Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of SOBIR1 accumulation and defence activation in an autoimmune mutant by specific components of ER quality control.

ii Preface . iii Table of contents . v List of figures . vii List of abbreviations . viii Acknowledgements . xi Chapter 1: Introduction . 1 1.1 Plant immunity . 1 1.2 Receptor-like kinases (RLKs) and receptor-like proteins (RLPs) . 3 1.3 Genetic analysis of defence responses regulated by BIR1 and SOBIR1 . 4 1.4 ER-QC in plant immunity . 7 Chapter 2: Regulation of SOBIR1 accumulation and activation of defence responses in bir1-1 by ER-quality control components CRT3, ERdj3b and SDF2 . 12 2.1 Introduction . 12 2.2 Results . 15 2.2.1 Identification and characterization of sobir3-1 bir1-1 pad4-1 . 15 2.2.2 SOBIR3 encodes CALRETICULIN 3 . 17 2.2.3 CRT3 is required for cell death and defence responses in bir1-1 . 19 2.2.4 Identification of an allele of erdj3b that supresses bir1-1 pad4-1 mutant phenotypes . 21 2.2. 5 ERdj3b is required for cell death and defence responses in bir1-1 . 23 2.2. 6 Identification of an allele of sdf2 that supresses bir1-1 pad4-1 mutant phenotypes . 25 2.2. 7 SDF2 is required for cell death and defence responses in bir1-1 . 27 2.2. 8 CRT3 and ERdj3b are required for the accumulation of SOBIR1 . 29 2.3 Discussion . 30 2.4 Experimental procedures . 32 2.4. 1 Plant material . 32 2.4. 2 Mutant characterization . 33 vi 2.4. 3 Analysis of SOBIR1 protein levels in crt3-1 and erdj3b-1 mutant plants . 34 Chapter 3: Regulation of SOBIR1 accumulation and activation of defence responses in bir1-1 by ER-quality control components UGGT and STT3a . 35 3.1 Introduction . 35 3.2 Results . 37 3.2.1 Identification and characterization of sobir6-1 bir1-1 pad4-1 . 37 3.2.2 SOBIR6 encodes UGGT . 38 3.2.3 UGGT is required for constitutive defence responses in bir1-1 . 41 3.2.4 The autoimmune phenotype of bir1-1 is partially suppressed by stt3a-2 . 42 3.2. 5 Accumulation of SOBIR1 is reduced in sobir6-1 but unaffected in stt3a-2 . 45 3.3 Discussion . 46 3.4 Experimental procedures . 48 3.4. 1 Plant material . 48 3.4. 2 Mutant characterization . 48 3.4. 3 Analysis of SOBIR1 protein levels in sobir6-1 and stt3a-2 mutant plants . 49 Chapter 4: Future directions and conclusions . 50 References: . 52
Comparison of ameliorative effects of Taraxacum syriacum and N-acetylcysteine against acetaminophen-induced oxidative stress in rat liver and kidney.

Taraxacum syriacum (TS) with natural antioxidant and pharmacological activities may be considered for treatment of oxidative stress induced by acetaminophen (APAP). The aim of the present study was to evaluate the ameliorative effects of the ethanol extract of TS root against hepatorenal toxicity induced by APAP in comparison to N-acetylcysteine (NAC) as a standard drug. Thirty male Wistar rat were randomly divided into five groups. Control group; APAP (1g/kg) group; APAP-NAC (160 mg/kg) group and APAP-TS100 and APAP-TS200 groups: APAP plus 100 and 200 mg/kg of TS extract, respectively. After 7 days treatment, serum and liver and kidney tissues were prepared and evaluated. TS extract ameliorated the increased lipid peroxidation level and decreased antioxidant enzymes activities and glutathione level in liver and kidney of APAP-treated rats. Moreover, treatment with the TS extract caused significant reduction in the histopathological damages and high levels of serum biochemical markers of hepatic and renal functions after APAP treatment. This study suggests that the extract of TS roots has dose-dependent ameliorative effect against APAP-induced oxidative damage in liver and kidney due to its free radical scavenging and antioxidant properties. The overall efficacy of the extract at 200 mg/kg dose is comparable with NAC.
Optimization of Parallel Structure of Planar Inductor Winding

