Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Triads Consisting of Ryanodine Receptors, Ca2+ Channels, and Ca2+-Activated K+ Channels in Bullfrog Sympathetic Neurons

Fluorescent ryanodine revealed the distribution of ryanodine receptors in the submembrane cytoplasm (less than a few micrometers) of cultured bullfrog sympathetic ganglion cells. Rises in cytosolic Ca2+ ([Ca2+]i) elicited by single or repetitive action potentials (APs) propagated at a high speed (150 μm/s) in constant amplitude and rate of rise in the cytoplasm bearing ryanodine receptors, and then in the slower, waning manner in the deeper region. Ryanodine (10 μM), a ryanodine receptor blocker (and/or a half opener), or thapsigargin (1–2 μM), a Ca2+-pump blocker, or ω-conotoxin GVIA (ω-CgTx, 1 μM), a N-type Ca2+ channel blocker, blocked the fast propagation, but did not affect the slower spread. Ca2+ entry thus triggered the regenerative activation of Ca2+-induced Ca2+ release (CICR) in the submembrane region, followed by buffered Ca2+ diffusion in the deeper cytoplasm. Computer simulation assuming Ca2+ release in the submembrane region reproduced the Ca2+ dynamics. Ryanodine or thapsigargin decreased the rate of spike repolarization of an AP to 80%, but not in the presence of iberiotoxin (IbTx, 100 nM), a BK-type Ca2+-activated K+ channel blocker, or ω-CgTx, both of which decreased the rate to 50%. The spike repolarization rate and the amplitude of a single AP-induced rise in [Ca2+]i gradually decreased to a plateau during repetition of APs at 50 Hz, but reduced less in the presence of ryanodine or thapsigargin. The amplitude of each of the [Ca2+]i rise correlated well with the reduction in the IbTx-sensitive component of spike repolarization. The apamin-sensitive SK-type Ca2+-activated K+ current, underlying the afterhyperpolarization of APs, increased during repetitive APs, decayed faster than the accompanying rise in [Ca2+]i, and was suppressed by CICR blockers. Thus, ryanodine receptors form a functional triad with N-type Ca2+ channels and BK channels, and a loose coupling with SK channels in bullfrog sympathetic neurons, plastically modulating AP.
Localization and fault growth in layered brittle‐ductile systems: Implications for deformations of the continental lithosphere

We present experiments and numerical simulations dealing with the growth of faults in thin brittle/ductile systems to understand deformation modes in the continental lithosphere. Experiments were uniaxial shortening of layers of dry sand and silicone putties of various viscous resistances. For large strength ratios between the brittle and ductile layers (R > 5–10), the deformation localizes into two shear bands; the fault pattern is created before reaching 10% shortening, and has fractal dimensions varying between 1.6 and 1.8. For small strength ratios (R < 5–10), deformation never localizes; the fault pattern is homogeneous with a trivial dimension of 2, and grows continuously during deformation. The transition between localized and homogeneous deformation occurs when the mechanical resistance of brittle layers is 5–10 times larger than the resistance of ductile layers. This transition was also investigated by means of electrical analog simulations. A fuse network, which represents an elasto-brittle layer, is coupled with a capacitor layer which models strain-rate dependent fluids. An AC potential is applied and the fuses progressively burned out until they form a connected network. The AC-potential frequency, ƒ, is a tuning parameter similar to the applied strain rate in experiments. A critical frequency is obtained marking a transition between a localization mode where the density of burned fuses decreases as the system size increases, and a delocalization mode where the density of burned fuses remains constant with increasing system size. The scaling dependency of the fracture process, as well as the critical frequency, are consistent with experimental results. Available information on the rheology of the continental lithosphere shows that this mechanical transition is bracketed by the possible range of brittle-to-ductile strength ratios.
Improving the Design of Existing Web Applications

