Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerating Dissociative Events in Molecular Dynamics Simulations by Selective Potential Scaling

Molecular dynamics (or MD) simulations can be a powerful tool for modeling complex dissociative processes such as ligand unbinding. However, many biologically relevant dissociative processes occur on timescales that far exceed the timescales of typical MD simulations. Here, we implement and apply an enhanced sampling method in which specific energy terms in the potential energy function are selectively “scaled” to accelerate dissociative events during simulations. Using ligand unbinding as an example of a complex dissociative process, we selectively scaled-up ligand-water interactions in an attempt to increase the rate of ligand unbinding. By applying our selectively scaled MD (or ssMD) approach to three cyclin-dependent kinase 2 (CDK2)-inhibitor complexes, we were able to significantly accelerate ligand unbinding thereby allowing, in some cases, unbinding events to occur within as little as 2 ns. Moreover, we found that we could make realistic estimates of the unbinding as well as the binding free energies (∆Gsim) of the three inhibitors from our ssMD simulation data. To accomplish this, we employed a previously described Kramers’-based rate extrapolation (KRE) method and a newly described free energy extrapolation (FEE) method. Because our ssMD approach is general, it should find utility as an easy-to-deploy, enhanced sampling method for modeling other dissociative processes.
Simulation and Optimization of a Reference Adaptive Control Model for a Gough-Stewart Platform

This paper presents the model reference adaptive control (MRAC), a combination of a Gough-Stewart platform with an adaptive control strategy for force control. For this purpose, firstly, the platform geometry is described followed by solving the inverse kinematic equations using the so-called vector method. Afterward, the dynamic robot model is built utilizing the MSC Adams software, with its linear form generated by the control plugin of the software, where the model takes the force as input and returns the displacement as output. As a next step, an adaptive control strategy is formulated to control the position of the robot operator and then simulated in MATLAB software. The control strategy has two components, namely the feedback and feedforward control strategies. The adaptive law is calculated based on the Lyapunov theory. Finally, the controller parameters are optimized through a genetic algorithm based on integral time squared error (ITSE) to minimize the system error over time. The results proved that the proposed system outputs are in agreement with the corresponding values for the model reference and that the controller performs well in presence of usual levels of noise and/or disturbance.
Experimental design for large scale omic studies

Molecular phenotyping has expanded from small sample sizes to larger complex studies and are now a common element in genetic studies. When large scale studies add a molecular phenotyping component, balancing omics batches for the factors of interest (e.g. treatment), regardless of the initial sample collection strategy always improves power. Where possible, confounding sources of experimental error that are not of interest (sample collection blocks and data collection plates) improves power as does planning batches for molecular phenotyping based on constraints during initial sample collection. Power for testing differences in molecular phenotypes is always higher when accounting for the entire experimental design during modeling. The inclusion of metadata that tracks sources variation is critical to our shared goals of enabling reproducible research.
Balancing nurses’ workload: A case study with nurse anaesthetists and intensive care nurses

DOI: 10.14254/2071789X.2020/13-2/1 ABSTRACT. Over the last two decades, intensive care has changed significantly. The nursing care intensity and the workload of nurses in the intensive care units have increased. In order to distribute tasks among nurse anaesthetists and intensive care nurses effectively and to balance their workload there is a need to implement nurses’ workload calculation techniques on a daily basis. The presented study aims to estimate the nurse anaesthetists and intensive care nurses’ workload by assessing nursing care intensity and patients’ severity in intensive care unit. The descriptive cross-sectional study design was employed for this study. The data was collected at a university hospital cardio-surgery intensive care unit. The total of 1147 assessments of nurses’ workload were performed. The relationship between TISS-28 components and nurses’ workload was analysed and a significant positive correlation among nurses’ workload, patients’ age and length of stay in the unit was determined. An excessive nursing workload increased by the overall nursing actions, support of cardiovascular, renal and metabolic system actions. The implementation of TISS-28 into nursing practice could help with showing the value of nursing practice and nurses’ input, also it would help calculating the nurses’ workload more accurately and improving the distribution of nurses in the workplace.
Pengaruh Implementasi Big Data Terhadap Auditdi Lembaga Pemerintah (Studi Pada Kantor Inspektorat Kabupaten Majalengka)

