Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling hydrophobicity to identify secondary structure signals in globular proteins

In globular proteins the hydrophobic effect is a well-known phenomenon that is more and more investigated in relation with protein folding. The Discrete Fourier Transform of the hydrophobic profile of the primary structure, resulting in the so-called amphipatic plots, allow to identify some regular structures. We present a modelling method, which aims to improve both the user-friendliness and the quality of the representation of the amphipatic plots.
Identification of multi-scale coherent eddy structures in a homogeneous isotropic turbulence

The coherent vortices of various scales are identified from a turbulent flow field obtained by a Direct Numerical Simulation (DNS). In this paper, the vorticity field of the database is filtered before the vortex-identifying method is applied, which enables the identification of large and middle scale coherent vortices from the turbulent flow field. The lattice Boltzmann method with a forcing scheme is used to obtain a statistically stationary three dimensional homogeneous and isotropic turbulence in a periodic box with a resolution of 128³. The vorticity field is filtered using sharp cut-off filters of different cut-off-wavenumbers to obtain different scales of coherent eddy structures. The Q criterion is applied to visualise the coherent vortices and the conditional sampling technique is used to investigate the energy spectrum of the coherent and incoherent parts, separately. By applying the filtering process prior to identification, flow fields of different scale structures are extracted and the energy spectrum of each is investigated.
Toward improvement of tracking performance nonlinear feedback for linear systems

A composite nonlinear feedback tracking control law based on a nominal linear controller is proposed. The design yields nonlinear feedback laws that both increase the speed of the closed-loop system response to the command input and reduce the overshoot, while not imperilling the small signal performance achieved by the nominal linear feedback controller in the face of actuator amplitude saturation. A modern flight control application is used to demonstrate the effectiveness of the design.
Development of a Novel Ex Vivo Porcine Hepatic Segmental Perfusion Proof-of-Concept Model Towards More Ethical Translational Research

Introduction Ex vivo machine perfusion describes the technique where organs are continuously perfused and oxygenated extracorporeally (at physiological conditions) to maintain the organs' viability. To our knowledge, there are currently no reported studies describing ex vivo perfusion of a single hepatic segment. Here, we describe the development of a porcine ex vivo hepatic segmental perfusion model to demonstrate proof of concept and support further research into the ex vivo perfusion of the human liver using discarded tissue. Methods Whole livers were retrieved from abattoir-derived pigs and connected to a normothermic extracorporeal perfusion circuit. Constant segmental perfusion via the common or segmental hepatic artery and portal vein with heparinised autologous blood was established. The viability of the perfused organ was assessed by monitoring perfusion pressures, flow rates and histology samples. Results Following perfusion and optimisation of the model for three hepatic segments, the third perfusion demonstrated viable hepatocytes centrally after 4 h of segmental perfusion. Conclusion Ex vivo hepatic segmental perfusion is technically challenging but its success in a porcine model and the principles learned should facilitate the development of an analogous human model using discarded tissue following formal liver resections. The model would use a healthy liver segment following a major formal resection such as a hemi-hepatectomy and ex vivo perfusion performed via a segmental hepatic artery and portal vein. If successful this model would represent a significant development and enable ethical translation research to assess the response of human livers to a variety of stressors, including toxicity and infection.
Active Vibration Suppression in Multi-degree-of-freedom Systems by Disturbance Observers

A novel approach to active vibration suppression in multi-degree-of-freedom (MDOF) systems is proposed based on disturbance observers for multi-input multi-output (MIMO) systems. The disturbance observer presented here has a simple structure equivalent to that of the internal model control (IMC), so there is therefore no need for the system inversion. Techniques to design the proposed disturbance observer are given. Furthermore, examples are given to illustrate the design of disturbance observers for MIMO systems, and to prove their efficacy in suppressing vibration in MDOF systems.
Decomposition of the difference between two rates and its consistency when more than two populations are involved

In recent years, many social scientists, in dealing with data of various kinds, have attempted to decompose the difference between two rates into effects of changes in the underlying factors. AU these studies can be divided into two categories, viz., the rate as a function of two or more factors (their product being a special case), and the rate as computed from cross‐classified data involving one or more factors. In the absence of general methods of decomposition to be used under these two circumstances, the researchers have devised their own ad hoc methods which in general produce meaningful results, but are sometimes less than satisfactory in terms of mathematical rigor and elegance. The objective of the present paper is to put together the general formulas that a researcher is expected to need for the two categories of decomposition problems for any number of factors. Applications of the use of the formulas under these two situations are illustrated by four examples. The paper also suggests a solution.
A performance measure for the fuzzy cluster validity