Despite several methodologies have been defined to support the disciplined development of Web applications, often such methodologies are not applied in the practice, mainly due to the short time-to-market and resource constraints. As a consequence, existing (i.e. legacy) Web applications often lack in design quality. This paper proposes a model-driven semi-automatic redesign approach to improve the design of existing Web applications. The approach analyzes the client side HTML pages of the application to recover its conceptual model according to the Ubiquitous Web Applications design methodology. The recovered model is then used as a starting point to define a new design for the application, adopting the Model-View-Controller architectural pattern and the Java Server Faces technology. A concrete example of the application of the approach to redesign a real world Web site is also described.
Giving advice to agents with hidden goals

This paper considers the problem of providing advice to an autonomous agent when neither the behavioural policy nor the goals of that agent are known to the advisor. We present an approach based on building a model of “common sense” behaviour in the domain, from an aggregation of different users performing various tasks, modelled as MDPs, in the same domain. From this model, we estimate the normalcy of the trajectory given by a new agent in the domain, and provide behavioural advice based on an approximation of the trade-off in utility between potential benefits to the exploring agent and the costs incurred in giving this advice. This model is evaluated on a maze world domain by providing advice to different types of agents, and we show that this leads to a considerable and unanimous improvement in the completion rate of their tasks.
A 10 000 fps CMOS Sensor With Massively Parallel Image Processing

A high-speed analog VLSI image acquisition and pre-processing system has been designed and fabricated in a 0.35 ¿m standard CMOS process. The chip features a massively parallel architecture enabling the computation of programmable low-level image processing in each pixel. Extraction of spatial gradients and convolutions such as Sobel or Laplacian filters are implemented on the circuit. For this purpose, each 35 ¿m × 35 ¿m pixel includes a photodiode, an amplifier, two storage capacitors, and an analog arithmetic unit based on a four-quadrant multiplier architecture. The retina provides address-event coded output on three asynchronous buses: one output dedicated to the gradient and the other two to the pixel values. A 64 × 64 pixel proof-of-concept chip was fabricated. A dedicated embedded platform including FPGA and ADCs has also been designed to evaluate the vision chip. Measured results show that the proposed sensor successfully captures raw images up to 10 000 frames per second and runs low-level image processing at a frame rate of 2000 to 5000 frames per second.
The role of cellular adhesion molecules in virus attachment and entry

As obligate intracellular parasites, viruses must traverse the host-cell plasma membrane to initiate infection. This presents a formidable barrier, which they have evolved diverse strategies to overcome. Common to all entry pathways, however, is a mechanism of specific attachment to cell-surface macromolecules or ‘receptors’. Receptor usage frequently defines viral tropism, and consequently, the evolutionary changes in receptor specificity can lead to emergence of new strains exhibiting altered pathogenicity or host range. Several classes of molecules are exploited as receptors by diverse groups of viruses, including, for example, sialic acid moieties and integrins. In particular, many cell-adhesion molecules that belong to the immunoglobulin-like superfamily of proteins (IgSF CAMs) have been identified as viral receptors. Structural analysis of the interactions between viruses and IgSF CAM receptors has not shown binding to specific features, implying that the Ig-like fold may not be key. Both proteinaceous and enveloped viruses exploit these proteins, however, suggesting convergent evolution of this trait. Their use is surprising given the usually occluded position of CAMs on the cell surface, such as at tight junctions. Nonetheless, the reason for their widespread involvement in virus entry most probably originates in their functional rather than structural characteristics.
On the Role of Atmospheric Teleconnections in Climate

Abstract In a recent application of networks to 500-hPa data, it was found that supernodes in the network correspond to major teleconnection. More specifically, in the Northern Hemisphere a set of supernodes coincides with the North Atlantic Oscillation (NAO) and another set is located in the area where the Pacific–North American (PNA) and the tropical Northern Hemisphere (TNH) patterns are found. It was subsequently suggested that the presence of atmospheric teleconnections make climate more stable and more efficient in transferring information. Here this hypothesis is tested by examining the topology of the complete network as well as of the networks without teleconnections. It is found that indeed without teleconnections the network becomes less stable and less efficient in transferring information. It was also found that the pattern chiefly responsible for this mechanism in the extratropics is the NAO. The other patterns are simply a linear response of the activity in the tropics and their role in thi.
Architecture-Driven Software Component Retrieval

