Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Identification and Analysis of TCP Transcription Factors Involved in the Formation of Leafy Head in Chinese Cabbage

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a widely cultivated and economically important vegetable crop with typical leaf curvature. The TCP (Teosinte branched1, Cycloidea, Proliferating cell factor) family proteins are plant-specific transcription factors (TFs) and play important roles in many plant biological processes, especially in the regulation of leaf curvature. In this study, 39 genes encoding TCP TFs are detected on the whole genome of B. rapa. Based on the phylogenetic analysis of TCPs between Arabidopsis thaliana and Brassica rapa, TCP genes of Chinese cabbage are named from BrTCP1a to BrTCP24b. Moreover, the chromosomal location; phylogenetic relationships among B. rapa, A. thaliana, and rice; gene structures and protein conserved sequence alignment; and conserved domains are analyzed. The expression profiles of BrTCPs are analyzed in different tissues. To understand the role of Chinese cabbage TCP members in regulating the curvature of leaves, the expression patterns of all BrTCP genes are detected at three development stages essential for leafy head formation. Our results provide information on the classification and details of BrTCPs and allow us to better understand the function of TCPs involved in leaf curvature of Chinese cabbage.
Development of a Virus-Induced Gene-Silencing System for Hexaploid Wheat and Its Use in Functional Analysis of the Lr21-Mediated Leaf Rust Resistance Pathway1

Virus-induced gene silencing (VIGS) is an important tool for the analysis of gene function in plants. In VIGS, viruses engineered to carry sequences derived from plant gene transcripts activate the host's sequence-specific RNA degradation system. This mechanism targets the RNAs of the viral genome for degradation, and as the virus contains transcribed plant sequence, homologous host mRNAs are also targeted for destruction. While routinely used in some dicots, no VIGS system was known for monocot plants until the recent report of silencing in barley (Hordeum vulgare) by barley stripe mosaic virus (BSMV). Here, we report development of protocols for use of BSMV to efficiently silence genes in hexaploid wheat (Triticum aestivum). The VIGS system was first optimized in studies silencing phytoene desaturase expression. Next, we used it to assay genes functioning in leaf rust resistance mediated by Lr21, which encodes a nucleotide binding site-leucine-rich repeat class resistance gene product. We demonstrated that infection with BSMV constructs carrying a 150-bp fragment of Lr21 caused conversion of incompatible interactions to compatible, whereas infection with a control construct or one that silences phytoene desaturase had no effect on resistance or susceptibility. Additionally, silencing the RAR1, SGT1, and HSP90 genes, known to be required in many but not all nucleotide binding site-leucine-rich repeat resistance pathways in diverse plant species, resulted in conversion to compatibility, indicating that these genes are essential in Lr21-mediated resistance. These studies indicate that BSMV-VIGS is a powerful tool for dissecting the genetic pathways of disease resistance in hexaploid wheat.
An evaluation of implicit surface tilers

The authors review the principal algorithms for the polygonization of implicit surfaces and provide a framework for identifying their conceptual similarities and practical differences. The algorithms' merits are evaluated according to topological disambiguation, implementation complexity, and triangle count. Special attention is devoted to the ambiguity problem, and proposed solutions are analyzed in the context of consistency and correctness. It is argued that consistency suffices for many purposes and is achievable with single-entry tetrahedral or cubical tables. <<ETX>>
Statistical inference for the doubly stochastic self-exciting process

We introduce and show the existence of a Hawkes self-exciting point process with exponentially-decreasing kernel and where parameters are time-varying. The quantity of interest is defined as the integrated parameter $T^{-1}\int_0^T\theta_t^*dt$, where $\theta_t^*$ is the time-varying parameter, and we consider the high-frequency asymptotics. To estimate it na\"ively, we chop the data into several blocks, compute the maximum likelihood estimator (MLE) on each block, and take the average of the local estimates. The asymptotic bias explodes asymptotically, thus we provide a non-na\"ive estimator which is constructed as the na\"ive one when applying a first-order bias reduction to the local MLE. We show the associated central limit theorem. Monte Carlo simulations show the importance of the bias correction and that the method performs well in finite sample, whereas the empirical study discusses the implementation in practice and documents the stochastic behavior of the parameters.
Systematic Performance Modeling and Characterization of Heterogeneous IP Networks

