Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient transgene-free genome editing in plants in the T0 generation based on a co-editing strategy

Transgene-free genome editing of plants in the T0 generation is highly desirable but challenging, especially in perennials and vegetatively propagated plants. Here, we investigated the co-editing strategy for generating transgene-free, gene-edited plants via Agrobacterium-mediated transient expression of cytosine base editor (CBE)/gRNA-Cas12a/crRNA-GFP in planta. Specifically, CBE/gRNA was used to base edit the ALS gene to confer resistance to herbicide chlorsulfuron as a selection marker, which has no negative effects on plant phenotypes; Cas12a/crRNA was used for editing genes(s) of interest; GFP was used for selecting transgene-free transformants. Using this approach, transgene-free genome-edited plants were efficiently generated for various genes (either individual or multiplex) in tomato, tobacco, potato, and citrus in the T0 generation. The biallelic/homozygous transgene-free mutation rates for target genes among herbicide-resistant transformants ranged from 8% to 50%. Whole genome sequencing further confirmed transgene-free and absence of off-target mutations in the edited plants. The co-editing strategy is efficient for generating transgene-free, genome-edited plants in the T0 generation, thus being a potent tool for plant genetic improvement.
The Emergence of Tuning to Global Shape Properties of Radial Frequency Patterns in the Ventral Visual Pathway

Radial frequency (RF) patterns, created by sinusoidal modulations of a circle's radius, are processed globally when RF is low. These closed shapes therefore offer a useful way to interrogate the human visual system for global processing of curvature. RF patterns elicit greater responses than those to radial gratings in V4 and more anterior face-selective regions of the ventral visual pathway. This is largely consistent with work on nonhuman primates showing curvature processing emerges in V4, but is evident also higher up the ventral visual stream. Rather than contrasting RF patterns with other stimuli, we presented them at varied frequencies in a regimen that allowed tunings to RF to be derived from 8 human participants (3 female). We found tuning to low RF in lateral occipital areas and to some extent in V4. In a control experiment, we added a high-frequency ripple to the stimuli disrupting the local contour. Low-frequency tuning to these stimuli remained in the ventral visual stream, underscoring its role in global processing of shape curvature. We then used representational similarity analysis to show that, in lateral occipital areas, the neural representation was related to stimulus similarity, when it was computed with a model that captured how stimuli are perceived. We therefore show that global processing of shape curvature emerges in the ventral visual stream as early as V4, but is found more strongly in lateral occipital regions, which exhibit responses and representations that relate well to perception. SIGNIFICANCE STATEMENT We show that tuning to low radial frequencies, known to engage global shape processing mechanisms, was localized to lateral occipital regions. When low-level stimulus properties were accounted for such tuning emerged in V4 and LO2 in addition to the object-selective region LO. We also documented representations of global shape properties in lateral occipital regions, and these representations were predicted well by a proxy of the perceptual difference between the stimuli.
Mechanosensitive channel MscS is critical for termination of the bacterial hypoosmotic permeability response

Free-living microorganisms are subjected to drastic changes in osmolarity. To avoid lysis under sudden osmotic down-shock, bacteria quickly expel small metabolites through the tension-activated channels MscL, MscS, and MscK. We examined five chromosomal knockout strains, ΔmscL, ΔmscS, a double knockout ΔmscS ΔmscK, and a triple knockout ΔmscL ΔmscS ΔmscK in comparison to the wild-type parental strain. Stopped-flow experiments confirmed that both MscS and MscL mediate fast osmolyte release and curb cell swelling, but osmotic viability assays indicated that they are not equivalent. MscS alone was capable of rescuing the cell population, but in some strains MscL did not rescue and additionally became toxic in the absence of both MscS and MscK. Furthermore, MscS was upregulated in the ΔmscL strain, suggesting either a cross-talk between the two genes/proteins or the influence of cell mechanics on mscS expression. The data shows that for the proper termination of the permeability response, the high-threshold (MscL) and the low-threshold (MscS/MscK) channels must act sequentially. In the absence of low-threshold channels, at the end of the release phase, MscL should stabilize membrane tension at around 10 mN/m. Patch-clamp protocols emulating the tension changes during the release phase indicated that the non-inactivating MscL, residing at its own tension threshold, flickers and produces a protracted leakage. The MscS/MscK population, when present, stays open at this stage to reduce tension below the MscL threshold and silence the large channel. When MscS reaches its own threshold, it inactivates and thus ensures proper termination of the hypoosmotic permeability response. This functional interplay between the high- and low-threshold channels is further supported by the compromised osmotic survival of bacteria expressing non-inactivating MscS mutants. Summary (for the table of contents) The kinetics of hypotonic osmolyte release from E. coli is analyzed in conjunction with bacterial survival. It is shown that MscL, the high-threshold ‘emergency release valve’, rescues bacteria from down-shocks only in the presence of MscS, MscK or other low-threshold channels that are necessary to pacify MscL at the end of the release phase.
Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation

Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where particular combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognise trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me3 during mitosis. We find that H3K4me3 hinders adjacent H3T3ph deposition in cells, and that the PHD domain of TAF3 can bind H3K4me3 in mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.
The Complexity of Checking Quasi-Identities over Finite Algebras with a Mal'cev Term

We consider finite algebraic structures and ask whether every solution of a given system of equations satisfies some other equation. This can be formulated as checking the validity of certain first order formulae called quasi-identities . Checking the validity of quasi-identities is closely linked to solving systems of equations. For systems of equations over finite algebras with finitely many fundamental operations, a complete P / NPC dichotomy is known, while the situation appears to be more complicated for single equations. The complexity of checking the validity of a quasi-identity lies between the complexity of term equivalence (checking whether two terms induce the same function) and the complexity of solving systems of polynomial equations. We prove that for each finite algebra with a Mal’cev term and finitely many fundamental operations, checking the validity of quasi-identities is coNP-complete if the algebra is not abelian, and in P when the algebra is abelian.
Unsteady hydromagnetic free convection flow with Hall current and mass transfer along an accelerated porous plate with time-dependent temperature and concentration

Unsteady free convective flow, with Hall currents and mass transfer, past an accelerated vertical porous plate is investigated in the presence of a transverse magnetic field while assuming the plate temperature and concentration to be functions of time. A similarity parameter, taken as a function of time, is introduced in the analysis. The suction or the injection velocity is then taken to be inversely proportional to the above parameter. The resulting similarity equations are then solved numerically and the effects of the Hall parameter, the magnetic parameter, and the Schmidt number on the primary and the secondary velocities are discussed and shown graphically. Finally, the corresponding x and z components of the skin friction are shown in tabular form.
Imaging Recommendations for Diagnosis, Staging, and Management of Soft Tissue Sarcomas

Abstract Soft tissue lesions are a wide range of tumors of mesenchymal cell origin, occurring anywhere in the body with a vast number of histological subtypes both benign and malignant. These are common in clinical practice and vast majority are benign. This article focuses on soft tissue sarcoma of the trunk and extremities and discusses their imaging guidelines.
Constrained Output Path-Following for Nonlinear Systems Using Predictive Control

We address the problem of steering the output of a nonlinear system along a given parametrized reference path, taking input and state constraints into account. Such problems are known as output path-following problems, which typically arise in vehicle and robot control and also in process control. We propose an efficient, continuous time, sampled-data state feedback, predictive control scheme which guarantees convergence to an output path in the presence of state and input constraints.
THE LINKS GOULD INVARIANT OF CLOSED 3-BRAIDS

In this paper, we study the Links–Gould invariant of closed 3-braids. We consider the algebra generated by the image of the 3-string braid group by the linear representation which yields the Links–Gould invariant. We find fundamental linear relations among natural generators of the algebra, and we obtain a basis of the algebra. The relations allow us to evaluate the invariant of closed 3-braids recursively. As an application we give a computer program to calculate the invariant for closed 3-braids.
The initial dispersion of soluble matter in three-dimensional flow

Abstract The dispersion of a passive solute in three-dimensional flow is examined for short times after the injection of solute. If the diffusivity is constant, the solute at first diffuses isotropically about the fluid particle originally coincident with the injection point whilst, at longer times, the effect of diffusion across a velocity shear becomes more important. An asymptotic expansion is derived for the concentration of solute at small times after its injection into the fluid flow and the use of the theory is illustrated for three representative flows. Some critical remarks on the applicability and limitations of the results conclude the note.
CFD Studies of Indoor Airflow and Contaminant Particle Transportation

This article presents a numerical study of indoor airflows and contaminant particle transportation in three ventilated rooms. The realizable k − ϵ model is employed to model the air-phase turbulence, while the Lagrangian particle tracking model is utilized for the particle-phase simulation. The predicted air-phase velocities and contaminant particle concentrations are validated against the experimental data obtained from the literature. In the first case, the realizable k − ϵ model successfully captures the flow trend and reasonably predicts the airflow velocity. The realizable k − ϵ model under-predicts the vertical air velocities along the vertical inlet jet axis by 11% at x = 0.219 m, which is slightly better than the standard k − ϵ model error of 17%. In a two-zone room case, the realizable k − ϵ model, combined with a Lagrangian particle tracking model, predicts the particle concentration decay with the highest normalized difference being 24%. In the third case, the influence of particle size, location of particle resource, and particle-wall collision on the particle concentrations is investigated by the realizable k − ϵ model and the Lagrangian model. It is found that for relatively small particles (diameter ≤ 10 μm), the particle concentration may be insensitive to the particle diameter. In addition it has been observed that the particle-collision model may have considerable effect on the particle concentration prediction.
Topology-induced effect in biomimetic propulsive wakes

