Miracle-dz/UniFAR-FTUs huggingface dataset:
Tomographic Analysis of EmaA Adhesin Glycosylation in Aggregatibacter actinomycetemcomitans

The numbers of antibiotic-resistant bacteria has rapidly increased in recent years, thus current research is directed at developing new therapies targeting colonization. Host adherence is frequently considered the first step in the infectious process and is crucial for colonization. A. actinomycetemcomitans is a Gram − bacterium involved in periodontal diseases and other systemic infections ( e.g. pneumonia, and endocarditis). These infections are associated with numerous virulence determinants, including extracellular matrix adhesins. EmaA (extracellular matrix protein adhesin A), a trimeric autotransporter adhesin, mediates the binding of this bacterium to collagen. EmaA forms antennae-like structures that protrude from the bacterial surface. The 30 nm distal region of the structure, which is further divided into three subdomains (SI, SII, SIII), contains the N-terminal sequences of the three monomers and encompasses the collagen binding activity [1]. Deletion of this region or any of the subdomains abrogates collagen binding. Furthermore, EmaA is glycosylated, and this post-translational modification is essential for the function of adhesin. Interestingly, this glycoprotein uses a similar synthesis pathway as the O-polysaccharide (O-PS) synthesis of lipopolysaccharides (LPS). Disabling sugar synthesis, transport, and glycan ligation in this pathway changes EmaA function [2]. Yet, the link between the modifications of the protein by glycosylation remains unclear. The aim of this study is to analyze the 3D structure of the functional domain of the EmaA adhesin from a mutant strain with a disrupted glycosylation mechanism. The waaL mutant strain lacks the O-antigen ligase, WaaL, which is an
The modified J-matrix method for short range potentials

We modify the J-matrix method for scattering to improve its convergence and reduce the computational cost. Our method applies to the oscillator basis J-matrix method. We distinguish three regions in the space of wavefunction coefficients. In the asymptotic region the free-space boundary conditions hold. In the far interaction region, semi-classical approximations to the matrix elements reduce the Schr? dinger equation to an inhomogeneous three-term recurrence relation, and in the near-interaction region one has the full Schr? dinger matrix equation. We apply the modified J-matrix method to scattering off a Yukawa potential. The examples show that the number of matrix elements that need to be calculated is significantly smaller than that for the J-matrix method.
Nanofabrication and plasma polymerization assisted surface modification of a transducer based on localized surface plasmon resonance of gold nanostructure arrays for biosensor applications

The nanofabrication and surface modification of a transducer based on localized surface plasmon resonance (LSPR) of gold nanostructure arrays for biosensing was studied. We used electron beam lithography for the nanopatterning technique, which let us choose LSPR sensor properties by providing immense control over nanostructural geometry. A critical step in the utilization of this transducer is to form a selective biolayer over the gold nanostructures. We applied plasma polymerization and wet chemistry techniques for ethylenediamine (EDA) modification and glutaraldehyde immobilization as intermediate layers, respectively. The gold nanostructure arrays were primarily modified using EDA in order to activate the surface with amine groups that are cross-linked with later added avidin molecules by the help of glutaraldhyde layer residing in between. The success of plasma polymerization was validated with x-ray photoelectron spectroscopy measurements. As a last step, we introduced biotin to the surface (biotin has a high affinity for avidin). We were able to detect the LSPR resonance wavelength shift in the transmission spectra at each step of modification, including the avidin-biotin interaction, which acts as a model for specific molecule detection using LSPR.
Ecohydrological optimality in the Northeast China Transect

Abstract. The Northeast China Transect (NECT) is one of the International Geosphere-Biosphere Program (IGBP) terrestrial transects, where there is a significant precipitation gradient from east to west, as well as a vegetation transition of forest–grassland–desert. It is remarkable to understand vegetation distribution and dynamics under climate change in this transect. We take canopy cover (M), derived from Normalized Difference Vegetation Index (NDVI), as an index to describe the properties of vegetation distribution and dynamics in the NECT. In Eagleson's ecohydrological optimality theory, the optimal canopy cover (M*) is determined by the trade-off between water supply depending on water balance and water demand depending on canopy transpiration. We apply Eagleson's ecohydrological optimality method in the NECT based on data from 2000 to 2013 to get M*, which is compared with M from NDVI to further discuss the sensitivity of M* to vegetation properties and climate factors. The result indicates that the average M* fits the actual M well (for forest, M* = 0.822 while M = 0.826; for grassland, M* = 0.353 while M = 0.352; the correlation coefficient between M and M* is 0.81). Results of water balance also match the field-measured data in the references. The sensitivity analyses show that M* decreases with the increase of leaf area index (LAI), stem fraction and temperature, while it increases with the increase of leaf angle and precipitation amount. Eagleson's ecohydrological optimality method offers a quantitative way to understand the impacts of climate change on canopy cover and provides guidelines for ecorestoration projects.
Verification of Quantum Optimizers

