Miracle-dz/UniFAR-FTUs huggingface dataset:
Early events in Agrobacterium-mediated genetic transformation of citrus explants.

BACKGROUND AND AIMS Genetic transformation of plants relies on two independent but concurrent processes: integration of foreign DNA into plant cells and regeneration of whole plants from these transformed cells. Cell competence for regeneration and for transformation does not always fall into the same cell type/developmental stage, and this is one of the main causes of the so-called recalcitrance for transformation of certain plant species. In this study, a detailed examination of the first steps of morphogenesis from citrus explants after co-cultivation with Agrobacterium tumefaciens was performed, and an investigation into which cells and tissues are competent for regeneration and transformation was carried out. Moreover, the role of phytohormones in the co-cultivation medium as possible enhancers of gene transfer was also studied. METHODS A highly responsive citrus genotype and well-established culture conditions were used to perform a histological analysis of morphogenesis and cell competence for transformation after co-cultivation of citrus epicotyl segments with A. tumefaciens. In addition, the role of phytohormones as transformation enhancers was investigated by flow cytometry. KEY RESULTS It is demonstrated that cells competent for transformation are located in the newly formed callus growing from the cambial ring. Conditions conducive to further development of this callus, such as treatment of explants in a medium rich in auxins, resulted in a more pronounced formation of cambial callus and a slower shoot regeneration process, both in Agrobacterium-inoculated and non-inoculated explants. Furthermore, co- cultivation in a medium rich in auxins caused a significant increase in the rate of actively dividing cells in S-phase, the stage in which cells are more prone to integrate foreign DNA. CONCLUSIONS Use of proper co-cultivation medium and conditions led to a higher number of stably transformed cells and to an increase in the final number of regenerated transgenic plants.
Strategies for initial sizing and operating point analysis of analog circuits

This work presents novel analog sizing flows based on analytical techniques. A graph-based operating point driven sizing approach provides operating point voltages and a rough sizing with respect to constraints. A voltage-range analysis method using linearized operating-point models obtains information about feasible voltage ranges. A direct-sizing method solves nonlinear algebraic circuit equations directly to obtain design parameters from specifications. All three methods require no or only minimum simulation effort and can provide quick insight into circuit design space and constraints in an early design stage. They allow flexible inclusion into state-of-the-art simulation-based optimization flows, where they lead to improved results with less optimization effort and prevent unnecessary simulation effort on unfeasible circuit topologies. The sizing flows are enhanced by a commercial optimization tool in order to obtain reliable circuits.
An Active Frequency Selective Surface Design Having Four Different Switchable Frequency Characteristics

Mutual interference between indoor adjacent wireless networks is becoming an important issue due to reducing the communication speed significantly. Control-ling the isolation of wireless networks by using frequency selective surfaces (FSSs) can be an efficient solution for such interference problems. Therefore, a switchable band-stop FSS design is presented in this work for unlicensed 2.4 and 5.8 GHz ISM (Industrial, Scientific and Medical) bands. In order to achieve desired frequency switch performance, a new theory is proposed in this paper by using PIN diodes. According to the proposed theory, PIN diodes should be placed in positions where high current densities are observed or where charges are collected. By using the proposed theory, a new FSS geometry design was carried out to control the targeted ISM bands. According to our best knowledge, there is no similar FSS work in the literature with four different frequency responses for 2.4 and 5.8 GHz ISM bands.
Outage Probability Minimization for Energy Harvesting Cognitive Radio Sensor Networks

The incorporation of cognitive radio (CR) capability in wireless sensor networks yields a promising network paradigm known as CR sensor networks (CRSNs), which is able to provide spectrum efficient data communication. However, due to the high energy consumption results from spectrum sensing, as well as subsequent data transmission, the energy supply for the conventional sensor nodes powered by batteries is regarded as a severe bottleneck for sustainable operation. The energy harvesting technique, which gathers energy from the ambient environment, is regarded as a promising solution to perpetually power-up energy-limited devices with a continual source of energy. Therefore, applying the energy harvesting (EH) technique in CRSNs is able to facilitate the self-sustainability of the energy-limited sensors. The primary concern of this study is to design sensing-transmission policies to minimize the long-term outage probability of EH-powered CR sensor nodes. We formulate this problem as an infinite-horizon discounted Markov decision process and propose an ϵ-optimal sensing-transmission (ST) policy through using the value iteration algorithm. ϵ is the error bound between the ST policy and the optimal policy, which can be pre-defined according to the actual need. Moreover, for a special case that the signal-to-noise (SNR) power ratio is sufficiently high, we present an efficient transmission (ET) policy and prove that the ET policy achieves the same performance with the ST policy. Finally, extensive simulations are conducted to evaluate the performance of the proposed policies and the impaction of various network parameters.
Argumentative Human Computer Dialogue for Automated Persuasion