Abstract It is known that the wake pattern observed in a cross-section behind swimming or flying animals is typically characterized by the presence of periodical vortex shedding. However, depending on species, propulsive wakes can differ according to the spatial ordering of the main vortex structures. We conducted a very precise experiment to analyse the role of the topology of the wake in the generation of propulsion by comparing two prototypical cases in a quasi-two-dimensional view. One configuration is jellyfish-like, with symmetric shedding of vortex pairs, and the other is fish-like, with alternating shedding of counter-rotating vortices. Self-propulsion is achieved by the flapping motion of two identical pitching rigid foils, separated by a distance $d$ . By keeping the momentum input unchanged, we compared both symmetric and asymmetric flapping modes. For the entire explored range of parameters, the symmetric jellyfish-like mode has shown to produce more thrust than the fish-like asymmetrical one. We show here that this difference is due to a pressure effect related to the ability of each wake to produce or not, strong fluctuations of transversal velocities in the near-wake region.
Interpretable Garment Workers’ Productivity Prediction in Bangladesh Using Machine Learning Algorithms and Explainable AI

Bangladesh’s garment industry is widely recognized and plays a significant role in the current global market. The nation’s per capita income and citizens’ living standards have risen significantly with the noteworthy hard work performed by the employees in this industry. The garment sector is more efficient once the target production can be achieved without any difficulties. But a frequent issue that comprises within this industry is, often the actual garment producing productivity of the people working there do not reach the previously determined target-productivity. The business suffers a significant loss when the productivity gap appears in this process. This approach seeks to address this issue by prediction of the actual productivity of the workers. To attain this goal, a machine learning approach is suggested for the productivity prediction of the employees, after experimentation with five machine learning models. The proposed approach displays a reassuring level of prediction accuracy, with a minimalist MAE (Mean Absolute Error) of 0.072, which is less than the existing Deep Learning model with a MAE of 0.086. This indicates that, application of this process can play a vital role in setting an accurate target production which might lead to more profit and production in the sector. Also, this work contains an explainable AI technique named SHAP for interpreting the model in order to see further information within it.
Prospects of NFMD for Power System Frequency and Amplitude Estimation

Power quality monitoring and parameter estimation are essential for the proper functioning of modern power grids. Various techniques have been proposed to estimate the characteristics of power signals and to gain insight into their dynamics. Non-stationary Fourier mode decomposition (NFMD) is a new interpretable time-frequency analysis framework for non-stationary and nonlinear signals. This work investigates the prospects of NFMD in the estimation of power-system characteristics such as fundamental frequency, amplitude and presence of disturbance components. Usage of NFMD as a noise removal technique is also explored in the current work. Results show that NFMD is robust to noisy disturbances and can perform well in noisy environments. The proposed methodology can be used for real-time analysis and interpretation of large volume of data from advanced smart metering techniques such as microphasor measurement units in microgrids.
Multimodal Emotion Recognition Using Heterogeneous Ensemble Techniques

Emotion recognition and sentiment analysis serve several purposes, from analyzing human behavior under specific conditions to the enhancement of customer experience for various services. In this paper, a multimodal approach is used to identify 4 classes of emotions by combining both speech and text features to improve classification accuracy. The methodology involves the implementation of six models for both audio and text domains combined using four different heterogeneous ensemble techniques - hard voting, soft voting, blending and stacking. The effects of each ensemble method on the accuracy for the multimodal classification task are also investigated. The results of this study show that the usage of ensemble learning to combine modalities greatly improves classification, with stacking being the best-performing ensemble technique for the selected collection of models. The proposed model outperforms several existing methods for 4-class emotion detection on the IEMOCAP dataset, obtaining a weighted accuracy of 81.2%.
Lifetime Prediction of Current-and Temperature-Induced Degradation in Silicone-Encapsulated 365 nm High-Power Light-Emitting Diodes