Perubahan pola penyimpanan dan jenis data di era digital membuat beberapa organisasi mencari cara agar tetap bertahan di tengah persaingan. Ledakan data tersebut memicu lahirnya era big data. Dimana dalam hal ini data memiliki peran penting dalam pengambilan keputusan strategis. Oleh karenanya, pihak yang mampu mengolah dan memanfaatkan data-data yang tersedia dalam volume besar, keragaman variatif, kompleksitas tinggi dan kecepatan penambahan data yang tinggi, dapat mengambil keuntungan yang besar. Sementara itu, selain untuk kegiatan bisnis big data juga digunakan dalam hal audit. Big Data dalam konteks audit maka menjadi penting untuk memahami perbedaan antara data elektronik yang akan digunakan oleh auditor saat ini menggunakan BDA dengan data yang digunakan secara tradisional untuk mendapatkan opini audit. Penelitian ini bertujuan untuk mengetahui pengaruh big data terhadap audit di lembaga pemerintah dan dalam hal ini adalah Kantor Inspektorat Kabupaten Majalengka. Kata kunci: Big data, Audit internal dan Data analysis
Energy Consumption Versus Greenhouse Gas Emissions in EU

Purpose: The article aims to trace out the interplay of the share of individual energy sources in the total consumption and greenhouse gas emissions from the European Union countries. Approach/Methodology/Design: By taking into account the share of individual energy sources in consumption in 2015, the EU countries were divided into 5 clusters. For each cluster, the values of the indicators for 2005 were determined to assess the changes. Additionally, energy dependence and greenhouse gas emissions factors were included. Findings: During the 2005-2015 period, the consumption of renewable energy increased, while the carbon dioxide emissions felt. It is difficult to say unequivocally whether limiting CO2 emissions through increased renewable energy sources consumption can be considered sufficient. It should also be pointed out that there was no clear link between the increase in the share of renewable energy sources and the decrease in energy dependence in EU countries. Practical Implications: The study directly refer to ongoing political debate on CO2 emissions at both the community and national levels in EU countries. Originality/Value: The study offers the first of its kind examination of the the interplay of the share of individual energy sources in the total consumption and greenhouse gas emissions from the European Union countries.
Characteristics of Plasma-activated Dielectric Film Surfaces for Direct Wafer Bonding

The low-temperature wafer bonding has been studied on two types of dielectric material (SiO, SiCN) as final bonding layers. It is important for the wafer bonding technology to obtain the higher interfacial energy between two bonding wafers, and oxygen and nitrogen (O2, N2) plasma treatments have been studied to properly activate the dielectric film surfaces prior to a bonding process that includes chemical-mechanical polishing, hydration with DI water and heat treatment. The surface activation by the plasma treatments with DI hydration formed ~ 10nm thick SiOx layer on the SiCN films. It is found that a newly formed surface SiOx layer played a role as a bonding medium. The dielectric film surfaces were treated by plasma treatment, then characterized by analyzing chemical binding states in the surface SiOx layer. The characteristics of the new SiOx layers were found to be dependent on the plasma species and bulk dielectric films. The obtained properties of the surface layer have been co-related to the initial bonding energy of the bonded wafers as well as the final bonding energy with heat treatment. As a result, the N2 plasma treatment to the dielectric films enhanced the initial bonding energy and SiCN-SiCN bonding wafers treated by the O2 plasma have the better initial bonding energy rather than SiO-SiO bonding due to high hydrogen contents in the surface oxide films. In addition, the chemical analysis (XPS) has revealed the surface activity of the films from the results of the chemical binding states of Si. Basically, we focus on the initial bonding energy and it is crucial to ensure that the Cu pads facing each other comes into contact prior to the heat treatment that causes Cu diffusion across the opposite Cu pads.
Activated carbon & carbon-cryogel composites for haemoperfusion based applications