Argumentation is an emerging topic in the field of human computer dialogue. In this paper we describe a novel approach to dialogue management that has been developed to achieve persuasion using a textual argumentation dialogue system. The paper introduces a layered management architecture that mixes task-oriented dialogue techniques with chatbot techniques to achieve better persuasiveness in the dialogue.
Code of practice for learning analytics

Introduction Learning analytics uses data about students and their activities to help institutions understand and improve educational processes, and provide better support to learners. It should be for the benefit of students, whether assisting them individually or using aggregated and anonymised data to help other students or to improve the educational experience more generally. It is distinct from assessment, and should be used for formative rather than summative purposes.
The structures of embedded clusters in the Perseus, Serpens and Ophiuchus molecular clouds

The young stellar population data of the Perseus, Ophiuchus and Serpens molecular clouds are obtained from the Spitzer Cores to Discs (c2d) legacy survey in order to investigate the spatial structure of embedded clusters using the nearest-neighbour (NN) and minimum-spanning tree method. We identify the embedded clusters in these clouds as density enhancements and analyse the clustering parameter Q with respect to source luminosity and evolutionary stage. This analysis shows that the older Class 2/3 objects are more centrally condensed than the younger Class 0/1 protostars, indicating that clusters evolve from an initial hierarchical configuration to a centrally condensed one. Only IC 348 and the Serpens core, the older clusters in the sample, show signs of mass segregation (indicated by the dependence of Q on the source magnitude), pointing to a significant effect of dynamical interactions after a few Myr. The structure of a cluster may also be linked to the turbulent energy in the natal cloud as the most centrally condensed cluster is found in the cloud with the lowest Mach number and vice versa. In general, these results agree well with theoretical scenarios of star cluster formation by gravoturbulent fragmentation.
Discovery of a Small Non-AUG-Initiated ORF in Poleroviruses and Luteoviruses That Is Required for Long-Distance Movement

Viruses in the family Luteoviridae have positive-sense RNA genomes of around 5.2 to 6.3 kb, and they are limited to the phloem in infected plants. The Luteovirus and Polerovirus genera include all but one virus in the Luteoviridae. They share a common gene block, which encodes the coat protein (ORF3), a movement protein (ORF4), and a carboxy-terminal extension to the coat protein (ORF5). These three proteins all have been reported to participate in the phloem-specific movement of the virus in plants. All three are translated from one subgenomic RNA, sgRNA1. Here, we report the discovery of a novel short ORF, termed ORF3a, encoded near the 5’ end of sgRNA1. Initially, this ORF was predicted by statistical analysis of sequence variation in large sets of aligned viral sequences. ORF3a is positioned upstream of ORF3 and its translation initiates at a non-AUG codon. Functional analysis of the ORF3a protein, P3a, was conducted with Turnip yellows virus (TuYV), a polerovirus, for which translation of ORF3a begins at an ACG codon. ORF3a was translated from a transcript corresponding to sgRNA1 in vitro, and immunodetection assays confirmed expression of P3a in infected protoplasts and in agroinoculated plants. Mutations that prevent expression of P3a, or which overexpress P3a, did not affect TuYV replication in protoplasts or inoculated Arabidopsis thaliana leaves, but prevented virus systemic infection (long-distance movement) in plants. Expression of P3a from a separate viral or plasmid vector complemented movement of a TuYV mutant lacking ORF3a. Subcellular localization studies with fluorescent protein fusions revealed that P3a is targeted to the Golgi apparatus and plasmodesmata, supporting an essential role for P3a in viral movement.
Allocating Resources Between Taking Action, Assessing Status, and Measuring Effectiveness of Conservation Actions

Abstract Millions of dollars are spent annually on biodiversity conservation projects at natural areas around the world. Managers of natural areas must achieve a balance between taking conservation action, evaluating the effectiveness of actions taken, and monitoring the general status of biodiversity conservation targets and the threats they face. Conservation practitioners often struggle with decisions regarding the allocation of limited resources among these competing needs. Many conservation projects have only a limited monitoring component while other projects have an inexplicably high investment in a single type of monitoring. We offer a conceptual framework to help guide conservation practitioners towards a logical allocation of resources between taking action and different types of monitoring depending on the situation that they are facing. The framework consists of a decision tree that includes an explicit evaluation of three questions: (1) Are there substantial threats facing the conservation entities? ; (2) Are there clear and feasible actions known to be effective at abating identified threats? ; and (3) Does the project team have high confidence in their understanding of the overall conservation situation? Based on this tree, we present five scenarios that illustrate a range of logical allocations of resources between taking action and different categories of monitoring.
Whole Genome Characterization of the Mechanisms of Daptomycin Resistance in Clinical and Laboratory Derived Isolates of Staphylococcus aureus

