Miracle-dz/UniFAR-FTUs huggingface dataset:
A Pattern-Based Approach to Semantic Relation Extraction Using a Seed Ontology

This paper presents our experiment on the "Badea" system. A system designed for the automated extraction of semantic relations from text using a seed ontology and a pattern based approach. We describe the experiment using a set of Arabic language corpora for extracting the antonym semantic relation. Antonyms from the seed ontology are used to extract patterns from the corpora, these patterns are then used to discover new antonym pairs, thus enriching the ontology. Evaluation results show that the system was successful in enriching the ontology with over 400% increase in size. The results also showed that only 2.7% of the patterns were useful in extracting new antonyms, and thus recommendations for pattern scoring are presented in this paper.
Development of the pulse tube refrigerator as an efficient and reliable cryocooler

This paper presents a review of the pulse tube refrigerator from its inception in the mid-1960s up to the present. Various factors are discussed which brought it from a laboratory curiosity to the point where it is now the most efficient of all cryocoolers and reliable enough to be used on space missions. Carnot efficiencies as high as about 20% at 80 K and temperatures as low as 2 K have been achieved in pulse tube refrigerators. The operating principles for the different types of pulse tube and thermoacoustic refrigerators are described. Pulse tube refrigerators operate with oscillating pressures and mass flows and have no moving parts in the cold end. For large industrial systems the mechanical compressor can be replaced with one of two types of thermoacoustic drivers to yield a refrigerator with no moving parts. Recent advances in understanding and reducing losses in various components are described that have led to the improved efficiencies. The major problems associated with cryocoolers are listed, and it is shown that pulse tube refrigerators have begun to overcome many of these problems. As a result, they are now being used or considered for many different applications. Some of these applications as well as example pulse tube refrigerators are described.
Toll-Like Receptors: Insights into Their Possible Role in the Pathogenesis of Lyme Neuroborreliosis

ABSTRACT Lyme neuroborreliosis is likely caused by inflammatory effects of the tick-borne spirochete Borrelia burgdorferi on the nervous system. Microglia, the resident macrophage cells within the central nervous system (CNS), are important in initiating an immune response to microbial products. In addition, astrocytes, the major CNS glial cell type, also can contribute to brain inflammation. TLRs (Toll-like receptors) are used by glial cells to recognize pathogen-associated molecular patterns (PAMPs), mediate innate responses, and initiate an acquired immune response. Here we hypothesize that because of their PAMP specificities, TLR1, -2, -5, and -9 may be involved in the pathogenesis of Lyme neuroborreliosis. Previous reports have shown that the rhesus monkey is the only animal model to exhibit signs of Lyme neuroborreliosis. Therefore, we used primary cultures of rhesus astrocytes and microglia to determine the role of TLRs in mediating proinflammatory responses to B. burgdorferi. The results indicate that microglia and astrocytes respond to B. burgdorferi through TLR1/2 and TLR5. In addition, we observed that phagocytosis of B. burgdorferi by microglia enhances not only the expression of TLR1, -2, and -5, but also that of TLR4. Taken together, our data provide proof of the concept that astrocyte and microglial TLR1, -2, and -5 are involved in the in vivo response of primate glial cells to B. burgdorferi. The proinflammatory molecules elicited by these TLR-mediated responses could be a significant factor in the pathogenesis of Lyme neuroborreliosis.
Leonardo da Vinci--the anatomist.

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Phosphite, an Analog of Phosphate, Suppresses the Coordinated Expression of Genes under Phosphate Starvation1

Phosphate (Pi) and its analog phosphite (Phi) are acquired by plants via Pi transporters. Although the uptake and mobility of Phi and Pi are similar, there is no evidence suggesting that plants can utilize Phi as a sole source of phosphorus. Phi is also known to interfere with many of the Pi starvation responses in plants and yeast (Saccharomyces cerevisiae). In this study, effects of Phi on plant growth and coordinated expression of genes induced by Pi starvation were analyzed. Phi suppressed many of the Pi starvation responses that are commonly observed in plants. Enhanced root growth and root to shoot ratio, a hallmark of Pi stress response, was strongly inhibited by Phi. The negative effects of Phi were not obvious in plants supplemented with Pi. The expression of Pi starvation-induced genes such as LePT1, LePT2,AtPT1, and AtPT2 (high-affinity Pi transporters); LePS2 (a novel acid phosphatase);LePS3 and TPSI1 (novel genes); andPAP1 (purple acid phosphatase) was suppressed by Phi in plants and cell cultures. Expression of luciferase reporter gene driven by the Pi starvation-induced AtPT2 promoter was also suppressed by Phi. These analyses showed that suppression of Pi starvation-induced genes is an early response to addition of Phi. These data also provide evidence that Phi interferes with gene expression at the level of transcription. Synchronized suppression of multiple Pi starvation-induced genes by Phi points to its action on the early molecular events, probably signal transduction, in Pi starvation response.
Asparaginyl Hydroxylation of the Notch Ankyrin Repeat Domain by Factor Inhibiting Hypoxia-inducible Factor*

