Miracle-dz/UniFAR-FTUs huggingface dataset:
KSRP: A checkpoint for inflammatory cytokine production in astrocytes

Chronic inflammation in the central nervous system (CNS) is a central feature of many neurodegenerative and autoimmune diseases. As an immunologically competent cell, the astrocyte plays an important role in CNS inflammation. It is capable of expressing a number of cytokines such as tumor necrosis factor alpha (TNF‐α) and interleukin‐1 beta (IL‐1β) that promote inflammation directly and through the recruitment of immune cells. Checkpoints are therefore in place to keep tight control over cytokine production. Adenylate/uridylate‐rich elements (ARE) in the 3′ untranslated region of cytokine mRNAs serve as a major checkpoint by regulating mRNA stability and translational efficiency. Here, we examined the impact of KH‐type splicing regulatory protein (KSRP), an RNA binding protein which destabilizes mRNAs via the ARE, on cytokine expression and paracrine phenotypes of primary astrocytes. We identified a network of inflammatory mediators, including TNF‐α and IL‐1β, whose expression increased 2 to 4‐fold at the RNA level in astrocytes isolated from KSRP−/− mice compared to littermate controls. Upon activation, KSRP−/− astrocytes produced TNF‐α and IL‐1β at levels that exceeded control cells by 15‐fold or more. Conditioned media from KSRP−/− astrocytes induced chemotaxis and neuronal cell death in vitro. Surprisingly, we observed a prolongation of half‐life in only a subset of mRNA targets and only after selective astrocyte activation. Luciferase reporter studies indicated that KSRP regulates cytokine gene expression at both transcriptional and post‐transcriptional levels. Our results outline a critical role for KSRP in regulating pro‐inflammatory mediators and have implications for a wide range of CNS inflammatory and autoimmune diseases. © 2012 Wiley Periodicals, Inc.
Numerical Simulation of Vector Wave Scattering From the Target and Rough Surface Composite Model With 3-D Multilevel UV Method

Numerical simulation of vector wave scattering from three-dimensional (3-D) target and rough surface composite model is investigated with a 3-D multilevel UV method. Due to the adoption of RWG basis functions for accurate modeling of vector current, the oscillation of the interaction matrix elements brings difficulty to directly apply the UV decomposition method. Based on the reordering of the interaction strength and the sampling according to the characteristics distribution of the interaction, an EM-interaction-based sampling algorithm is developed for the accurate reconstruction of the far interaction submatrix with UV decomposition method. Combined with multilevel division of the total composite model, the 3-D multilevel UV method incorporating the new sampling algorithm is developed for vector wave scattering from 3-D complex target above or on a random rough surface. The 3-D multilevel UV method yields a complexity of O(N log N) for the setup time of the impedance matrix, the solve time of the matrix iterative solution and also for the memory requirements. The accuracy and the efficiency of the 3-D multilevel UV method is compared and validated with the full MOM method and the ACA method in the tested cases. Finally, the applications of a target above or on the rough surface, for example, a ship on the sea surface, have been accomplished and analyzed.
Applied Dental Materials

Science of dental materials . Properties used to characterise materials . Gypsum products for dental casts . Waxes . Investments and refractory dies . Metals and alloys . Gold and alloys of noble metals . Base metal casting alloys . Casting . Steel and wrought alloys . Ceramics and porcelain fused to metal (PFM) . Synthetic polymers . Denture base polymers . Denture lining materials . Artificial teeth . Impression materials: Classification and requirements . Non-elastic impression materials . Elastic impression materials: Hydrocolloids . Elastic impression materials: Synthetic elastomers . Requirements of direct filing materials and historical perspectives . Dental amalgam . Resin-based filling materials . Adhesive restorative materials: bonding of resin-based materials . Glass-ionomer restorative materials (polyalkenoates) . Resin-modified glass-ionomers and related materials . Temporary crown and bridge resins . Requirements of dental cements for lining, base and luting applications . Cements based on phosphoric acid . Cements based on organometallic chelate compounds . Polycarboxylates, glass-ionomers and resin-modified glass-ionomers for luting and lining Index
Quasi-biennial oscillations extracted from the monthly NAO index and temperature records are phase-synchronized

