Miracle-dz/UniFAR-FTUs huggingface dataset:
SGML Documents: Where Does Quality Go?

Quality control in electronic publications should be one of the major concerns of everyone who is managing a project. Big projects, like digital libraries, try to gather information from a series of different sources: libraries, museums, universities, and other scientific or cultural organizations. Collecting and treating information from several different sources raises very interesting problems, one being the assurance of quality. Quality in electronic publications can be reflected in several forms, from the visual aspects of the interface, to linguistic and literary aspects, to the correctness of data. With SGML we can solve part of the problem, structural/syntactic correctness. SGML provides a nice way to specify the structure of documents keeping a complete separation between structure (syntax) and typesetting. Today there are lots of editors and environments that can assist the user producing well-formed and valid SGML documents (validating their structure). However, current software still gives the user too much freedom. The user has full control of the data being introduced, creating a margin for errors. In this context there are situations where pre-conditions over the information being introduced should be enforced in order to prevent the user from introducing erroneous data; we shall call this process data semantics validation. The idea is to constrain the values of some structural elements of a document according to its final purpose. This way the user (who writes the documents according to that DTD) will not have full control of his data; he will be forced to obey certain domain range limitations or certain information relationships. SGML does not have the necessary constructs to implement this extra validation task. In this paper we will present and discuss ways of associating a constraint language with the SGML model. We will present the steps towards the implementation of that language. In the end, we present a new SGML authoring and processing model which has an extra validation task: semantic validation. Along the paper we will show some case studies that could have their quality improved with this new working scheme.
[Peptic ulcer of the esophagus].

Peptic ulcer has been diagnosed in eighty-eight out of more than 4,000 cases of esophageal disease in fortytwo years of my experience. Of these eighty-eight cases, twenty-one were active ulcers and sixty-seven were scars probably due to preceding peptic ulcers. This, however, is not a sound basis on which to esti¬ mate the infrequency of the disease, because until recent years few opportunities have been afforded for esophagoscopy, and when done at all it has been only in the presence of symptoms of esophageal obstruction. Peptic ulcer of the esophagus is for a long time not obstructive and the symptoms are erroneously consid¬ ered gastric. When the time shall have come when
When does hearing laughter draw attention to happy faces? Task relevance determines the influence of a crossmodal affective context on emotional attention

Prior evidence has shown that a person's affective context influences attention to emotional stimuli. The present study investigated whether a crossmodal affective context that is induced by remembering an emotional sound modulates attention to visual emotional stimuli. One group of participants had to remember a positive, negative, or neutral sound during each trial of a dot probe paradigm. A second group of participants also had to encode the valence of the sound. The results revealed that attention was preferentially deployed to stimuli that were emotionally congruent to the affective context. However, this effect was only evident when participants had to encode the valence of the affective context. These findings suggest that a crossmodal affective context modulates the deployment of attention to emotional stimuli provided that the affective connotation of the context is task-relevant.
Input–output robustness in simple bacterial signaling systems

Biological signaling systems produce an output, such as the level of a phosphorylated protein, in response to defined input signals. The output level as a function of the input level is called the system's input–output relation. One may ask whether this input–output relation is sensitive to changes in the concentrations of the system's components, such as proteins and ATP. Because component concentrations often vary from cell to cell, it might be expected that the input–output relation will likewise vary. If this is the case, different cells exposed to the same input signal will display different outputs. Such variability can be deleterious in systems where survival depends on accurate match of output to input. Here we suggest a mechanism that can provide input–output robustness, that is, an input–output relation that does not depend on variations in the concentrations of any of the system's components. The mechanism is based on certain bacterial signaling systems. It explains how specific molecular details can work together to provide robustness. Moreover, it suggests an approach that can help identify a wide family of nonequilibrium mechanisms that potentially have robust input–output relations.
Inward rectifier potassium (Kir) current in dopaminergic periglomerular neurons of the mouse olfactory bulb

