Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and Preliminary Biochemical Characterization of MppQ, a PLP-Dependent Aminotransferase from Streptomyces hygroscopicus

MppQ is an enzyme of unknown function from Streptomyces hygroscopicus that is involved in the biosynthesis of the nonproteinogenic amino acid L-enduracididine (L-End). Since L-End is a component of several peptides showing high activity against methicillin-resistant Staphylococcus aureus (MRSA), a complete understanding of its biosynthetic pathway is of utmost importance for developing chemoenzymatic routes for syntheses of novel antibiotics. In this work, we report high-resolution X-ray crystal structures of MppQ complexed with pyridoxal-5’-phosphate (PLP) and pyridoxamine-5’-phosphate (PMP). The structure of MppQ shares a fold with known Type I PLP-dependent aminotransferases, consisting of an N-terminal extension, large domain, and a small domain. We also report the first functional characterization of MppQ, which we incubated with enzymatically produced 2-ketoenduracidine and observed conversion to L-End via mass spectroscopy. Additionally, we have observed that MppQ has a relatively high affinity for 2-ketoarginine, a shunt product in the L-End biosynthetic pathway, indicating a possible role of MppQ in increasing efficiency of L-End biosynthesis by converting 2-ketoarginine back to the starting material, L-arginine.
Biological responses to terahertz radiation with different power density in primary hippocampal neurons

Background Terahertz (THz) radiation is a valuable imaging and sensing tool which is widely used in industry and medicine. However, it biological effects including genotoxicity and cytotoxicity are not clear, particularly on the nervous system. In this study, we investigated how THz radiation with different frequency and intensity would affect the morphology, cell growth and function of rat hippocampal neurons in vitro. Methods Primary hippocampal neuronal cells were isolated from newborn Wistar rat pups and were exposed to THz radiation with the frequencies of 0.12 THz and 0.141 THz, at an power intensities of 10 mW/cm2 and 30 mW/cm2 respectively. The cellular activities were evaluated by Cell Counting Kit-8 after exposure for 10 min and 30 min. The cellular apoptosis was examined by Annexin V staining using flow cytometry and the ultrastructure was detected by electron microscopy. Moreover, the amount of amino acid in the cultured neurons was measured by high performance liquid chromatography (HPLC). Results No obvious morphological changes, such as axon length and axon number, could be detected in primary neurons after exposure to 10mW/cm2 or 50 mW/cm2 THz for 30 min. However, the overall cellular activities were differentially affected by 10mW/cm2 and 50 mW/cm2 THz. Obvious cellular apoptosis was induced by both 10mW/cm2 and 50 mW/cm2 exposure. We also found that the amounts of most amino acids did not change significantly after exposure to these two types of THz radiation. Conclusions The effects of THz radiation on hippocampal neurons depend on frequency, power, exposure time as well as the measurement time after the exposure. These results will provide important information for further investigation of the effect of THz radiation on the nervous system.
Molecular differences in APOBEC3 counteraction by primate herpesviruses reveal an evolutionary link between the genesis of APOBEC3B and novel viral ribonucleotide reductase function

Viruses have evolved diverse mechanisms to antagonize host immunity. A recently discovered example is the direct inhibition and relocalization of cellular APOBEC3B (A3B) by the Epstein-Barr virus (EBV) ribonucleotide reductase (RNR) subunit BORF2. Recent reports also indicate interactions between the RNRs of other human herpesviruses and A3B, as well as interactions with the homologous APOBEC3A (A3A) enzyme. Here, we investigate the conservation of this APOBEC3 (A3) counteraction mechanism and reveal novel insights into its evolutionary origin. First, we found that herpesvirus RNRs bind to A3s via partially distinct surfaces. Second, we show that RNR-mediated relocalization and enzymatic inhibition of cellular A3s depend on binding to different regions of the A3 catalytic domain and that the inhibition is specific to A3B. Finally, we show that the ability of viral RNRs to counteract A3s is conserved in herpesviruses that infect humans and Old World monkeys, but absent in viruses infecting New World monkeys that naturally lack A3B. These results combine to indicate that the genesis of A3B at a critical branchpoint in primate evolution may have been a driving force in selecting herpesviruses with an expanded RNR functionality through counteraction of this antiviral enzyme.
Thermal effect on endurance performance of 3-dimensional RRAM crossbar array*