Using the extension of Monte Carlo Singular Sys- tem Analysis (MC SSA), based on evaluating and testing the regularity of the dynamics of the SSA modes against the col- ored noise null hypothesis, we demonstrate detection of os- cillatory modes with period of about 27 months in records of monthly average near-surface air temperature from sev- eral European locations, as well as in the monthly North At- lantic Oscillation index. According to their period, the de- tected modes can be attributed to the quasi-biennial oscilla- tions (QBO). The QBO modes extracted from the temper- ature and from the NAO index underwent synchronization analysis and their phase synchronization has been confirmed with high statistical significance.
Single Document Keyphrase Extraction Using Sentence Clustering and Latent Dirichlet Allocation

This paper describes the design of a system for extracting keyphrases from a single document The principle of the algorithm is to cluster sentences of the documents in order to highlight parts of text that are semantically related. The clusters of sentences, that reflect the themes of the document, are then analyzed to find the main topics of the text. Finally, the most important words, or groups of words, from these topics are proposed as keyphrases.
Optimal sampling schedule for chemical exchange saturation transfer

The sampling schedule for chemical exchange saturation transfer imaging is normally uniformly distributed across the saturation frequency offsets. When this kind of evenly distributed sampling schedule is used to quantify the chemical exchange saturation transfer effect using model‐based analysis, some of the collected data are minimally informative to the parameters of interest. For example, changes in labile proton exchange rate and concentration mainly affect the magnetization near the resonance frequency of the labile pool. In this study, an optimal sampling schedule was designed for a more accurate quantification of amine proton exchange rate and concentration, and water center frequency shift based on an algorithm previously applied to magnetization transfer and arterial spin labeling. The resulting optimal sampling schedule samples repeatedly around the resonance frequency of the amine pool and also near to the water resonance to maximize the information present within the data for quantitative model‐based analysis. Simulation and experimental results on tissue‐like phantoms showed that greater accuracy and precision (>30% and >46%, respectively, for some cases) were achieved in the parameters of interest when using optimal sampling schedule compared with evenly distributed sampling schedule. Hence, the proposed optimal sampling schedule could replace evenly distributed sampling schedule in chemical exchange saturation transfer imaging to improve the quantification of the chemical exchange saturation transfer effect and parameter estimation. Magn Reson Med 70:1251–1262, 2013. © 2013 Wiley Periodicals, Inc.
A micromechanical approach to the behaviour of single wood fibers and wood fracture at cellular level

Mechanical and fracture behaviors of wood are defined by the morphology and mechanical properties of wood fibers and their bonding medium. Parallel orientation of wood fibers makes them the most influential microstructural elements from the mechanical point of view. On the other hand, in wood fracture, the difference between the properties of fiber and bonding medium (which make weak cleavage plates) plays a more important role. Experiments show that the mechanical behavior of a single wood fiber under axial tension is complex, although the cause of this complexity has still not been clearly understood. In this thesis, in order to explain the mechanism underlying the mechanical behavior of wood fibers and the fracture of wood specimens at fiber level, a micromechanical approach has been used. Confocal laser scanning microscopy was used to investigate the pattern of the distribution of microfibrils in different wood fibers. It was shown that the microfibril angle within a single fiber is non-uniform and this non-uniformity in radial walls of earlywood fibers, which contain the bordered pits, is higher than tangential walls of earlywood fibers and also higher than in latewood fibers. Tensile and cyclic tensile tests on single spruce fibers were carried out and their non-linear and force-history dependent behaviors under axial tension were shown. It was found that the fiber behavior is affected by the range of microfibril angle non-uniformities and other defects. After a certain force limit, wood fiber undergoes irreversible strains and the elastic limit of the fiber increases in the tensile loading. To explain these results, a model based on the assumption of helical and non-uniform distribution of cellulose microfibrils in the fiber and damage of the hemicellulose and lignin matrix after yielding, was proposed. The model indicated that multi-damage and evolution of microfibrils in the damages segments are the main governing mechanisms of the tensile behavior of wood fiber. Difficulties of considering the porous and heterogeneous microstructure of wood in a continuum-based fracture model, led us to develop a mixed lattice-continuum model. The three-dimensional geometry of lattice, composed of different beam elements which represent the bonding medium and alternation of earlywood and latewood fibers, enabled us to detect the propagation of cracks in both cross sections and longitudinal sections at the fiber level. Model showed that in Mode I fracture, parallel to the fibers, the location of the developed crack and the resulting stress-strain curves have a good agreement with the experimental evidence.
Ionic materials to improve charge injection in polymer electroluminescent devices

