Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations

Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org) helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC) and two types of system shapes (rectangular and hexagonal) are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.
Unified Compact ECC-AES Co-Processor with Group-Key Support for IoT Devices in Wireless Sensor Networks

Security is a critical challenge for the effective expansion of all new emerging applications in the Internet of Things paradigm. Therefore, it is necessary to define and implement different mechanisms for guaranteeing security and privacy of data interchanged within the multiple wireless sensor networks being part of the Internet of Things. However, in this context, low power and low area are required, limiting the resources available for security and thus hindering the implementation of adequate security protocols. Group keys can save resources and communications bandwidth, but should be combined with public key cryptography to be really secure. In this paper, a compact and unified co-processor for enabling Elliptic Curve Cryptography along to Advanced Encryption Standard with low area requirements and Group-Key support is presented. The designed co-processor allows securing wireless sensor networks with independence of the communications protocols used. With an area occupancy of only 2101 LUTs over Spartan 6 devices from Xilinx, it requires 15% less area while achieving near 490% better performance when compared to cryptoprocessors with similar features in the literature.
Highly selective solid electrolyte sensor for the analysis of gaseousmixtures

Abstract. The operation principle of a commercially available solid electrolyte sensor was modified with respect to applications in flowing gaseous mixtures containing H2 and O2. For this purpose the generally applied coulometric or potentiometric operation mode was replaced by cyclic voltammetry. By varying the sensor temperature, electrode area and potential scan rate, the conditions for the characteristic peak formation for every gas component were determined. While hydrogen oxidation peaks arise at potential scan rates up to 100 mV s−1, oxygen reduction peaks develop between 200 and 1000 mV s−1. A linear relationship between peak area/peak height and concentration was found at concentrations ϕ (H2)
Failure of resistance spot welds: tensile shear versus coach peel loading conditions

Abstract This paper aims at investigating the failure behaviour of resistance spot welds under tensile shear (TS) and coach peel (CP) loading conditions. A failure mechanism was proposed to describe both interfacial and pullout failure modes in each loading condition. The mechanisms were confirmed by SEM investigations, examining the cross-sections of the fractured welds to detail the fracture path. The experimental results showed that in the pullout failure mode during TS testing, necking is initiated at the nugget circumference in the base metal, and then failure propagates along the nugget circumference in the sheet, leading to the final fracture, while pullout failure during the CP test occurred by crack initiation and propagation near the weld nugget/heat affected zone boundary. The interfacial failure to pullout failure mode transition in the TS and CP tests was also studied. The critical weld nugget size required to ensure the pullout failure mode was obtained for each loading condition. The critical fusion zone size to ensure pullout failure mode during the TS test was larger than that of the CP test. It was found that the load bearing capacity of the spot welds under CP is significantly lower than that of the TS test.
An Expanded Multi-Organ Disease Phenotype Associated with Mutations in YARS

Whole exome sequence analysis was performed in a Swedish mother–father-affected proband trio with a phenotype characterized by progressive retinal degeneration with congenital nystagmus, profound congenital hearing impairment, primary amenorrhea, agenesis of the corpus callosum, and liver disease. A homozygous variant c.806T > C, p.(F269S) in the tyrosyl-tRNA synthetase gene (YARS) was the only identified candidate variant consistent with autosomal recessive inheritance. Mutations in YARS have previously been associated with both autosomal dominant Charcot-Marie-Tooth syndrome and a recently reported autosomal recessive multiorgan disease. Herein, we propose that mutations in YARS underlie another clinical phenotype adding a second variant of the disease, including retinitis pigmentosa and deafness, to the spectrum of YARS-associated disorders.
Delivery of bone morphogenetic protein-2 and substance P using graphene oxide for bone regeneration

In this study, we demonstrate that graphene oxide (GO) can be used for the delivery of bone morphogenetic protein-2 (BMP-2) and substance P (SP), and that this delivery promotes bone formation on titanium (Ti) implants that are coated with GO. GO coating on Ti substrate enabled a sustained release of BMP-2. BMP-2 delivery using GO-coated Ti exhibited a higher alkaline phosphatase activity in bone-forming cells in vitro compared with bare Ti. SP, which is known to recruit mesenchymal stem cells (MSCs), was co-delivered using Ti or GO-coated Ti to further promote bone formation. SP induced the migration of MSCs in vitro. The dual delivery of BMP-2 and SP using GO-coated Ti showed the greatest new bone formation on Ti implanted in the mouse calvaria compared with other groups. This approach may be useful to improve osteointegration of Ti in dental or orthopedic implants.
Surface characterization of plasma‐treated poly‐p‐xylylene films