Planar magnetic components have the advantages of high operating frequency, high efficiency, and low susceptibility to interference, and are widely used in high-frequency and miniaturized power supply systems. However, due to the limitation of the copper thickness of the PCB winding, multiple parallel connections are required to reduce the current density in high current applications. This paper completes the design of the planar inductor based on the two-stage Buck-Boost integrated LLC converter(BBLLC). Three different parallel structures are proposed, which called direct parallel structure, interleaved parallel structure, and sandwich parallel structure. The loss of three different structures will be analyzed, and the simulation is verified by ANASYS Maxwell software. The purposed structure improves the current sharing ability between layers and reduces the current density, which compares to the unparalleled structure. The AC resistance of the purposed structure is the smallest, which minimizes the copper loss of the inductor and improves the efficiency of the converter.
Metabolic tuning of inhibition regulates hippocampal neurogenesis in the adult brain

Significance Our the brain actively responds to changes in the environment by remodeling neural circuits. One important aspect of neuroplasticity is adult neurogenesis, which involves the generation, survival, and incorporation of new neurons into existing circuits and is unique to two discrete areas of the mammalian brain. The hippocampus, critical for learning and memory, is one such area that exhibits ongoing neurogenesis throughout an individual’s lifetime. Although recent studies have confirmed that hippocampal behaviors regulate neurogenesis, the mechanistic pathways governing that regulatory activity remain poorly understood. In this work, we found that hippocampal behaviors increase inhibitory circuit activity through a metabolic pathway, and established a computational model to quantitively model the relationship between circuit activity and control of hippocampal neurogenesis. Hippocampus-engaged behaviors stimulate neurogenesis in the adult dentate gyrus by largely unknown means. To explore the underlying mechanisms, we used tetrode recording to analyze neuronal activity in the dentate gyrus of freely moving adult mice during hippocampus-engaged contextual exploration. We found that exploration induced an overall sustained increase in inhibitory neuron activity that was concomitant with decreased excitatory neuron activity. A mathematical model based on energy homeostasis in the dentate gyrus showed that enhanced inhibition and decreased excitation resulted in a similar increase in neurogenesis to that observed experimentally. To mechanistically investigate this sustained inhibitory regulation, we performed metabolomic and lipidomic profiling of the hippocampus during exploration. We found sustainably increased signaling of sphingosine-1-phosphate, a bioactive metabolite, during exploration. Furthermore, we found that sphingosine-1-phosphate signaling through its receptor 2 increased interneuron activity and thus mediated exploration-induced neurogenesis. Taken together, our findings point to a behavior-metabolism circuit pathway through which experience regulates adult hippocampal neurogenesis.
A tale of two genomes: role of a chloroplast signal in coordinating nuclear and plastid genome expression

Plant cells coordinately regulate the expression of nuclear and plastid genes that encode components of the photosynthetic apparatus. Nuclear genes that regulate chloroplast development and chloroplast gene expression provide part of this coordinate control. However, there is compelling evidence that information also flows in the opposite direction, from chloroplasts to the nucleus. This hypothesised, second pathway functions to coordinate the expression of nuclear genes encoding components of the photosynthetic apparatus with the functional state of the chloroplast. Here we review the evidence for the signal transduction pathway from the chloroplasts to the nucleus and suggest possible signal molecules.
Convolutional Neural Network with Multi-Valued Neurons

In this paper, a convolutional neural network (CNN) based on multi-valued neurons (MVNs) with complex-valued weights is presented. Convolutional neural networks are known as one of the best tools for solving such problems as image and speech recognition. The vast majority of researches and users so far employ a classical CNN, which operates with real-valued inputs/outputs and is based on classical neurons with a sigmoidal activation function. Recently complex-valued CNNs were introduced, but their neurons employ an activation function, which is a complex-valued generalization of a sigmoidal one. While such complex-valued neurons are more flexible when they learn and make it possible to process complex-valued data, their generalization capability is basically not higher than the one of real-valued neurons. At the same time there exists a complex-valued neuron (a multi-valued neuron – MVN) with a phase dependent activation function whose functionality is higher than the one of neurons with a sigmoidal activation function. It is also known that a multilayer neural network with multi-valued neurons (MLMVN) outperforms a classical multilayer peceptron in terms of speed of learning and generalization capability. Hence our goal was to develop a convolutional neural network based on multi-valued neurons (CNNMVN). We consider in detail a learning algorithm for CNNMVN, which is derivative free as well as the one for MLMVN. We also suggested the max pool operation for complex numbers. These results are illustrated by simulations showing that CNNMVN with even a minimal convolutional topology is able to solve image recognition problems with pretty high accuracy.
Robust Segmentation of 3D Brain MRI Images in Cross Datasets by Integrating Supervised and Unsupervised Learning