We describe here the fabrication and characterization of novel organic electro-optic materials composed of self-assembled superlattices. The SAS structures are intrinsically acentric and exhibit large second harmonic generation and electro-optic responses. This approach using SAS electro-optic materials has advantages such as not requiring poling for creating nonlinearity in the films and efficient film growth on a variety of substrates over large areas. Prototype waveguide electro-optic modulators have been fabricated usgin SAS films integated with low-loss polymeric materials functioning as partial guiding and cladding layers. The waveguide EO modulators are fabricated using a multistep process including e-beam deposition, plasma-enhanced chemical vapor deposition, photolithography, and reactive ion etching. Electro-optic parameters such as the half-wave voltage and the effective electro-optic coefficient, and the velocity mismatch between the optical and radio frequency waves have been evaluated.
Latent semantic analysis and the construction of coherent extracts

We describe a language-neutral automatic summarization system which aims to produce coherent extracts. It builds an initial extract composed solely of topic sentences, and then recursively fills in the topical lacunae by providing linking material between semantically dissimilar sentences. While experiments with human judges did not prove a statistically significant increase in textual coherence with the use of a latent semantic analysis module, we found a strong positive correlation between coherence and overall summary quality.
Comparing phonological skills and spelling abilities in children with reading and language impairments.

BACKGROUND Bishop and Snowling (2004) proposed that children with language impairments (LI) and children with reading difficulties (RD) can be considered to be on a (phonological) continuum of risk for reading impairments. AIMS The first aim of the present study was to address two specific hypotheses about the relationship between RD and LI. The severity hypothesis proposes that LI is a more severe form of RD. In contrast, the dyslexia-plus hypothesis proposes that children with LI share the same phonological deficit as children with RD, but also have impairments in non-phonological language skills. The second aim of the study was to further our understanding of the spelling skills of children with LI. METHODS & PROCEDURES Twenty-three children with primary language impairments (LI) and 22 children with primary reading impairments (RD) matched on chronological and reading age were compared with typically developing children. The children's performance on tests of phoneme deletion, phonological memory, and spelling accuracy and phonetic spelling was compared. OUTCOMES & RESULTS Children with LI showed poorer phonological memory performance than children with RD and age controls, whereas both clinical groups performed significantly worse than the age controls on the phoneme deletion task and comparably to reading-age controls. Children with LI and RD were impaired for their age at phonetic spelling, the children with LI showing the more severe impairment. Further exploration of the data identified two different profiles among children with LI; some of these children had poorer phonological skills than predicted from receptive vocabulary, supporting the severity hypothesis. The other group showed a profile with concurrent impairments in vocabulary and phonological skills, in line with the dyslexia-plus hypothesis. CONCLUSIONS The findings suggest that a subgroup of children with LI may be experiencing a severe form of dyslexia. The results further suggest that children with LI have difficulty producing phonologically plausible spellings.
Underwater photosynthesis in flooded terrestrial plants: a matter of leaf plasticity.

