Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX1/FER/RALF growth regulatory module

Plant cell growth involves coordination of numerous processes and signaling cascades among the different cellular compartments to concomitantly enlarge the protoplast and the surrounding cell wall. In Arabidopsis thaliana, the cell wall integrity-sensing process involves the extracellular LRX (LRR-Extensin) proteins that bind RALF (Rapid ALkalinization Factor) peptide hormones and, in vegetative tissues, interact with the transmembrane receptor kinase FERONIA (FER). This LRX/RALF/FER signaling module influences cell wall composition and regulates cell growth. The numerous proteins involved in or influenced by this module are beginning to be characterized. In a genetic screen, mutations in Apyrase 7 (APY7) were identified to suppress growth defects observed in lrx1 and fer mutants. APY7 encodes a Golgi-localized NTP-diphosphohydrolase, but opposed to other apyrases of Arabidopsis, APY7 revealed to be a negative regulator of cell growth. APY7 modulates the growth-inhibiting effect of RALF1, influences the cell wall architecture, and alters the pH of the extracellular matrix, all of which affect cell growth. Together, this study reveals a function of APY7 in cell wall formation and cell growth that is connected to growth processes influenced by the LRX/FER/RALF signaling module.
DRPBind: prediction of DNA, RNA and protein binding residues in intrinsically disordered protein sequences

DRPbind predicts three components: deoxyribonucleic acid (DNA) binding, ribonucleic acid (RNA) binding and protein-binding residues of query protein sequences. DRPbind utilizes independent sources of information encoded for each component predictor and relies on the information-rich profiles of protein evolutionary-based features, protein physicochemical-based features, and protein structural-based features. DRPbind employs protein profile-based features extracted from the bigrams of PSSM and HMM profiles. It also extracts features from physicochemical and structural attributes. DRPbind takes primary protein sequences as input, and through the Support Vector Machine (SVM) classifier, it provides the binding prediction. DRPbind is optimized based on a specific binding type and shown superior performance in terms of simultaneously predicting the DNA-binding, RNA-binding and protein-binding residues. The source code is available at https://github.com/roneshsharma/DNA-RNA-Protein-Binding/wiki
Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses

Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, Florida, USA, after emerging among horses in South America. In the early 21st century the American lineage of EIV diverged into two ‘Florida’ clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV. (242 words) IMPORTANCE The emergence of viruses in new hosts is a threat to human and animal health. The H3N8 equine influenza virus (EIV) emerged in 1963 by transfer of an avian influenza virus, and the H3N8 canine influenza virus (CIV) subsequently emerged in 1999 when EIV transferred to dogs. H3N8 CIV persistently circulated in only a few locations in the USA, and has not been detected since 2016. In the same period H3N8 EIV has circulated as two separate clades, one in North America and other regions of the world, while the other currently appears to be found only in Central Asia. By comparing the hosts, epidemiology, and evolution of these influenza viruses we explain how these lineages had different evolutionary fates, and show why elucidating these evolutionary processes is key to understanding zoonotic disease and viral emergence. (137 words)
Microsaccades Track Location-Based Object Rehearsal in Visual Working Memory

Besides controlling eye movements, the brain’s oculomotor system has been implicated in the control of covert spatial attention and the rehearsal of spatial information in working memory. We investigated whether the oculomotor system also contributes to rehearsing visual objects in working memory when object location is never asked about. To address this, we tracked the incidental use of locations for mnemonic rehearsal via directional biases in microsaccades while participants maintained two visual objects (coloured oriented gratings) in working memory. By varying the stimulus configuration (horizontal, diagonal, and vertical) at encoding, we could quantify whether microsaccades were more aligned with the configurational axis of the memory contents, as opposed to the orthogonal axis. Experiment 1 revealed that microsaccades continued to be biased along the axis of the memory content several seconds into the working-memory delay. In Experiment 2, we confirmed that this directional microsaccade bias was specific to memory demands, ruling out lingering effects from passive and attentive encoding of the same visual objects in the same configurations. Thus, by studying microsaccade directions, we uncover oculomotor-driven rehearsal of visual objects in working memory through their associated locations. SIGNIFICANCE STATEMENT How humans rehearse information in working memory is a foundational question in psychology and neuroscience. To provide insight into the cognitive and neural bases of working-memory rehearsal, we turned to microsaccades – small eye-movements produced by the brain’s oculomotor system. We reveal how microsaccades track the locations of visual objects during memory rehearsal, even when object locations are never asked about. This brings three advances. From a psychology standpoint, it demonstrates how memory rehearsal automatically engages object locations. From a neuroscience standpoint, it demonstrates how such location-based rehearsal relies on brain circuitry that also controls our eyes. Finally, from a practical standpoint, it demonstrates how microsaccades can be utilised to track the properties of working-memory rehearsal across space and time.
Scale choosing based on spectrum analysis in a novel wavelet principle for fault line selection

