidence that usage-based reading is an efficient reading technique.
A Benchmark Parallel Sort for Shared Memory Multiprocessors

The first parallel sort algorithm for shared memory MIMD (multiple-instruction-multiple-data-stream) multiprocessors that has a theoretical and measured speedup near linear is exhibited. It is based on a novel asynchronous parallel merge that evenly partitions data to be merged among any number of processors. A benchmark sorting algorithm is proposed that uses this merge to remove the linear time bottleneck inherent in previous multiprocessors sorts. This sort, when applied to data set on p processors, has a time complexity of O((n log n)/p)+O((n log p)/p) and a space complexity of 2n, where n is the number of keys being sorted. Evaluations of the merge and benchmark sort algorithms on a 12-processor Sequent Balance 21000 System demonstrate near-linear speedup when compared to sequential Quicksort. >
Epicardial Border Zone Overexpression of Skeletal Muscle Sodium Channel SkM1 Normalizes Activation, Preserves Conduction, and Suppresses Ventricular Arrhythmia: An In Silico, In Vivo, In Vitro Study

Background— In depolarized myocardial infarct epicardial border zones, the cardiac sodium channel (SCN5A) is largely inactivated, contributing to low action potential upstroke velocity (&OV0312; max), slow conduction, and reentry. We hypothesized that a fast inward current such as the skeletal muscle sodium channel (SkM1) operating more effectively at depolarized membrane potentials might restore fast conduction in epicardial border zones and be antiarrhythmic. Methods and Results— Computer simulations were done with a modified Hund-Rudy model. Canine myocardial infarcts were created by coronary ligation. Adenovirus expressing SkM1 and green fluorescent protein or green fluorescent protein alone (sham) was injected into epicardial border zones. After 5 to 7 days, dogs were studied with epicardial mapping, programmed premature stimulation in vivo, and cellular electrophysiology in vitro. Infarct size was determined, and tissues were immunostained for SkM1 and green fluorescent protein. In the computational model, modest SkM1 expression preserved fast conduction at potentials as positive as −60 mV; overexpression of SCN5A did not. In vivo epicardial border zone electrograms were broad and fragmented in shams (31.5±2.3 ms) and narrower in SkM1 (22.6±2.8 ms; P=0.03). Premature stimulation induced ventricular tachyarrhythmia/fibrillation >60 seconds in 6 of 8 shams versus 2 of 12 SkM1 (P=0.02). Microelectrode studies of epicardial border zones from SkM1 showed membrane potentials equal to that of shams and &OV0312; max greater than that of shams as membrane potential depolarized (P<0.01). Infarct sizes were similar (sham, 30±2.8%; SkM1, 30±2.6%; P=0.86). SkM1 expression in injected epicardium was confirmed immunohistochemically. Conclusions— SkM1 increases &OV0312; max of depolarized myocardium and reduces the incidence of inducible sustained ventricular tachyarrhythmia/fibrillation in canine infarcts. Gene therapy to normalize activation by increasing &OV0312; max at depolarized potentials may be a promising antiarrhythmic strategy.
User authentication based on mouse movement data using normalized features

This paper presents a user authentication system based on mouse movement data. An available logging tool named Recording User Input (RUI) is used to collect three types of mouse actions — Mouse Move, Point-and-Click on Left or Right mouse button and Drag-and-Drop. Collected data are divided into N-number of blocks consisting of specific number of actions. From each block seventy four features are extracted to form feature vectors where number of new features is forty eight. Two types of classifiers are used to identify the user: Support Vector Machine (SVM) and Artificial Neural Network (ANN) are used to identify the user. A benchmark data is used to train and test the system. Experimental result shows that for both classifiers system with proposed features perform better. The results also show that Support Vector Machine outperforms the Artificial Neural Network Classifier.
Selective elasticity data acquisition on 3D deformable objects for virtualized reality applications

This paper proposes the use of self-organizing architectures, particularly the growing neural gas, for the purpose of automatically guiding elasticity data acquisition based on a sparse vision and elasticity point-cloud of a 3D object. The proposed solution allows for the identification of regions where changes in the elastic behavior of the object occur. Additional data can then be collected in these areas in order to better characterize the elastic characteristics of a certain object. Experimental results for different non-homogeneous objects are presented in order to validate the proposed solution.
Small versus Large Iron Oxide Magnetic Nanoparticles: Hyperthermia and Cell Uptake Properties