Dopaminergic (DA) periglomerular (PG) neurons are critically placed at the entry of the bulbar circuitry, directly in contact with both the terminals of olfactory sensory neurons and the apical dendrites of projection neurons; they are autorhythmic and are the target of numerous terminals releasing a variety of neurotransmitters. Despite the centrality of their position, suggesting a critical role in the sensory processing, their properties -and consequently their function- remain elusive. The current mediated by inward rectifier potassium (Kir) channels in DA-PG cells was recorded by adopting the perforated-patch configuration in thin slices; IKir could be distinguished from the hyperpolarization-activated current (Ih) by showing full activation in <10 ms, no inactivation, suppression by Ba2+ in a typical voltage-dependent manner (IC50 208 μM) and reversal potential nearly coincident with EK. Ba2+ (2 mM) induces a large depolarization of DA-PG cells, paralleled by an increase of the input resistance, leading to a block of the spontaneous activity, but the Kir current is not an essential component of the pacemaker machinery. The Kir current is negatively modulated by intracellular cAMP, as shown by a decrease of its amplitude induced by forskolin or 8Br-cAMP. We have also tested the neuromodulatory effects of the activation of several metabotropic receptors known to be present on these cells, showing that the current can be modulated by a multiplicity of pathways, whose activation in some case increases the amplitude of the current, as can be observed with agonists of D2, muscarinic, and GABAA receptors, whereas in other cases has the opposite effect, as it can be observed with agonists of α1 noradrenergic, 5-HT and histamine receptors. These characteristics of the Kir currents provide the basis for an unexpected plasticity of DA-PG cell function, making them potentially capable to reconfigure the bulbar network to allow a better flexibility.
Automatic baggage detection and classification

In this paper we propose an enhanced approach to automatic baggage detection in CCTV video footage that addresses some of the shortcomings of state-of-the-art algorithms and a novel approach to the subsequent recognition of their type. The proposed approach consists of standard steps used in baggage detection, namely, the estimation of moving direction of humans carrying baggage and the alignment of a temporal human-like template with the best matched view-specific exemplars. In addition, unique to the proposed approach is the connected baggage separation algorithm to achieve accurate baggage detection. A further key novel contribution is baggage type classification which is based on the determination of the position of the bag in relevance to the human body carrying it. The proposed system has been extensively tested for its effectiveness on PETS 2006 dataset and additional CCTV video footage captured to cover specific test scenarios. The experimental results suggest that the proposed algorithm is capable of superseding the functional performance of state-of-the art baggage detection algorithms and is able to achieve accurate baggage type classification.
Testing the Temperature Limits of GaN-Based HEMT Devices

The high temperature stability of AlGaN/GaN and lattice-matched InAlN/GaN heterostructure FETs has been evaluated by a stepped temperature test routine under large-signal operation. While AlGaN/GaN high-electron mobility transistors (HEMTs) have failed in an operating temperature range of 500°C, InAlN/GaN HEMTs have been operated up to 900°C for 50 h (in vacuum). Failure is thought to be still contact metallization stability related, indicating an extremely robust InAlN/GaN heterostructure configuration.
Effect of Fluorescent Dyes on In Vitro-Differentiated, Late-Stage Plasmodium falciparum Gametocytes

ABSTRACT Plasmodium falciparum gametocytes are not associated with clinical symptoms, but they are responsible for transmitting the pathogen to mosquitoes. Therefore, gametocytocidal interventions are important for malaria control and resistance containment. Currently available drugs and vaccines are not well suited for that purpose. Several dyes have potent antimicrobial activity, but their use against gametocytes has not been investigated systematically. The gametocytocidal activity of nine synthetic dyes and four control compounds was tested against stage V gametocytes of the laboratory strain 3D7 and three clinical isolates of P. falciparum with a bioluminescence assay. Five of the fluorescent dyes had submicromolar 50% inhibitory concentration (IC50) values against mature gametocytes. Three mitochondrial dyes, MitoRed, dihexyloxacarbocyanine iodide (DiOC6), and rhodamine B, were highly active (IC50s < 200 nM). MitoRed showed the highest activity against gametocytes, with IC50s of 70 nM against 3D7 and 120 to 210 nM against clinical isolates. All compounds were more active against the laboratory strain 3D7 than against clinical isolates. In particular, the endoperoxides artesunate and dihydroartemisinin showed a 10-fold higher activity against 3D7 than against clinical isolates. In contrast to all clinically used antimalarials, several fluorescent dyes had surprisingly high in vitro activity against late-stage gametocytes. Since they also act against asexual blood stages, they shall be considered starting points for the development of new antimalarial lead compounds.
Studying the effect of particle size and coating type on the blood kinetics of superparamagnetic iron oxide nanoparticles