Accurate measurement and modeling of IP networks is essential for network design, planning, and management. Efforts are being made to detect the state of the network from end-to-end measurements using different techniques and paradigms. In this paper we present a novel concept to use in the modeling of real network scenarios under measurement and analysis. We called this new concept service condition. We explain our proposal's motivations and we show how to apply the service condition concept to the study of real heterogeneous network scenarios. To show the real applicability of our proposal results from a performance evaluation study over real heterogeneous networks (where the integration of LAN, UMTS and GPRS is present) are given
Crowdsourced Exploration of Mobile App Features: A Case Study of the Fort McMurray Wildfire

The ubiquity of mobile devices has led to unprecedented growth in not only the usage of apps, but also their capacity to meet people's needs. Smart phones take on a heightened role in emergency situations, as they may suddenly be among their owner's only possessions and resources. The 2016 wildfire in Fort McMurray, Canada, intrigued us to study the functionality of the existing apps by analyzing social media information. We investigated a method to suggest features that are useful for emergency apps. Our proposed method called MAPFEAT, combines various machine learning techniques to analyze tweets in conjunction with crowdsourcing and guides an extended search in app stores to find currently missing features in emergency apps based on the needs stated in social media. MAPFEAT is evaluated by a real-world case study of the Fort McMurray wildfire, where we analyzed 69,680 unique tweets recorded over a period from May 2nd to May 7th, 2016. We found that (i) existing wildfire apps covered a range of 28 features with not all of them being considered helpful or essential, (ii) a large range of needs articulated in tweets can be mapped to features existing in non-emergency related apps, and (iii) MAPFEAT's suggested feature set is better aligned with the needs expressed by general public. Only six of the features existing in wildfire apps is among top 40 crowdsourced features explored by MAPFEAT, with the most important one just ranked 13th. By using MAPFEAT, we proactively understand victims' needs and suggest mobile software support to the people impacted. MAPFEAT looks beyond the current functionality of apps in the same domain and extracts features using variety of crowdsourced data.
Dynamic Pricing in Social Networks: The Word of Mouth Effect

We study the problem of optimal dynamic pricing for a monopolist selling a product to consumers in a social network. In the proposed model, the only means of spread of information about the product is via Word of Mouth communication; consumers' knowledge of the product is only through friends who already know about the product's existence. Both buyers and non-buyers contribute to information diffusion while buyers are more likely to get engaged. By analyzing the structure of the underlying endogenous process, we show that the optimal dynamic pricing policy for durable products with zero or negligible marginal cost, drops the price to zero infinitely often. By attracting low-valuation agents with free-offers and getting them more engaged in the spread, the firm can reach out to potential high-valuation consumers in parts of the network that would otherwise remain untouched without the price drops. We provide evidence for this behavior from smartphone app market, where price histories indicate frequent free-offerings. Moreover, we show that despite infinitely often drops of the price to zero, the optimal price trajectory does not get trapped near zero. We demonstrate the validity of our results in face of strategic forward-looking agents, homophily-based engagement in word of mouth, network externalities, and consumer inattention to price changes. We further unravel the key role of the product type in the drops by showing that the price fluctuations disappear after a finite time for a nondurable product.
Colonia : Corpus of Historical Portuguese

This paper presents a new linguistic resource for Portuguese, Colonia: Corpus of Historical Portuguese. It is a collection of textual material from the 16th to the early 20th century with a user-friendly interface. Colonia is a diachronic corpus available online with over 5,1 million tokens divided into five sub-corpora by century. The corpus was POS tagged using TreeTagger and the framework used to process queries is Corpus WorkBench (CWB) and Corpus Query Processor (CQP). On top of this architecture, CQPWeb provides the interface between query language and users. The methods for corpus compilation as well as the characteristics of the data are presented in detail in this paper.
Faring with Facets: Building and Using Databases of Student Misconceptions

A number of educational researchers have developed pedagogical approaches that involve the teacher in discovering and helping to correct misconceptions that students bring to their study of their subject matter. During the last decade, several computer systems have been developed to support teaching and learning using this kind of approach. A central conceptual construct used by these systems is the "facet" of understanding: an atomic diagnosable unit of belief. A formidable challenge to applying such pedagogical approaches to new topic areas is the task of discovering and organizing the facets for the new subject area. This paper presents a taxonomy of misconceptions and a methodology for going about the task of preparing a database of facets. Important issues include the generality and diagnosability of facets, granularity of facets, and their placement on a scale of problematicity. Examples are drawn from the subjects of physics and computer science and in the context of two computer systems: the Diagnoser and INFACT. Editors: Patrick McAndrew (Open University, UK). Reviewers: Paul Horwitz (Concord Consortium, USA) and Ruth Thomas (Jelsim Partnership, UK).
FMI-based co-simulation of hybrid closed-loop control system models