Three-dimensional (3D) crossbar array architecture is one of the leading candidates for future ultra-high density nonvolatile memory applications. To realize the technological potential, understanding the reliability mechanisms of the 3D RRAM array has become a field of intense research. In this work, the endurance performance of the 3D 1D1R crossbar array under the thermal effect is investigated in terms of numerical simulation. It is revealed that the endurance performance of the 3D 1D1R array would be seriously deteriorated under thermal effects as the feature size scales down to a relatively small value. A possible method to alleviate the thermal effects is provided and verified by numerical simulation.
Molecular basis of neurodevelopmental disorder-causing mutation in nonsense-mediated mRNA decay factor UPF3B

UPF3B is a key nonsense-mediated mRNA decay (NMD) factor required for surveillance of mRNA and regulation of eukaryotic gene expression. Mutations in UPF3B cause intellectual disability. The underlying molecular mechanisms remain unexplored as the mutations lie in an uncharacterized region of UPF3B. Here, we show that UPF3B shares structural and functional homology to the Drosophila Behavior/Human Splicing protein family comprising an RNA-recognition motif-like domain (RRM-L), a NONA/paraspeckle-like domain (NOPS-L), and extended α-helical domains essential for ribosome- and RNA-binding and RNA-induced oligomerization. A co-crystal structure of UPF3B with the third middle domain of eukaryotic initiation factor 4G (MIF4GIII) of UPF2 reveals an unexpectedly intimate binding interface. UPF3B’s disease-causing mutation Y160D located in the NOPS-L domain reduces the UPF2 binding affinity ~40-fold compared to wildtype UPF3B. UPF3B’s paralogue UPF3A, an NMD antagonist which is upregulated in patients with the UPF3B-Y160D mutation, binds UPF2 with ~10-fold higher affinity than UPF3B, leading to impaired NMD activity and upregulation of mRNAs involved in neurodevelopment.
Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome

The human Mixed Lineage Leukemia-1 (MLL1) complex orchestrates methylation of histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, WDR5, RbBp5, Ash2L, and DPY-30, have revealed variation in the docking of MLL1-WRAD on nucleosomes and left ambiguous portions of Ash2L and the position of DPY30. We used an integrated approach combining cryo-electron microscopy and mass spectrometry-crosslinking to determine structures of the MLL1-WRAD complex bound to ubiquitinated nucleosomes containing the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The subunits in all four states are positioned on the nucleosome in manner that is similar to a previous structure of MLL1-WRAD bound to ubiquitinated nucleosome, but that differs from structures with unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex. Significance The Mixed Lineage Leukemia-1 (MLL1) complex plays a role in activating transcription by methylating lysine 4 in histone H3, a reaction that is stimulated by the presence of ubiquitin conjugated to histone H2B. Recent structures of the core MLL1 complex, termed MLL1-WRAD, have revealed the existence of multiple docking states and have also left ambiguous portions of the structure. Here we combine mass spectrometry-cross linking with cryo-EM to model additional regions of the MLL1-WRAD complex and identify a series of states that light on complex assembly and the role that ubiquitin plays in orienting MLL1-WRAD on nucleosomes.
COMPARISON OF 3D REALITY CAPTURE TECHNOLOGIES FOR THE SURVEY OF STONE WALLS