Purpose: Magnetic resonance imaging (MRI), one of the most powerful imaging techniques available, usually requires the use of an on-demand designed contrast agent to fully exploit its potential. The blood kinetics of the contrast agent represent an important factor that needs to be considered depending on the objective of the medical examination. For particulate contrast agents, such as superparamagnetic iron oxide nanoparticles (SPIOs), the key parameters are particle size and characteristics of the coating material. In this study we analyzed the effect of these two properties independently and systematically on the magnetic behavior and blood half-life of SPIOs. Methods: Eleven different SPIOs were synthesized for this study. In the first set (a), seven carboxydextran (CDX)-coated SPIOs of different sizes (19–86 nm) were obtained by fractionating a broadly size-distributed CDX–SPIO. The second set (b) contained three SPIOs of identical size (50 nm) that were stabilized with different coating materials, polyacrylic acid (PAA), poly-ethylene glycol, and starch. Furthermore, small PAA–SPIOs (20 nm) were synthesized to gain a global insight into the effects of particle size vs coating characteristics. Saturation magnetization and proton relaxivity were determined to represent the magnetic and imaging properties. The blood half-life was analyzed in rats using MRI, time-domain nuclear magnetic resonance, and inductively coupled plasma optical emission spectrometry. Results: By changing the particle size without modifying any other parameters, the relaxivity r2 increased with increasing mean particle diameter. However, the blood half-life was shorter for larger particles. The effect of the coating material on magnetic properties was less pronounced, but it had a strong influence on blood kinetics depending on the ionic character of the coating material. Conclusion: In this report we systematically demonstrated that both particle size and coating material influence blood kinetics and magnetic properties of SPIO independently. These data provide key information for the selection of a contrast agent for a defined application and are additionally valuable for other nano areas, such as hyperthermia, drug delivery, and nanotoxicology.
Searches for exploitable biochemical differences between normal and cancer cells. IV. Utilization of neucleosides and nucleotides.

Ear l ie r papers of th is series (5, 6) have been concerned wi th the capac i ty of tumors a n d normal t issues in vivo to ut i l ize p re formed pur ines and precursors of pur ines as sources of nucleic acid purines. An obvious extension of these studies is to pur ine nucleosides and nucleotides. Compounds of these classes have been shown to be u t i l ized for nucleic acid synthes is b y m a m m a l i a n sys tems in vitro (9-12, 21) and in vivo (8, 13-17, 19, 20); however, the only repor t in which tumors and normal t issue were compared in vivo was t ha t of Weinfe ld et al. (20), who s tudied the u t i l iza t ion of adenos ine-3 ' -phosphate and a mix tu re of guanosine-2 ' and 3 ' -phosphates by Sarcoma 180 and by the mixed viscera of the hos t Swiss mice. I n cont inuat ion of our studies on pur ine me tabo l i sm by tumors and normal t issues in vivo, this paper deals wi th the ut i l iza t ion of a series of pur ine nucleosides and nucleot ides b y Sarcoma 180 and by a h u m a n sarcoma grown in the cor t isonet reated hamster .
Ubiquitination of basal VEGFR2 regulates signal transduction and endothelial function

ABSTRACT Cell surface receptors can undergo recycling or proteolysis but the cellular decision-making events that sort between these pathways remain poorly defined. Vascular endothelial growth factor A (VEGF-A) and vascular endothelial growth factor receptor 2 (VEGFR2) regulate signal transduction and angiogenesis, but how signaling and proteolysis is regulated is not well understood. Here, we provide evidence that a pathway requiring the E1 ubiquitin-activating enzyme UBA1 controls basal VEGFR2 levels, hence metering plasma membrane receptor availability for the VEGF-A-regulated endothelial cell response. VEGFR2 undergoes VEGF-A-independent constitutive degradation via a UBA1-dependent ubiquitin-linked pathway. Depletion of UBA1 increased VEGFR2 recycling from endosome-to-plasma membrane and decreased proteolysis. Increased membrane receptor availability after UBA1 depletion elevated VEGF-A-stimulated activation of key signaling enzymes such as PLCγ1 and ERK1/2. Although UBA1 depletion caused an overall decrease in endothelial cell proliferation, surviving cells showed greater VEGF-A-stimulated responses such as cell migration and tubulogenesis. Our study now suggests that a ubiquitin-linked pathway regulates the balance between receptor recycling and degradation which in turn impacts on the intensity and duration of VEGF-A-stimulated signal transduction and the endothelial response. Summary: Ubiquitin-mediated modulation of membrane trafficking and turnover of an endothelial receptor tyrosine kinase (VEGFR2) thus regulates proteolysis, receptor activation, signal transduction and downstream cellular responses. This article has an associated First Person interview with the first author of the paper as part of the supplementary information.
Fuzzy Controller Based QoS Routing Algorithm with a Multiclass Scheme for MANET

A mobile ad hoc network (MANET) consists of a set of mobile hosts that can communicate with each other without the assistance of base stations. Due to the dynamic nature of the network topology and restricted resources, quality of service (QoS) and multicast routing in MANET are challenging tasks which attract the interests of many people. In this paper, we present a fuzzy controller based QoS routing algorithm with a multiclass scheme (FQRA) in mobile ad hoc networks. The performance of this scheduler is studied using NS2 (Network Simulator version 2) and evaluated in terms of quantitative measures such as packet delivery ratio, path success ratio and average end-to-end delay. Simulations show that the approach is efficient, promising and applicable in ad hoc networks.
Automated detection and tracking of many cells by using 4D live-cell imaging data