The primary concern with the use of any clustering is how well it has identified the structure that is present in the data. This is the "cluster validity problem". In this paper, we define G as a measure of the quality of clustering which is based on the mini-max filter concept and fuzzy theory. It measures the overall average compactness and separation of a fuzzy c-partition and explore the properties of G, and we define I/sub G/ as a more suitable measure to compare the clustering result of one fuzzy c/sub 1/-partition with another c/sub 2/-partition of a data set. We show the measure I/sub G/ can be used to select an optimal number of clusters.
On the strength of Ramsey's theorem for pairs

Abstract We study the proof–theoretic strength and effective content of the infinite form of Ramsey's theorem for pairs. Let RTkn denote Ramsey's theorem for k–colorings of n–element sets, and let RT<∞n denote (∀k)RTkn. Our main result on computability is: For any n ≥ 2 and any computable (recursive) k–coloring of the n–element sets of natural numbers, there is an infinite homogeneous set X with X″ ≤T 0(n). Let IΣn and BΣn denote the Σn induction and bounding schemes, respectively. Adapting the case n = 2 of the above result (where X is low2) to models of arithmetic enables us to show that RCA0 + IΣ2 + RT22 is conservative over RCA0 + IΣ2 for Π11 statements and that RCA0 + IΣ3 + RT<∞2 is Π11-conservative over RCA0 + IΣ3. It follows that RCA0 + RT22 does not imply BΣ3. In contrast, J. Hirst showed that RCA0 + RT<∞2 does imply BΣ3, and we include a proof of a slightly strengthened version of this result. It follows that RT<∞2 is strictly stronger than RT22 over RCA0.
Path Planning of Slender Tensegrities Based on the Artificial Potential Field Method

Focusing on the constraints of obstacle avoidance and compliance of structural geometry, a path planning method is proposed for slender morphing tensegrities in this paper based on the artificial potential field method. An analytical kinematic equation is established for tensegrities under member length actuation. The expressions of the elongations of active members are derived for the specified motion with elastic and rigid-body deformations, respectively. The mathematical models of the repulsive fields induced by obstacles and the attractive fields generated by target points are given to define the artificial potential field. For any configuration on the kinematic path, the nodes in the repulsive fields and the guide nodes in the attractive fields are forced to move in the steepest descent directions of their potential energies. The motion directions of nodes are then adjusted for the compliance of structural geometry. A numerical strategy is proposed to trace the kinematic path of a tensegrity step by step in the artificial potential field. The path plannings are performed on an illustrative slender tensegrity consisting of stacked modules by considering the motions with elastic and rigid-body deformations, respectively; and the validity of the proposed method is verified by investigating the obstacle avoidance, the compliance of structural geometry, the slack prevention of cables, and the structural stability for the obtained kinematic paths.
Nonsinusoidal torque of permanent-magnet couplings

This paper presents new structures of permanent-magnet couplings and ways of calculating their characteristics. The analytical formulas of the force between two magnets are used to calculate the torque of the couplings. This allows optimization of the structures and easy comparison for several criteria. The presented structures are fitted with magnets on one rotor, which do not have the same angular width, and magnets on the other rotor, which are not necessarily jointive and do not necessarily have the same angular width. As a result, these structures appear to be very interesting in terms of maximum torque, torque-to-weight ratio, and magnet volume. Such devices are particularly interesting for applications such as screwing devices.
A two-dimensional hybrid simulation for micro dielectric barrier discharges operated in atmospheric pressure

A plasma display panel cell is one example of micro dielectric barrier discharges operated in near atmospheric pressure. It is difficult to measure the phenomena experimentally in such a small discharge at atmospheric pressure. In most cases, atmospheric pressure discharges are simulated with a fluid model using drift-diffusion approximation and local field approximation. However, it was proved in our research that the drift-diffusion approximation is not applicable to heavy ions even at a high pressure. Especially, Xe ion motion is overestimated in the fluid code. In order to investigate the discharge characteristics and analyze the effects of cell size and Xe-content of more than 10%, a hybrid model has been developed which adopts a fluid model for electrons and a particle-in-cell (PIC) model for ions. Using the hybrid code, the discharge characteristics are investigated with the diagnostics for the electric field intensity, charged and excited particles distributions, energy and angle distributions of the ions at the boundary. Conventional diagnostics for a light device are also included such as luminance, power consumption, and luminous efficacy . We compared the result with experiment to confirm adequacy of the simulation.
Neuronal circuits within the homing pigeon hippocampal formation