This paper argues that retrieval of complex hardware components is based on the use of architectural descriptions rather than functional descriptions, and explores the idea of basing software component retrieval on architectural descriptions. Architecture-driven retrieval is contrasted with retrieval based on keywords that characterize a few relevant properties and with deductive retrieval based on functional descriptions. A simple example, development of a component-based compiler, is used to explain how specification patterns in a architecture description language (Acme) can be used to drive component selection.
Direct Measurements of Black Hole Charge with Future Astrometrical Missions

Recently, Zakharov et al. (2005a, New Astron., 10, 479) considered the possibility of evaluating the spin parameter and the inclination angle for Kerr black holes in nearby galactic centers by using future advanced astrometrical instruments. A similar approach which uses the characteristic properties of gravitational retro-lensing images can be followed to measure the charge of a Reissner-Nordstrom black hole. Indeed, in spite of the fact that their formation might be problematic, charged black holes are objects of intensive investigations. From a theoretical point of view, it is well-known that a black hole is described by only three parameters, namely, its mass M , angular momentum J , and charge Q . Therefore, it would be important to have a method for measuring all these parameters, preferably by independent model of any. In this paper, we propose a procedure to measure the black hole charge by using the size of the retro-lensing images that can be revealed by future astrometrical missions. A discussion of the Kerr-Newmann black hole case is also offered.
On Harvesting Energy from Tree Trunks for Environmental Monitoring

This work describes an experimental study on the possibilities of harvesting energy from tree trunks in order to power sensor nodes for environmental monitoring, particularly in wild forests. As the trunk of a living tree can be divided into isothermal subvolumes, which are generally referred to as annual rings, and the trunk is a good heat storage material, depending on the tree dimensions and its species, it can potentially offer different temperature gradients according to the tree trunk depths. The hypothesis is to consider the application of this temperature gradient on the faces of a Peltier cell to obtain electrical energy. In order to evaluate this hypothesis, a wireless sensor network was developed for measuring internal temperature of trunks from different trees. The experimental results show that it is possible to obtain a sufficient temperature gradient to harvest energy from tree trunks. Additionally, it is also shown that it is possible to harvest thermal energy during the day and during the night while photovoltaic cell only works under sunlight.
The presumptive CDR3 regions of both T cell receptor alpha and beta chains determine T cell specificity for myoglobin peptides

The T cell receptor alpha/beta (TCR-alpha/beta) is encoded by variable (V), diversity (D), joining (J), and constant (C) segments assembled by recombination during thymocyte maturation to produce a heterodimer that imparts antigenic specificity to the T cell. Unlike immunoglobulins (Igs), which bind free antigen, the ligands of TCR-alpha/beta are cell surface complexes of intracellularly degraded antigens (i.e., peptides) bound to and presented by polymorphic products of the major histocompatibility complex (MHC). Therefore, antigen recognition by T cells is defined as MHC restricted. A model has been formulated based upon the similarity between TCR-alpha/beta V region and Ig Fab amino acid sequences, and the crystal structure of the MHC class I and Ig molecules. This model predicts that the complementarity determining regions (CDR) 1 and 2, composed of TCR V alpha and V beta segments, primarily contact residues of the MHC alpha helices, whereas V/J alpha and V/D/J beta junctional regions (the CDR3 equivalent) contact the peptide in the MHC binding groove. Because polymorphism in MHC proteins is limited relative to the enormous diversity of antigenic peptides, the TCR may have evolved to position the highly diverse junctional residues (CDR3), where they have maximal contact with antigen bound in the MHC peptide groove. Here, we demonstrate a definitive association between CDR3 sequences in both TCR alpha and beta chains, and differences in recognition of antigen fine specificity using a panel of I-Ed-restricted, myoglobin-reactive T cell clones. Acquisition of these data relied in part upon a modification of the polymerase chain reaction that uses a degenerate, consensus primer to amplify TCR alpha chains without foreknowledge of the V alpha segments they utilize.
Pre-hospital Delay in Treatment after Acute Myocardial Infarction

