Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Features of the Nucleosomal DNA Modulate the Functional Binding of a Transcription Factor and Productive Transcription

A small non-histone protein of budding yeast, Nhp6 has been reported to specifically influence the transcription of a yeast gene, SNR6. The gene is essential, transcribed by the enzyme RNA polymerase III, and codes for the U6snRNA required for mRNA splicing. A translationally positioned nucleosome on the gene body enables the assembly factor TFIIIC binding by juxtaposing its otherwise widely separated binding sites, boxes A and B. We found histone depletion results in the loss of U6 snRNA production. Changing the rotational phase of the boxes and the linear distance between them with deletions in 5 bp steps displayed a helical periodicity in transcription, which gradually reduced with incremental deletions up to 40 bp but increased on further deletions enclosing the pseudoA boxes. Nhp6 influences the transcription in a dose-dependent manner, which is modulated by its previously reported co-operator, an upstream stretch of seven T residues centered between the TATA box and transcription start site. Nhp6 occupancy on the gene in vivo goes up at least 2-fold under the repression conditions. Nhp6 absence, T7 disruption, or shorter A–B box distance all cause the downstream initiation of transcription. The right +1 site is selected with the correct placement of TFIIIC before the transcription initiation factor TFIIIB. Thus, the T7 sequence and Nhp6 help the assembly and placement of the transcription complex at the right position. Apart from the chromatin remodelers, the relative rotational orientation of the promoter elements in nucleosomal DNA, and Nhp6 regulate the transcription of the SNR6 gene with precision.
A Recombinant Porcine Reproductive and Respiratory Syndrome Virus Stably Expressing a Gaussia Luciferase for Antiviral Drug Screening Assay and Luciferase-Based Neutralization Assay

The reverse genetics system is a valuable tool in the virological study of RNA viruses. With the availability of reverse genetics, the porcine reproductive and respiratory syndrome virus (PRRSV) has been utilized as a viral vector for the expression of foreign genes of interest. Here, we constructed a full-length cDNA clone of a highly pathogenic PRRSV (HP-PRRSV) TA-12 strain. Using this cDNA clone, we generated a reporter virus expressing a gaussia luciferase (Gluc) via an additional subgenomic RNA between ORF7 and 3′UTR. This reporter virus exhibited similar growth kinetics to the wild-type (WT) virus and remained genetically stable for at least ten passages in MARC-145 cells. In cells infected with this reporter virus, the correlation between the expression levels of Gluc in culture media and the virus titers suggested that Gluc is a good indicator of the reporter virus infection. With this reporter virus, we further established the Gluc readout-based assays for antiviral drug screening and serum neutralizing antibody detection that exhibited comparable performance to the classical assays. Taken together, we established a reverse genetics system of HP-PRRSV and generated a novel reporter virus that could serve as a valuable tool for antiviral drug screening and serum neutralizing antibody detection.
Correlations Between Wake Phenomena and Fatigue Loads Within Large Wind Farms: A Large-Eddy Simulation Study

This work proposes a methodology aiming at simulating the whole wind farm behavior, from the wake phenomena to the wind turbine fatigue loads, in a both accurate and efficient way and for a large range of operating conditions. This approach is based on Large Eddy Simulation (LES), coupled to an Actuator Disk (AD) approach. In order to recover pertinent fatigue loads with that wind turbine model, the blade trajectories are replicated through the disk and the AD aerodynamic forces are interpolated onto these “virtual blades” at each time step. The wake centerline is also tracked in the whole wind farm, in order to highlight the correlations between the wake phenomena and the wind turbine fatigue damage. The described methodology is deployed in simulations of the Horns Rev wind farm for several wind directions. The time-averaged power production is first compared to measurements and other LES results, with a very good agreement for large wind sectors. We then investigate the fatigue loads for several machines inside the wind farm and wind directions. We clearly show the link between the upstream wake movement and the resulting high and low frequency oscillations of the root bending moments and of the yaw and tilt moments, and therefore on the resulting fatigue equivalent loads. This study demonstrates the capacity of the numerical tool to accurately capture the wind farm flow and the rotor behaviors, as well as the correlations between the wake phenomena and the resulting fatigue loads.
Interpersonal Mindfulness, Intergroup Anxiety, and Intercultural Communication Effectiveness Among International Students Studying in Russia