The current study aimed to reveal in detail patterns of intrahippocampal connectivity in homing pigeons (Columba livia). In light of recent physiological evidence suggesting differences between dorsomedial and ventrolateral hippocampal regions and a hitherto unknown laminar organization along the transverse axis, we also aimed to gain a higher‐resolution understanding of the proposed pathway segregation. Both in vivo and high‐resolution in vitro tracing techniques were employed and revealed a complex connectivity pattern along the subdivisions of the avian hippocampus. We uncovered connectivity pathways along the transverse axis that started in the dorsolateral hippocampus and continued to the dorsomedial subdivision, from where information was relayed to the triangular region either directly or indirectly via the V‐shaped layers. The often‐reciprocal connectivity along these subdivisions displayed an intriguing topographical arrangement such that two parallel pathways could be discerned along the ventrolateral (deep) and dorsomedial (superficial) aspects of the avian hippocampus. The segregation along the transverse axis was further supported by expression patterns of the glial fibrillary acidic protein and calbindin. Moreover, we found strong expression of Ca2+/calmodulin‐dependent kinase IIα and doublecortin in the lateral but not medial V‐shape layer, indicating a difference between the two V‐shaped layers. Overall, our findings provide an unprecedented, detailed description of avian intrahippocampal pathway connectivity, and confirm the recently proposed segregation of the avian hippocampus along the transverse axis. We also provide further support for the hypothesized homology of the lateral V‐shape layer and the dorsomedial hippocampus with the dentate gyrus and Ammon's horn of mammals, respectively.
Experimental observation of resonances in modulated turbulence

The response of turbulence to a periodic forcing of the Reynolds number is studied. The turbulent flow is produced in a closed geometry between two counter-rotating disks. The time series of both the global injected power and the local velocity are measured. It is found that the injected power fluctuations exhibit resonances for well-determined values of the modulation frequency, making it possible to estimate a turbulent cascade time. For modulation periods larger than the measured cascade time, the response of the velocity fluctuations is simply proportional to the modulation of the forcing. For high-frequency modulations, the velocity fluctuations are strongly damped: their amplitude decreases as the inverse of the modulation frequency.
A 2D model of laser grooved silicon solar cell

A two-dimensional model of the grooved solar cell has been developed, based on an approximate analysis that allows a closed-form solution to the fundamental transport equations of the device to be obtained. Thus, a flexible tool for the analysis of the cell is available, both for understanding the basis of its operation and as a design tool. Due to the two-dimensional carrier distribution in the base layer, it is demonstrated that this kind of structures exhibits higher short-circuit current, owing to the improved spectral response (particularly in the range of long wavelengths). <<ETX>>
Automatic Verification of Hypothesized Phonemic Strings in Continuous Speech

A procedure is described for mapping a phonemic string onto a computer representation of an interval of continuous speech. The procedure has as its inputs a hypothesized phonemic string and a matrix of labels and probabilities obtained by computer analysis of a complete utterance. These two inputs are mapped by an iterative technique which (1) searches for individual phonemes in an appropriate order, not necessarily left to right; (2) continuously adjusts for phoneme duration variations; and (3) can deal with intraword coarticulation effects. The mapping procedure yields estimated time boundaries and a goodness‐of‐match score for the hypothesized phoneme string. A computer program has been written using this algorithm which performs automatic recognition of words and phrases within an operating continuous speech understanding system. Examples and current results from this system are presented.
IRS spectroscopic studies of ULIRGs at z ~ 2

Abstract We present a result of IRS spectroscopy of 14 Ultra-Luminous Infrared Galaxies (ULIRGs) in the Extended Groth Strip region. These galaxies are massive and have very high star formation rate. Four objects of this sample are detected in the HST/WFC3 near-infrared imaging. They show very diversified rest-frame optical morphologies, including string-like, extended/diffused, and even spiral with a possible bulge, implying different formation processes for these galaxies. We also search for signatures of active galactic nucleus (AGN) in our sample in the X-ray, mid-infrared and radio bands. This sample is dominated by objects with intensive star formation, only 14–29% of them have AGN activities.
Application of the Preisach model to the calculation of magnetization curves and power losses in ferromagnetic materials

The ability of Preisach-type scalar models to describe static and dynamic hysteresis properties is discussed. Three aspects are addressed in particular: the description of reversible magnetization processes, the characterization of magnetic interactions, and the calculation of dynamic hysteresis loops. Applications of the standard Preisach model and of the moving Preisach model to the description of Henkel plots in recording media and to the prediction of power losses in metallic soft magnetic materials are discussed. >
A search for peculiar objects in young open clusters II. A new Be star, the optical counterpart of IRAS 19564+3224 and a new open cluster in Vulpecula ?