A number of pathological conditions are associated with the build up of toxic substances within the systemic circulation. For example, renal and hepatic failure can lead to the accumulation of metabolites which are usually processed by these organs. There has been much interest over a number of years in techniques such as haemoperfusion that could help clear these toxins from the body and improve patient outcome. Haemoperfusion is an extracorporeal blood purification technique in which a patient’s blood is passed over a column containing a material designed to adsorb a board spectrum of biological toxic molecules. Direct blood contact with the adsorbent requires a material that is able to display good haemocompatibility whilst maintaining adsorption efficiency. Activated carbons (AC) have great adsorption capacity and have previously been used as haemoadsorbents. However the haemocompatibility of carbons has been questioned and they are often coated with biocompatible polymers that increase their haemocompatibility but also act as a barrier to the removal of larger toxins and middle molecules.
Ten years of hardware Trojans: a survey from the attacker's perspective

Hardware Trojan detection techniques have been studied extensively. However, to develop reliable and effective defenses, it is important to figure out how hardware Trojans are implemented in practical scenarios. The authors attempt to make a review of the hardware Trojan design and implementations in the last decade and also provide an outlook. Unlike all previous surveys that discuss Trojans from the defender's perspective, for the first time, the authors study the Trojans from the attacker's perspective, focusing on the attacker's methods, capabilities, and challenges when the attacker designs and implements a hardware Trojan. First, the authors present adversarial models in terms of the adversary's methods, adversary's capabilities, and adversary's challenges in seven practical hardware Trojan implementation scenarios: in-house design team attacks, third-party intellectual property vendor attacks, computer-aided design tools attacks, fabrication stage attacks, testing stage attacks, distribution stage attacks, and field-programmable gate array Trojan attacks. Second, the authors analyse the hardware Trojan implementation methods under each adversarial model in terms of seven aspects/metrics: hardware Trojan attack scenarios, the attacker's motivation, feasibility, detectability (anti-detection capability), protection and prevention suggestions for the designer, overhead analysis, and case studies of Trojan implementations. Finally, future directions on hardware Trojan attacks and defenses are also discussed.
Technical Analysis of Liquid Sugar Production Process of Raw Sago Starch Using the Enzymatic Hydrolisis Method of Pilot Plant Scale

Indonesia has the potential for sago around 50% of the world sago production but has not been used optimally. Technologically, the process of making liquid sugar from sago starch has been developed. Therefore, further research to improve the color quality of liquid sugar is needed. The research objective is to conduct a technical study of liquid sugar production process made from raw sago starch by doing purification treatment using activated charcoal and ion-exchange resin. The liquid sugar production process of raw sagu starch using hydrolysis method is in the condition of the ratio of starch to water is 1:4, the liquidation process is at the temperature of 90°C for 90 minutes with the addition of enzyme α-amylase 1.2 mL kg−1 of starch with pH of 5. Saccharification process is at the temperature of 50 °C for 72 hours with the addition of enzyme glucoamylase 1.2 mL kg−1 starch with pH of 4.5. Purification by ion-exchange resin and evaporation by a vacuum evaporator are at 80° C for 90 minutes with pressure of 0.4 atm. Technically, the technology of liquid sugar production process using the enzymatic hydrolysis method could be developed for the pilot plant and industrial scale.
Genotype-sensitive reversible and time-dependent CYP 2 D 6 inhibition in human liver microsomes