The stability and activity of hypoxia-inducible factor (HIF) are regulated by the post-translational hydroxylation of specific prolyl and asparaginyl residues. We show that the HIF asparaginyl hydroxylase, factor inhibiting HIF (FIH), also catalyzes hydroxylation of highly conserved asparaginyl residues within ankyrin repeat (AR) domains (ARDs) of endogenous Notch receptors. AR hydroxylation decreases the extent of ARD binding to FIH while not affecting signaling through the canonical Notch pathway. ARD proteins were found to efficiently compete with HIF for FIH-dependent hydroxylation. Crystallographic analyses of the hydroxylated Notch ARD (2.35Å) and of Notch peptides bound to FIH (2.4–2.6Å) reveal the stereochemistry of hydroxylation on the AR and imply that significant conformational changes are required in the ARD fold in order to enable hydroxylation at the FIH active site. We propose that ARD proteins function as natural inhibitors of FIH and that the hydroxylation status of these proteins provides another oxygen-dependent interface that modulates HIF signaling.
New Essays on Singular Thought

Introduction I THE STRUCTURE OF SINGULAR THOUGHT 1. Getting a Thing Into a Thought 2. Three Perspectives on Quantifying In 3. On Singularity II CONDITIONS ON SINGULAR THOUGHT 4. Singular Thought: Acquaintance, Semantic Instrumentalism, and Cognitivism 5. Singular Thought: In Defense of Acquaintance DEMONSTRATIVE AND COMMUNICATION-BASED REFERENCE AND THOUGHT 6. Demonstrative Reference, the Relational View of Experience, and the Proximality Principle 7. We Are Acquainted With Ordinary Things 8. Millian Externalism IV THINKING OF NOTHING 9. Fictional Singular Imaginings 10. Intentionality Without Exotica Index
Preliminary Studies for Machine Generated Index Vocabularies

The studies form part of a programme in which a computer will be used to generate an “index vocabulary” appropriate for the indexing and retrieval of documents in various scientific disciplines; the computer will then index a suitable collection of documents and retrieve documents in response to specific enquiries. The present paper describes how such a system works for a particularly simple text. Then, ten evaluation methods are put forward, and used to assess individual descriptors, indexing rules, and the system as a whole. In this exercise the evaluation methods themselves are on trial and four are selected as being more generally useful than the others. For evaluating whole retrieval systems a type of random enquiry is used for which the perfect answer is computable; relevance and recall ratios can then be objectively determined.
Aliiroseovarius pelagivivens gen. nov., sp. nov., isolated from seawater, and reclassification of three species of the genus Roseovarius as Aliiroseovarius crassostreae comb. nov., Aliiroseovarius halocynthiae comb. nov. and Aliiroseovarius sediminilitoris comb. nov.

A Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated GYSW-22T, was isolated from seawater off Geoje Island in the South Sea, South Korea. Strain GYSW-22T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain GYSW-22T and the type strains of Roseovarius crassostreae, Roseovarius halocynthiae and Roseovarius sediminilitoris form a coherent cluster, independent of phylogenetic lineages or clusters comprising the type strains of other species of the genus Roseovarius. Strain GYSW-22T exhibited 16S rRNA gene sequence similarities of 97.2, 96.6 and 96.3% to R. halocynthiae MA1-10T, R. crassostreae CV919-312T and R. sediminilitoris M-M10T, respectively, and of 92.6-94.7% to the type strains of other species of the genus Roseovarius. Strain GYSW-22T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain GYSW-22T was 59.0 mol% and its mean DNA-DNA relatedness value with R. halocynthiae MA1-10T was 15 %. On the basis of the data presented, we propose strain GYSW-22T represents a novel species of a new genus, Aliiroseovarius pelagivivens gen. nov., sp. nov. The type strain of the type species is GYSW-22T ( = KCTC 42459T = CECT 8811T). In this study, it is also proposed that Roseovarius crassostreae, Roseovarius halocynthiae and Roseovarius sediminilitoris be reclassified into the new genus as Aliiroseovarius crassostreae comb. nov. (type strain CV919-312T = ATCC BAA-1102T = DSM 16950T), Aliiroseovarius halocynthiae comb. nov. (type strain MA1-10T = KCTC 23462T = CCUG 60745T) and Aliiroseovarius sediminilitoris comb. nov. (type strain M-M10T = KCTC 23959T = CCUG 62413T), respectively.
Brain MRI‐markers Associate Differentially with Cognitive Versus Functional Decline Leading to Dementia

