Miracle-dz/UniFAR-FTUs huggingface dataset:
Dominant Mutations of the TREX1 Exonuclease Gene in Lupus and Aicardi-Goutières Syndrome*

TREX1 is a potent 3′→5′ exonuclease that degrades single- and double-stranded DNA (ssDNA and dsDNA). TREX1 mutations at amino acid positions Asp-18 and Asp-200 in familial chilblain lupus and Aicardi-Goutières syndrome elicit dominant immune dysfunction phenotypes. Failure to appropriately disassemble genomic DNA during normal cell death processes could lead to persistent DNA signals that trigger the innate immune response and autoimmunity. We tested this concept using dsDNA plasmid and chromatin and show that the TREX1 exonuclease locates 3′ termini generated by endonucleases and degrades the nicked DNA polynucleotide. A competition assay was designed using TREX1 dominant mutants and variants to demonstrate that an intact DNA binding process, coupled with dysfunctional chemistry in the active sites, explains the dominant phenotypes in TREX1 D18N, D200N, and D200H alleles. The TREX1 residues Arg-174 and Lys-175 positioned adjacent to the active sites act with the Arg-128 residues positioned in the catalytic cores to facilitate melting of dsDNA and generate ssDNA for entry into the active sites. Metal-dependent ssDNA binding in the active sites of the catalytically inactive dominant TREX1 mutants contributes to DNA retention and precludes access to DNA 3′ termini by active TREX1 enzyme. Thus, the dominant disease genetics exhibited by the TREX1 D18N, D200N, and D200H alleles parallel precisely the biochemical properties of these TREX1 dimers during dsDNA degradation of plasmid and chromatin DNA in vitro. These results support the concept that failure to degrade genomic dsDNA is a principal pathway of immune activation in TREX1-mediated autoimmune disease.
Kernel and random extreme learning machine applied to submersible motor pump fault diagnosis

This paper presents an extension of a comparative study of classifier architectures for automatic fault diagnosis, with a special emphasis on the Extreme Learning Machine (ELM), with and without kernel mapping. Besides the explanation of the ELM model, an attempt is made to find theoretical hints of the excellent generalization capabilities of this model, based on the findings of Cover about dichotomies and the equivalence of Mean Squared Error minimization in the high-dimensional feature spaces induced by kernels, and spaces defined by a finite sample set. The field of application is a practical problem in the context of offshore petroleum exploration where sophisticated submersible motor pumps are extensively tested before being deployed. The work juxtaposes the performance of ELM to an existing statistically sound comparison of state of the art classifier methods for a hand-crafted feature model tailored specially to the spectra of the vibrational signals of the pump. The results suggest the remarkably good generalization capability of ELM, exhibiting the highest scores for the chosen F-measure performance criterion.
Topic ontology-based efficient tag recommendation approach for blogs

Efficient tag recommendation systems are required to help users in the task of searching, indexing and browsing appropriate blog content. Tag generation has become more popular to annotate web content, other blogs, photos, videos and music. Tag recommendation is an action of signifying valuable and informative tags to a budding item based on the content. We propose a novel approach based on topic ontology for tag recommendation. The proposed approach intelligently generates tag suggestions to blogs. In this paper, we effectively construct the technology entitled Ontology based on Wikipedia categories and WordNet semantic relationship to make the ontology more meaningful and reliable. Spreading activation algorithm is applied to assign interest scores to existing blog content and tags. High quality tags are suggested based on the significance of the interest score. Evaluation proves that the applicability of topic ontology with spreading activation algorithm helps tag recommendation more effective when compared to collaborative tag recommendations. Our proposed approach offers several solutions to tag spamming, sentiment analysis and popularity. Finally, we report the results of an experiment which improves the performance of tag recommendation approach.
Characterizing Functional Domains for TIM-Mediated Enveloped Virus Entry

