Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel predictor of ACE2-binding ability among betacoronaviruses

Abstract Background Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in ~4.8 million deaths worldwide as of this writing. Almost all conceivable aspects of SARS-CoV-2 have been explored since the virus began spreading in the human population. Despite numerous proposals, it is still unclear how and when the virus gained the ability to efficiently bind to and infect human cells. In an effort to understand the evolution of receptor binding domain (RBD) of the spike protein of SARS-CoV-2, and specifically, how the ability of RBD to bind to angiotensin-converting enzyme 2 receptor (ACE2) of humans evolved in coronaviruses, we have applied an alignment-free technique to infer functional relatedness among betacoronaviruses. This technique, concurrently being optimized for identifying novel prions, was adapted to gain new insights into coronavirus evolution, specifically in the context of the ongoing COVID-19 pandemic. Novel methods for predicting the capacity for coronaviruses, in general, to infect human cells are urgently needed. Methodology proposed method utilizes physicochemical properties of amino acids to develop fully dynamic waveform representations of proteins that encode both the amino acid content and the context of amino acids. These waveforms are then subjected to dynamic time warping (DTW) and distance evaluation to develop a distance metric that is relatively less sensitive to variation in sequence length and primary amino acid composition. Results and Conclusions Using our proposed method, we show that in contrast to alignment-based maximum likelihood (ML) and neighbor-joining (NJ) phylogenetic analyses, all bat betacoronavirus spike protein RBDs known to bind to the ACE2 receptor are found within a single physicochemical cluster. Further, other RBDs within that cluster are from pangolin coronaviruses, two of which have already been shown to bind to ACE2 while the others are suspected, yet unverified ACE2 binding domains. This finding is important because both severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 use the host ACE2 receptor for cell entry. Surveillance for coronaviruses belonging to this cluster could potentially guide efforts to stifle or curtail potential and/or early zoonotic outbreaks with their associated deaths and financial devastation. Lay Summary Robust methods for predicting human ACE2 receptor binding by the spike protein of coronaviruses are needed for the early detection of zoonotic coronaviruses and biosurveillance to prevent future outbreaks. Here we present a new waveform-based approach that utilizes the physicochemical properties of amino acids to determine the propensity of betacoronaviruses to infect humans. Comparison with the established phylogenetic methods demonstrates the usefulness of this new approach in the biosurveillance of coronaviruses.
The effects of post-deposition processes on polysilicon Young's modulus

Polysilicon films deposited by low pressure chemical deposition (LPCVD) are the most widely used structural material for microelectromechanical systems (MEMS). However, the properties of LPCVD polysilicon are known to vary significantly, depending on deposition conditions as well as post-deposition processes. This paper presents extensive experimental results, investigating the effects of phosphorus doping and texture on Young's modulus of polysilicon films. Polysilicon films are deposited at 585, 605 and 625 to a thickness of 2 m. Specimens with varying phosphorus doping levels are prepared by diffusion doping at various temperatures and times using both and phosphosilicate glass (PSG) as the source. Young's modulus is calculated by taking the average of the values calculated from the resonant frequencies of four different-size lateral resonators. Our results show that Young's modulus decreases with increasing doping concentration, and increases with increasing texture. The polysilicon grain size and grain boundaries could also have an influence on Young's modulus, which remains to be further investigated.
Subgroup Identification for Time-to-event Data Based on AFT Model

Considering the problem of identifying subgroup in a randomized clinical trial with respect to survival time, we present an analysis strategy to find subgroup of enhanced treatment effect. We fit univariate accelerated failure time (AFT) models with covariate-treatment interactions to identify predictive covariates. The false discovery rate is controlled by Benjamini-Hochberg procedure. Then a composite score conversion is employed to transform the set of identified covariates for each patient into a univariate score. To classify patient subgroups, a change-point algorithm is applied to searching for the threshold cutoff instead of using the median. Moreover, we adopted a biomarker adaptive design to check whether the treatment effect exists within certain subgroup. The simulation results show that the change-point method is remarkably superior to the median cutoff particularly when the subgroup sizes vary considerably. Furthermore, the 2-stage adaptive design has good power properties in detecting treatment effect while the type I error is generally controlled. As an illustration, we apply the proposed methods to an AIDS study. In conclusion, when the sample size is sufficient and the censoring rate is mild, the AFT model combined with change-point algorithm performs well in identifying subgroup. Keywords: accelerated failure time model; adaptive design; change-point algorithm; false discovery rate; precision medicine; subgroup identification
Decreased Sound Tolerance and Tinnitus Retraining Therapy (TRT)