Methods for finding ground states of classical spin models are of great importance in optimization and are gaining additional relevance now for verifying the results quantum optimizers. We combine the state-of-the-art branch and bound method for solving such optimization problems via converging upper- and lower-bounds with ideas from polynomial optimization and semidefinite programming (SDP). The resulting chordal branch and bound (CBB) algorithm can exploit the locality and resulting sparsity in relevant Ising spin models in a systematic way. This yields certified solutions for many of the problems that are being used to benchmark quantum annealing devices more efficiently and for larger system sizes. We are able to verify the output of a D-Wave 2000Q device for the largest triangular lattice that can be embedded in the hardware and provide exact ground states for cases in which the quantum annealer returns a configuration with almost minimal energy but markedly different spin pattern. The method always yields provable polynomial time upper and lower bounds on the ground state energy. We benchmark our method against further planar and non-planar graphs and show that these bounds often converge after a small number of steps, even though the NP-hardness of general Ising models implies that exponentially many steps are required in the worst case. This new tool is a flexible and scalable solution for the verification and benchmarking of the next generation of quantum optimization devices.
Mobile computing technology for monitoring advanced Parkinson ’ s disease

This paper presents the development and evaluation of Information Technology-based methods and systems for supporting assessment of symptoms and enabling remote monitoring of Parkinson‟s disease (PD) patients. In this paper, data from a mobile device test battery, collected during a three year clinical study, was used for the development and evaluation of methods. The data was gathered from a series of tests, consisting of self-assessments and motor tests (tapping and spiral drawing). These tests were carried out repeatedly in a telemedicine setting during week-long test periods. A computer method was developed to process traced spiral drawings and generate a score representing PD-related drawing impairments. The data processing part consisted of using discrete wavelet transform and principal component analysis. When this computer method was evaluated against human clinical ratings, the results showed that it could perform quantitative assessments of drawing impairment in spirals comparatively well. Furthermore, an information system was designed and evaluated for delivering assessment support information to the treating clinical staff for monitoring PD symptoms in their patients. The system consisted of a patient node for data collection based on the mobile device test battery, a service node for data storage and processing, and a web application for data presentation. The evaluation results for this integrated system indicate that it can be used as a tool for frequent PD symptom assessments in home environments.
On the Existence of Global Weak Solutions to 1D Pollutant Transport Model

We consider a one-dimensionnal bilayer model coupling shallow water and Reynolds lubrication equations with a molecular interactions between molecules. These molecular interactions give rise to intermolecular forces, namely the long-range van der Waals forces and short-range Born intermolecular forces. In this paper, an expression will be used to take into account all these intermolecular forces. Our model is a similar model studied in (Roamba, Zabsonr\'{e}\& Zongo, 2017). The model considered is represented by the two superposed immiscible fluids. A similar model was studied in (Zabsonr\'{e} Lucas \& Fernandez-Nieto, 2009) but the authors do not take into account the intermolecular forces. Without hypothesis about the unknowns as in (Roamba, Zabsonr\'{e}\& Zongo, 2017), we show the existence of global weak solution in time in a periodic domain.
Simulation of quantum circuits by low-rank stabilizer decompositions

Recent work has explored using the stabilizer formalism to classically simulate quantum circuits containing a few non-Clifford gates. The computational cost of such methods is directly related to the notion of stabilizerrank, which for a pure state ψ is defined to be the smallest integer χ such that ψ is a superposition of χ stabilizer states. Here we develop a comprehensive mathematical theory of the stabilizer rank and the related approximate stabilizer rank. We also present a suite of classical simulation algorithms with broader applicability and significantly improved performance over the previous state-of-the-art. A new feature is the capability to simulate circuits composed of Clifford gates and arbitrary diagonal gates, extending the reach of a previous algorithm specialized to the Clifford+T gate set. We implemented the new simulation methods and used them to simulate quantum algorithms with 40-50 qubits and over 60 non-Clifford gates, without resorting to high-performance computers. We report a simulation of the Quantum Approximate Optimization Algorithm in which we process superpositions of χ∼106 stabilizer states and sample from the full n-bit output distribution, improving on previous simulations which used ∼103 stabilizer states and sampled only from single-qubit marginals. We also simulated instances of the Hidden Shift algorithm with circuits including up to 64 T gates or 16 CCZ gates; these simulations showcase the performance gains available by optimizing the decomposition of a circuit's non-Clifford components.
Demonstrating the “unit hydrograph” and flow routing processes involving active student participation – a university lecture experiment