On the basis of traditional signal spectrum analysis, scale choosing in a novel wavelet principle for fault line selection is analyzed in detail. The relation between spectrum and wavelet transform modulus maxima of transient fault signal is discussed in detail, which provides a theoretical foundation for choosing scale in the new wavelet criterion as well as an important analyzing method for more wavelet applications in other fields of power system.
Fault detection for chemical process based on locally linear embedding

As industrial processes become more complex,on-line monitoring of the processes are gaining importance for plant safety,maintenance,and product quality.To handle the nonlinear problem for process monitoring,a novel fault detection method was proposed by combining locally linear embedding(LLE)with support vector data description(SVDD). Firstly,LLE manifold learning algorithm was performed for nonlinear dimensionality reduction and thus the main feature of the collected data was extracted.Then,the mapping matrix from data space to feature space was calculated by using local linear regression which guaranteed the real-time property of the algorithm.Next,in order to avoid the influence of data noise on the traditional statistics,a fault detection model was established based on SVDD in the feature space,while a corresponding statistic and its control limit were determined at the same time.Finally,the feasibility and efficiency of the proposed method were shown through a numerical simulation and the Tennessee Eastman(TE)benchmark process.
A mechanical model for dissolution–precipitation creep based on the minimum principle of the dissipation potential

In contrast to previous approaches that consider dissolution–precipitation creep as a multi-stage process and only simulate its governing subprocess, the present model treats this phenomenon as a single continuous process. The applied strategy uses the minimum principle of the dissipation potential according to which a Lagrangian consisting of elastic power and dissipation is minimized. Here, the elastic part has a standard form while the assumption for dissipation stipulates the driving forces to be proportional to two kinds of velocities: the material-transport velocity and the boundary-motion velocity. A Lagrange term is included to impose mass conservation. Two ways of solution are proposed. The strong form of the problem is solved analytically for a simple case. The weak form of the problem is used for a finite-element implementation and for simulating more complex cases.
The relation between the Wentzel-Kramers-Brillouin and the Thomas-Fermi approximations

It is shown that two essential approximations are made in using the customary Thomas-Fermi formula for the sum of the eigenvalues in any one-dimensional problem. The first is to start from the Wentzel-Kramers-Brillouin formula for the individual eigenvalues, and the second is to replace the summation by an integration. The three-dimensional central field problem is then considered, and by similar arguments, though with an additional approximation, the usual Thomas-Fermi energy formula is again obtained. Possible ways of correcting the errors introduced by integrating instead of summing are discussed and illustrative examples given. In the three-dimensional case particular attention is given to the Coulomb field problem. Finally, brief reference is made to the possibility of correcting for the errors of the Wentzel-Kramers-Brillouin formula.
GLOBAL ASYMPTOTIC OUTPUT TRACKING FOR A CLASS OF NONLINEAR SYSTEMS

This paper considers a global asymptotic output tracking problem with a prescribed constant reference signal for a class of single-input and single output-output nonlinear systems. It is shown that under some mild conditions on such a system there is a smooth output feedback achieving global asymptotic output tracking and such a smooth output controller is explicitly constructed by a new design method proposed. The usefulness of our result is illustrated by a numerical example.
Analytic solution of rectangular plates loaded with vertical force on an elastic half space

The method of double Fourier transform was introduced for the analysis of an elastic half space loaded with vertical force,and an integral representation for displacements of an elastic half space was presented.The analytic solution of an elastic rectangular plate on an elastic half space was also given by combining the analytic solution of an elastic rectangular plate with four free edges.Some examples were analyzed and the results were compared with those from the literature which used other methods such as finite element method.The agreement was found to be satisfactory which proved the validity of the new method in solving the problem of a rectangular plate on an elastic half space with four free edges.This new method would be feasible in practical applications.
Semi‐coupled air/water immersed boundary approach for curvilinear dynamic overset grids with application to ship hydrodynamics