With the rapid development of machine learning technology in recent years, image segmentation technology based on supervised learning or unsupervised learning has also made important progress and achieved many successful applications, such as the applications to medical imaging in the same time. However, both supervised and unsupervised segmentation methods have their own strong and weak points. In order to address this dilemma, in this paper, we proposed a robust method for 3D image segmentation that can not only maintain the advantages of the two kinds of learning methods, but also overcome their disadvantages, by integrating supervised and unsupervised learning technologies into one method effectively. The proposed method has been applied to brain MRI image segmentation with a variety of experiments on several open 3D brain MRI datasets. Experimental results obtained in the work show that the proposed method, with strong adaptability and robustness, outperforms other state of the art segmentation approaches including both the supervised and unsupervised ones when applied to a new MRI dataset or a cross dataset without needing to be retrained by using the annotation information of the dataset.
Study on the coordination agent system of Sn-Ag-Cu ternary alloy co-deposition

With the developing of Surface packaging technology, the requirement of electronic components on coating is getting more and more rigorous. Sn-Ag-Cu ternary alloy coating has the advantages of low melting point, good weldability and so on. It is considered to be the best choice to replace Sn-Pb coating. However, due to the large difference in deposition potentials of Sn2+, Ag+ and Cu2+, it is difficult to co-deposit. It is necessary to add coordination agent in the plating solution to make the deposition potentials of Sn2+, Ag+ and Cu2+ close to each other and stabilize the plating solution. In this paper, the co-deposition of Sn-Ag-Cu was achieved by using EDTA-2Na, ammonium citrate and thiourea as additives. The effects of EDTA-2Na, ammonium citrate and thiourea on Sn, Ag and Cu Sheet metal and Sn-Ag-Cu alloys were analyzed by Potentiometric scanning curve. It was found that the three additives could make the deposition potentials of Sn2+, Ag+ and Cu2+ close to each other. The kinds and proportions of additives were changed in order to find a suitable coordination agent system. The bath with ammonium citrate and EDTA-2Na was more stable than that with thiourea. The surface morphology of the coating was observed by Scanning Electronic Microscopy (SEM). It is found that the coating with compact structure and smooth surface can be obtained by adding thiourea in the plating solution.
Anomalous IP Address Detection on Traffic Logs Using Novel Word Embedding

This paper presents an anomalous IP address detection algorithm for network traffic logs. It is based on word embedding techniques derived from natural language processing to extract the representative features of IP addresses. However, the features extracted from vanilla word embeddings are not always compatible with machine learning-based anomaly detection algorithms. Therefore, we developed an algorithm that enables the extraction of more compatible features of IP addresses for anomaly detection than conventional methods. The proposed algorithm optimizes the objective functions of word embedding-based feature extraction and anomaly detection, simultaneously. According to the experimental results, the proposed algorithm outperformed conventional approaches; it improved the detection performance from 0.876 to 0.990 in the area under the curve criterion in a task of detecting the IP addresses of attackers from network traffic logs.
WoTnectivity: A Communication Pattern for Different Web of Things Connection Protocols

The Web of Things proposes an IoT device definition framework, the Thing Description. Conceptually, this definition covers a wide range of devices, protocols, and data types. On the other hand, the proliferation of IoT devices and the traits that they usually exhibit, such as limited number of resources, leads to the emergence of bottlenecks that cause the slowdown of requests and even the shutdown of devices. To solve these problems, we introduce the concept of Digital Dice, a digital representation of an IoT device based on microservices that uses the framework established by the W3C Web of Things. This article describes WoTnectivity, a mechanism that allows the connection of multiple protocols on IoT devices by means of several common communication patterns. Besides, establishing the possibility of connecting with different protocols, WoTnectivity has been developed with future expansion in mind, thus an explanation on how to add more protocols is also studied in this paper.
Effect of Annealing on the Microstructure and SERS Performance of Mo-48.2% Ag Films