Efficient use of magnetic hyperthermia in clinical cancer treatment requires biocompatible magnetic nanoparticles (MNPs), with improved heating capabilities. Small (~34 nm) and large (~270 nm) Fe3O4-MNPs were synthesized by means of a polyol method in polyethylene-glycol (PEG) and ethylene-glycol (EG), respectively. They were systematically investigated by means of X-ray diffraction, transmission electron microscopy and vibration sample magnetometry. Hyperthermia measurements showed that Specific Absorption Rate (SAR) dependence on the external alternating magnetic field amplitude (up to 65 kA/m, 355 kHz) presented a sigmoidal shape, with remarkable SAR saturation values of ~1400 W/gMNP for the small monocrystalline MNPs and only 400 W/gMNP for the large polycrystalline MNPs, in water. SAR values were slightly reduced in cell culture media, but decreased one order of magnitude in highly viscous PEG1000. Toxicity assays performed on four cell lines revealed almost no toxicity for the small MNPs and a very small level of toxicity for the large MNPs, up to a concentration of 0.2 mg/mL. Cellular uptake experiments revealed that both MNPs penetrated the cells through endocytosis, in a time dependent manner and escaped the endosomes with a faster kinetics for large MNPs. Biodegradation of large MNPs inside cells involved an all-or-nothing mechanism.
Experimental Testing to Determine Concrete Fracture Energy Using Simple Laboratory Test Setup

Insight into reinforced concrete structural behavior can be provided and experimental investigation can be complemented by nonlinear finite element analysis. Specification of material parameters, including post-peak tensile response curve shape, fracture energy, and concrete tensile strength is typically required in a concrete structure finite element model's development. A number of different tests for fracture energy and post-cracking response determination has resulted from previous research. A very stiff, closed-loop test machine typically needs to be used in these methods so load application can be performed under displacement control since extremely brittle response is exhibited by test specimens. A recommended fracture energy test method was employed in a recently computed University of Washington study, with an open-loop testing machine and test specimens modified to include counterweights. Test-generated post-cracking response data and fracture energy data fall within the typically observed recommended test range. Additionally, the laboratory-observed load-displacement response was reproduced, with acceptable accuracy through using these data for concrete constitutive model calibration for nonlinear finite element analyses.
Comment on "Quantifying Long-term Scientific Impact"

The paper comments on "Quantifying long-term scientific impact". It indicates that there is a mistake of [D. S. Wang , C. Song, A. L. Barabasi, Quantifying long-term scientific impact, Science 342, 127 (2013), arXiv:1306.3293].
Learning Relational Navigation Policies

Navigation is one of the fundamental tasks for a mobile robot. The majority of path planning approaches has been designed to entirely solve the given problem from scratch given the current and goal configurations of the robot. Although these approaches yield highly efficient plans, the computed policies typically do not transfer to other, similar tasks. We propose to learn relational decision trees as abstract navigation strategies from example paths. Relational abstraction has several interesting and important properties. First, it allows a mobile robot to generalize navigation plans from specific examples provided by users or exploration. Second, the navigation policy learned in one environment can be transferred to unknown environments. In several experiments with real robots in a real environment and in simulated runs, we demonstrate the usefulness of our approach
Recommendation in the Social Web

Recommender systems are a means of personalizing the presentation of information to ensure that users see the items most relevant to them. The social web has added new dimensions to the way people interact on the Internet, placing the emphasis on user-generated content. Users in social networks create photos, videos and other artifacts, collaborate with other users, socialize with their friends and share their opinions online. This outpouring of material has brought increased attention to recommender systems, as a means of managing this vast universe of content. At the same time, the diversity and complexity of the data has meant new challenges for researchers in recommendation. This article describes the nature of recommendation research in social web applications and provides some illustrative examples of current research directions and techniques. It is difficult to overstate the impact of the social web. This new breed of social applications is reshaping nearly every human activity from the way people watch movies to how they overthrow governments. Facebook allows its members to maintain friendships whether they live next door or on another continent. With Twitter, users from celebrities to ordinary folks can launch their 140 character messages out to a diverse horde of ‘‘followers. ” Flickr and YouTube users upload their personal media to share with the world, while Wikipedia editors collaborate on the world’s largest encyclopedia.
Improving protein identification from tandem mass spectrometry data by one-step methods and integrating data from other platforms