BACKGROUND Flooding causes substantial stress for terrestrial plants, particularly if the floodwater completely submerges the shoot. The main problems during submergence are shortage of oxygen due to the slow diffusion rates of gases in water, and depletion of carbohydrates, which is the substrate for respiration. These two factors together lead to loss of biomass and eventually death of the submerged plants. Although conditions under water are unfavourable with respect to light and carbon dioxide supply, photosynthesis may provide both oxygen and carbohydrates, resulting in continuation of aerobic respiration. SCOPE This review focuses on evidence in the literature that photosynthesis contributes to survival of terrestrial plants during complete submergence. Furthermore, we discuss relevant morphological and physiological responses of the shoot of terrestrial plant species that enable the positive effects of light on underwater plant performance. CONCLUSIONS Light increases the survival of terrestrial plants under water, indicating that photosynthesis commonly occurs under these submerged conditions. Such underwater photosynthesis increases both internal oxygen concentrations and carbohydrate contents, compared with plants submerged in the dark, and thereby alleviates the adverse effects of flooding. Additionally, several terrestrial species show high plasticity with respect to their leaf development. In a number of species, leaf morphology changes in response to submergence, probably to facilitate underwater gas exchange. Such increased gas exchange may result in higher assimilation rates, and lower carbon dioxide compensation points under water, which is particularly important at the low carbon dioxide concentrations observed in the field. As a result of higher internal carbon dioxide concentrations in submergence-acclimated plants, underwater photorespiration rates are expected to be lower than in non-acclimated plants. Furthermore, the regulatory mechanisms that induce the switch from terrestrial to submergence-acclimated leaves may be controlled by the same pathways as described for heterophyllous aquatic plants.
A rank-based statistical test for measuring synergistic effects between two gene sets

MOTIVATION Due to recent advances in high-throughput technologies, data on various types of genomic annotation have accumulated. These data will be crucially helpful for elucidating the combinatorial logic of transcription. Although several approaches have been proposed for inferring cooperativity among multiple factors, most approaches are haunted by the issues of normalization and threshold values. RESULTS In this article, we propose a rank-based non-parametric statistical test for measuring the effects between two gene sets. This method is free from the issues of normalization and threshold value determination for gene expression values. Furthermore, we have proposed an efficient Markov chain Monte Carlo method for calculating an approximate significance value of synergy. We have applied this approach for detecting synergistic combinations of transcription factor binding motifs and histone modifications. AVAILABILITY C implementation of the method is available from http://www.hgc.jp/~yshira/software/rankSynergy.zip. CONTACT yshira@hgc.jp SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Bandwidth Expansion Shannon Mapping for Analog Error-Control Coding

Based on an initial idea of Shannon, we investigate an approach, named Shannon mapping, for transmission of analog messages, that is fundamentally different from current digital communication methods. We investigate 1:2 bandwidth expansion Shannon mapping based on two specific mapping curves. We demonstrate that bandwidth expansion Shannon mapping using a mapping curve does not introduce any delay and its encoding and decoding processes exhibit very low complexity. More importantly, our simulations show that the distortion performance of 1:2 bandwidth expansion Shannon mapping is significantly better than the rate-distortion bound without bandwidth expansion at moderate to high SNRs, and about 3-5 dB inferior to the rate-distortion bound with the same bandwidth expansion.
Enhanced chemotherapy delivery by intraarterial infusion and blood‐brain barrier disruption in the treatment of cerebral metastasis

Cerebral metastases are clinically significant in 10% to 30% of patients with neoplasia. Multiple cerebral metastases are typically treated with palliative radiotherapy. There is no consensus on the role of enhanced chemotherapy delivery as an adjuvant treatment modality in this disease. In this report, the authors detailed their experience with intraarterial (IA) chemotherapy infusion with and without blood‐brain barrier disruption (BBBD) in patients with multiple cerebral metastases.
A Speech Based Approach to Surveillance Video Retrieval