1. Full-time Lecturer at Ewha Women’s University Corresponding author: Kyungeh An, PhD, RN, Ewha Women’s University, College of Nursing, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750, Korea Tel: 822-3277-3926 Fax: 822-3277-2875 E-mail: kaan@ewha.ac. kr This study was supported by the Inje University Research Grant for New Faculty. Received April 10, 2001 ; Accepted November 26, 2001 Significance of the study. Acute myocardial infarction (AMI) is a major cause of death. Most of the deaths from AMI, if diagnosed and treated early enough, can be prevented. Delay in treatment may cause unnecessary exacerbation of the disease and even death in AMI patients.
Professional Summarizing: No Cognitive Simulation Without Observation

Professional summarizing includes the cognitive processes of abstracting, indexing, and classifying as performed by expert summarizers who prepare records for bibliographic information systems. In order to simulate their skilled performance, a “grounded” (or “naturalistic”) cognitive model of expert summarization has been developed, using 54 working processes of 6 experts recorded by thinking-aloud protocols. The working processes comprise up to 140 working steps. The model is explained in the following using the abstracting step Trueby-2 executed by the expert Marliese. Components of the model are a toolbox of empirically founded strategies, principles of process organization, and interpreted working steps where the interaction of cognitive strategies can be investigated. In the computerized simulation, the SimSum (Simulation of Summarizing) system, cognitive strategies are represented by object-oriented agents grouped around dedicated blackboards. While the main scientific goal of the system is to check and improve the cognitive model, the system also serves practical presentation purposes. It will be distributed on CD-ROM as part of a textbook and thus help to explain the cognitive task of summarizing. © 1998 John Wiley & Sons, Inc.
ESTABLISHING BOUNDING INTERNAL DOSE ESTIMATES FOR THORIUM ACTIVITIES AT ROCKY FLATS

As part of an evaluation of a Special Exposure Cohort petition filed on behalf of workers at the Rocky Flats Plant, the National Institute for Occupational Safety and Health (NIOSH) was required to demonstrate that bounding values could be established for radiation doses due to the potential intake of all radionuclides present at the facility. The main radioactive elements of interest at Rocky Flats were plutonium and uranium, but much smaller quantities of several other elements, including thorium, were occasionally handled at the site. Bounding potential doses from thorium has proven challenging at other sites due to the early historical difficulty in detecting this element through urinalysis methods and the relatively high internal dose delivered per unit intake. This paper reports the results of NIOSH’s investigation of the uses of thorium at Rocky Flats and provides bounding dose reconstructions for these operations. During this investigation, NIOSH reviewed unclassified reports, unclassified extracts of classified materials, material balance and inventory ledgers, monthly progress reports from various groups, and health physics field logbooks, and conducted interviews with former Rocky Flats workers. Thorium operations included: (1) an experimental metal forming project with 240 kg of thorium in 1960; (2) the use of pre-formed parts in weapons mockups; (3) the removal of 228Th from 233U; (4) numerous analytical procedures involving trace quantities of thorium; and (5) the possible experimental use of thorium as a mold coating compound. The thorium handling operations at Rocky Flats were limited in scope, well-monitored and documented, and potential doses can be bounded.
Airborne dust in Saudi Arabia : source areas, entrainment, simulation and composition

