Miracle-dz/UniFAR-FTUs huggingface dataset:
A simple and reliable PCR-restriction fragment length polymorphism assay to identify Candida albicans and its closely related Candida dubliniensis

Candida dubliniensis is an emerging pathogen capable of causing superficial as well as systemic infections. Due to its close similarity to C. albcians, conventional methods based on phenotypic traits are not always reliable in identification of C. dubliniensis. In this study, we developed a PCR-restriction fragment length polymorphism (RFLP) assay to identify and discriminate between the two closely related species. The D1/D2 region of 28S rDNA was amplified by PCR and enzymatically digested by ApaI and BsiEI respectively. PCR products of both species were digested into two fragments by ApaI, but those of other yeast species were undigested. BsiEI cut the PCR products of C. albicans into two fragments but not those of C. dubliniensis. Thus two species were differentiated. We evaluated 10 reference strains representing 10 yeast species, among which C. albicans and C. dubliniensis were successfully identified. A total of 56 phenotypically characterized clinical isolates (42 C. albicans isolates and 14 C. dubliniensis isolates) were also investigated for intra-species variability. All tested isolates produced identical RFLP patterns to their respective reference strains except one initially misidentified isolate. Our method offers a simple, rapid and reliable molecular method for the identification of C. albicans and C. dubliniensis.
Tests of the precursory accelerating moment release model using a synthetic seismicity model for Wellington, New Zealand

[1] We have constructed a synthetic seismicity model of the Wellington region, New Zealand, including seven superfaults and 500 subfaults which are randomly positioned. From this model, a synthetic catalogue of 2000 years duration, containing events of magnitude 5.0 or more, has been generated. The properties of the catalogue, such as the long-term slip rates, b value, average activity rate, and hypocenter distribution, are in accord with paleoseismic studies and the real seismicity over the last 40 years. Such a synthetic catalogue can replace the short, incomplete, and inhomogeneous historic and instrumental records in research which needs a long time duration and many strong shocks. We have used our catalogue to examine tests for the existence of accelerating moment release (AMR) before large events and compared the results with those from random (Poisson) catalogues. We find that (1) the apparent success rate is very dependent on the rules used to define the test window; (2) when appropriately defined, the AMR pattern occurs before about 20% of the strong (M ≥ 7.0) shocks with a typical precursor time of about 22 years; (3) the AMR pattern is found almost equally frequently before large events in random catalogues; and (4) there are some false alarms (AMR pattern without a large event). This extended study reinforces the conclusion in our preliminary report: that in synthetic catalogues of the kind we have constructed, the AMR pattern is essentially an artefact of the method of sampling.
Folding rate prediction using complex network analysis for proteins with two- and three-state folding kinetics

It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.
Preference Dominance Approaches for Conversational Recommender Systems

Conversational recommender systems typically involve iteratively showing the user a small set of options for them to choose between. In order to choose an appropriate set to display at each stage, it is useful to have information regarding the user’s relative preference between options: specifically whether an option is dominated by others with respect to the user’s preference relation. This paper describes a simple semantic framework for preference dominance, and two instances of the framework are developed for a recent kind of conversational recommender system. The first is based on a basic quantitative preferences formalism, where products are compared using sums of weights of features, and the input language involves comparisons between options. The second is a qualitative preference formalism, where models are a kind of generalised lexicographic order, and the inputs are comparative preference statements (in a language generalising CP-nets). A key feature of both methods is that deductions of preference dominance can be made efficiently, since this procedure needs to be applied for many pairs of products. The two approaches have been implemented, with encouraging experimental results.
Study of the Activity of 3-benzyl-5-(4-chloro-arylazo)-4-thioxo-imidazolidin-2-one against Schistosomiasis Mansoni in Mice