The maintenance of the external fabric of historic buildings constitutes a large portion of overall building life cycle costs.Advanced reality capture and data processing technologies have the potential to transform existing survey practice,providing surveyors with objective data pertaining to building fabric, in a more rapid (frequent), safe and cost-effectivemanner. In this paper, we present a unique evaluation of several Terrestrial Laser Scanning (TLS) and photogrammetric(PG) systems that assess their relative strengths for the survey of stone walls. The assessment is conducted using anhistoric building selected for its representativeness of form, fabric and condition. The work considers performance interms of data accuracy and precision, data completeness, and process efficiency. The results show that, while TLSprovides good geometric data to generate accurate and valuable 3D models, the quality of PG reconstructions can bealso be sufficient in such contexts. And considering the relatively low-cost and portability of modern digital camerascompared to laser scanners, photogrammetry can constitute a realistic alternative to TLS. In addition, mounting a cameraon a UAV could further solve access issues, preventing the need for any additional infrastructure (e.g. scaffolding), whichwould be required when employing TLS. However, a lesson drawn from this work is that effective acquisition ofphotogrammetric data requires careful planning to select the appropriate camera settings and picture density (andlocations) to ensure accurate and reliable photogrammetric reconstruction. This process may be referred to as: Planningfor Photogrammetry (P4P).
Moxifloxacin-mediated killing of Mycobacterium tuberculosis involves respiratory downshift, reductive stress, and ROS accumulation

Moxifloxacin is central to treatment of multidrug-resistant tuberculosis. Effects of moxifloxacin on Mycobacterium tuberculosis redox state were explored to identify strategies for increasing lethality and reducing the prevalence of extensively resistant tuberculosis. A non-invasive redox biosensor and an ROS-sensitive dye revealed that moxifloxacin induces oxidative stress correlated with M. tuberculosis death. Moxifloxacin lethality was mitigated by supplementing bacterial cultures with an ROS scavenger (thiourea), an iron chelator (bipyridyl), and, after drug removal, an antioxidant enzyme (catalase). Lethality was also reduced by hypoxia and nutrient starvation. Moxifloxacin increased the expression of genes involved in the oxidative stress response, iron-sulfur cluster biogenesis, and DNA repair. Surprisingly, and in contrast with Escherichia coli studies, moxifloxacin decreased expression of genes involved in respiration, suppressed oxygen consumption, increased the NADH/NAD+ ratio, and increased the labile iron pool in M. tuberculosis. Lowering the NADH/NAD+ ratio in M. tuberculosis revealed that NADH-reductive stress facilitates an iron-mediated ROS surge and moxifloxacin lethality. Treatment with N-acetyl cysteine (NAC) accelerated respiration and ROS production, increased moxifloxacin lethality, and lowered the mutant prevention concentration. Moxifloxacin induced redox stress in M. tuberculosis inside macrophages, and co-treatment with NAC potentiated the anti-mycobacterial efficacy of moxifloxacin during nutrient starvation, inside macrophages, and in mice where NAC restricted the emergence of resistance. Thus, oxidative stress, generated in a novel way, contributes to moxifloxacin-mediated killing of M. tuberculosis. The results open a way to make fluoroquinolones more effective anti-tuberculosis agents and provide a mechanistic basis for NAC-mediated enhancement of fluoroquinolone lethality in vitro and in vivo. Author Summary A new paradigm was revealed for stress-mediated bacterial death in which moxifloxacin treatment of M. tuberculosis decreases respiration rate (respiration increases in E. coli). Although moxifloxacin-induced, ROS-mediated bacterial death was observed, it derived from elevated levels of NADH and iron, a phenomenon not seen with antibiotic-treated E. coli. Nevertheless, stimulation of respiration and ROS by N-acetyl cysteine (NAC) enhanced moxifloxacin-mediated killing of M. tuberculosis, thereby reinforcing involvement of ROS in killing. NAC stimulation of moxifloxacin-mediated killing of M. tuberculosis and restriction of the emergence of resistance in a murine model of infection emphasize the importance of lethal action against pathogens. The work, plus published benefits of NAC to TB patients, encourage studies of NAC-based enhancement of fluoroquinolones.
Bacterial sirtuin CobB and PRPP synthase crosstalk in regulation of protein acetylation