Brain MRI‐markers are risk factors of dementia and decline in cognition and daily functioning. It is unknown to what extent the associations of brain MRI‐markers with cognition and daily functioning are part of the pathway leading to dementia. We aimed to investigate associations of brain MRI‐markers with change in cognition and daily functioning during 15 years of follow‐up, including their relation to dementia.
Societal Grounding Is Essential to Meaningful Language Use

Language engineers often point to tight connections between their systems' linguistic representations and accumulated sensor data as a sign that their systems really mean what they say. While we believe such connections are an important piece in the puzzle of meaning, we argue that perceptual grounding alone does not suffice to explain the specific, stable meanings human speakers attribute to each other. Instead, human attributions of meaning depend on a process of societal grounding by which individual language speakers coordinate their perceptual experience and linguistic usage with other members of their linguistic communities. For system builders, this suggests that implementing a strategy of societal grounding would justify the attribution of bona fide linguistic meaning to a system even if it had little perceptual experience and only modest perceptual accuracy. We illustrate the importance and role of societal grounding using an implemented dialogue system that collaboratively identifies visual objects with human users.
Private and verifiable interdomain routing decisions

Existing secure interdomain routing protocols can verify validity properties about individual routes, such as whether they correspond to a real network path. It is often useful to verify more complex properties relating to the route decision procedure - for example, whether the chosen route was the best one available, or whether it was consistent with the network's peering agreements. However, this is difficult to do without knowing a network's routing policy and full routing state, which are not normally disclosed. In this paper, we show how a network can allow its peers to verify a number of nontrivial properties of its interdomain routing decisions without revealing any additional information. If all the properties hold, the peers learn nothing beyond what the interdomain routing protocol already reveals; if a property does not hold, at least one peer can detect this and prove the violation. We present SPIDeR, a practical system that applies this approach to the Border Gateway Protocol, and we report results from an experimental evaluation to demonstrate that SPIDeR has a reasonable overhead.
Proton MR spectroscopy of polymicrogyria and heterotopia.

BACKGROUND AND PURPOSE Proton MR spectroscopy of the brain allows noninvasive in vivo assessment of metabolites, which may be useful in understanding the biology of malformations of cortical development. The aim of this study was to determine the MR spectroscopic characteristics of polymicrogyria and heterotopia compared with those of normal frontal lobe white matter. METHODS We recruited 22 patients with radiographic findings characteristic of polymicrogyria, nine patients with radiographic findings characteristic of heterotopia, and 10 control subjects into the study. The MR imaging technique consisted of high-spatial-resolution axial dual-echo and gradient-echo 3D volume imaging. A single-voxel point-resolved technique (1600/135 [TR/TE]) was used to acquire spectra from the region of neocortical malformation and from frontal lobe white matter in control subjects. The differences in N-acetyl moieties (NA)/creatine (Cr), NA/choline (Cho), and Cho/Cr ratios among patients with heterotopia, those with polymicrogyria, and control subjects were compared by using the Kruskal-Wallis test followed by the Mann-Whitney U (Wilcoxon) test. RESULTS No statistically significant differences were noted in the NA/Cr, NA/Cho, and Cho/Cr ratios between the polymicrogyria group and controls, the heterotopia group and controls, or the polymicrogyria and heterotopia groups. CONCLUSION Both heterotopia and polymicrogyria are malformations of cortical development that occur at a relatively late stage of brain development. The neurons and glia in these lesions are mature, and the metabolites appear to be similar to those of normal adult frontal white matter.
Vritthi - a theoretical framework for IT recruitment based on machine learning techniques applied over Twitter, LinkedIn, SPOJ and GitHub profiles

In this model, we propose an innovative recruitment system using social networking websites like Twitter and LinkedIn along with code repository hosting website GitHub and competitive coding platforms like SPOJ. It is aimed to develop advanced search engines to automatically sort the job-seekers based on job offer requirements using various data mining and machine learning techniques. Vritthi allows job-seekers to quantify their job preparedness and offer a list of specific areas for them to focus on. We propose the formulation of VPQF (Vritthi Professional Quotient) that involves the use of K-means algorithm to classify users into appropriate clusters and provide them with appropriate suggestions for improvement. Using classic data mining techniques like filtration, classification, clustering, profiling as well as string matching & user profiling, this tool will enable recruiters to effectively select candidates who fit their organization in a hassle-free automated manner.
Dynamics of periodic node states on a model of static networks with repeated-averaging rules