In modern psychology, mindfulness is an important resource for psychological well-being and intergroup relations, but its role in intercultural communication effectiveness has not been sufficiently studied. This research aims to identify the interrelationship between interpersonal mindfulness, intergroup anxiety, and intercultural communication effectiveness among international students. The sample includes 337 (Mage = 22.93, SD = 3.11) international students (41.5% of females) from different countries studying in Russian Universities. Interpersonal mindfulness was measured using the Interpersonal Mindfulness Scale, Intergroup anxiety using ten items adapted from Stephan and Stephan and used in Gudykunst and Nishida, and Intercultural communication effectiveness using the eight items adapted from Gudykunst’s Perceived Effectiveness of Communication measure. Descriptive analysis, correlations, and mediation analyses were used to process the data. The research findings showed that interpersonal mindfulness has both a direct effect on intercultural communication effectiveness and a mediation effect on intercultural communication effectiveness through intergroup anxiety among the international students.
Revisiting the Relationship Between the Strength of Environmental Regulation and Foreign Direct Investment

Interest in sustainability is increasing, and research on ESG management continues. The first issue to be discussed in the present situation is the environment. The study between the environment and internationalization was conducted around two conflicting arguments. First, the pollution haven hypothesis states that multinational corporations move to countries with looser regulations depending on environmental regulation. Next is the Porter Hypothesis, which argues that well-designed environmental regulations offset the cost of compliance and ultimately help firms gain a competitive advantage through innovation that enhances performance. However, the two arguments have not yet reached a consensus conclusion. In addition, studies on the national level and studies considering the distance between countries, an important factor in international management, are lacking. This manuscript aims to revisit the relationship between the strength of environmental regulation and foreign direct investment (FDI) in the context of increasing environmental concerns. Differences between countries are an important field of international management, but research on environmental regulations is lacking. The purpose of this study is to examine the relationship between existing environmental regulations and FDI and to discuss how the distance between countries can affect existing theories.
Strategies to Improve the Targeting of Retinal Cells by Non-Viral Gene Therapy Vectors

Retinal diseases lead to severe vision loss and are currently a major cause of vision impairment in industrialized countries. The significant number of genetic defects of the retina underlying these disorders, coupled to the absence of effective treatments, require new therapeutic solutions. Recent gene therapy developments in the field of ophthalmic research reveal the great potential of this approach. In recent years, non-viral vectors have been extensively studied due to their properties such as large gene packaging capacity and low immunogenicity. Hitherto, their development and optimisation for retinal gene therapy have been hindered by their inability to directly target retinal cells. The goal of this review is to summarize the most promising strategies to direct non-viral vectors for retinal cells to avoid off-target effects and promote their specific uptake, gene expression and overall efficiency.
Identification, High-Density Mapping, and Characterization of New Major Powdery Mildew Resistance Loci From the Emmer Wheat Landrace GZ1

Powdery mildew is one of the most devastating diseases of wheat which significantly decreases yield and quality. Identification of new sources of resistance and their implementation in breeding programs is the most effective way of disease control. Two major powdery mildew resistance loci conferring resistance to all races in seedling and adult plant stages were identified in the emmer wheat landrace GZ1. Their positions, effects, and transferability were verified using two linkage maps (1,510 codominant SNP markers) constructed from two mapping populations (276 lines in total) based on the resistant GZ1 line. The dominant resistance locus QPm.GZ1-7A was located in a 90 cM interval of chromosome 7AL and explains up to 20% of the trait variation. The recessive locus QPm.GZ1-2A, which provides total resistance, explains up to 40% of the trait variation and was located in the distal part of chromosome 2AL. The locus was saturated with 14 PCR-based markers and delimited to a 0.99 cM region which corresponds to 4.3 Mb of the cv. Zavitan reference genome and comprises 55 predicted genes with no apparent candidate for the QPm.GZ1-2A resistance gene. No recessive resistance gene or allele was located at the locus before, suggesting the presence of a new powdery mildew resistance gene in the GZ1. The mapping data and markers could be used for the implementation of the locus in breeding. Moreover, they are an ideal base for cloning and study of host–pathogen interaction pathways determined by the resistance genes.
Detecting Key Functional Components Group and Speculating the Potential Mechanism of Xiao-Xu-Ming Decoction in Treating Stroke