MOTIVATION Many approaches have been proposed for the protein identification problem based on tandem mass spectrometry (MS/MS) data. In these experiments, proteins are digested into peptides and the resulting peptide mixture is subjected to mass spectrometry. Some interesting putative peptide features (peaks) are selected from the mass spectra. Following that, the precursor ions undergo fragmentation and are analyzed by MS/MS. The process of identification of peptides from the mass spectra and the constituent proteins in the sample is called protein identification from MS/MS data. There are many two-step protein identification procedures, reviewed in the literature, which first attempt to identify the peptides in a separate process and then use these results to infer the proteins. However, in recent years, there have been attempts to provide a one-step solution to protein identification, which simultaneously identifies the proteins and the peptides in the sample. RESULTS In this review, we briefly introduce the most popular two-step protein identification procedure, PeptideProphet coupled with ProteinProphet. Following that, we describe the difficulties with two-step procedures and review some recently introduced one-step protein/peptide identification procedures that do not suffer from these issues. The focus of this review is on one-step procedures that are based on statistical likelihood-based models, but some discussion of other one-step procedures is also included. We report comparative performances of one-step and two-step methods, which support the overall superiorities of one-step procedures. We also cover some recent efforts to improve protein identification by incorporating other molecular data along with MS/MS data.
A model-based auditory scene analysis approach and its application to speech source localization

Localization and classification of acoustic signals in a complex auditory scene is an every day task of the human auditory system. However, this problem presents a significant challenge for a computational system. In this paper, we propose a framework that allows the detection of different classes of signals (e.g. speech, music) and the localization of the signal sources. As a special application of this framework, we describe a method for localization of human speech in a complex acoustic scene and low SNR, based on vowel detection. In contrast to other works, we detect and extract parts of the signal mixture that correspond to a single class exclusively, using a prior model of the target signals. Herewith, a reliable localization of signal sources is possible.
IT Architecture and Information Quality in Data Warehouse and Business Intelligence Environments

Organizations are currently investing more in information technology to store and process a vast amount of information. Generally, this information does not comply with any standard, which hinders the decision-making process. The cause of the difficulties can be attributed to Information Quality (IQ), which has technical characteristics related to the architecture used in Data Warehouse (DW) and Business Intelligence (BI) environments. On the basis of the relevant literature in IQ, DW, and BI, a research model was created to identify the relations between components of DW/BI architecture and IQ dimensions. This research model was applied in a real case study (Big Financial Company in Brazil). This case study involved semi-structured interviews with managers and analysts. This chapter attempts to provide a better understanding of the relations between IT architecture and IQ in DW and BI environments. The authors hope to motivate the discussion around the development of IQ-oriented architectures for BI and the relationship between these concepts. Samuel Otero Schmidt University of Sao Paulo, Brazil Edmir Parada Vasques Prado University of Sao Paulo, Brazil DOI: 10.4018/978-1-4666-4892-0.ch006
Torque control strategies for snake robots

We present three methods of achieving compliant motion with a snake robot by controlling the torques exerted by the joints of the robot. Two strategies command joint torques based solely on the robot's local curvature (i.e. joint angles). A third strategy commands joint angles, velocities, and torques based on the recorded feedback from the robot while executing a previously defined motion under position control. The three control strategies are implemented and compared on a snake robot that includes series elastic actuation (SEA) and torque sensing at each joint, and demonstrate compliant locomotion that adapts automatically to the robot's surrounding terrain.
Design of high frequency ultrasonic array transducers for medical imaging

Ultrasonic transducers have been widely used in the medical applications. High frequency array transducers have recently attracted many research interests, since it provides not only the electronic beamforming but also the very fine image resolution. The transducers are usually either annular or linear arrays. This study concentrates on the design of both types of array in high frequency applications. The annular array is firstly investigated, and an optimized design of array geometry is developed including the kerfs influence which is usually neglected in the design of high frequency arrays. The improved imaging performance is found by this optimized design. More interestingly, the conventional annular array with element having the same surface area has a relatively large sidelobe closest to the main lobe. Two methods are applied to suppress the sidelobe. The method of using high-impedance single matching to enlarge the element bandwidth only shows very limited lobe suppression, however, a novel matching approach is found. Another method of changing the array geometry from equal area elements to equal width ones successfully suppressed the sidelobe. The imaging results suggest that the novel equal width array shows a good improvement. The linear array is then analyzed. The kerfs influence again is found to be significant for the array especially for high frequency. It is essential to use a high attenuated kerfs material in the linear array design. More importantly, the limitation of current fabrication techniques forces the linear array to concede a high grating lobe in the imaging field if it operates in a relatively high frequency. A novel linear array is developed to suppress the grating lobe without using advanced fabrication techniques. The imaging results show that the novel linear array has a general reduction of -6dB for the lobe suppression. The novel design made the linear array operate in a very high frequency without strong grating lobe, and the array can be fabricated by current techniques.
A ug 2 00 4 Local Fields in Boundary Conformal QFT

Conformal field theory on the half-space x > 0 of Minkowski spacetime (“boundary CFT”) is analyzed from an algebraic point of view, clarifying in particular the algebraic structure of local algebras and the bi-localized charge structure of local fields. The field content and the admissible boundary conditions are characterized in terms of a non-local chiral field algebra.