Background Daptomycin remains one of our last-line anti-staphylococcal agents. This study aims to characterize the genetic evolution to daptomycin resistance in S. aureus. Methods Whole genome sequencing was performed on a unique collection of isogenic, clinical (21 strains) and laboratory (12 strains) derived strains that had been exposed to daptomycin and developed daptomycin-nonsusceptibility. Electron microscopy (EM) and lipid membrane studies were performed on selected isolates. Results On average, six coding region mutations were observed across the genome in the clinical daptomycin exposed strains, whereas only two mutations on average were seen in the laboratory exposed pairs. All daptomycin-nonsusceptible strains had a mutation in a phospholipid biosynthesis gene. This included mutations in the previously described mprF gene, but also in other phospholipid biosynthesis genes, including cardiolipin synthase (cls2) and CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase (pgsA). EM and lipid membrane composition analyses on two clinical pairs showed that the daptomycin-nonsusceptible strains had a thicker cell wall and an increase in membrane lysyl-phosphatidylglycerol. Conclusion Point mutations in genes coding for membrane phospholipids are associated with the development of reduced susceptibility to daptomycin in S. aureus. Mutations in cls2 and pgsA appear to be new genetic mechanisms affecting daptomycin susceptibility in S. aureus.
Decreased expression of lncRNA Malat1 in rat spinal cord contributes to neuropathic pain by increasing neuron excitability after brachial plexus avulsion

Purpose: Neuropathic pain (NP) is a challenging clinical problem due to its complex pathogenesis. In our previous study using microarray, we found that the levels of lncRNA Malat1 were decreased in the spinal cord of NP rat after brachial plexus avulsion, but its contribution to NP remain unclear. The purpose of this study was to investigate its role in the pathogenesis of NP. Methods: In the NP model of complete brachial plexus avulsion rat, spinal cords were harvested, and fluorescence in situ hybridization (FISH) was used to test the spatial expression of Malat1 and qRT-PCR was used to confirm the quantitative expression of Malat1. In primary cultured neurons, Malat1 expression interfered with adenovirus. Spontaneous electric activities of neurons were tested using multi-electrode arrays and apoptosis of neurons was tested using TUNEL method. The change of intracellular calcium concentration was analyzed using calcium imaging method. Results: Decreased Malat1 expression was confirmed using qRT-PCR, and Malat1 was identified in the cytoplasm of neurons in spinal cord, but not in glia. In vitro, the decrease of Malat1 resulted in an increase in the frequency of spontaneous electric activity in neurons but had no effect on neuronal apoptosis. Further analysis indicated during glutamate stimulation, the change of intracellular calcium concentration in neurons with downregulated Malat1 expression was significantly greater than that in normal neurons. Conclusion: Reduced Malat1 expression may induce NP by increasing neuronal excitability in the spinal cord via regulation of calcium flux.
On contrast combinations for visual saliency detection

Saliency detection is an important task in computer vision and image processing. The most influential factor in bottom-up visual saliency is contrast operation. In this paper, we propose a unified model to combine widely used contrast measurements, namely, center-surround, corner-surround and global contrast to detect visual saliency. The proposed model benefits from the advantages of each individual contrast operation, and thus produces more robust and accurate saliency maps. Extensive experimental results on natural images show the effectiveness of the proposed model for visual saliency detection task, and demonstrate the combination is superior than individual subcomponent.
Optimal Design of a Push-Pull-Forward Half-Bridge (PPFHB) Bidirectional DC–DC Converter With Variable Input Voltage

This paper presents a low-cost bidirectional isolated dc-dc converter, derived from dual-active-bridge converter for the power sources with variable output voltage like super capacitors. The proposed converter consists of push-pull-forward circuit half-bridge circuit (PPFHB) and a high-frequency transformer; this structure minimizes the number of the switching transistors and their associate gate driver components. With phase-shift control strategy, all the switches are operated under zero-voltage switching (ZVS) condition. Furthermore, in order to optimize the converter performance and increase efficiency, optimal design methods and criteria are investigated, including coupled inductors design, bidirectional power flow analysis, harmonics analysis, and ZVS range extension. Based on all the optimal parameters, higher efficiency can be achieved. Finally, prototypes are built in laboratory controlled by digital signal processor for comparison purpose. Detailed test results verify the theoretical analysis and demonstrate the validity of optimization design method.
Assessment of the Effect of Energy Consumption on Trajectory Improvement for a Car-like Robot