In recent years, co-simulation and model exchange approaches have become ever more popular within the context of model-based design and analysis. This trend has led to the development of the Functional Mock-up Interface (FMI) specification - the de facto standard for model exchange and co-simulation - and a growing number of FMI-compliant tools. This paper addresses the FMI-based co-simulation of hybrid models representing closed-loop control systems, where a continuous time-based plant model is connected to a discrete event-driven controller model. The semantics of execution and data flow of such models are discussed and demonstrated with the help of a model that has been inspired by real-world applications. An example illustrates that popular proprietary simulation environments are not necessarily able to properly capture the semantics of these models. Furthermore, it is shown how existing concepts and tools can be successfully applied to implement such simulations properly.
Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages

There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.
Precision fuzzy sliding-mode tracking control with DNLRX model based friction feed-forward compensator

This study developed a precision tracking controller with friction compensation for precision stage. This controller includes two parts, the DNLRX (Dynamic NonLinear Regression with direct application of eXcitation) model based feed-forward controller and sliding-mode feedback controller with adaptive fuzzy uncertainty estimator. Experimental results are shown to demonstrate the efficiency of the proposed controller. The performance of the proposed controller also compared with the integral sliding-mode controller that has been reported recently. The experimental results show that the proposed controller can improve the tracking performance of the system one step further.
Micro-blog Keyword Extraction Method Based on Graph Model and Semantic Space

There have been many domain-specific keyword extraction researches, but micro-blog- oriented keyword extraction is just beginning. This paper researches into the keyword extraction from Chinese micro-blog. Taking the characteristics of micro-blog into account, such as short, topic divergence, etc., we propose a Chinese micro-blog keyword extraction method based on the combination of multi features. Firstly create the graph model based on the co-occurrence between words, get a kind of weight based on the created graph model. The weight based on the graph model is sometimes same. In order to solve this problem, this method secondly proposes to create the semantic space based on the topic detection method, and get the statistical weight based on the semantic space. Finally, we take the location of words into account during the extraction, which is proved to be a very effective feature. Experimental results show that the proposed keyword extraction method is very successful.
Characterization of a novel carbonized foam electrode for wearable bio-potential recording

A novel dry disposable electrode using carbonized foam as conductive material is presented. The conductive material is flexible and the manufacturing of it is inexpensive. In this paper, the preparation of the conductive material and the electrical properties of the electrode are investigated. A test protocol is designed to compare the in-vitro impedance, skin-electrode interface and the signal quality of the proposed electrode with that of the wet Ag/AgCl electrode. Experimental results reveal that the carbonized foam has good flexibility and conductivity. The proposed electrode can acquire ECG signal of promising signal quality when compared with Ag/AgCl electrode in the case of static and motion. Furthermore, raw data with less power line interference was observed by proposed electrodes without noise suppression circuits or algorithms. All these make the novel electrode a promising candidate for wearable bio-potential recording.
A Goal-based Classification of Web Information Tasks

While researchers have been studying user activity on the Web since its inception, there remains a lack of understanding of the high level tasks in which users engage on the Web. We have recently conducted a field study in which participants were asked to annotate all web usage with a task description and categorization. Based on our analysis of participants’ recorded tasks during the field study, as well as previous research, we have developed a goal-based classification of information tasks which describes user activities on the Web.
A study of the key genes and inflammatory signaling pathways involved in HLA-B27-associated acute anterior uveitis families

The present study was conducted to investigate the key genes and the inflammatory signaling pathways involved in HLA-B27-associated acute anterior uveitis (AAU) families. Four families with HLA-B27-positive AAU patients and their HLA-B27-positive blood relatives were included in the study. Peripheral blood monocytes were isolated from the subjects and stimulated by lipopolysaccharides (LPS). Gene expression microarrays were used to identify the differentially expressed genes (DEGs), and the DEGs were analyzed by a range of bioinformatics-based techniques, including Gene Ontology (GO), Pathway analysis, Signal-Net analysis and Gene Relation Network (Gene-Rel-Net). Finally, ELISA was used to quantify cytokines in the supernatant. The gene expression microarrays identified 801 DEGs, including 349 upregulated and 452 downregulated genes. The GO analysis revealed several important functions, including metabolic, immune and inflammatory responses. The pathway analysis highlighted the enhanced activity of Staphylococcus aureus infection, chemokine and metabolic signaling pathways, as well as cytokine-to-cytokine receptor interactions. A total of 18 DEGs that were found to play critical roles by Signal-Net and Gene-Rel-Net and verified by quantitative polymerase chain reaction analysis were identified as key genes. In conclusion, monocytes from the AUU patients were more sensitive and exhibited a more prominent inflammatory response to stimulation by LPS compared with monocytes from healthy HLA-B27-positive blood relatives. These characterized DEGs may provide new evidence for the pathogenesis of AAU and help identify new therapeutic targets.
Bringing Structure into Summaries: Crowdsourcing a Benchmark Corpus of Concept Maps