The unit hydrograph (UH) has been one of the most widely employed hydrological modelling techniques to predict rainfall–runoff behaviour of hydrological catchments, and is still used to this day. Its concept is based on the idea that a unit of effective precipitation per time unit (e.g. mm h −1 ) will always lead to a specific catchment response in runoff. Given its relevance, the UH is an important topic that is addressed in most (engineering) hydrology courses at all academic levels. While the principles of the UH seem to be simple and easy to understand, teaching experiences in the past suggest strong difficulties in students' perception of the UH theory and application. In order to facilitate a deeper understanding of the theory and application of the UH for students, we developed a simple and cheap lecture theatre experiment which involved active student participation. The seating of the students in the lecture theatre represented the hydrological catchment in its size and form. A set of plastic balls, prepared with a piece of magnetic strip to be tacked to any white/black board, each represented a unit amount of effective precipitation. The balls are evenly distributed over the lecture theatre and routed by some given rules down the catchment to the catchment outlet , where the resulting hydrograph is monitored and illustrated at the black/white board. The experiment allowed an illustration of the underlying principles of the UH, including stationarity, linearity, and superposition of the generated runoff and subsequent routing. In addition, some variations of the experimental setup extended the UH concept to demonstrate the impact of elevation, different runoff regimes, and non-uniform precipitation events on the resulting hydrograph. In summary, our own experience in the classroom, a first set of student exams, as well as student feedback and formal evaluation suggest that the integration of such an experiment deepened the learning experience by active participation. The experiment also initialized a more experienced based discussion of the theory and assumptions behind the UH. Finally, the experiment was a welcome break within a 3 h lecture setting, and great fun to prepare and run.
INCREASING ACCURACY OF ACTIVE POWER MEASUREMENT OF NON-COHERENTLY SAMPLED SIGNALS BY TIME DOMAIN SIGNAL PROCESSING

The paper analyses an effective method of increasing accuracy of active power measurement (and energy measurement) by non-coherent sampling. The measurement bias caused by non-coherent sampling are reduced by windowing the instantaneous power sequence of samples by various generalized cosine windows. Active power is found by processing signal in time domain, without using FFT. Newly obtained analytical formulae are given, a comparison to classical method and numerical simulations verifying the derived formulae are presented. A simple method of compensation multiplexing delay by measurement using multiplexing DAQ plug-in board is explained and verified both in simulation and measurement. Application of windowing for measurement of multifrequency signals is also included, formula for standard uncertainty of active power estimate is given. Basic numerical integration methods applied to quantized input signals in power computation are briefly compared, and numerical values showing decrease in power bias for selected windows are shown.
Amine-Functionalized Mesoporous Silica Nanoparticles: A New Nanoantibiotic for Bone Infection Treatment

Abstract This manuscript reports an effective new alternative for the management of bone infection by the development of an antibiotic nanocarrier able to penetrate bacterial biofilm, thus enhancing antimicrobial effectiveness. This nanosystem, also denoted as “nanoantibiotic”, consists in mesoporous silica nanoparticles (MSNs) loaded with an antimicrobial agent (levofloxacin, LEVO) and externally functionalized with N-(2-aminoethyl)-3- aminopropyltrimethoxysilane (DAMO) as targeting agent. This amine functionalization provides MSNs of positive charges, which improves the affinity towards the negatively charged bacteria wall and biofilm. Physical and chemical properties of the nanoantibiotic were studied using different characterization techniques, including Xray diffraction (XRD), transmission electron microscopy (TEM), N2 adsorption porosimetry, elemental chemical analysis, dynamic light scattering (DLS), zeta (ζ)-potential and solid-state nuclear magnetic resonance (NMR). “In vial” LEVO release profiles and the in vitro antimicrobial effectiveness of the different released doses were investigated. The efficacy of the nanoantibiotic against a S. aureus biofilm was also determined, showing the practically total destruction of the biofilm due to the high penetration ability of the developed nanosystem. These findings open up promising expectations in the field of bone infection treatment.
COMPARATIVE ANALYSIS OF ANTICANCER ACTIVITY OF RUBIA CORDIFOLIA L . & ADULTERANT ON MCF-7 CELLS AND SCAR MARKER DEVELOPMENT