Mo-48.2% Ag films were fabricated by direct current (DC) magnetron sputtering and annealed in an argon atmosphere. The effects of annealing on the surface morphology, resistivity and surface-enhanced Raman scattering (SERS) performance of Mo-48.2% Ag films were investigated. Results show a mass of polyhedral Ag particles grown on the annealed Mo-48.2% Ag films’ surface, which are different from that of as-deposited Mo-Ag film. Moreover, the thickness and the resistivity of Mo-48.2% Ag films gradually decrease as the annealing temperature increases. Furthermore, finite-difference time-domain (FDTD) simulations proved that the re-deposition Ag layer increases the “hot spots” between adjacent Ag nanoparticles, thereby greatly enhancing the local electromagnetic (EM) field. The Ag layer/annealed Mo-48.2% Ag films can identify crystal violet (CV) with concentration lower than 5 × 10−10 M (1 mol/L = 1 M), which indicated that this novel type of particles/films can be applied as ultrasensitive SERS substrates.
Antimicrobial Peptides as New Combination Agents in Cancer Therapeutics: A Promising Protocol against HT-29 Tumoral Spheroids

Antimicrobial peptides are molecules synthetized by a large variety of organisms as an innate defense against pathogens. These natural compounds have been identified as promising alternatives to widely used molecules to treat infections and cancer cells. Antimicrobial peptides could be viewed as future chemotherapeutic alternatives, having the advantage of low propensity to drug resistance. In this study, we evaluated the efficiency of the antimicrobial peptide gramicidin A (GA) and the anticancer drug, doxorubicin (Doxo) against the spheroids from colorectal cancer cells (HT-29). The two drugs were applied separately against HT-29 spheroids as well as together to determine if they can act synergistically. The spheroid evolution, cell viability, and ATP levels were monitored at 24 and 48 h after the applied treatments. The results show significant drops in cell viability and cellular ATP levels for all the experimental treatments. The simultaneous use of the two compounds (GA and Doxo) seems to cause a synergistic effect against the spheroids.
Bright Mid-Infrared (MIR) Photoluminescence Sources and their Application in Imaging and Sensing

Mid-infrared (MIR) spectroscopy and imaging underpin many applications, ranging from industrial process monitoring to environmental analysis, and offer a new era in healthcare and clinical diagnostics. The spectral region from 1.5 to $12\ \mu \mathrm{m}$ is of interest since it contains strong characteristic absorption peaks associated with the vibrational transitions of many important molecules. A principal requirement for rapid measurement is bright, fibre-based, sources that, if possible, should also be robust and low cost. This paper describes our work to use sources based on the photoluminescence from Pr3+ and Dy3+ doped GeAsGaSe fibres to provide affordable carbon dioxide (CO2) sensing in heritage buildings. Limitations to the Beer Lambert law, previously reported by others, were observed in the sensing system, and the sensors were consequently calibrated empirically. Simulation results show that the use of commercial filters provides a promising approach to realising more compact, real-time, sensing.
A Tool for Non-Intrusive and Privacy-Preserving Developers' Programming Activity Data Collection

The quality of software products is closely related to software developers. A good psychological state can improve the quality of software products to a certain extent. More and more researchers are beginning to study how to effectively identify the psychological state of developers to help their work. However, many of these works have a significant intrusion into developers and are not suitable for long-term deployment in real enterprises. In this paper, we present a tool for IDE-based programming activity data collection for software developers. A conceptual model is presented for raw data collection and hierarchical concept encapsulation. We implement this tool in the form of an IDE plug-in for popular IDEs including IntelliJ IDEA and Android Studio, which can collect and process developers' in-IDE activity data in a non-intrusive and privacy-preserving manner. To demonstrate its usefulness, we deploy the proposed tool in a real enterprise environment. Based on this tool and the data collected in the real enterprise environment, we build applications including programming activity statistics and flow state recognition. The experiment results suggest the proposed approach can effectively capture the detailed programming activities and perform flow state recognition. The recognition accuracy is 80.14%.
Emotion Recognition Techniques for Geriatric Users: A Snapshot