Previous studies conducted with the imidazolidinic derivative 3-benzyl-5-(4-chloro-arylazo)-4-thioxo-imidazolidin-2-one (LPSF-PT05) show outstanding activity against adult Schistosoma mansoni worms in vitro. In the first phase of this study, S. mansoni-infected mice were treated, orally, with 100 mg/Kg of the LPSF-PT05 in three formulations: Tween 80 and saline solution, oil/water (70 : 30) emulsion, and solid dispersion with polyethylene glycol (PEG). In the second phase, three other doses of the LPSF-PT05 in PEG were tested: 3, 10, 30 mg/kg. These treatment regimens significantly reduced the number of recovered worms due to increases in the solubility of the compound in this formulation; the greatest reduction (70.5%) was observed at the dose of 100 mg/kg. There was no changes in the pattern of mature egg compared to immature eggs; however there was a significant increase in the number of dead eggs. Histopathological analysis of liver tissue showed changes in morphological aspects of the hepatic parenchyma with decrease exudative-productive hepatic granuloma stages, although we found no significant differences in IFN-γ, IL-4, IL-10, or NO production in response to the specific antigen SEA. The results show the derivative LPSF-PT05 to be a potential candidate in the etiological treatment of schistosomiasis with a possible dampening effect of the granulomatous process.
Feedback/feedforward schemes for motion control of the cybercarpet

Abstract The CyberCarpet is an actuated platform that allows unconstrained locomotion possibilities to a walking user for VR exploration. The platform has two actuating devices (linear and angular) and the motion control problem is dual to that of nonholonomic wheeled mobile robots. The main control objective is to keep the walker close to the platform center. Simple but global kinematic control schemes are presented, addressing in particular the handling of singularity issues. The feedback stabilizing part, which is based only on the user's pose information, is complemented by a feedforward term derived from a walker's velocity observer. Numerical and graphical simulation results are presented.
Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors

Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion.
Experiences on Teaching Software Engineering Concepts for the Design of Communication Protocols

Protocols undoubtedly play a key role in computer networks and distributed and real-time embedded software. Therefore, Telecommunications Engineering and other related curricula usually include a specific subject for the design of communication protocols at the undergraduate level. Traditionally, these subjects focus on using standards and formal methods related to the International Telecommunications Union (ITU-T) or the International Organization for Standardization (ISO). Because the academic focus is generally on design (and validation) these approaches are indeed appropriate, but a gap exists between high-level protocol designs and their actual implementation as part of complex systems in industry. This paper describes the experiences in one of these subjects that now includes software engineering concepts and methods for the design of protocols. The objective is to fill the gap between design and implementation through the use of communication frameworks and middleware, with a focus on high-performance and reliability.
A Fog based system model for cooperative IoT node pairing using matching theory

The revolutionized vision of IoT has united heterogeneous devices to foster the systems of cohesive intelligent things. In addition, Fog computing has also envisioned a new form of cloud computing paradigm. Therefore, Fog provides edge computing to such IoT devices with varied capabilities and resources. However, a balanced and efficient pairing or matching strategy for edge IoT nodes is crucial to achieve the user requisite. Hence, this paper addresses the utility based matching or pairing problem within the same domain of IoT nodes by using Irving's matching algorithm under the node specified preferences to endure a stable IoT node pairing. We studied the performance of the proposed matching algorithm through simulation. The simulation results show the higher utility gain of the node pairs through refined matching algorithm over greedy approach.
EMI prediction and filter design for MHz GaN based LLC half-bridge converter

In this paper, EMI research and filter design with shielding method for a MHz switching frequency Gallium Nitride (GaN) based LLC half-bridge resonant DC-DC converter is explored. Firstly, a high-frequency model considering overall electromagnetic coupling effects for both common mode and differential mode is proposed. And EMI prediction during the frequency spectrum from 150 kHz to 30 MHz is illustrated. Then, improved inductor with shielding method is designed. According to the accurate EMI prediction and the designed inductor, high-frequency CM and DM EMI filters of the GaN based LLC converter are designed and implemented. To achieve that, different filter topologies are compared and CLC type is selected. It is confirmed that the proposed EMI filter is a convenient and cost-effective approach to suppress the EMI noise largely by both practical experiments and theoretical analysis. Moreover, to further improve the performance of the system, an optimized prototype with planar transformer is designed and implemented, which demonstrates that planar transformer can achieve smaller size, lower loss, higher power density and efficiency compared to traditional transformer.
Biological Activities of Aerial Parts Extracts of Euphorbia characias