For many problems in ship hydrodynamics, the effects of air flow on the water flow are negligible (the frequently called free surface conditions), but the air flow around the ship is still of interest. A method is presented where the water flow is decoupled from the air solution, but the air flow uses the unsteady water flow as a boundary condition. The authors call this a semi‐coupled air/water flow approach. The method can be divided into two steps. At each time step the free surface water flow is computed first with a single‐phase method assuming constant pressure and zero stress on the interface. The second step is to compute the air flow assuming the free surface as a moving immersed boundary (IB). The IB method developed for Cartesian grids (Annu. Rev. Fluid Mech. 2005; 37:239–261) is extended to curvilinear grids, where no‐slip and continuity conditions are used to enforce velocity and pressure boundary conditions for the air flow. The forcing points close to the IB can be computed and corrected under a sharp interface condition, which makes the computation very stable. The overset implementation is similar to that of the single‐phase solver (Comput. Fluids 2007; 36:1415–1433), with the difference that points in water are set as IB points even if they are fringe points. Pressure–velocity coupling through pressure implicit with splitting of operators or projection methods is used for water computations, and a projection method is used for the air. The method on each fluid is a single‐phase method, thus avoiding ill‐conditioned numerical systems caused by large differences of fluid properties between air and water. The computation is only slightly slower than the single‐phase version, with complete absence of spurious velocity oscillations near the free surface, frequently present in fully coupled approaches. Validations are performed for laminar Couette flow over a wavy boundary by comparing with the analytical solution, and for the surface combatant model David Taylor Model Basin (DTMB) 5512 by comparing with Experimental Fluid Dynamics (EFD) and the results of two‐phase level set computations. Complex flow computations are demonstrated for the ONR Tumblehome DTMB 5613 with superstructure subject to waves and wind, including 6DOF motions and broaching in SS7 irregular waves and wind. Copyright © 2008 John Wiley & Sons, Ltd.
An Improved SIFT Algorithm and Its Application in Medical Image Registration

Feature extraction is the basis of medical image registration.The accuracy of feature points directly affects matching result.It often use manpower to do feature extraction at present,but the accuracy is poor and the workload is heavy.The features extracted with SIFT are invariant to image scale and rotation,and provide robust matching.SIFT algorithm has been widely used in image registration.As the SIFT algorithm is very strict about matching condition,the number of feature points often can not meet the needs of medical image registration,and there are some false matches to a certain extent.In order to increase the number of feature points and improve the matching accuracy,the Euclid distance has been adopted to determine the similarity between feature points and low contrast points have been retained according to the characteristics of medical images.The experiment results demonstrate the effectiveness of this method.
‘They say we are all zombies’: Rethinking the role of audiences in a mediatized international conflict

This article contributes to the conceptualization of international conflict mediatization through the lenses of ‘audience logic’ instead of the usual ‘media logic’ perspective. The former is defined here as beliefs about the workings of the media system that are held by audiences and constructions of their own identities as media users. The empirical analysis is about strategies used by Baltic Russian-speakers in making sense of media and news during the Russia-Ukraine conflict during 2013–2019. The authors propose elaborating the conceptualization of the audience and further inquiry into the resources for audience empowerment to alter today’s asymmetrical publics/elites power dynamics.
The Occurrence of Folate Biosynthesis Genes in Lactic Acid Bacteria from Different Sources

SUMMARY Research background Lactic acid bacteria (LAB) are known to produce folate. However, this ability is highly strain-dependent. Folate synthesis in specific LAB strains is affected by the availability of folate, which can be consumed by other LAB under certain conditions. Moreover, differences in folate synthesis capabilities are related to the presence of folate biosynthesis-related genes and regulation of this pathway. Experimental approach As basic information to better understand the regulation of folate biosynthesis among different LAB species and strains, folate biosynthetic genes were screened and identified in folate-producing and non-folate-producing LAB isolated from various local food sources in Indonesia. The extracellular folate productivity amounts of the isolates were analyzed using high-performance liquid chromatography with a diode array detector (HPLC-DAD). Results and conclusions Eleven of the thirteen tested LAB isolates had all of the eight genes involved in folate biosynthesis (folE, folQ, folB, folK, folP, folC1, folA and folC2). Furthermore, these isolates produced extracellular folate ranging from 10.37 to 31.10 µg/mL. In contrast, two non-folate-producing isolates lacked several folate biosynthetic genes, such as folQ, folP and folA, which is possibly the reason for their inability to synthesize folate de novo. Phylogenetic tree construction revealed that the folate biosynthetic genes (excluding folK and folP) from six distinct species of folate-producing LAB isolates were monophyletic with homologous genes from other LAB species in the database. Novelty and scientific contribution In this study, the distribution of folate biosynthetic genes in various LAB species was determined. The findings from this research support the use of folate biosynthesis marker genes in the genotypic screening for folate-producing LAB.
The velocity field within a vortex ring with a large elliptical cross-section