Plasma-treated poly-p-xylylene films have been characterized by neutron activation oxygen analysis, internal reflection (IRS) and transmission infrared spectroscopy, transmission electron microscopy (TEM), and surface contact angle measurements. The results indicate that an oxygen plasma roughens the surface and that oxygen is incorporated into the surface. Oxygen is not detected in the bulk of the sample. The infrared transmission spectra exhibited no carbonyl band, but the relative band intensities changed, indicating a change in ring substitution by a loss of chlorine in the chlorinated poly-p-xylylenes. The IRS spectra of the surface of films treated with oxygen plasma did contain carbonyl bands at 1730 and 1640 cm−1. Argon and helium plasmas generally decreased the water contact angle measured on plasma-treated poly-p-xylylene surfaces more than oxygen or nitrogen plasma treatments. Regardless of the plasma utilized, the water contact angles increased with time after the treatment but did not recover to the original level. IRS spectra of the surface of films treated with argon plasma contained carbonyl bands at 1730 and 1695 cm−1. The adhesion of a polyurethane thermosetting material to a poly-p-xylylene surface is greatly improved if a plasma treatment is used prior to the application of the polyurethane. The degree of improvement in adhesion was dependent on the type of plasma and the treatment time.
The use of Ge-doped optical fibres in external beam radiotherapy dosimetry

The need for better characteristics of a radiation dosimeter arises from the requirement to verify the advanced techniques now employed in radiotherapy such as Intensity Modulated Radiation Therapy (IMRT), Intensity Guided Radiation Therapy (IGRT) and Cyberknife. To-date, one of the most promising dosimeter is thermoluminescent (TL) Ge-doped silica dioxide (SiO2) optical fibre. It has been established that it provides excellent spatial resolution, flexibility, modest cost, a nonhygroscopic nature, and excellent radiation response characteristics. In this study, the TL yield of 9 μm Ge-doped optical fibres (Ge-9 μm) has been investigated, establishing their key dosimetric characteristics: for verification of dose distributions in IMRT prostate dosimetry; for measuring out-of-field photon. These results show that the fibres offer consistent linearity between TL yield and dose for doses from 0.05 Gy up to 10 Gy for photon and electron beam energies, with reproducibility of better than 5%. For all investigated megavoltage photon and electron beam energies, the fibres also offer angular-, dose rate-, and temperature-independence, while a small energy-dependent response was found, of between 6 to 11%. However, at kilovoltage potentials there is significant energy dependence. When held at room temperature results show fading of 11% 133 days post-irradiation. In addition, Ge-doped optical fibre was observed to verify doses to within 3% of the IMRT radiotherapy treatment planning system predicted doses and LiF TLDs (TLD-100 and TLD-700) for the 6 MV and 15 MV energy photon beams used. The fibres have demonstrated potential for use in measuring IMRT out-of-field photon dose when using 6 MV photons, however when conducting 15MV irradiations, the fibres’ response needs to be corrected to account for the activation neutron dose. Ge-doped fibres also represent a viable system for use in mailed audit radiotherapy programmes; in particular measuring beam output under reference conditions as demonstrated in a postal dosimetry audit at selected Malaysian radiotherapy centres. The audit methodology has been developed with an expanded uncertainty of 4.22 % at 95% confidence interval for the energy photon beams used.
Feasibility of repeated self-measurements of maximum step length and gait speed by community-dwelling older persons

Objectives Self-management of mobility and fall risk can be important in fall prevention; however, it remains unstudied. Therefore, the current study assessed whether community-dwelling older persons were able to repeatedly self-assess maximum step length (MSL) and gait speed (GS) in their own home for a 6-month period, how these tests changed during this period and if these changes were related to falling. Design This is a prospective study. Setting This study was conducted at home. Participants A total of 56 community-dwelling older adults (24 women (43%), mean age 76.2 (SD 3.9) years) entered the study; of which, 45 completed the study. Methods Participants performed MSL and GS once a week in their own home during a 6-month period. Primary and secondary outcomes Repeated MSL and GS measurements were the primary outcomes. Falls, self-management and mobility were the secondary outcomes. Results Self-assessment of MSL and GS by older persons is feasible. Compliance of repeatedly self-measuring MSL and GS was good; the median number of weekly measurements was 23.0 (88%) and 21.0 (81%) for MSL and GS, respectively. Drop-outs showed less self-management abilities compared to the participants who completed the study (p=0.049). Linear mixed models showed a small significant improvement in MSL and GS over time (p<0.001), without an influence on falling. Conclusions Most community-dwelling older persons are able and willing to repeatedly assess their MSL and GS. Self-managing mobility and fall risk did not increase fall occurrence. The fact that older persons can be actively involved in their own healthcare is clinically relevant. Further studies are needed to examine the (cost-)effectiveness of self-management in fall prevention interventions.
Measurement of patient safety: a systematic review of the reliability and validity of adverse event detection with record review