The aim of the present study was to evaluate antioxidant, antimicrobial, anti-HIV, and cholinesterase inhibitory activities of aqueous and alcoholic extracts from leaves, stems, and flowers of Euphorbia characias. The extracts showed a high antioxidant activity and were a good source of total polyphenols and flavonoids. Ethanolic extracts from leaves and flowers displayed the highest inhibitory activity against acetylcholinesterase and butyrylcholinesterase, showing potential properties against Alzheimer's disease. Antimicrobial assay showed that leaves and flowers extracts were active against all Gram-positive bacteria tested. The ethanolic leaves extract appeared to have the strongest antibacterial activity against Bacillus cereus with MIC value of 312.5 μg/mL followed by Listeria monocytogenes and Staphylococcus aureus that also exhibited good sensitivity with MIC values of 1250 μg/mL. Moreover, all the extracts possessed anti-HIV activity. The ethanolic flower extract was the most potent inhibitor of HIV-1 RT DNA polymerase RNA-dependent and Ribonuclease H with IC50 values of 0.26 and 0.33 μg/mL, respectively. The LC-DAD metabolic profile showed that ethanolic leaves extract contains high levels of quercetin derivatives. This study suggests that Euphorbia characias extracts represent a good source of natural bioactive compounds which could be useful for pharmaceutical application as well as in food system for the prevention of the growth of food-borne bacteria and to extend the shelf-life of processed foods.
NSSAC: Negative selection-based self adaptive classifier

In this paper, a novel algorithm for classification called “NSSAC” is proposed, which is based on negative selection method in the human immune system. Artificial immune based classifiers have two important challenges: (1) the recognition distance threshold which choosing an appropriate recognition distance threshold is a difficult task because it necessitates the understanding of the data set in detail, (2) A detector generation algorithm that all classifiers used randomized algorithm to generate memory cell. In this paper for resolve above problems a deterministic algorithm is used to generate memory cell and an adaptive method is used for calculation the recognition distance threshold. Therefore the generated detectors have a good quality of the distribution and on the other hand, NSSAC can be adapted automatically to each data set. The classifier was tested on three benchmark data sets and the results show that our algorithm is useful for classification problems.
Training in virtual environments via a hybrid dynamic trainer model

This thesis presents a novel virtual reality (VR) training concept that integrates the trainer or the trainer model into training sessions. As an extension to conventional VR training systems that rely only on realistic interaction, the students are given the chance to be corrected by the trainer in a multi-user schema. The trainer is connected to the same virtual environment as the student via an individual haptic display. As an alternative, task performing skill of the trainer is captured with hybrid identification methods and the trainer is replaced with the identified model allowing for a single-user training schema. Two different identification approaches are successfully applied and presented in this thesis: The weighted K-means clustering-based method and the stochastically switching dynamics method. Observations and corrections of the trainer or trainer model are multi-modal, i.e. can be represented in the form of visual, acoustic and/or haptic signals. The combination of these possible signals allows for the definition of different training strategies. Enhancing the training systems with extra features that are not available in a real task is investigated as well. Two different VR scenarios are developed as test-beds: A bone drilling medical training system and a push button system. The efficiency of the different training strategies is checked through a series of user tests. To assess the training results objectively, a metric depending on the distance between the trainer and student in n dimensional Euclidean space is introduced and applied. The results validate the efficiency and usability of the training strategies and hybrid identification methods.
The Weather Safety Education Program at 45th Weather Squadron

The 45th Weather Squadron (45 WS) conducts an extensive weather safety education program. This program is summarized below. The authors hope this paper will encourage increased and improved weather safety education by others. The 45 WS also supports special missions, such as the Space Shuttle Ferry Flight (Priselac et al., 1997). Other special missions include transport of large components on oversized aircraft such as the Super Guppy, transport of large components on barges across the Gulf of Mexico to the east coast of Florida, and astronaut rescue exercises. Another special mission is space launch with radioactive material onboard (Boyd et al., 2004). 2. BACKGROUND
Adaptive Resource Allocation for Layer-Encoded IPTV Multicasting in IEEE 802.16 WiMAX Wireless Networks