We introduce a simple model of static networks, where nodes are located on a ring structure, and two accompanying dynamic rules of repeated averaging on periodic node states. We assume nodes can interact with neighbors, and will add long-range links randomly. The number of long-range links, E, controls structures of these networks, and we show that there exist many types of fixed points, when E is varied. When E is low, fixed points are mostly diverse states, in which node states are diversely populated; on the other hand, when E is high, fixed points tend to be dominated by converged states, in which node states converge to one value. Numerically, we observe properties of fixed points for various E's, and also estimate points of the transition from diverse states to converged states for four different cases. This kind of simple network models will help us understand how diversities that we encounter in many systems of complex networks are sustained, even when mechanisms of averaging are at work,and when they break down if more long-range connections are added.
Long-acting reversible contraception: Findings from the Understanding Fertility Management in Contemporary Australia survey

Objectives The aim of this research was to investigate awareness, perceived reliability and consideration of use of long-acting reversible contraception (LARC) among Australians of reproductive age. Methods A sample of 18- to 50-year-old women and men (N = 2235) was randomly recruited from the Australian electoral roll in 2013. Respondents completed a self-administered, anonymous questionnaire. Data were weighted to reduce non-response bias. Factors associated with perceived reliability and consideration of use of LARC were identified in multivariable analyses. Results Most respondents had heard of implants (76.5%) and intrauterine contraception (63.7%). However, most did not think implants (56.3%) or IUDs (63.9%) were reliable and would not consider using implants (71.6%) or IUDs (77.5%). Those significantly more likely to perceive LARC as reliable were younger, did not regard religion as important in fertility choices, had private health insurance, had been pregnant and had had an abortion; and women who had a partner. Those more likely to consider using LARC were younger and did not regard religion as important in fertility choices; women who had private health insurance, lived in an area of socioeconomic advantage and had had an abortion; and men without a partner, born in Australia and comfortable talking to a health care provider about contraceptive matters. Conclusions Despite high awareness of LARC among Australian adults, its perceived reliability and willingness to use it remain low in certain groups. Targeted interventions that aim to increase knowledge of the benefits and reliability of LARC and allow informed use are recommended.
Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis.

Nutrient scarcity is a common condition in nature, but the resulting extremely low growth rates (below 0.025 h(-1) ) are an unexplored research area in Bacillus subtilis. To understand microbial life in natural environments, studying the adaptation of B. subtilis to near-zero growth conditions is relevant. To this end, a chemostat modified for culturing an asporogenous B. subtilis sigF mutant strain at extremely low growth rates (also named a retentostat) was set up, and biomass accumulation, culture viability, metabolite production and cell morphology were analysed. During retentostat culturing, the specific growth rate decreased to a minimum of 0.00006 h(-1) , corresponding to a doubling time of 470 days. The energy distribution between growth and maintenance-related processes showed that a state of near-zero growth was reached. Remarkably, a filamentous cell morphology emerged, suggesting that cell separation is impaired under near-zero growth conditions. To evaluate the corresponding molecular adaptations to extremely low specific growth, transcriptome changes were analysed. These revealed that cellular responses to near-zero growth conditions share several similarities with those of cells during the stationary phase of batch growth. However, fundamental differences between these two non-growing states are apparent by their high viability and absence of stationary phase mutagenesis under near-zero growth conditions.
Robust real-time attention-based head-shoulder detection for video surveillance

Robust head-shoulder detection has widely been utilized in video surveillance applications. However, most state-of-the-art approaches are very time-consuming and unable to effectively handle videos with radical pose and viewpoint changes. In this paper, we introduce a robust and rapid head-shoulder detection method, which is invariant to pose and viewpoint for video surveillance. The proposed method combines an attention-based foreground segmentation module and a multiview head-shoulder detection cascade to achieve high performance in both accuracy and speed. Specifically, the attention-based foreground segmentation module firstly detects not only active regions that involve motions but also static areas where people stand or sit still in video frames. These regions are then provided to a two-layer head-shoulder detection cascade which is composed of a preliminary linear classifier which eliminates most obvious non-head-shoulder windows rapidly, and a set of histogram intersection kernel (HIK) based multi-view classifiers that can precisely detect head-shoulders with different pose and viewpoint. When compared to the leading methods in the challenging PETS 2009 benchmark dataset, our approach obtains highly competitive results in terms of effectiveness and efficiency.