Stroke is a cerebrovascular event with cerebral blood flow interruption which is caused by occlusion or bursting of cerebral vessels. At present, the main methods in treating stroke are surgical treatment, statins, and recombinant tissue-type plasminogen activator (rt-PA). Relatively, traditional Chinese medicine (TCM) has widely been used at clinical level in China and some countries in Asia. Xiao-Xu-Ming decoction (XXMD) is a classical and widely used prescription in treating stroke in China. However, the material basis of effect and the action principle of XXMD are still not clear. To solve this issue, we designed a new system pharmacology strategy that combined targets of XXMD and the pathogenetic genes of stroke to construct a functional response space (FRS). The effective proteins from this space were determined by using a novel node importance calculation method, and then the key functional components group (KFCG) that could mediate the effective proteins was selected based on the dynamic programming strategy. The results showed that enriched pathways of effective proteins selected from FRS could cover 99.10% of enriched pathways of reference targets, which were defined by overlapping of component targets and pathogenetic genes. Targets of optimized KFCG with 56 components can be enriched into 166 pathways that covered 80.43% of 138 pathways of 1,012 pathogenetic genes. A component potential effect score (PES) calculation model was constructed to calculate the comprehensive effective score of components in the components-targets-pathways (C-T-P) network of KFCGs, and showed that ferulic acid, zingerone, and vanillic acid had the highest PESs. Prediction and docking simulations show that these components can affect stroke synergistically through genes such as MEK, NFκB, and PI3K in PI3K-Akt, cAMP, and MAPK cascade signals. Finally, ferulic acid, zingerone, and vanillic acid were tested to be protective for PC12 cells and HT22 cells in increasing cell viabilities after oxygen and glucose deprivation (OGD). Our proposed strategy could improve the accuracy on decoding KFCGs of XXMD and provide a methodologic reference for the optimization, mechanism analysis, and secondary development of the formula in TCM.
Moyamoya Disease With Initial Ischemic or Hemorrhagic Attack Shows Different Brain Structural and Functional Features: A Pilot Study

Objective Cerebral ischemia and intracranial hemorrhage are the two main phenotypes of moyamoya disease (MMD). However, the pathophysiological processes of these two MMD phenotypes are still largely unknown. Here, we aimed to use multimodal neuroimaging techniques to explore the brain structural and functional differences between the two MMD subtypes. Methods We included 12 patients with ischemic MMD, 10 patients with hemorrhagic MMD, and 10 healthy controls (HCs). Each patient underwent MRI scans and cognitive assessment. The cortical thickness of two MMD subtypes and HC group were compared. Arterial spin labeling (ASL) and diffusion tensor imaging (DTI) were used to inspect the cerebral blood flow (CBF) of cortical regions and the integrity of related white matter fibers, respectively. Correlation analyses were then performed among the MRI metrics and cognitive function scores. Results We found that only the cortical thickness in the right middle temporal gyrus (MTG) of hemorrhagic MMD was significantly greater than both ischemic MMD and HC (p < 0.05). In addition, the right MTG showed higher ASL-CBF, and its associated fiber tract (arcuate fasciculus, AF) exhibited higher fractional anisotropy (FA) values in hemorrhagic MMD. Furthermore, the cortical thickness of the right MTG was positively correlated with its ASL-CBF values (r = 0.37, p = 0.046) and the FA values of right AF (r = 0.67, p < 0.001). At last, the FA values of right AF were found to be significantly correlated with cognitive performances within patients with MMD. Conclusions Hemorrhagic MMD shows increased cortical thickness on the right MTG in comparison with ischemic MMD and HCs. The increased cortical thickness is associated with the higher CBF values and the increased integrity of the right AF. These findings are important to understand the clinical symptoms and pathophysiology of MMD and further applied to clinical practice.
Early Bioinformatic Implication of Triacidic Amino Acid Motifs in Autophagy-Dependent Unconventional Secretion of Mammalian Proteins