In this paper, we study the utility-based resource allocation problem for layer-encoded IPTV multicast service over WiMAX networks. In this problem, each video stream is encoded into multiple layers. We regard each layer as a multicast subsession. Each layer of a video stream is assigned a utility value, and the number of layers for each program each user can receive is adjustable. The objective is to maximize the total utility (i.e., all users' satisfaction) and the system resource utilization, subject to users' channel conditions, the popularity of a video program, and the total available radio resource. We design a polynomial-time solution to this problem, and show that the difference in the performance of our proposed mechanism and the optimal solution is tightly bounded. Our mechanism supports both unicast and multicast, and both single layer and multi-layer environments. Most importantly, it can be integrated with the multicast mechanism defined in WiMAX standards, and can also be applied to any kind of wireless networks which support adaptive modulation and coding schemes. The performance of our scheme is evaluated by simulation. The simulation results show that this scheme can allocate resource flexibly according to the utility function of each program, the popularity of each program, and the amount of total resource available in the network.
Impact of metal artefacts due to EEG electrodes in brain PET/CT imaging

The goal of this study is to investigate the impact of electroencephalogram (EEG) electrodes on the visual quality and quantification of 18F-FDG PET images in neurological PET/CT examinations. For this purpose, the scans of 20 epilepsy patients with EEG monitoring were used. The CT data were reconstructed with filtered backprojection (FBP) and with a metal artefact reduction (MAR) algorithm. Both data sets were used for CT-based attenuation correction (AC) of the PET data. Also, a calculated AC (CALC) technique was considered. A volume of interest (VOI)-based analysis and a voxel-based quantitative analysis were performed to compare the different AC methods. Images were also evaluated visually by two observers. It was shown with simulations and phantom measurements that from the considered AC methods, the MAR-AC can be used as the reference in this setting. The visual assessment of PET images showed local hot spots outside the brain corresponding to the locations of the electrodes when using FBP-AC. In the brain, no abnormalities were observed. The quantitative analysis showed a very good correlation between PET-FBP-AC and PET-MAR-AC, with a statistically significant positive bias in the PET-FBP-AC images of about 5–7% in most brain voxels. There was also good correlation between PET-CALC-AC and PET-MAR-AC, but in the PET-CALC-AC images, regions with both a significant positive and negative bias were observed. EEG electrodes give rise to local hot spots outside the brain and a positive quantification bias in the brain. However, when diagnosis is made by mere visual assessment, the presence of EEG electrodes does not seem to alter the diagnosis. When quantification is performed, the bias becomes an issue especially when comparing brain images with and without EEG monitoring.
Computer aided design and evaluation of new anatomic fixation system on entire pelvic model

This paper presented a special computer aided procedure to design a new sacroliliac anatomic bar-plate internal fixation system, and evaluated its biomechanical properties on an accurate patient-specific finite element model of entire pelvis, compared with two conventional internal fixation methods. Based on virtual anatomical measure of 30 digital pelvic models reconstructed from CT, an anatomic plate was designed according to the complicated structure of the outer table of the posterior ilium, and was integrated into the complete fixation system. Then, an ad hoc semi-automatic mesh generator was employed to construct a patient-specific finite element model of whole pelvis, including elaborate sacroiliac joints, important pelvic ligaments, and interpubic disc, as well as position-dependent cortical thickness and trabecular bone elastic modulus. Following, one side of sacroiliac joint related ligaments were deleted to simulate a complete unilateral sacroiliac joint disruption. Then the new anatomic fixation system was integrated to fix the fracture, and two comparing models including iliosacral screw fixation and front reconstruction plate fixation were also generated. Finally, all models were simulated under same loading conditions. The results demonstrated that the mechanical stability of the new anatomic fixation system was superior, with obviously improved stress distribution and little displacement, which implied an effective internal fixation method for potential clinical application.
Yeast mitochondrial outer membrane specifically binds cytoplasmically‐synthesized precursors of mitochondrial proteins

The precursor of cytochrome b2 (a cytoplasmically‐synthesized mitochondrial protein) binds to isolated mitochondria or to isolated outer membrane vesicles. Binding does not require an energized inner membrane, is diminished by trypsin treatment of the membranes and is not observed with the partially processed (intermediate) form of the cytochrome b2 precursor or with non‐mitochondrial proteins. Upon energization of the mitochondria, the bound precursor is imported and cleaved to the mature form. Similar results were obtained with the precursor of citrate synthase. This receptor‐like binding activity was present in isolated outer, but not inner membrane. It was solubilized from outer membrane with non‐ionic detergent and reconstituted into liposomes.