The main objective of Tinnitus Retraining Therapy (TRT) is habituation of activation of the autonomic nervous system, evoked by signals present in the auditory pathways. Sound therapy aims at decreasing the strength of these signals. The same systems in the brain are involved in tinnitus and decreased sound tolerance, and the same basic neurophysiological mechanisms are utilised for decreasing the tinnitusrelated neuronal activity and, in case of hyperacusis, abnormally enhanced activity induced by external sounds. The similarity of TRT treatment between tinnitus and misophonia is even closer, as in both situations the goal is to achieve extinction of functional connections between the auditory and the limbic and autonomic nervous systems. The increased gain within the auditory pathways that are presumably responsible for hyperacusis could enhance the tinnitus signal, thus it is possible to expect coexistence of tinnitus and hyperacusis, and the predisposition of hyperacusis patients to develop tinnitus. As such, for some patients tinnitus and hyperacusis may be considered the double manifestation of the same internal phenomenon.
Preservice Teachers Learning about Teaching for Conceptual Change through Slowmation.

This study reports on research into the use of Slowmation in a general science methods program in teacher education as a productive way of teaching student teachers how to recognize and respond to students' alternative conceptions in science. The preservice teachers first experienced Slowmation themselves as modelled by their lecturers in their teacher education program, they then used Slowmation during their school practicum with their school students. On returning to the university after their practicum they reviewed their learning about teaching with Slowmation in ways designed to encourage deep reflection on their practicum experiences in relation to their students' conceptions of science. The results of this study show that as a consequence of teaching Slowmation that these student teachers came to recognise and respond to students' alternative conceptions.
Cumulative Ductility Spectra for Seismic Design of Ductile Structures Subjected to Long Duration Motions: Concept and Theoretical Background

A seismic design procedure that does not take into account the maximum and cumulative plastic deformation demands that a structure will likely undergo during severe ground motion could lead to unreliable performance. Damage models that quantify the severity of repeated plastic cycling through plastic energy are simple tools that can be used for practical seismic design. The concept of constant cumulative ductility strength spectra, developed from one such model, is a useful tool for performance-based seismic design. Particularly, constant cumulative ductility strength spectra can be used to identify cases in which low-cycle fatigue may become a design issue, and provides quantitative means to estimate the design lateral strength that should be provided to a structure to adequately control its cumulative plastic deformation demands during seismic response. Design expressions can be offered to estimate the strength reduction factors associated to the practical use of constant cumulative ductility strength spectra.
Comportamento da alface tipo americana sob diferentes tensões da água no solo, em ambiente protegido

Seeking to define a criteria for irrigation scheduling of lettuce cultivated in a protected environment in the region of Lavras - MG, Brazil, the purpose of this work was to evaluate the effects of different soil water tensions in the crisphead lettuce, Raider cv. , on productive behavior. The experiment was carried out in a greenhouse following the completely randomized blocks design with four replications. The treatments consisted of six water tensions as indicatives of the irrigation schedule criteria. Preset tensions were 15; 30; 45; 60; 75 and 90 kPa. Results allowed concluding that under tensions around 15 kPa at a 0.15 m depth, there is a tendency in obtaining taller plants, featuring more fresh matter weight of marketable head, and lower dry matter contents in the marketable part. It was also possible to obtain a better efficiency water use (469.22 kg ha-1 mm-1) under tensions around 15 kPa.
Field behaviour of granular pile-anchors in expansive soils

Different innovative foundation techniques have been suggested for controlling the detrimental volume change behaviour of expansive soils. The efficacy of a recent innovation in the form of granular pile-anchors in controlling heave of expansive clay beds and improving the engineering behaviour of the ambient soil has also been reported, based on results obtained from laboratory model tests. Before suggesting granular pileanchor foundations for installation in field practices, however, an in situ study of the behaviour of granular pile-anchors is also required as a support to the laboratory study. This paper describes an extensive field study of the behaviour of granular pile-anchor foundations of expansive clay beds. The field study was performed to study the rate of heave, reduction of heave and variation of heave with radial distance and with depth. Heave was found to be reduced by about 90% upon installation of granular pile-anchors. Final heave was reached in just about half the time required for fin.
Towed mapping of the effluent plume from a coastal ocean outfall

The dispersion of effluent from coastal ocean sewage outfalls has continued to be a difficult problem to study in situ. The spatial extent of the detectable effluent field is an important question for understanding the range of potential impacts from the effluent plume. Sampling around large southern California sewage outfalls is done using automated water column profilers (i.e., CTDs) at designated stations, typically centered on the outfall. Discrete water samples, if taken, are collected at predefined depths. While this method of sampling allows for analysis of the environmental impacts to the receiving water from these outfalls, the data have shown that the studies are inadequate for determining the vertical and horizontal spatial extents of these subsurface wastewater fields. To address this issue, the Orange County Sanitation District (OCSD), California supplemented its normal receiving water sampling by using a Guildline Minibat towed underwater vehicle, equipped with a CTD and in situ pumping system, to map the distribution of physical, bio-optical, chemical, and bacterial variables in the vicinity of its outfall. The mapping demonstrates that the plume is clearly present for distances of at least 12.5 km in either direction from the outfall, depending on the current direction. The mapping results allow comparison with results from traditional receiving water monitoring and plume models of initial height, dilution, and thickness.
Implementing lean production systems: research areas and opportunities for future studies