Several elderly people prefer their independence, however due to cognitive impairment or other age-related ailments they cannot necessarily be left on their own. In order to aid the elderly in living independently, we consider the use of emotion recognition as a relatively autonomous monitoring approach for geriatric people. An analysis and comparison among various emotion recognition studies has shown that close to none of these studies have taken age related cognitive decline into account, which comes with various issues. The aim of this paper is to provide an overview of current emotion recognition techniques and why they may not necessarily be suitable or feasible for geriatric people. This analysis serves as a foundation for a proposed conceptual framework toward an autonomous monitoring system for geriatric people which could minimize the need for explicit user input or interaction while still monitoring the geriatric person(s) well-being.
Orthohantaviruses, Emerging Zoonotic Pathogens

Orthohantaviruses give rise to the emerging infections such as of hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in Eurasia and the Americas, respectively. In this review we will provide a comprehensive analysis of orthohantaviruses distribution and circulation in Eurasia and address the genetic diversity and evolution of Puumala orthohantavirus (PUUV), which causes HFRS in this region. Current data indicate that the geographical location and migration of the natural hosts can lead to the orthohantaviruses genetic diversity as the rodents adapt to the new environmental conditions. The data shows that a high level of diversity characterizes the genome of orthohantaviruses, and the PUUV genome is the most divergent. The reasons for the high genome diversity are mainly caused by point mutations and reassortment, which occur in the genome segments. However, it still remains unclear whether this diversity is linked to the disease’s severity. We anticipate that the information provided in this review will be useful for optimizing and developing preventive strategies of HFRS, an emerging zoonosis with potentially very high mortality rates.
Reduction of MOS Interface Defects in TiN/Y₂O₃/Si₀.₇₈Ge₀.₂₂ Structures by Trimethylaluminum Treatment

We report improvement of TiN/Y<sub>2</sub>O<sub>3</sub>/ Si<sub>0.78</sub>Ge<sub>0.22</sub> metal-oxide-semiconductor (MOS) interface properties by employing the trimethylaluminum (TMA) pretreatment before Y<sub>2</sub>O<sub>3</sub> deposition. It is found that the optimum number of the TMA pretreatment cycles for minimizing interface trap density (<inline-formula> <tex-math notation="LaTeX">${D}_{\text {it}}$ </tex-math></inline-formula>) and slow trap density (<inline-formula> <tex-math notation="LaTeX">$\Delta {N}_{\text {st}}$ </tex-math></inline-formula>) of TiN/Y<sub>2</sub>O<sub>3</sub>/SiGe interfaces with post metallization annealing (PMA) at 450 °C is ten cycles. The reduction in <inline-formula> <tex-math notation="LaTeX">${D} _{\text {it}}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\Delta ~{N} _{\text {st}}$ </tex-math></inline-formula> is attributable to less amounts of Ge–O bonds at the SiGe interfaces. On the other hand, an increase in <inline-formula> <tex-math notation="LaTeX">${D} _{\text {it}}$ </tex-math></inline-formula> with further increasing the number of TMA pretreatment is attributable to more amounts of Al–O bonds in ILs.
Investigating the Understanding of Plagiarism: A Case Study of Code Plagiarism in China

Plagiarism is a matter of great concern in academic. Especially, colleges and universities which involve homework, exams, credits and degrees, are the hardest hit area for plagiarism. Although it is a common sense about plagiarism for teachers and students that plagiarism is forbidden, a blurred boundary line is always there when plagiarism happens in real cases. In computer science, the problem is more severe as the definition of code plagiarism is more ambiguous and difficult than the text plagiarism. The assignments and projects for computer science students include not only documents, but also codes, which contain variables, functions, comments etc. This research is a case study on the code plagiarism in a programming course. Questionnaires were conducted to get general ideas about code plagiarism from several universities in China. The problems of code plagiarism are discussed in this study. Some thoughts are raised on the measure of the code plagiarism and the strategies from management point of view.