Summary Reducing the energy consumed by a car-like mobile robot makes it possible to move at a lower cost, yet it takes more working time. This paper proposes an optimization algorithm for trajectories with optimal times and analyzes the consequences of restricting the energy consumed on the trajectory obtained for a car-like robot. When modeling the dynamic behavior of the vehicle, it is necessary to consider its inertial parameters, the behavior of the motor, and the basic properties of the tire in its interaction with the ground. To obtain collision-free, minimum-time trajectories quadratic sequential optimization techniques are used, where the objective function is the time taken by the robot to move between two given configurations. This is subject to constraints relating to the vehicle and tires as well as the energy consumed, which is the basis for this paper. We work with a real random distribution of consumed energy values following a normal Gaussian distribution in order to analyze its influence on the trajectories obtained by the vehicle. The energy consumed, the time taken, the maximum velocity reached, and the distance traveled are analyzed in order to characterize the properties of the trajectories obtained. The proposed algorithm has been applied to 101 examples, showing that the computational times needed to obtain the solutions are always lower than those required to realize the trajectories. The results obtained allow us to reach conclusions about the energy efficiency of the trajectories.
Evidence for adaptive responses to historic drought across a native plant species range

As climatic conditions change, species will be forced to move or adapt to avoid extinction. Exacerbated by ongoing climate change, California recently experienced a severe and exceptional drought from 2011 to 2017. To investigate whether an adaptive response occurred during this event, we conducted a “resurrection” study of the cutleaf monkeyflower (Mimulus laciniatus), an annual plant, by comparing trait means and variances of ancestral seed collections (“pre‐drought”) with contemporary descendant collections (“drought”). Plants were grown under common conditions to test whether this geographically restricted species has the capacity to respond evolutionarily to climate stress across its range. We examined if traits shifted in response to the recent, severe drought and included populations across an elevation gradient, including populations at the low‐ and high‐elevation edges of the species range. We found that time to seedling emergence in the drought generation was significantly earlier than in the pre‐drought generation, a response consistent with drought adaptation. Additionally, trait variation in days to emergence was reduced in the drought generation, which suggests selection or bottleneck events. Days to first flower increased significantly by elevation, consistent with climate adaptation across the species range. Drought generation plants were larger and had greater reproduction, which was likely a carryover effect of earlier germination. These results demonstrate that rapid shifts in trait means and variances consistent with climate adaptation are occurring within populations, including peripheral populations at warm and cold climate limits, of a plant species with a relatively restricted range that has so far not shifted its elevation distribution during contemporary climate change. Thus, rapid evolution may mitigate, at least temporarily, range shifts under global climate change. This study highlights the need for better understanding rapid adaptation as a means for plant communities to cope with extraordinary climate events.
Relevance and Support calculation for Health information

Consumer health information search (CHIS) is a forum of information retrieval that has organized two tasks to be performed. The first task includes the identification that whether a given query is relevant or irrelevant to the sentences available in the document. The second tasks talks about finding the nature of support of a sentence in the document to the query. Task 1 i.e identification of relevance is done by performing different similarity measures calculations and finally averaging the obtained score to find the relevance nature of a sentence. The second task is solved by using a special type of support vector machine called C-support vector machines that can handle multiclass support. The results obtained from CHIS organizers shown that model developed for second task shown promising results than that of the model developed for the first task.
Two-Dimensional DOA Estimation of Sound Sources Based on Weighted Wiener Gain Exploiting Two-Directional Microphones

We propose a new method for estimating directions of arrival (DOAs) of sound sources, both in azimuthal and elevation angle, using two directional microphones. This method adopts weighted Wiener gain (WWG) for DOA estimation. WWG is an estimate of the Wiener gain that we proposed for use in automatic gain control to enhance speech that is degraded by additive noise. Angular resolution of WWG arises from spectral subtraction (SS)-based noise reduction involved in the WWG calculation, which enhances the signal from the look direction while suppressing signals from other directions. Because WWG involves two-channel SS, which can deal with instantaneous noise, noise sources need not to be stationary, as they must be with ordinary single-channel SS. We further propose the exploitation of a pair of directional microphones whose front directions are arranged in rotational symmetry. The time difference and amplitude difference between the two-channel signal provided by the microphones are utilized to yield a two-dimensional resolution of DOA. We evaluated the proposed method through computer simulations and compared it to three DOA estimation methods that are based on a cross-correlation function and two popular high-resolution methods of multiple signal classification and minimum variance method. Evaluation results of the source detection rate and estimation accuracy demonstrate the remarkable superiority of our method compared to the other methods in conditions where multiple speech sources exist