Concept maps can be used to concisely represent important information and bring structure into large document collections. Therefore, we study a variant of multi-document summarization that produces summaries in the form of concept maps. However, suitable evaluation datasets for this task are currently missing. To close this gap, we present a newly created corpus of concept maps that summarize heterogeneous collections of web documents on educational topics. It was created using a novel crowdsourcing approach that allows us to efficiently determine important elements in large document collections. We release the corpus along with a baseline system and proposed evaluation protocol to enable further research on this variant of summarization.
Modeling and localized feedforward control of thermal deformations induced by a moving heat load

This paper deals with the modeling and control of thermal induced deformations that are the result of a position dependent heat load. These deformations are modeled using a combination of spectral methods and FEM. For systems of this type, a distributed feedforward controller is proposed that acts only around the location of the heat load. The results of this controller show a significant reduction of thermal induced deformations of a flexible beam.
Evaluating melt iron features by computer aided recognition of thermal analysis cooling curves

A relation database of thermal analysis cooling curves, composition, microstructure and mechanical properties of various cast irons under fixed casting condition has been set up. Based on the pattern recognition principle, the authors developed an approach to precisely evaluate the melt iron features and predict the mechanical properties of the corresponding casting by finding a corresponding cooling curve from the database which is most similar to the measured one. This method is self-adaptive to the production condition and has been put into application in several foundries.
Ultrasonographic evaluation of complications related to transfemoral arterial procedures

The transfemoral arterial approach is used to gain access for angiography, percutaneous coronary interventions, or various endovascular therapies. To decrease the risk of procedure-related vascular complications, it is recommended to puncture the common femoral artery in its middle segment. However, due to inadequate access or anatomical variability, various complications, including hematoma, pseudoaneurysm, arteriovenous fistula, thrombosis, or dissection, can occur after transfemoral arterial interventions. Duplex ultrasound has proven to be an excellent noninvasive modality that provides not only anatomic but also hemodynamic information, effectively detecting and differentiating various femoral puncture-related complications. Radiologists should be familiar with the characteristic sonographic findings of the entire spectrum of transfemoral puncture-related vascular complications for early detection and proper treatment.
Amyloid-beta and Proinflammatory Cytokines Utilize a Prion Protein-Dependent Pathway to Activate NADPH Oxidase and Induce Cofilin-Actin Rods in Hippocampal Neurons

Neurites of neurons under acute or chronic stress form bundles of filaments (rods) containing 1:1 cofilin:actin, which impair transport and synaptic function. Rods contain disulfide cross-linked cofilin and are induced by treatments resulting in oxidative stress. Rods form rapidly (5–30 min) in . 80% of cultured hippocampal or cortical neurons treated with excitotoxic levels of glutamate or energy depleted (hypoxia/ischemia or mitochondrial inhibitors). In contrast, slow rod formation (50% of maximum response in , 6 h) occurs in a subpopulation ( , 20%) of hippocampal neurons upon exposure to soluble human amyloid-b dimer/trimer (A b d/t) at subnanomolar concentrations. Here we show that proinflammatory cytokines (TNF a , IL-1 b , IL-6) also induce rods at the same rate and within the same neuronal population as A b d/t. Neurons from prion (PrP C )-null mice form
A new hybrid cuckoo search and firefly optimization

Abstract In this paper, we present a new hybrid algorithm which is a combination of a hybrid Cuckoo search algorithm and Firefly optimization. We focus in this research on a hybrid method combining two heuristic optimization techniques, Cuckoo Search (CS) and Firefly Algorithm (FA) for the global optimization. Denoted as CS-FA. The hybrid CS-FA technique incorporates concepts from CS and FA and creates individuals in a new generation not only by random walk as found in CS but also by mechanisms of FA. To analyze the benefits of hybridization, we have comparatively evaluated the classical Cuckoo Search and Firefly Algorithms versus the proposed hybridized algorithms (CS-FA).