The increasing use of lean production (LP) by companies from several sectors has substantially increased the amount of publications and different emphases on the subject, which amplifies the need for organisation of that knowledge. This article aims to identify the research areas on LP implementation and to propose research opportunities. The literature review was based on 102 studies published in the years between 1996 and 2012. The studies were divided into six research areas, named: (a) structure and scope of LP systems; (b) factors that influence in the LP implementation; (c) methods for implementing LP systems; (d) LP assessment methods; (e) results of implementing LP systems; and (f) adaptation of LP to particular sectors. The findings suggested that the substantial increase on the amount of publications on LP implementation has created fragmented and dissociated areas that would benefit from integration.
The collective praise intervention: A brief intervention highlighting prosocial behavior reduces hostility towards Muslims

Muslims are consistently the target of dehumanization and hostile policies. Previous research shows that interventions that highlight the hypocrisy wherein people collectively blame entire groups for the heinous acts of individual members of outgroups but not ingroups are effective in reducing animosity towards Muslims. However, these interventions rely on aversive materials (e.g., terrorist acts), which can hinder the scalability of interventions due to individuals’ tendency to resist/avoid challenging and aversive stimuli. In three preregistered studies (combined N = 2,635), we developed and tested a nonaversive, hypocrisy-based intervention that highlights the hypocrisy involved in attributing ingroup members’ prosocial acts to the entire ingroup (i.e., Christians) but not doing the same for outgroup members (i.e., Muslims). Results indicated that this collective praise intervention reliably reduces dehumanization of Muslims, anti-Muslim policy support, and collective blame of Muslims. We argue that the intervention’s use of nonaversive stimuli allows for both practical and scalable applications.
Optical Durability of Candidate Solar Reflectors

Concentrating solar power (CSP) technologies use large mirrors to collect sunlight to convert thermal energy to electricity. The viability of CSP systems requires the development of advanced reflector materials that are low in cost and maintain high specular reflectance for extended lifetimes under severe outdoor environments. The long-standing goals for a solar reflector are specular reflectance above 90% into a 4 mrad half-cone angle for at least 10 years outdoors with a cost of less than $13.8/m 2 (the 1992 $10.8/m 2 goal corrected for inflation to 2002 dollars) when manufactured in large volumes. Durability testing of a variety of candidate solar reflector materials at outdoor test sites and in laboratory accelerated weathering chambers is the main activity within the Advanced Materials task of the CSP Program at the National Renewable Energy Laboratory (NREL) in Golden, Colorado. Test results to date for several candidate solar reflector materials will be presented. These include the optical durability of thin glass, thick glass, aluminized reflectors, front-surface mirrors, and silvered polymer mirrors. The development, performance, and durability of these materials will be discussed. Based on accelerated exposure testing the glass, silvered polymer, and front-surface mirrors may meet the 10 year lifetime goals, but at this time because of significant process changes none of the commercially available solar reflectors and advanced solar reflectors have demonstrated the 10 year or more aggressive 20 year lifetime goal.
Preliminary analysis of single flash combined with binary system using thermodynamic assessment: a case study of Dieng geothermal power plant

This paper addressed the performance of single flash combined with a binary system that was proposed in the Dieng geothermal power plant by applying thermodynamic assessment methods. A set of mathematical equations from the plant was developed and solved iteratively using engineering equation solver. The results showed that the available exergy of the produced fluid from production wells is 66,204 kW. The performance of an existing single-flash power plant indicated 24,300 kW of net power output. The proposed design of single flash combined with a binary system improves the power output by 17.16% to 27,786 kW. The second law efficiency increases from 36.7% to 41.97% while the first law efficiency increases from 11.62% to 13.61%.
Multi-Scale Modeling of High Power Density Data Centers