Rubia cordifolia Linn. (Rubiaceae) commonly known as Indian Madder, Majith, Manjistha etc. is widely dispersed throughout the lower hills of Indian. The plant is famous important drug in the Ayurvedic treatments. Extracts of this plant have shown many important medicinal properties. In this study we compared the therapeutic potential of methanolic extract of R. cordifolia Linn. and its adulterant on breast cancer cell line MCF-7. The adulterant exhibited significantly low anticancer activity in comparison to the authentic R. cordifolia as authentic plant showed IC50 value 400 μg/mL while the adulterant have not showed any significant cytotoxicity to the same. For the correct identification of the R. cordifolia we developed RAPD based easy and cheap SCAR markers (Rb-F and Rb-R). Developed SCAR markers were also validated with respect to the market samples.
The [a,b]-domination and [a,b]-total Domination of Graphs

A subset $S$ of the vertices of $G = (V, E)$ is an $[a, b]$-set if for every vertex $v$ not in $S$ we have the number of neighbors of $v$ in $S$ is between $a$ and $b$ for non-negative integers $a$ and $b$, that is, every vertex $v$ not in $S$ is adjacent to at least $a$ but not more than $b$ vertices in $S$. The minimum cardinality of an $[a, b]$-set of $G$ is called the $[a, b]$-domination number of $G$. The $[a, b]$-domination problem is to determine the $[a, b]$-domination number of a graph. In this paper, we show that the [2,b]-domination problem is NP-complete for $b$ at least $3$, and the [1,2]-total domination problem is NP-complete. We also determine the [1,2]-total domination and [1,2] domination numbers of toroidal grids with three rows and four rows.
Top-Down Control of Perceptual Decision Making by the Prefrontal Cortex

Although most work on perceptual decision making has focused on the processing within the visual, temporal, and parietal lobes, recent research points to an underappreciated but critical role of the prefrontal cortex (PFC). PFC provides high-level control of perception, but it is unclear whether this control can be subdivided into different processes and whether different PFC regions have different roles. Here I review evidence that prefrontal top-down control is organized in the processes of selection control, decision control, and evaluation. These three processes overlap and interact with each other while at the same time maintaining a temporal hierarchy. Further, these different stages are supported by dissociable regions within the PFC that control hierarchically organized cognition. The current proposal for PFC’s role in perceptual control can serve as the basis for a deeper understanding of both the functional organization of PFC and the processes underlying perceptual decision making.
The Effect of Anterior Teeth Forms in Smile Esthetics

Background and objective: Smile play a great role on the face attractiveness. A good-looking smile advances the individual’s acceptability by affecting the social interactions. This study aimed to evaluate the effects of different anterior teeth forms on smile esthetics in people referred to dental faculty clinic in Ardabil, Iran. Materials and methods: For this survey, six photos of different shapes of central and lateral incisors (round, round-square, and square), and canines (pointed and flat) were shown to 469 people in the dental faculty of Ardabil, Iran, including 248 females and 221 males. Each image was scored from one to ten. Results: According to this study, no significant difference was observed between age, gender, and educational stage of participant (P>0.05). According to the groups judgments, the scores of images of pointed tip canine and round incisors and flat canine and round incisors were the highest and the images of pointed tip canine and square incisors and flat canine and square incisors were scored the least. Regarding the results of the Wilcoxon test, the pointed canine type was not effective in the esthetic judgment. The participants similarly rated the photos of pointed and flat canines (P>0.05). Conclusion: The age, gender, and educational stage was not correlated to the preferences about esthetics of the aforementioned photos. Generally, the smile with anterior teeth with round incisal edges was preferred.
Coordinated Freight Routing With Individual Incentives for Participation

The sharp increase in e-commerce over the last few years has led to an increase in the volume of trucks both in ports and in commercial areas. Truck traffic has a negative impact on traffic flow in general due to the size of trucks and their slower dynamics. The continuously increasing use of navigation apps has led drivers to make their routing decisions in an independent manner in an effort to minimize their own individual travel time, with possible significant deviation from a socially optimum solution. In this paper, we consider the use of coordinated routing in order to achieve load balancing. Users send their OD matrices as well as their preferred departure time to the coordinator who gives them routing instructions based on a socially optimum cost. This design enables us to derive sufficient conditions under which we prove the existence of mechanisms which are truthful in equilibrium, budget balanced on average and create individual incentives for voluntary participation of the truck drivers. Subsequently, we design our mechanism in a way that only uses a minimal set of sufficient conditions in order to guarantee the existence of a solution and maximize its efficiency. Finally, the extensive simulation results of our approach in the Braess and the Sioux Falls networks demonstrate that the proposed mechanism can approach the system optimum solution.