Spatial and temporal characteristics of dust storm activity in Saudi Arabia has been established using coarse-particle (PM10) dust concentrations recorded by the KACST monitoring network during the 2000-2003 period, backward trajectory analysis and satellite imagery. Thirty three major dust episodes impacted Riyadh city during the 2000-2003 period. The majority of these intense dust episodes are experienced during the March-August period with interannual and monthly variability in both intensity and frequency. Using TOMS images in conjunction with the backward trajectories corresponding to these 33 major episodes, the dust source regions have been identified. The most vulnerable dust source areas within these identified source regions have also been determined by compiling satellite images of dusty days from the true color SeaWiFs and high resolution MODIS archives over a six-year period (2000-2005). In total 45 dust-source areas have been identified in 9 local source regions and 4 external ones. Furthermore, 38 episodes of high fine-particle (PM2.5) and PM10 dust concentrations were observed at Riyadh city and 16 and 6 episodes of elevated PM10 dust concentrations were observed at Dammam and Jeddah cities, respectively, during March-September 2006, corresponding to the dust season in Saudi Arabia. During these episodes, Riyadh city was significantly impacted by dust from the southern Iraqi source areas and the eastern source areas located to the north and to the northeast of the city, respectively. Moreover, Dammam city was also significantly impacted by dust from the southern Iraqi source areas whereas Jeddah city was evenly impacted by dust from northeastern-northwestern sources to the city, with somewhat higher PM10 concentrations from African dust source areas, located to the northwest of the city. Analysis of meteorological maps of surface pressure as well as upper air data associated with high airborne dust concentrations in Saudi Arabia was successfully performed. This analysis revealed seven common types of dust storms, triggered by a clear seasonal distribution of meteorological conditions: (1) frontal, (2) Haboob, (3) jets convergence, (4) jet streak, (5) Shamal, (6) cyclonic, and (7) gap. The majority of dust episodes that impacted Riyadh city during the study period were triggered by Haboob (~ 42 %) and Shamal (~ 37 %). Additional analyses, including elemental, ionic and biological analyses as well as model analyses were used to further characterize the airborne dust in Saudi Arabia.
Inferring ancestral chloroplast genomes with inverted repeat

Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions/deletions and gene order rearrangements. Reconstruction of phylogeny based on gene order changes has been limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many Chloroplast genomes, the inference of inverted repeats is needed in ancestral genome reconstruction. We apply GRAPPA-IR to reconstruct ancestral chloroplast genomes containing duplicated genes. A test of GRAPPA-IR using divergent chloroplast genomes from land plants and green algae recovers the phylogeny congruent with prior studies, while analysis that do not consider IR structure fail to obtain the accepted topology. The ancestral genome structure suggests that genome rearrangement in chloroplasts is probably limited by inverted repeats with a conserved core region. In addition, the boundaries of inverted repeats are hot spots for gene duplications or deletions.
How Do Agents Comply with Norms?

The import of the notion of institution in the design of MASs requires to develop formal and efficient methods for modeling the interaction between agents' behaviour and normative systems. This paper discusses how to check whether agents' behaviour complies with the rules regulating them. The key point of our approach is that compliance is a relationship between two sets of specifications: the specifications for executing a process and the specifications regulating it. We propose a formalism for describing both the semantics of normative specifications and the semantics of compliance checking procedures.
Use of passive-microwave data to monitor spatial and temporal variations of snow cover at tree line near Churchill, Manitoba, Canada

Abstract We evaluated the contribution of Special Sensor Microwave/Imager (SSM/I) passive-microwave data to the monitoring of spatial and temporal variability of snow cover in the Churchill area, Manitoba, Canada. Because of the coarse spatial resolution of current passive-microwave sensors, the estimation of snow water equivalent using empirical equations with these instruments is largely compromised in complex areas such as Churchill (forest–tundra ecotone). However, with its high frequency of observations and the availability of a long time series (1988–99), passive-microwave data from the SSM/I radiometer remain a very valuable tool for monitoring the temporal evolution of snow cover at various spatial scales. Through winter 1997/98, we first examined the passive-microwave signatures at the local scale and we identified the major stages of the snow period. Principal-component analysis (PCA) applied on spectral-difference (Tb(19H) - Tb(37H))time series (1988–99) enabled us to identify spatio-temporal effects over a large area. PCA also permitted the extraction of indices of relevance for monitoring climatic variability and climate change (annual snow-cover duration, dates of snow-cover appearance and disappearance).