Data center facilities, which house thousands of servers, storage devices and computing hardware, arranged in 2 meter high racks are providing many thermal challenges. Each rack can dissipate 10–15 kW, and with facilities as large as tens of thousands of square feet, the net power dissipated is typically on the order of several MW. The cost to power these facilities alone can be millions of dollars a year, with the cost to provide adequate cooling not far behind. Significant savings can be realized for the end user by improved design methodology of these high power density data centers. The fundamental need for improved characterization is motivated by inadequacies of simple energy balances to identify local ‘hot spots’ and ultimately provide a reliable modeling framework by which the data centers of the future can be designed. Recent attempts in computational fluid dynamics (CFD) modeling of data centers have been based around a simple rack model, either as a uniform heat generator or specified temperature rise across the rack. This desensitizes the solution to variations of heat load and corresponding flow rate needed to cool the servers throughout the rack. Heat generated at the smaller scales (the chip level) produces changes in the larger length scales of the data center. Accurate simulations of these facilities should attempt to resolve the range of length scales present. In this paper, a multi-scale model where each rack is subdivided into a series of sub-models to better mimic the behavior of individual servers inside the data center is proposed. A Reynolds-averaged Navier-Stokes CFD model of a 110 m2 (1,200 ft2 ) representative data center with the raised floor cooling scheme was constructed around this multi-scale rack model. Each of the 28 racks dissipated 4.23 kW, giving the data center a power density of 1076 W/m2 (100 W/ft2 ) based on total floor space. Parametric studies of varying heat loads within the rack and throughout the data center were performed to better characterize the interactions of the sub-rack scale heat generation and the data center. Major results include 1) the presence of a nonlinear thermal response in the upper portion of each rack due to recirculation effects and 2) significant changes in the surrounding racks (up to 10% increase in maximum temperature) observed in response to changes in rack flow rate (50% decrease). Copyright © 2003 by ASME
Advanced signal processing algorithms for 3rd generation wireless mobile systems

These Ecole polytechnique federale de Lausanne EPFL, n° 2550 (2002)Section des systemes de communicationFaculte informatique et communicationsInstitut EurecomJury: Sergio Benedetto, Pierre Comon, Raymond Knopp, Bixio Rimoldi, Rudiger Urbanke Public defense: 2002-4-19 Reference doi:10.5075/epfl-thesis-2550Print copy in library catalog Record created on 2005-03-16, modified on 2016-08-08
Rheumatoid Arthritis Revealed by Myocardial Infarction in a Type 1 Diabetic Patient

The association of rheumatoid arthritis (RA), Hashimoto thyroiditis and type 1 diabetes mellitus (T1D) is rarely reported. Herein, we report the case of a sixty-year old female, with a history of non-complicated type 1 diabetes and well-substituted Hashimoto thyroiditis who had a myocardial infarction at the age of 48 year-old. Our patient did not have classical risk factors for coronary heart disease, clinical and laboratory investigations showed the diagnosis of rheumatoid arthritis. The association of RA and the autoimmune endocrinopathies is not a fortuitous finding and coronary disease in well equilibrated T1D patient should encourage physician to search another aetiology.
HVAC optimisation studies: Component modelling methodology

Significant changes in the way HVAC systems are designed would be made possible by the application of optimal search techniques to find the 'best' design for any given criterion. A suite of programs has been developed which implements this type of optimisation; it was necessary to develop HVAC component models which are more extensive than the conventional performance or energy models used in contemporary system simulation. The paper describes the development of component models which: reproduce the characteristics of ranges of manufactured products; execute quickly when linked to form system models; and model on three levels: performance, economics and constraints. An example is given of the use of the models in the optimisation of a heat pump system for minimum energy consumption.
Characteristics of Smoothed-power Output Topology of Stand-alone Renewable Power System Using EDLC

Analysis of characteristics of smoothed-power output topology of Stand-alone Renewable Power System (SARPS) is presented in this paper. To prolong the service life of battery, decrease maintenance cost and power loss of SARPS by realizing smoothed-power output supply, An Electric Double Layer Capacitor (EDLC) is paralleled with battery as a part of storage system, and connected by a bi-directional Buck/Boost compensation topology. The EDLC stores fluctuant component and compensate battery current through proposed topology and switch control. Whereas the changeful natural condition and initial power condition, an appointed fluctuant power condition as an example to analysis the validity of proposed method in simulation firstly and also be validated in later experiment example. Analyze the frequency characteristics and system transformation with same characteristic based on state-space average model. The design method for general smoothed-power supply system is also presented as follows. The obtained smoothed-power output of battery satisfied the criterion of smooth precision.
Experimental Testing and Numerical Simulation of a Six-Story Structure Incorporating Two-Degree-of-Freedom Nonlinear Energy Sink

AbstractThe nonlinear energy sink (NES) is a fully passive attachment used to rapidly dissipate a significant portion of energy induced in a linear primary structure to which it is attached. In this study, the performance of a Type III NES in reducing the response of a large primary structure when subjected to a shock-type loading is evaluated experimentally. The Type III NES is a two-degree-of-freedom device comprising two relatively lightweight masses in series coupled together and to the primary structure through essentially nonlinear (i.e., nonlinearizable) stiffness elements. The essential stiffness nonlinearity of the NES and the corresponding lack of preferential resonance frequencies enable it to resonantly interact with multiple structural modes over broad frequency and energy ranges. Hence a local NES can induce global effects in the dynamics of the structure to which it is attached. In this study, and for the first time, specially shaped polyurethane bumpers are employed for realizing these ess.