This paper describes the anatomy of a pilot surveillance system with a speech-based interface for content-based retrieval of video data. The proposed system relies on an ontology-based information sharing architecture and lets components of the system communicate among each other through TCP/IP communication channels. The aim of developing the pilot system was to explore dependencies between image analysis, event detection, video annotation, and speech- based retrieval of the video content in the context of a broader spoken dialogue system.
Colorimetric Detection Based on Localised Surface Plasmon Resonance Optical Characteristics for the Detection of Hydrogen Peroxide Using Acacia Gum–Stabilised Silver Nanoparticles

The use of nanoparticles in sensing is attracting the interest of many researchers. The aim of this work was to fabricate Acacia gum–stabilised silver nanoparticles (SNPs) using green chemistry to use them as a highly sensitive and cost-effective localised surface plasmon resonance (LSPR) colorimeter sensor for the determination of reactive oxygen species, such as hydrogen peroxide (H2O2). Silver nanoparticles were fabricated by the reduction of an inorganic precursor silver nitrate solution (AgNO3) using white sugar as the reducing reagent and Acacia gum as the stabilising reagent and a sonication bath to form uniform silver nanoparticles. The fabricated nanoparticles were characterised by visual observation, ultraviolet-visible (UV-Vis) spectrophotometry, transmission electron microscopy (TEM) analysis, energy-dispersive X-ray spectroscopy (EDAX), thermogravimetric analysis (TGA), and Fourier transform infrared spectroscopy (FT-IR). The TEM micrographs of the synthesised nanoparticles showed the presence of spherical nanoparticles with sizes of approximately 10 nm. The EDAX spectrum result confirmed the presence of silver (58%), carbon (30%), and oxygen (12%). Plasmon colorimetric sensing of H2O2 solution was investigated by introducing H2O2 solution into Acacia gum–capped SNP dispersion, and the change in the LSPR band in the UV-Vis region of spectra was monitored. In this study, it was found that the yellow colour of Acacia gum–stabilised SNPs gradually changed to transparent, and moreover, a remarkable change in the LSPR absorbance strength was observed. The calibration curve was linear over 0.1–0.00001 M H2O2, with a correlation estimation (R2) of . 953. This was due to the aggregation of SNPs following introduction of the H2O2 solution. Furthermore, the fabricated SNPs were successfully used to detect H2O2 solution in a liquid milk sample, thereby demonstrating the ability of the fabricated SNPs to detect H2O2 solution in liquid milk samples. This work showed that Acacia gum–stabilised SNPs may have the potential as a colour indicator in medical and environmental applications.
AstRoMap European Astrobiology Roadmap

Abstract The European AstRoMap project (supported by the European Commission Seventh Framework Programme) surveyed the state of the art of astrobiology in Europe and beyond and produced the first European roadmap for astrobiology research. In the context of this roadmap, astrobiology is understood as the study of the origin, evolution, and distribution of life in the context of cosmic evolution; this includes habitability in the Solar System and beyond. The AstRoMap Roadmap identifies five research topics, specifies several key scientific objectives for each topic, and suggests ways to achieve all the objectives. The five AstRoMap Research Topics are • Research Topic 1: Origin and Evolution of Planetary Systems • Research Topic 2: Origins of Organic Compounds in Space • Research Topic 3: Rock-Water-Carbon Interactions, Organic Synthesis on Earth, and Steps to Life • Research Topic 4: Life and Habitability • Research Topic 5: Biosignatures as Facilitating Life Detection It is strongly recommended that steps be taken towards the definition and implementation of a European Astrobiology Platform (or Institute) to streamline and optimize the scientific return by using a coordinated infrastructure and funding system. Key Words: Astrobiology roadmap—Europe—Origin and evolution of life—Habitability—Life detection—Life in extreme environments. Astrobiology 16, 201–243.
Semantic models for knowledge management

We explore the use of a semantic model to support a group of strategic business analysts in their daily work. In particular, we present a set of modeling constructs for representing goals, events and actors that are relevant to the work of analysts. We also describe a qualitative goal analysis procedure which makes it possible to reason about a goal model under different assumptions. The paper also reports on an incremental document classification scheme that can be used to classify relevant documents with respect to the concepts constituting the semantic model.