Objectives Record review is the most used method to quantify patient safety. We systematically reviewed the reliability and validity of adverse event detection with record review. Design A systematic review of the literature. Methods We searched PubMed, EMBASE, CINAHL, PsycINFO and the Cochrane Library and from their inception through February 2015. We included all studies that aimed to describe the reliability and/or validity of record review. Two reviewers conducted data extraction. We pooled κ values (κ) and analysed the differences in subgroups according to number of reviewers, reviewer experience and training level, adjusted for the prevalence of adverse events. Results In 25 studies, the psychometric data of the Global Trigger Tool (GTT) and the Harvard Medical Practice Study (HMPS) were reported and 24 studies were included for statistical pooling. The inter-rater reliability of the GTT and HMPS showed a pooled κ of 0.65 and 0.55, respectively. The inter-rater agreement was statistically significantly higher when the group of reviewers within a study consisted of a maximum five reviewers. We found no studies reporting on the validity of the GTT and HMPS. Conclusions The reliability of record review is moderate to substantial and improved when a small group of reviewers carried out record review. The validity of the record review method has never been evaluated, while clinical data registries, autopsy or direct observations of patient care are potential reference methods that can be used to test concurrent validity.
Tierless Web Programming in the Large

Tierless Web programming languages allow combining client-side and server-side programming in a single program. This allows defining expressions with both client and server parts, and at the same time provides good static guarantees regarding client-server communication. However, these nice properties come at a cost: most tierless languages offer very poor support for modularity and separate compilation. To regain this modularity and offer a larger-scale notion of composition, we propose to leverage a well-known tool: ML-style modules. In modern ML languages, the module system is a layer separate from the expression language. Eliom is an extension of OCaml for tierless Web programming which provides type-safe communication and an efficient execution model. In this article, we present how the Eliom module system combines the flexibility of tierless Web programming languages with a powerful module system, thus providing good support for abstraction, modularity and separate compilation. We also show that we can provide all these advantages while providing seamless integration with OCaml and its ecosystem.
A hybrid recommendation approach based on attributes of products using genetic algorithm and naive Bayes classifier

Recommender system technology can present personalised offers to customers of companies. This technology suffers from the cold-start and sparsity problems. On the other hand, in most researches, less attention has been paid to user's preferences varieties in different product categories and also explicit and implicit attributes of products. Since users express their opinions implicitly based on some specific attributes of products, this paper proposes a hybrid recommendation approach based on attributes of products to address these problems. After product category and taxonomy formation and attributes extraction for each category, explicit-based module provides recommendations through naive Bayes classifier. Implicit-based module considers the weight vector of implicit attributes for users as chromosomes in genetic algorithm. This algorithm optimises the weights according to historical rating. Finally, recommendations are generated using the results of two modules. The main contributions are addressing sparsity and cold-start problem using naive Bayes classifier and weight optimisation by genetic algorithm.
PPT: A Push Pull Traffic Algorithm to Improve QoS Provisioning in IoT-NDN Environment

Internet of Things (IoT) is the convergence of connecting people, things, data, and processes. Named data networking (NDN) is a recent paradigm perceived for the future internet architecture to tackle the exponential increase in the volume of global IoT traffic. Traditionally, NDN supports PULL traffic, but IoT applications embrace both PULL and PUSH traffic. In this letter, we propose a hybrid PUSH–PULL traffic (PPT) model, for efficient data exchange in IoT applications. Simulation results indicate that our PPT algorithm can reduce the network load by 50% compared with the traditional IPv6, which in turn helps in almost 98% packet delivery ratio and no packet drop. The average throughput of our PPT model is 50% better than the IPv6 approach, which ensures a reliable IoT model.
Facile Synthesis of CaCo3 and CaCo3:Eu3+ Phosphors by Solid State Reaction at Room Temperature and the Luminescence Properties