Cytochrome P450 (CYP) 2D6 metabolizes a wide range of xenobiotics and is characterized by a huge interindividual variability. A recent clinical study highlighted differential magnitude of CYP inhibition as a function of CYP2D6 genotype. The aim of this study was to investigate the effect of CYP2D6 genotype on the inhibition of dextromethorphan O-demethylation by duloxetine and paroxetine in human liver microsomes (HLMs). The study focused on genotypes defined by the combination of two fully functional alleles (activity score 2, AS 2, n = 6), of one fully functional and one reduced allele (activity score 1.5, AS 1.5, n = 4) and of one fully functional and one non-functional allele (activity score 1, AS 1, n = 6), which all predict extensive metabolizer phenotype. Kinetic experiments showed that maximal reaction velocity was affected by CYP2D6 genotype, with a decrease in 33% of Vmax in AS 1 HLMs compared to AS 2 (P = 0.06). No difference in inhibition parameters Ki , KI and kinact was observed neither with the competitive inhibitor duloxetine nor with the time-dependent inhibitor paroxetine. Among the genotypes [. ] STORELLI, Flavia, DESMEULES, Jules Alexandre, DAALI, Youssef. Genotype-sensitive reversible and time-dependent CYP2D6 inhibition in human liver microsomes. Basic & Clinical Pharmacology & Toxicology, 2018
Bacteria associated with soft coral from Mot island - Nha Trang bay and their antimicrobial activities

Microbial communities associated with invertebrates had been considered as a new source of bioactive compounds. The soft coral associated bacteria in Mot island, Nha Trang bay were isolated, extracted and assessed for antagonistic activity against human and coral pathogens, the strongly active strains were identified by 16S rRNA analysis. The soft coral associated bacterium SCN10 had abcd antibacterial pattern which was named for inhibition towards Bacillus subtilis (pattern a), Escherichia coli (pattern b), Salmonella typhimurium (pattern c) and Serratia marcescens (pattern d). It was the nearest strain to the wellknown antibiotic producer Bacillus amyloliquefaciens with 99% sequence similarity. Whereas strain SCL19 had abde pattern which means inhibition of the growth of B. subtilis, E. coli, S. marcescens and Vibrio parahaemolyticus (pattern e). This strain SCL19 affiliated with Bacillus sp. strain A-3-23B with 99.8% identity. In addition to antimicrobial activity to the aforementioned tested bacteria, the isolate SCX15 also inhibited Vibrio alginolyticus (pattern f) and Candida albicans (pattern g), so this isolate possessed abcdefg antimicrobial pattern. The coral associated isolate SCX15 was identified as Bacillus velezensis with 99% sequence similarity. Among the 78 screened strains, 25 isolates possessed antibacterial activity against at least one of seven tested microorganisms and exhibited 12 different types of antimicrobial activities, suggesting that they can produce many different natural substances with antibacterial activity.
CHALLENGES OF COPING WITH THE ECONOMIC CONSEQUENCES OF THE GLOBAL PANDEMIC COVID-19.

Currently, the COVID-19 coronavirus epidemic has devastated the Chinese economy and is spreading around the world. The nature of the infection and its economic consequences remain highly unpredictable, making it difficult to develop a policy that is an effective solution for macroeconomic policy. In order to mitigate the negative economic consequences, the article discusses some of the proposed measures and strategies that will help individuals and businesses, as well as the state, deal with the consequences of COVID-19. The current study begins with an analysis of the points of view of world experts, in particular economists in the US, who have proposed a number of measures that will benefit the entire economy in uncertain times. The article considers some areas of state support in overcoming the consequences of the global crisis in the practice of the Republic of Uzbekistan. These scenarios demonstrate the scale of costs that can be avoided by increasing investment in social support programs.
An update on engineering issues concerning stratospheric aerosol injection for geoengineering

Solar Radiation Management (SRM) geoengineering is a proposed response to anthropogenic global warming (AGW). Stratospheric aerosol injection (SAI) is one proposed method, reliant on lofting material into the stratosphere. Engineering reviews related to this technology approach have been sparse, with most major primary analyses now at least five years old. We attempt to bridge this gap—with a short, qualitative review of recent developments in various fields of engineering that have potential applicability to SAI. Our analysis shows that a new conventional aircraft design is still likely to be the most dependable and affordable technology solution (cost estimates start around $1000–1500 per ton lofted), with hybrid or vacuum airships a potential challenger. Rockets, gas guns and MAGLEV/coilguns show some potential—although they lack the inherent level-flight capability that would be needed for direct aerosol distribution (versus distribution of gaseous precursors), without substantial additional engineering. Should very high-altitude access be required, rockets, jet-hybrid rockets, and various guns (especially light-gas guns) potentially offer the required capability. Costs and performance for tethered balloons remain highly uncertain. Towers are not found to be promising. The extreme accessibility of free balloons suggests that this method may be used primarily for reasons of political leverage, as opposed to being an optimal engineering solution.
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease

A central challenge in human genomics is to understand the cellular, evolutionary, and clinical significance of genetic variants. Here we introduce a unified population-genetic and machine-learning model, called Linear Allele-Specific Selection InferencE (LASSIE), for estimating the fitness effects of all potential single-nucleotide variants, based on polymorphism data and predictive genomic features. We applied LASSIE to 51 high-coverage genome sequences annotated with 33 genomic features, and constructed a map of allele-specific selection coefficients across all protein-coding sequences in the human genome. We show that this map is informative about both human evolution and disease.
Assessment of the sculpin stock complex in the Bering Sea and Aleutian Islands

The Bering Sea and Aleutian Island (BSAI) sculpin complex is managed in Tier 5. The last full BSAI sculpin assessment was performed in 2016. The 2016 full assessment can be found at http://www.afsc. noaa.gov/REFM/stocks/assessments.htm. This document consists of an executive summary.
A State of De-Stress: Examining the Relationship Between Subjective Well-Being, Self-Compassion, and Empathy

University can be a period of stress caused by academic, social, or personal demands. Yet most are able to rise above the adversity and grow from their experiences. Research on stress has found that a negative association exists with subjective well-being broadly conceptualized as life happiness (Denovan & Macaskill, 2017; Zhang, 2009). There are also positive relationships demonstrated between selfcompassion and empathy with subjective well-being (Bluth et al., 2016; Thomas et al., 2007). This study examined the relationship between perceived stress and subjective well-being in a non-clinical university population. The study also examined the relationship between stress and subjective well-being, and how that relationship was moderated by the self-compassion and mediated by empathy.
Assessment the effect of phosphorus on plant growth of purslane (Portulaca oleracea L.)

Phosphorus is vital to plant growth and its functions cannot be performed by any other nutrients. The adequate supply of P is required for optimum growth and reproduction. Phosphorus is classified as a major nutrient meaning that it is frequently deficient for crop production and is required by crop in relatively large amount. Field experiments were conducted during 2 seasons (summer 2016-2017) to investigate the effect of P level on growth of purslane throughout 3 stages (vegetative, flowering and fruiting). The results of this study revealed that, in the first season, the mean values of total leaves, axis length, leaf area, fresh weight of leaves and flowers number were significantly increased with increased of the level of P. In the second season for the three stages (vegetative, flowering and fruiting) the results revealed that numbers of branches, leaves in each branch and total leaves were significantly decreased when P level increased, while axis length, leaves area, flowers number fresh and dry weights of leaves were significantly increased with increasing in P level.
Comparison of power factor between permanent magnet assisted synchronous reluctance motor with neodymium-iron-boron and ferrite magnets

In this paper, the design of a permanent magnet assisted synchronous reluctance motor (PMASynRM or PMASRM) is presented as a replacement for a suitable permanent magnet in a simulated synchronous reluctance motor (synrm). In addition to solving the important problems faced by typical synchronous reluctance motors (low power factor and high torque ripple) it can provide more power of coping and then other common motors such as induction motors (IM). A common motor model was created for simulation in Maxwell finite element software. Then, ferrite and neodymium-iron-boron (NdFeB) magnets were compared as the permanent magnet The results show that the fields of average torque, Back-emf voltage and efficiency, and the torque ripple are all greater in the neodymium-iron-boron magnet than the ferrite magnet. Finally the power factors for both magnets are calculated from the power, voltage and current simulations as 0.68 in ferrite magnet and 0.89 in neodymium-iron-boron magnet. The results also indicated that a higher power factor in the second model than the first one.