ABSTRACT T-cell immunoglobulin and mucin domain 1 (TIM-1) and other TIM family members were recently identified as phosphatidylserine (PtdSer)-mediated virus entry-enhancing receptors (PVEERs). These proteins enhance entry of Ebola virus (EBOV) and other viruses by binding PtdSer on the viral envelope, concentrating virus on the cell surface, and promoting subsequent internalization. The PtdSer-binding activity of the immunoglobulin-like variable (IgV) domain is essential for both virus binding and internalization by TIM-1. However, TIM-3, whose IgV domain also binds PtdSer, does not effectively enhance virus entry, indicating that other domains of TIM proteins are functionally important. Here, we investigate the domains supporting enhancement of enveloped virus entry, thereby defining the features necessary for a functional PVEER. Using a variety of chimeras and deletion mutants, we found that in addition to a functional PtdSer-binding domain PVEERs require a stalk domain of sufficient length, containing sequences that promote an extended structure. Neither the cytoplasmic nor the transmembrane domain of TIM-1 is essential for enhancing virus entry, provided the protein is still plasma membrane bound. Based on these defined characteristics, we generated a mimic lacking TIM sequences and composed of annexin V, the mucin-like domain of α-dystroglycan, and a glycophosphatidylinositol anchor that functioned as a PVEER to enhance transduction of virions displaying Ebola, Chikungunya, Ross River, or Sindbis virus glycoproteins. This identification of the key features necessary for PtdSer-mediated enhancement of virus entry provides a basis for more effective recognition of unknown PVEERs. IMPORTANCE T-cell immunoglobulin and mucin domain 1 (TIM-1) and other TIM family members are recently identified phosphatidylserine (PtdSer)-mediated virus entry-enhancing receptors (PVEERs). These proteins enhance virus entry by binding the phospholipid, PtdSer, present on the viral membrane. While it is known that the PtdSer binding is essential for the PVEER function of TIM-1, TIM-3 shares this binding activity but does not enhance virus entry. No comprehensive studies have been done to characterize the other domains of TIM-1. In this study, using a variety of chimeric proteins and deletion mutants, we define the features necessary for a functional PVEER. With these features in mind, we generated a TIM-1 mimic using functionally similar domains from other proteins. This mimic, like TIM-1, effectively enhanced transduction. These studies provide insight into the key features necessary for PVEERs and will allow for more effective identification of unknown PVEERs.
Large-scale Use of FACTS Technology for Damping Inter-Area Oscillations in the Mexican System

This paper discusses the results of preliminary studies conducted to evaluate the potential for application of static VAR compensators (SVCs) and thryristor controlled series capacitors (TCSCs) on the Mexican interconnected system. The work synthesizes the progress in a research effort to study means to remove power transfer limitations in the 400/230 kV transmission system. The study compares the results and effectiveness of large-scale application of SVCs and TCSCs for enhancing global, large-scale system performance. Detailed system studies are conducted to assess the impact of existing FACTS controllers on system damping as well as to identify potential sites for FACTS applications. Coordination of multiple FACTS controllers is studied for the purpose of achieving global stabilization and improved transient performance. Study results include the use of SVCs and TCSCs to enhance system damping and voltage stability. Issues addressed include characterizing the influence of existing and planned devices on transient oscillations and voltage stability, and the design of modulation controllers. Time domain, frequency response, and eigenvalue studies are used for siting and designing system controllers.
Decentralized two-stage control for active power real time dispatch in islanded AC microgrids

Microgrid is a typical small-scale cyber-physical system in which computing, communication, and control technologies are tightly integrated. A two-stage control framework is introduced for active power real time dispatch in islanded ac microgrids. Then a decentralized hybrid method consisting of two control schemes is developed. In the method, an adaptive droop scheme using local physical information is employed in the first stage to provide rapid control for frequency regulation. Based on the peer-to-peer communication in the cyber system, a consensus scheme is implemented in the second stage to realize frequency restoration and economic dispatch simultaneously. Simulation results are presented to demonstrate the effectiveness of the proposed method.
Many-Objective Evolutionary Algorithms Based on Coordinated Selection Strategy

Selection strategy, including mating selection and environmental selection, is a key ingredient in the design of evolutionary multiobjective optimization algorithms. Existing approaches, which have shown competitive performance in low-dimensional multiobjective optimization problems with two or three objectives, often encounter considerable challenges in many-objective optimization, where the number of objectives exceeds 3. This paper first provides a comprehensive analysis on the selection strategies in the current evolutionary many-objective optimization algorithms. Afterward, we propose a coordinated selection strategy to improve the performance of evolutionary algorithms in many-objective optimization. This selection strategy considers three crucial factors: 1) the new mating selection criterion considers both the quality of each selected parent and the effectiveness of the combination of selected parents; 2) the new environmental selection criterion directly focuses on the performance of the whole population rather than single individual alone; and 3) both selection steps are complement to each other and the coordination between them in the evolutionary process can achieve a better performance than each of them used individually. Furthermore, in order to handle the curse of dimensionality in many-objective optimization problems, a new convergence measure by distance and a new diversity measure by angle are developed in both selection steps. Experimental results on both DTLZ and WFG benchmark functions demonstrate the superiority of the proposed algorithm in comparison with six state-of-the-art designs in terms of both solution quality and computational efficiency.
Evaluation of risk in farm planning: a case study