We report on the degradation mechanisms and dynamics of silicone encapsulated ultraviolet A (UV-A) high-power light-emitting diodes (LEDs), with a peak wavelength of <inline-formula> <tex-math notation="LaTeX">${\mathrm {365~ \text {n} \text {m} }}$ </tex-math></inline-formula>. The stress tests were carried out for a period of 8665 hours with forward currents between <inline-formula> <tex-math notation="LaTeX">${\mathrm {350~ \text {m} \text {A} }}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">${\mathrm {700~ \text {m} \text {A} }}$ </tex-math></inline-formula> and junction temperatures up to 132°C. Depending on stress condition, a significant decrease in optical power could be observed, being accelerated with higher operating conditions. Devices stressed at a case temperature of 55 °C indicate a decrease in radiant flux between 10- <inline-formula> <tex-math notation="LaTeX">${\mathrm {40~\%}}$ </tex-math></inline-formula> varying with measurement current, whereas samples stressed at higher case temperatures exhibit crack formation in the silicone encapsulant accompanied by electromigration shorting the active region. The analyzed current and temperature dependency of the degradation mechanisms allows to propose a degradation model to determine the device lifetime at different operating parameters. Additional stress test data collected at different aging conditions is used to validate the model’s lifetime predictions.
Two-photon absorption of hydrocarbons at visible wavelengths

The two-photon absorption properties of brunched π-conjugated hydrocarbons at visible wavelengths, up to 400 nm measured by using the femtosecond open-aperture Z-scan method are presented. The hydrocarbons, phenylethynylsubstituted benzenes, shows moderate (several hundreds GM) or very large (~20,000 GM) two-photon absorption cross sections, suggesting such a hydrocarbons can be efficient two-photon absorption chromophores in the wavelength region.
An Element Selection Enhanced Hybrid Relay-RIS Assisted Communication System

In this letter, we propose a simple yet efficient element selection (ES) enhanced hybrid relay-reconfigurable intelligent surface (RIS) assisted communication system, where a subset of RIS elements is selected from the whole element set to connect with an additional power amplifier (PA) for realizing the active RIS. In contrast, the remanent elements reflect the signals passively without amplification serving as the passive RIS. To obtain the optimal active RIS element set, we propose to utilize a 0–1 diagonal ES matrix in the conventional RIS-assisted systems to express the connection relationship between the RIS elements and the PA. Then, we relax the 0–1 constraint and jointly optimize the ES matrix and RIS coefficients with an alternating optimization (AO) method. Due to the particular form of the ES matrix, the optimization problem can be transformed into a linear programming form, which indicates that the optimal solution of the ES matrix is the boundary of the constraint set, i.e., 0 or 1, which compensates for the influence of linear relaxation. The corresponding simulation results demonstrate that the proposed ES scheme was capable of outperforming the sub-connected scheme and the HR-RIS scheme without ES.
Similarity and reduction for time varying linear systems with well posed boundary conditions

The classical theory of similarity and reduction of causal and anti-causal systems is generalized and extended to time varying linear systems with well-posed boundary conditions. Two main problems are solved. The first is to determine to what extent a system with boundary conditions can be simplified by similarity and reduction. The second problem is to find the invariants of such a simplification. Special attention is given to the time invariant case.
A Hybrid Deep Cascade-ResNet Model for Detecting Alzheimer's Stages in MR Images

Neuroimaging is used for diagnosing neuropathological disorders, such as Alzheimer's disease (AD). In this study, a hybrid convolutional neural network (CNN) model is evaluated for its ability to improve AD diagnosis. Accordingly, we determine that using the CascadeNet and ResNet algorithms, we can precisely classify Alzheimer's disease stages in magnetic resonance imaging (MRI). Based on Kaggle datasets, we validate the proposed architecture and compare its performance with that of similar deep learning methods. We achieved 99.02% accuracy using quaternary classification. There was an accuracy of quaternary classification between all AD subtypes in the proposed model. Cascade-ResNet has better classification accuracy and processing complexity than other deep CNNs. The proposed model outperforms the current state-of-the-art deep learning methods when applied to MRI. Furthermore, the hybrid Cascade-ResNet performed well without the need for feature extraction and was insensitive to existing noise in the imaging. Consequently, untrained operators are able to apply the proposed model to digital patient imaging data. By distinguishing between AD patients and healthy individuals, this research can enhance value-based care in clinical settings.
Development of microwave-enhanced spark-induced breakdown spectroscopy

We propose microwave-enhanced spark-induced breakdown spectroscopy with the same measurement and analysis processes as in laser-induced breakdown spectroscopy, but with a different plasma generation mechanism. The size and lifetime of the plasma generated can contribute to increased measurement accuracy and expand its applicability to industrial measurement, such as an exhaust gas analyzer for automobile engine development and its regulation, which has been hard to operate by laser at an engineering evaluation site. The use of microwaves in this application helps lower the cost, reduce the system size, and increase the ease of operation to make it commercially viable. A microwave frequency of 2.45 GHz was used to enhance the volume and lifetime of the plasma at atmospheric condition even at elevated pressure.