A serendipitous sky eld in Vulpecula was observed with Johnson BVR photometry and slitless spec- troscopy in the 5600{8000 A range, looking for emission line and late spectral type stars. We discovered that the B2V star LS II +32 9, most probably a member of the Vul OB4 association, is now an H emitter. Furthermore, we identied the optical counterpart of the IRAS source IRAS 19564+3224 as a C star. Photometric study of the surrounding stellar eld revealed that this object lies inside the sky area of a previously undetected open cluster of intermediate age. We discuss the possible cluster membership of the Carbon star and its implications. Some hints about the galactic structure along the line of sight of the observed eld are also given
A Guide to LP, The Larch Prover

This guide provides an introduction to LP (the Larch Prover), Release 2.2. It describes how LP can be used to axiomatize theories in a subset of multisorted first-order logic and to provide assistance in proving theorems. It also contains a tutorial overview of the equational term-rewriting technology that provides, along with induction rules and other user-supplied nonequational rules of inference, part of LP’s inference engine.
A fast moment method algorithm using spectral domain wavelet concepts

A multiresolution wavelet algorithm is developed for the fast solution of electromagnetic scattering problems. A multiscale feature of the spectral domain Green's function is observed in the joint spectral-spatial representation. Owing to the multiscale nature of the electrodynamic Green's function in the spectral domain, wavelet application in the spectral domain (KDWT) is more appropriate in representing the Green's function than the wavelet transform applied in the space domain (SDWT). Using the KDWT, a sparse moment impedance matrix, which is a discretized form of the Green's function, is obtained and a fast multiresolution moment method algorithm is developed in conjunction with the conjugate gradient solver. For a square cylinder the sparsity of the moment method matrix and the resulting time performance are compared with those from the conventional moment method. It is found that the KDWT algorithm leads to a matrix-vector multiplication which scales with an order less than N2.
Properties of bilayers based on Mo films for transition-edge sensors

Transition-edge sensors (TES) are promising devices for materials science and space applications due to their spectroscopic capabilities and good count rates. In this work, we report details on fabrication and characterization of Mo films and Mo/Ag bilayers that, being immiscible and nonreactive with each other, should have a long time stability. Both single superconducting films and bilayers of normal-superconducting materials have been deposited in UHV by e-gun. Structural and morphological properties have been investigated by x-ray diffraction and AFM. Bilayers with transition widths of 1 mK are achievable, adequate to realize high sensitivity thermometers.
Phytate-Induced Dose-Response Auto-Activation of Enzyme in Commercial Recombinant Phytase From Escherichia coli

Background: Microbial phytase is one of the most widely used enzymes in food industries like cattle, poultry, and aquaculture food. Therefore, understanding the kinetic properties of the enzyme is very important to evaluate and predict its behavior in the digestive system of livestock. Working on phytase is one of the most challenging experiments because of some problems, including free inorganic phosphate (FIP) impurity in phytate (substrate) and interference reaction of the reagent with both phosphates (product and phytate impurity). Objective: In the present study, FIP impurity of phytate was removed, and then it was shown that the substrate (phytate) has a dual role in enzyme kinetics: substrate and activator. Material and Methods: phytate impurity was decreased by two-step recrystallization prior to the enzyme assay. The impurity removal was estimated by the ISO30024:2009 method and confirmed by Fourier-transform infrared (FTIR) spectroscopy. The kinetic behavior of phytase activity was evaluated using the purified phytate as substrate by non-Michaelis-Menten analysis, including Eadie-Hofstee, Clearance, and Hill plots. The possibility of an allosteric site on phytase was assessed by molecular docking. Results: The results showed a 97.2% decrease in FIP due to recrystallization. The phytase saturation curve had a sigmoidal appearance, and Lineweaver-Burk plot with a negative y-intercept indicated the positive homotropic effect of the substrate on the enzyme activity. A right-side concavity of Eadie-Hofstee plot confirmed it. Hill coefficient was calculated to be 2.26. Molecular docking also showed that Escherichia coli phytase molecule has another binding site for phytate very close to the active site, called “allosteric site”. Conclusions: The observations strongly propose the existence of an intrinsic molecular mechanism in Escherichia coli phytase molecules to be promoted for more activity by its substrate, phytate (positive homotropic allosteric effect). In silico analysis showed that phytate binding to the allosteric site caused new substrate-mediated inter-domain interactions, which seems to lead to a more active conformation of phytase. Our results provide a strong basis for animal feed development strategies, especially in the case of poultry food and supplements, regarding a short food passage time in their gastrointestinal tract and variable concentration of phytate along with it. Additionally, the results strengthen our understanding of phytase auto-activation as well as allosteric regulation of monomeric proteins in general.
Towards an h-adaptive immersed boundary method for the unsteady incompressible Navier-Stokes equations

textabstractThis paper treats the development and validation of a numerical method for the solution of the unsteady incompressible Navier-Stokes equations in two dimensions. The method of choice is a Godunov-type pressure-free correction method similar to the method developed by Lee and LeVeque. Validation is done by considering a two-dimensional boundary-layer flow along a flat-plate. The resulting method provides a starting point for the development of an h-adaptive immersed boundary method to be applied to the flapping flexible filament problem proposed by Zhu and Peskin.