Many studies suggest that farmers frequently show risk averse attitudes, and choose the “riskminimizing” and “safety first” survival strategy rather than pursuing the profit maximization. This article reports on a study of the impact of risk caused by different events: climate, stock levels, price volatility and other causes affecting the yield and price variability of agricultural crops. This study will simulate the risk in farm decisions using a sumex utility function that allows to parameterize the risk for specific traits of the function, and MOTAD (minimization of total absolute deviations) to simulate an efficient combination of crops in the whole farm planning (WFP). The empirical analysis is represented by a case study consisting in the risk simulation of a farm of 100 Ha, growing vegetable crops located in the Northern region of Italy. The risk is modelled using 15 years historical observations with discrete probability distribution of some of the most diffused cereal and oilseed crops (source: Eurostat). The objective is to evaluate the risk aversion by designing a utility frontier of crop combinations using a LP approximation model. The results indicate the trade off between expected returns and risk: if the value of gross income is expected to increase, the farmers tend to specialize in the most profitable portfolio enterprise while it is not so evident that the diversification will contribute to curb the risk.
SOCIAL MEDIA’S CHALLENGE TO THE PROMOTION OF YOUNG PEOPLE’S SEXUAL HEALTH

Drawing from young people’s accounts of Facebook practice, this paper challenges current public health attempts to promote sexual health via social media, arguing that health interventions must engage with the complexities of young people’s online intimacies. Social media plays a significant role in young people’s everyday practices of intimacy and friendship. Health promotion strategies increasingly note the value of social media in young people’s lives and often approach social network sites (SNS) as channels through which to access young people. In utilising social media, such initiatives rarely deviate from public health social marketing paradigms committed to developing and disseminating static messages to their target population. While these strategies often include consultations with young people, such as through campaign development focus groups, this does not extend to seeing young people as partners, stakeholders, or co- producers of social media interventions. This paper will begin by arguing that young people’s sexual health practices are contexualised by, and mediated through, everyday practices of friendship and intimacy. Focusing on Australian cultures of young people’s heterosex, and drawing from focus groups conducted in the state of New South Wales, I argue that to engage with social media, sexual health interventions from government, non-government, and other research institutions must reform their traditional approaches.
Indoor air quality measurements in 35 schools of South-Western Europe

The ClimACT project has been developed under the priority axis “Low Carbon Economy” of the Interreg SUDOE program. It aims to support the transition to a low carbon economy in schools. Environmental audits addressing energy and water consumptions, waste management, travels to school, procurements and green spaces have been carried out in 38 pilots schools of Portugal, Spain, France and Gibraltar. Indoor air quality and ventilation measurements were also achieved. The concentrations of 9 aldehydes and 10 selected VOCs were measured from passive sampling in two classrooms of each school. In addition, TVOC, CO2, CO, PM2.5 and PM10 concentrations were monitored for a period of 2 days or 1 week in French schools. Of all the individual VOCs and aldehydes investigated, only formaldehyde exhibit some concentrations over the guideline. On the other hand, PM10, PM2.5, CO2 and TVOC concentrations during the class hours are over the guidelines in 64%, 45%, 43% and 20% of classrooms, respectively. The time series of concentrations highlight that a significant part of TVOCs originates from the occupants. Similarly, PM10 concentrations over the guideline are mainly contributed by biogenic emissions and resuspension of settled particles. Another interesting conclusion coming from the study is that there are no significant differences in the characteristics of the air pollution in secondary schools, high schools and universities, when compared to primary schools. However, the characteristics of indoor air pollution in classrooms may be slightly different in Spain, Portugal, Gibraltar and France.
Ranked Search Over Structured and Semi-Structured Data

Traditionally, relational database systems have been designed for precise queries over structured data, while information retrieval systems have been designed for more flexible ranked keyword search queries over unstructured (text) data. However, many new and emerging applications require data management capabilities that combine the benefits of database and information retrieval systems, e.g., e-commerce and content management applications. In this dissertation, we have proposed and initiated steps toward the larger goal of integrating relational database and information retrieval systems. First, we consider the problem of ranked text search in relational databases, where the traditional ranking paradigms and techniques developed for stand-alone unstructured documents are not directly applicable. We thus propose a new ranking paradigm that uses structured data values to score the results of text search queries. Our experimental results on real and synthetic data sets show that we can support the new ranking paradigm efficiently in relational databases. Second, we explore a novel problem of discovering rich relationships in databases based on user queries with text search and structural query conditions. Toward this end, we have introduced the notion of data, topology and developed efficient algorithms for computing ranked topologies based on user queries. We have evaluated our algorithms using a real biological database, the Biozon database (http://www.biozon.org). Third, we consider the problem of efficiently producing results for keyword search queries over semi-structured XML documents. We present the XRANK system that is built to address the novel challenges for effective XML keyword search as apposed to HTML keyword search. Our experimental results show that XRANK offers both space and performance benefits when compared with existing approaches.
Presence in immersive virtual environments