The CaCO3 and CaCO3:Eu3+ phosphors have been synthesized by solid state reaction at room temperature without further sintering treatment. The morphology, crystalline structure, and fluorescent properties of the samples were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), spectrofluorometer, respectively. Also, the influences of Eu3+-doping concentration on the photoluminescence (PL) properties were investigated in detail. The results indicate that the morphology of as-prepared CaCO3 particles are irregular cubic in shape and about 200-400nm in size, while the CaCO3:Eu3+ particles are the aggregates of many small nanoparticles with nearly 30nm in size, indicating that Eu3+ ions have a great influence on the CaCO3 particle morphology and size. The lines around 392nm in luminescence excitation spectrum is the most noticeable. Upon excitation at 392nm, the PL emission spectrum is composed of two band and strong peaks at 589nm and at 613nm. The peaks at 589nm is attributed to magnetic dipole transition 5D0–7F1 and with the increase of the Eu3+-doped concentration, the intensity decreases gradually; but it shows the opposite trend for the peak at 613nm which is attributed to the hyper sensitively forced electric dipole transition5D0–7F2.
Crystallinity and orientation development upon hot multistage drawing of PET multifilament yarn

In this research, poly(ethylene terephthalate) (PET) multifilament yarn was drawn on an industrial drawing machine at hot multistage. By varying draw ratio, a number of drawn fibers with different internal structures were obtained. Total draw ratio was changed from 4.68 to 6.24. Crystallinity and molecular orientation of the drawn samples were investigated using differential scanning calorimetry, birefringence, infrared spectroscopy, and X-ray diffraction. The results show that the high population of gauche conformer in as-spun fiber decreased rapidly with fiber orientation. The absence of crystallization peak and clear T g in the drawn samples has been explained by orientation development as well as crystalline–amorphous interactions. Microstructural changes in the drawn PET fibers have been discussed in terms of the applied heat and mechanical deformation upon hot multistage drawing.
Velocity Control Strategies to Improve Automated Vehicle Driving Comfort

Automated vehicles are rapidly emerging as the new generation of transport tools. Relevant research mainly focuses on collision avoidance, lane keeping, and coordination control to ensure driving safety and improve efficiency, with little emphasis on passenger comfort. This paper proposes a set of comfortbased velocity control strategies on the basis of driving safety. Driving comfort was evaluated by multiple accelerometers fixed inside vehicles. Power spectral density analysis and one-third octave band filtering were applied to derive the weighted root mean square acceleration as an evaluation indicator for comfort. The annoy rate model is proposed to describe individual sensitivity to vibration. Field tests were conducted to investigate interactions between pavement roughness, speed, and comfort, and multiple linear relationships were identified. Three typical processes were considered: deceleration phase, uniform speed phase and abnormal occasions. The hyperbolic tangent function was utilized to provide moderate deceleration. Model parameters were set to guarantee maximal deceleration and jerk within acceptable limits. Nonlinear programming was used to balance between rapid deceleration and bumps caused by abnormal obstacles. The proposed strategy can potentially be applied for automated vehicles to improve the perceived quality of automated driving.
ULTRASONIC MACHINING—A COMPREHENSIVE REVIEW

Ultrasonic machining (USM) is a mechanical material removal process used to erode holes and cavities in hard or brittle workpieces by using shaped tools, high-frequency mechanical motion, and an abrasive slurry. The fundamental principles of stationary ultrasonic machining, the material removal mechanisms involved, proposed models for estimation of machining rate, the effect of operating parameters on material removal rate, tool wear rate, and workpiece surface finish, research work reported on rotary mode USM, hybrid USM, process capabilities of USM have been extensively reviewed in this article. The limitations of USM, gaps observed from the literature review, and the directions for future research have also been presented. Overall, this article presents a comprehensive review of USM process for advancement of the process through fundamental insights into the process.
Share or Split : which is more efficient?

In this paper, we investigate two different feature representations in convolutional neural networks (CNN): (a) Share all classes share the same feature space, and a fully connected layer is used to decode class activation, and (b) Split each class has its own feature space and a class is activated if its corresponding feature vector has a large norm. This is inspired by Capsules (Sabour et al. (2017)) which splits the feature space. We compare these two representations on a transformed MNIST dataset, which adds random scales and translations on the original digits. The experimental results show that Split has better performance when data is limited, while Share is better when data is big.
On Physical Layer Security in Finite-Area Wireless Networks: An Analysis Framework

This paper analyzes the information theoretic secrecy performance in finite-area wireless networks based on a stochastic geometry framework. Unlike most prior works, which explored the physical layer security with a large number of transmitters, legitimate receivers and eavesdroppers in infinite regions, we consider a finite downlink wireless network composing of a transmitter, a legitimate receiver and several eavesdroppers. The legitimate receiver attempts to receive confidential data from the transmitter in the presence of the eavesdroppers. We present the probabilistic characteristics of the achievable secrecy rates and average secrecy rates in both disk regions and regular L-sided convex polygon regions. As shown by extensive numerical results, the proposed framework could be leveraged to efficiently analyze the secrecy performance of finite-area networks, and give insights for network designers on how to achieve good secrecy performance in finite-area networks.