Motivation: Automated fluorescence microscopes produce massive amounts of images observing cells, often in four dimensions of space and time. This study addresses two tasks of time-lapse imaging analyses; detection and tracking of the many imaged cells, and it is especially intended for 4D live-cell imaging of neuronal nuclei of Caenorhabditis elegans. The cells of interest appear as slightly deformed ellipsoidal forms. They are densely distributed, and move rapidly in a series of 3D images. Thus, existing tracking methods often fail because more than one tracker will follow the same target or a tracker transits from one to other of different targets during rapid moves. Results: The present method begins by performing the kernel density estimation in order to convert each 3D image into a smooth, continuous function. The cell bodies in the image are assumed to lie in the regions near the multiple local maxima of the density function. The tasks of detecting and tracking the cells are then addressed with two hill-climbing algorithms. The positions of the trackers are initialized by applying the cell-detection method to an image in the first frame. The tracking method keeps attacking them to near the local maxima in each subsequent image. To prevent the tracker from following multiple cells, we use a Markov random field (MRF) to model the spatial and temporal covariation of the cells and to maximize the image forces and the MRF-induced constraint on the trackers. The tracking procedure is demonstrated with dynamic 3D images that each contain >100 neurons of C.elegans. Availability: http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014 Supplementary information: Supplementary data are available at http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014 Contact: yoshidar@ism.ac.jp
Tungsten as a Chemically-Stable Electrode Material on Ga-Containing Piezoelectric Substrates Langasite and Catangasite for High-Temperature SAW Devices

Thin films of tungsten on piezoelectric substrates La3Ga5SiO14 (LGS) and Ca3TaGa3Si2O14 (CTGS) have been investigated as a potential new electrode material for interdigital transducers for surface acoustic wave-based sensor devices operating at high temperatures up to 800 °C under vacuum conditions. Although LGS is considered to be suitable for high-temperature applications, it undergoes chemical and structural transformation upon vacuum annealing due to diffusion of gallium and oxygen. This can alter the device properties depending on the electrode nature, the annealing temperature, and the duration of the application. Our studies present evidence for the chemical stability of W on these substrates against the diffusion of Ga/O from the substrate into the film, even upon annealing up to 800 °C under vacuum conditions using Auger electron spectroscopy and energy-dispersive X-ray spectroscopy, along with local studies using transmission electron microscopy. Additionally, the use of CTGS as a more stable substrate for such applications is indicated.
Exploring the Structure of Complex Software Designs: An Empirical Study of Open Source and Proprietary Code

This paper reports data from a study that seeks to characterize the differences in design structure between complex software products. We use design structure matrices (DSMs) to map dependencies between the elements of a design and define metrics that allow us to compare the structures of different designs. We use these metrics to compare the architectures of two software products---the Linux operating system and the Mozilla Web browser---that were developed via contrasting modes of organization: specifically, open source versus proprietary development. We then track the evolution of Mozilla, paying attention to a purposeful “redesign” effort undertaken with the intention of making the product more “modular. ” We find significant differences in structure between Linux and the first version of Mozilla, suggesting that Linux had a more modular architecture. Yet we also find that the redesign of Mozilla resulted in an architecture that was significantly more modular than that of its predecessor and, indeed, than that of Linux. Our results, while exploratory, are consistent with a view that different modes of organization are associated with designs that possess different structures. However, they also suggest that purposeful managerial actions can have a significant impact in adapting a design's structure. This latter result is important given recent moves to release proprietary software into the public domain. These moves are likely to fail unless the product possesses an “architecture for participation. ”
Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods

Ageing is a highly complex biological process that is still poorly understood. With the growing amount of ageing-related data available on the web, in particular concerning the genetics of ageing, it is timely to apply data mining methods to that data, in order to try to discover novel patterns that may assist ageing research. In this work, we introduce new hierarchical feature selection methods for the classification task of data mining and apply them to ageing-related data from four model organisms: Caenorhabditis elegans (worm), Saccharomyces cerevisiae (yeast), Drosophila melanogaster (fly), and Mus musculus (mouse). The main novel aspect of the proposed feature selection methods is that they exploit hierarchical relationships in the set of features (Gene Ontology terms) in order to improve the predictive accuracy of the Naïve Bayes and 1-Nearest Neighbour (1-NN) classifiers, which are used to classify model organisms' genes into pro-longevity or anti-longevity genes. The results show that our hierarchical feature selection methods, when used together with Naïve Bayes and 1-NN classifiers, obtain higher predictive accuracy than the standard (without feature selection) Naïve Bayes and 1-NN classifiers, respectively. We also discuss the biological relevance of a number of Gene Ontology terms very frequently selected by our algorithms in our datasets.