Several proteins are secreted outside the cell, and in many cases, they may be identified by a characteristic signal peptide. However, more and more studies point to the evidence for an “unconventional” secretion, where proteins without a hitherto unknown signal are secreted, possibly in conditions of starvation. In this work, we analyse a set of 202 RNA binding mammalian proteins, whose unconventional secretion has recently been established. Analysis of these proteins secreted by LC3 mediation, the largest unconventionally secreted dataset to our knowledge, identifies the role of KKX motif as well as triacidic amino acid motif in unconventional secretion, the latter being an extension of the recent implicated diacidic amino acid motif. Further data analysis evolves a hypothesis on the sequence or structural proximity of the triacidic or KKX motifs to the LC3 interacting region, and a phosphorylatable amino acid such as serine as a statistically significant feature among these unconventionally secreted proteins. This hypothesis, although needs to be validated in experiments that challenge the specific details of each of these aspects, appears to be one of the early steps in defining what may be a plausible signal for unconventional protein secretion.
Characterization of lncRNA Profiles of Plasma-Derived Exosomes From Type 1 Diabetes Mellitus

Backgrounds Exosomes contain several types of transcripts, including long non-coding RNAs (lncRNAs), and have been shown to exert important effects in human diseases. However, the roles of exosomal lncRNAs in type 1 diabetes mellitus (T1DM) have not been well investigated. In the present study, we characterized the plasma-derived exosomal lncRNAs expression profiles of T1DM and predict their potential function in the pathogenesis of T1DM. Material and Methods Exosomal lncRNA expression profiles were detected by Illumina Hiseq platform (T1DM subjects N=10; age-, sex- matched Control subjects N=10). Six exosomal lncRNAs were selected to validate their expression level by using quantitative real-time PCR (qRT-PCR) (T1DM subjects N=30; age-, sex- matched Control subjects N=30). Bioinformatics analysis approaches were carried out to explore the potential biological function of differentially expressed lncRNAs. Results A total of 162 differentially expressed exosomal lncRNAs were identified in T1DM patients compared with control subjects, among which 77 up-regulated and 85 down-regulated. The expression level of the selected six lncRNAs didn’t show significant difference in the following qRT-PCR analysis. Gene Ontology analysis enriched terms such as activation of phospholipase D activity, neuronal cell body membrane, and calcium sensitive guanylate cyclase activator activity for cis-acting genes of lncRNAs, and metal ion binding for trans-acting genes. The most enriched Kyoto Encyclopedia of Genes and Genomes pathways for the lncRNAs were associated with oxidative phosphorylation and Parkinson’s disease for cis-acting genes, and pathways in cancer as well as focal adhesion for trans-acting genes. Conclusions This study characterized the lncRNA profiles of plasma-derived exosomes from T1DM for the first time and these results highlighted the potential role of exosomal lncRNAs in T1DM pathogenesis. A better understanding of exosomal lncRNA profiling will provide novel insights into its molecular mechanisms.
Implementing random unitaries in an imperfect photonic network

We numerically investigate the implementation of Haar-random unitarity transformations and Fourier transformations in photonic devices consisting of beam splitters and phase shifters, which are used for integrated photonics implementations of boson sampling. The distribution of reflectivities required to implement an arbitrary unitary transformation is skewed towards low values, and this skew becomes stronger the larger the number of modes. A realistic implementation using Mach-Zehnder interferometers is incapable of doing this perfectly and thus has limited fidelity. We show that numerical optimisation and adding extra beam splitters to the network can help to restore fidelity.
Coarse-to-Fine Evolutionary Method for Fast Horizon Detection in Maritime Images