Protein lysine acetylation, regulates a wide range of cellular functions and is controlled by protein deacetylases called sirtuins. In eukaryotes, sirtuins activity is coupled to the spatiotemporally-controlled NAD+ level. However, regulation of the bacterial sirtuin CobB and its coupling to the NAD+ metabolism is not well understood. In this work we show that such coordination in Escherichia coli cells is achieved through a CobB interaction with PRPP synthase Prs, an enzyme necessary for NAD+ synthesis. Probing CobB protein-protein interactions, we demonstrate that it forms a stable complex with Prs. This assembly stimulates CobB deacetylase activity and partially protects it from inhibition by nicotinamide. We provide evidence that Prs acetylation is not necessary for CobB binding but affects the global acetylome and CobB activity in vivo. Consequently, we show that Prs acetylation status affects bacterial growth under different metabolic regimes. Therefore, we propose that CobB-Prs crosstalk orchestrates the NAD+ metabolism and protein acetylation in response to environmental cues.
Endfire Circularly-Polarized Antipodal Linearly Tapered Slot Antenna Fed by Slotted Width-Tapered SIW

A low-profile single-layer endfire circularly-polarized (CP) antipodal linearly tapered slot antenna (ALTSA) is proposed and investigated through simulations and experiments. This antenna is a composite structure consisting of a novel width-tapered slotted substrate-integrated waveguide (SIW) and an ALTSA fed by the SIW. The former also serves as a radiator to produce vertically polarized radiation, which is crucial to achieve a fully planar endfire CP antenna when a thin substrate is deployed. Compared to the previous ALTSA fed by the SIW, this proposed antenna utilizes slots on the spare broad walls of the SIW to form an extra slotted width-tapered SIW radiator, which presents an extension of the conventional width-uniform slotted SIW. Moreover, there are no space harmonics in the slotted width-tapered SIW; it is a slow wave that produces the vertically polarized radiation. The proposed antenna is demonstrated at 28 GHz, which is one of the millimeter-wave bands specified for 5G. An experimental prototype of the antenna has an impedance bandwidth of about 9 GHz from 23.8 to 32.8 GHz and an axial ratio bandwidth of about 1.4 GHz from 27.35 to 28.75 GHz, which coincide well with simulated results.
Task Migration Policy for Thermal-Aware Dynamic Performance Optimization in Many-Core Systems

The steady downsizing of semiconductor technology nodes in recent years has led to a rapid increase in the density of power consumption on chips which, in turn, renders temperature a major issue for many-core systems, adversely affecting their performance, reliability, leakage, cost, etc. In this context, task migration is a powerful technique that is widely used for controlling the temperature profile of many-core systems under dynamic workloads with the goal to improve their performance, utilization, reliability, etc. In this paper, we present a task migration policy for thermal-aware performance optimization in heterogeneous many-core systems. The proposed policy is developed based on an analytical and thermally safe power-budgeting scheme and uses Dynamic Voltage and Frequency Scaling (DVFS) for power and thermal management of the system. Our migration policy aims at maximizing the system’s performance and, at the same time, proactively enforcing thermal safety using DVFS. To that end, it iteratively adapts the distribution of active cores in the system (through proper migration decisions) to maximize the thermally safe power budget of active cores and, thereby, enable them to operate on higher frequencies without violating their safe thermal threshold. Experimental results demonstrate that the proposed policy offers 2× higher performance gain in comparison to existing approaches which aim at greedily reducing the average, variance, or gradient of temperature as an indirect means to enhance performance.
Enhancing Creativity in the Magazine Industry: A Cross-Cultural Comparison of German and Chinese Editors