Immersive virtual environments (IVEs) provide a tightly coupled human-computer interface; input to the sensory organs of the human participant are directly generated through computer displays, in the visual, auditory, tactile and haptic modalities. Some of the results of a pilot experimental study of presence in IVEs are outlined. This is a contribution to a project involved in constructing a system for architectural walkthrough, where architects and their clients are able to navigate through and effect changes to a virtual building interior. Emphasis is placed on the interface provided by the virtual environment generator (VEG) to the human user, and initially on the problem of the establishment of the presence of the human inside the virtual environment (VE). <<ETX>>
Bifurcation analysis with AUTO

In this lecture, we will learn how to do a bifurcation analysi s with the computer program AUTO. AUTO is built into xppaut , which is where theaut part of the name comes from, so we can just continue to use the tool we started to learn in the las t lecture. We will proceed by example, working with the autocatalator m odel we started to study last time. Because AUTO is a tricky piece of software, the instruc tions given in this set of notes will be much more detailed regarding the operation of the softwar e than would otherwise be the case. Recall that thexpp input file is
Parietal lobe mechanisms for directed visual attention.

1. Experiments were made on the cortex of the inferior parietal lobule in 10 hemispheres of six alert, behaving monkeys. The electrical signs of the impulse discharges of single cortical cells were recorded as the monkeys executed tasks requiring them to fixate stationary visual targets, track those which moved slowly, and to make saccadic movements to foveate those which suddenly jumped from one locus to another within the field of view. A total of 907 neurons of area 7 were identified in terms of their physiological properties, particularly the correlation of their activity with the oculomotor components of these behavioral acts of directed visual attention; 480 of these were located by cytoarchitectural layer. Most identifiable cells of area 7 are visuomotor neurons, in a special and conditional sense. Their discharge frequencies increase before and during those steady fixations and movements of the eyes which secure and maintain foveation of objects, but only if the visual targets engaged are linked by a strong motivational drive; in our experiments, one between thirst and the light whose dimming the animal has learned to detect for liquid reward. We have identified and studied three major classes of neurons in area 7. 2. The visual fixation neurons (57%) accelerate discharge synchronously with fixation of a visual object the animal desires. The incremented discharge continues until reward, but then declines abruptly even when there is no immediate shift of the line of gaze. Fixation neurons are relatively inactive during those casual fixations by which the animal insepcts the surrounding environment. Mist fixation neurons subtend gaze fields limited to one quadrant or half of the total gaze field. The sum of the gaze fields of the fixation neurons in one hemisphere is weighted moderately toward the contralateral side. Fixation cells also discharge during slow pursuit movements in any direction so long as the movement stays within the gaze field of the neuron under study. About 40% of fixation cells are suppressed before and during saccadic movements of the eyes to a new target within the gaze field of the fixation cell. Those suppressed are located preferentially in layer V of the cortex. Suppression is maximal for saccades directed contralaterally to the hemisphere under study. 3. Visual tracking neurons are active during oculomotor pursuit of slowly moving visual objects, not during steady fixations. They show a marked directional but no laterality relation, and are suppressed before and during a visually evoked saccade superimposed on the smooth pursuit movement. The rate of discharge is a flat function of tracking speed so that these cells do not appear to emit signals which specify the speed of smooth pursuit movements. 4. The saccade neurons are active before and during visually evoked saccadic movements of the eyes but not before spontaneous saccades, no matter whether made in light or near darkness. The discharge of saccade neurons leads the eye movement by as much as 150 ms (mean, 73 ms).
Multi-target direction finding in MIMO radar exploiting nested array

In this paper, a novel multi-target direction finding approach is proposed for multiple input multiple output (MIMO) radar exploiting nested array. In our MIMO radar model, the transmit antennas are widely spaced to enable transmit diversity, while the receiver of the MIMO radar is configured with a 2-level nested array to enable direction finding. The nested array is an emerging non-uniform linear array (NLA) which can contain a large number of virtual sensors in MIMO radar system. When multiple targets are closely located in spatial domain, the proposed approach can significantly enhance the resolution and estimation accuracy relative to the conventional method with uniform linear array (ULA). In the proposed approach, no peaking searching is needed. Notably, it fits the situation that the number of targets is equal or even larger than that of the receive sensors, which is unavailable for the conventional MIMO radar system. The simulations validate the performance of the proposed approach.