The velocity field within a steady toroidal vortex is found for arbitrary mean core radius and section ellipticity. The problem is solved by transforming to coordinates that define invariant sets. The method allows the properties of the coordinate system metric tensor to be exploited in the continuity equation in order to obtain the solution. The vorticity is found to decrease monotonically with distance from the symmetry axis. For a given outer radius and outer perimeter velocity, the circulation of the vortex ring can be either smaller or larger than that of Hill's spherical vortex.
Understanding Gender in the Dynamics of the Hidden Curriculum: An ELT Colombian Case Study

This article describes the main findings of a Colombian case study in which an English language teacher, who was enrolled in a gender-based optional course, carries out small-scale research to understand gender in her ELT practices. The study aims at describing what and how English language teachers learn when they incorporate their gender consciousness in their teaching practices. The study focuses on Martha’s case who seeks to understand how her learning comes about when integrating the gender perspective in her educational practices and teaching context. The qualitative analysis indicates, among other things, that Martha becomes aware of how the dynamics of the hidden curriculum affect her students’ gender subjectivities. Through this learning process, Martha adopts discourses and practices to promote gender equity, eradicate differential treatments, and contribute positively to her students’ learning experience.
High-Resolution Stratospheric Tracer Fields Estimated from Satellite Observations Using Lagrangian Trajectory Calculations

Abstract A technique is introduced by which high-resolution tracer fields may be constructed from low-resolution satellite observations. The technique relies upon the continual cascade of tracer variance from large to small scales and makes use of wind fields generated by a data assimilation scheme. To demonstrate its usefulness, the technique has been applied in a study of isentropic distributions of nitrous oxide in the winter midstratosphere, using measurements made by the Improved Stratospheric and Mesospheric Sounder instrument on the Upper Atmosphere Research Satellite. The results show that the high-resolution fields significantly increase the amount of information that is available from the satellite observations. The fields give insights into the characteristic structure and evolution of tracer distributions at scales that are normally obscured from view. Two results are particularly noteworthy. First, at the interface between low and middle latitudes there is evidence of active mixing. This mixi.
The thermistor: A problem in heat and current flow

The thermistor is an electrical device that can be used as a current surge protector. The basis of its operation is the temperature-dependent electrical conductivity that drops by 4 to 5 orders of magnitude over a temperature range of 100–200°C. In the present work the coupled heat and electrical current problems are examined with the conductivity modeled by a step function. A numerical scheme is suggested for the nonlinear coupled problem. Convergence of this scheme for some boundary conditions is demonstrated and some numerical results are given.
AN ALGORITHM FOR THE MIXED INTEGER PROBLEM

Abstract : An algorithm is given for the numerical solution of the 'mixed integer' linear programming problem, the problem of maximizing a linear form in finitely many variables constrained both by linear inequalities and the requirement that a proper subset of the variables assume only integral values. The algorithm is an extension of the cutting plane technique for the solution of the 'pure integer' problem.
A novel cyber intrusion detection model based on improved hybrid sampling

The class imbalance of samples of network traffic will cause the poor classification performance of intrusion detection models based on machine learning. To solve this problem, this paper researches sampling algorithm and deep learning for intrusion detection in imbalanced network traffic. This paper proposes a deep recurrent neural network (delayed long short-term memory (DLSTM)) intrusion detection model based on the balanced samples. First, an improved hybrid sampling (IHS) method based on chaotic particle swarm optimization (CPSO) algorithm is proposed as the sampling algorithm to balance the imbalanced samples. Next, a DLSTM with long short-term memory (LSTM) function is proposed to realize high-precision classification of intrusion behaviours. Finally, the method is validated on the standard network traffic dataset. The experimental results show that the DLSTM intrusion detection model based on the IHS method outperforms other comparative models at accuracy. The model is available to the computer network information security defence system.