Creativity is of significant strategic importance in the media industry since creative content represents a source of a company’s competitive advantages. As a consequence, it is crucial for media companies to know how to promote the creative performance of their employees. Especially in the transitional media industry of China, publishing houses aim at offering creative products to their customers and therefore need editors that perform creatively. Previous researches have focused on how the work environment affects creativity but these findings have neither been applied in the field of media management nor have cultural differences been respected. This publication, therefore, aims at confirming factors of the work environment that enhance or hinder creativity in the media industry and compares perceptions in Germany and in China. Applying a qualitative, interpretative approach, 28 in-depth interviews were used to analyse the opinions of German and Chinese editors from female magazines. Findings show substantial cultural differences in the manifestations of particular factors.
Computer Intelligent Stock Prediction Model with Mathematical Statistics and Machine Learning Techniques

As we look into the financial markets, or more straightforwardly, the stock market, the unstable stock price is always a problem existing in the stock market. Whether the price will go up or down and by how much, has always been an unavoidable issue for the investors. Although the price is relatively unstable, many people come up with methods to predict the future stock prices in order to make the price more predictable and hence make a huge number of profits. A relatively successful prediction on the stock price can help you earn a large amount of money from it, increasing the attention and motivation to find different methods of predicting price. The objective of this paper is to summarize and review some of the popular methods of stock price forecasting both in a traditional statistical method and the machine learning or deep learning methods as well as the more favored approach adopted today and the relevant research on them.
Chi Running A Revolutionary Approach To Effortless Injury Free Running

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Resources and Benchmarks for Keyword Search in Spoken Audio From Low-Resource Indian Languages

This paper presents the resources and benchmarks developed for keyword search (KWS) in spoken audio from six low-resource Indian languages (from two families), namely Gujarati, Hindi, Marathi, Odia, Tamil, and Telugu. The current work on constructing keywords and building benchmark KWS systems is inspired by the popular IARPA Babel program and the subsequent works on low-resource KWS. The keywords are constructed by taking into account their properties i.e., occurrence, length, and average confusability; and their effects on the evaluation metric - the term-weighted value (TWV). We make use of freely available speech datasets, and reprocess them to create resources for KWS, thereby adding value to the existing speech resources. Four ASR-based KWS systems are built, and their performance is analyzed across the three keyword properties on all the six languages. The prepared keywords and other related resources to replicate our experiments are made available for the public. We believe that the analysis and guidelines provided in this paper will not only help the research community, but also practitioners and engineers to easily create KWS resources for newer languages, datasets, and scenarios.
UAV Electric Patrol Path Planning Based on Improved Ant Colony Optimization-A* Algorithm

Due to the control accuracy and the complexity of three-dimensional path planning, it is difficult for multi rotor UAV to locate accurately according to point cloud data. In order to overcome these problems, according to the control accuracy of UAV and taking the minimum how much the energy is consumed as the objective function, an improved ant colony-A* optimization algorithm based on UAV performance and wind speed constrained path planning model is established in this paper. The improved ant colony-A* algorithm is used to find the approximate optimal trajectory on the premise of covering all shooting points. The simulation results show that compared with the air transmission line UAV patrol image shooting manual, the how much the energy is consumed of the improved algorithm is greatly reduced.
Design and Performance Analysis of ZYNQ Based Incremental PID-PWM Controller

With the rapid development of digital control techniques, there have been a great rise for using digital processors due to their adaptability, reduced cost, size and reliability. This paper presents a designed IP core of an incremental PID (Proportion, Integration, Differentiation) and PWM (Pulse Power Modulation) on Xilinx Zynq7035, aiming at simplifying the close-loop control of motor position, which driven by pulse powers. Firstly, PWM block is designed in Vivado2017 with Verilog Hardware Description Language (VHDL). Secondly, an incremental PID is built in Vivado High Level Synthesis (HLS) in C++, after C simulation, C synthesis and Co-simulation, it is packaged as intellectual property (IP) core for further applications. Thirdly, to demonstrate the effectiveness of our strategy, testbench is designed in HLS for the PID IP core, simulations are designed for both the PWM IP and the combined two IPs. All the results have shown our designed IP core is not only simple but precise in the close-loop position control of motor driven by pulse power. Moreover, usage of HLS leads to lower development time and rational allocation of hardware resources, which can be a powerful tool for realization of more complicated algorithms.