SUMMARY Horizon detection is useful in maritime image processing for various purposes, such as estimation of camera orientation, registration of consecutive frames, and restriction of the object search region. Existing horizon detection methods are based on edge extraction. For accuracy, they use multiple images, which are ﬁltered with di ﬀ erent ﬁlter sizes. However, this increases the processing time. In addition, these methods are not robust to blurting. Therefore, we developed a horizon detection method without extracting the candidates from the edge information by formulating the horizon detection problem as a global optimization problem. A horizon line in an image plane was represented by two parameters, which were optimized by an evolutionary algorithm (genetic algorithm). Thus, the local and global features of a horizon were concurrently utilized in the optimization process, which was accelerated by applying a coarse-to-ﬁne strategy. As a result, we could detect the horizon line on high-resolution maritime images in about 50 ms . The performance of the proposed method was tested on 49 videos of the Singapore marine dataset and the Buoy dataset, which contain over 16000 frames under di ﬀ erent scenarios. Experimental results show that the proposed method can achieve higher accuracy than state-of-the-art methods.
LTL Model Checking for Register Pushdown Systems

SUMMARY A pushdown system (PDS) is known as an abstract model of recursive programs. For PDS, model checking methods have been studied and applied to various software veriﬁcation such as interprocedural data ﬂow analysis and malware detection. However, PDS cannot manipulate data values from an inﬁnite domain. A register PDS (RPDS) is an extension of PDS by adding registers to deal with data values in a restricted way. This paper proposes algorithms for LTL model checking problems for RPDS with simple and regular valuations, which are labelings of atomic propositions to conﬁgurations with reasonable restriction. First, we introduce RPDS and related models, and then deﬁne the LTL model checking problems for RPDS. Second, we give algorithms for solving these problems and also show that the problems are EXPTIME-complete. As practical examples, we show solutions of a malware detection and an XML schema checking in the proposed framework.
Fogcached: A DRAM/NVMM Hybrid KVS Server for Edge Computing

SUMMARY With the development of IoT devices and sensors, edge computing is leading towards new services like autonomous cars and smart cities. Low-latency data access is an essential requirement for such services, and a large-capacity cache server is needed on the edge side. However, it is not realistic to build a large capacity cache server using only DRAM because DRAM is expensive and consumes substantially large power. A hybrid main memory system is promising to address this issue, in which main memory consists of DRAM and non-volatile memory. It achieves a large capacity of main memory within the power supply capabilities of current servers. In this paper, we propose Fogcached, that is, the extension of a widely-used KVS (Key-Value Store) server program (i.e., Memcached) to exploit both DRAM and non-volatile main memory (NVMM). We used Intel Optane DCPM as NVMM for its prototype. Fogcached implements a Dual-LRU (Least Recently Used) mechanism that seamlessly extends the memory management of Memcached to hybrid main memory. Fogcached reuses the segmented LRU of Mem-cached to manage cached objects in DRAM, adds another segmented LRU for those in DCPM and bridges the LRUs by a mechanism to automatically replace cached objects between DRAM and DCPM. Cached objects are autonomously moved between the two memory devices according to their access frequencies. Through experiments, we conﬁrmed that Fogcached improved the peak value of a latency distribution by about 40% compared to Memcached. key words: Fogcached, KVS, Key-Value-Store, Middleware, edge, edge computing
Using Topic Generation Model to explore the French Parliamentary Debates during the early Third Republic (1881-1899)

In this long paper, we use NLP techniques to explore two decades (1881-1899) of parliamentary debates of the French Third Republic (1870-1940), and more specifically to analyse the importance of the army in the political debate. We use Latent Dirichlet Allocation to partition the vocabulary into topics, and then study the distribution of the topic “army” over time. We also examine its connection with other topics, in relation to the main political and military events of the period.