pinecone/core-2020-05-10-deduplication huggingface dataset:
A focal plane processor for continuous-time 1-D optical correlation applications

El pdf es la versión post-print.This chapter describes a 1-D Focal Plane Processor, which has been designed to run continuous-time optical correlation applications. The chip contains 200 sensory processing elements, which acquire light patterns through a 2mm ×10.9μm photodiode. The photogenerated current is scaled at the pixel level by five independent 3-bit programmable-gain current scaling blocks. The correlation patterns are defined as five sets of two hundred 3-bit numbers (from 0 to 7), which are provided to the chip through a standard I2C interface. Correlation outputs are provided in current form through 8-bit programmable gain amplifiers (PGA), whose configurations are also defined via I2C. The chip contains a mounting alignment help, which consists of three rows of 100 conventional active pixel sensors (APS) inserted at the top, middle and bottom part of the main photodiode array. The chip has been fabricated in a standard 0.35μm CMOS technology and its maximum power consumption is below 30mW. Experimental results demonstrate that the chip is able to process interference patterns moving at an equivalent frequency of 500kHz.This work has been partially funded by CICE/JA, MICINN, and CDTI (Spain) through projects 2006-TIC-2352, TEC2009-11812, and Cenit EeE.Peer Reviewe
Poxviral TNFRs: Properties and Role in Viral Pathogenesis

Tumor necrosis factor (TNF) is the prototypical member of a large superfamily of structurally related cytokines that are involved in a wide range of activities involved in the regulation of the immune response and developmental processes and that signal mainly through an equally diverse array of receptors included in the TNF receptor superfamily (TNFRSF). TNF has an essential role in the activation of the antiviral immune response, where it acts both directly on virus-infected cells as a cell death-inducing cytokine and indirectly in the activation of the innate and adaptive immune responses against the invading pathogen. Consequently, viruses from different families have devised strategies to evade or modulate these TNF-driven responses. Most strategies involve the expression of virus-encoded intracellular proteins that are able to bind to different proteins of the TNFR signal transduction pathways. Uniquely, poxviruses express secreted TNFR homologues that can bind to soluble TNF, inhibiting its activity by preventing it from binding to the cellular receptors. In the recent years, we have been interested in studying the activity and function of these viral TNFRs (vTNFRs) both in vitro and during infection. We describe recent advances in this field.Peer reviewe
Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells

Budding yeast (Saccharomyces cerevisiae) has been widely used as a model system to study fundamental biological processes. Genetic and biochemical approaches have allowed in the last decades to uncover the key components involved in many signaling pathways. Generally, most techniques measure the average behavior of a population of cells, and thus missed important cell-to-cell variations. With the recent progress with fluorescent proteins, new avenues have been opened to quantitatively study the dynamics of signaling in single living cells. In this chapter, we describe several techniques based on fluorescence measurements to quantify the activation of biological pathways. Flow cytometry allows for rapid quantification of the total fluorescence of a large number of single cells. In contrast, microscopy offers a lower throughput but allows to follow with a high temporal resolution the localization of proteins at sub-cellular resolution. Finally, advanced functional imaging techniques such as FRET and FCS offer the possibility to directly visualize the formation of protein complexes or to quantify the activity of proteins in vivo. Together these techniques present powerful new approaches to study cellular signaling and will greatly increase our understanding of the regulation of signaling networks in budding yeast and beyond
XtreemOS: a Sound Foundation for Cloud Infrastructure and Federations

International audienceXtreemOS is a Linux-based operating system with native support for virtual organizations (VO's), for building large-scale resource federations. XtreemOS has been designed as a grid operating system, supporting the model of resource sharing among independent administrative domains. We argue, however, that the VO concept can be used to establish either resource sharing or resource isolation, or even both at the same time. We outline XtreemOS' fundamental properties and how its native VO support can be used to implement cloud infrastructure and cloud federations
Geometric and Electromagnetic Aspects of Fusion Pore Making

For regulated exocytosis, we model the morphology and dynamics of the making
of the fusion pore or porosome as a cup-shaped lipoprotein structure (a dimple
or pit) on the cytosol side of the plasma membrane. We describe the forming of
the dimple by a free boundary problem. We discuss the various forces acting and
analyze the magnetic character of the wandering electromagnetic field wave
produced by intracellular spatially distributed pulsating (and well observed)
release and binding of calcium ions anteceding the bilayer membrane vesicle
fusion of exocytosis. Our approach explains the energy efficiency of the
observed dimple forming prior to hemifusion and fusion pore, and the observed
flickering in secretion. It provides a frame to relate characteristic time
length of exocytosis to the frequency, amplitude and direction of propagation
of the underlying electromagnetic field wave.Comment: To appear as the closing chapter in a monograph "BetaSys - Systems
  Biology of Regulated Exocytosis in Pancreatic Beta-Cells", Vol. 4 of the
  Springer-Verlag Series in Systems Biolog
Parsimonious selection of useful genes in microarray gene expression data

Machine Learning methods have of late made significant efforts to solving multidisciplinary problems in the field of cancer classification in microarray gene expression data. These tasks are characterized by a large number of features and a few observations, making the modeling a non-trivial undertaking. In this work we apply entropic filter methods for gene selection, in combination with several off-the-shelf classifiers. The introduction of bootstrap resampling techniques permits the achievement of more stable performance estimates. Our findings show that the proposed methodology permits a drastic reduction in dimension, offering attractive solutions both in terms of prediction accuracy and number of explanatory genes; a dimensionality reduction technique preserving discrimination capabilities is used for visualization of the selected genes.Postprint (author’s final draft
Global optimization in systems biology: stochastic methods and their applications

Mathematical optimization is at the core of many problems in systems biology: (1) as the underlying hypothesis for model development, (2) in model identification, or (3) in the computation of optimal stimulation procedures to synthetically achieve a desired biological behavior. These problems are usually formulated as nonlinear programing problems (NLPs) with dynamic and algebraic constraints. However the nonlinear and highly constrained nature of systems biology models, together with the usually large number of decision variables, can make their solution a daunting task, therefore calling for efficient and robust optimization techniques. Here, we present novel global optimization methods and software tools such as cooperative enhanced scatter search (eSS), AMIGO, or DOTcvpSB, and illustrate their possibilities in the context of modeling including model identification and stimulation design in systems biology.This work was supported by the Spanish MICINN project ”MultiSysBio”\ud
(ref. DPI2008-06880-C03-02), and by CSIC intramural project ”BioREDES” (ref. PIE-201170E018).Peer reviewe
Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Esti- mating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell–cell variability. We propose a novel com- bination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and ef- ficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In ad- dition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place
What is the source level of pile-driving noise in water?

This article was published in the journal, Advances in Experimental Medicine and Biology [© Springer]. The definitive version is available at: http://www.springerlink.com/content/kl8v22033073051t/To meet the growing demand for carbon-free energy sources, the European Union (EU) has ambitious plans to increase its capacity for generation of offshore wind power. The United Kingdom and The Netherlands, for example, plan to increase their offshore power-generating capacity to 33 and 6 GW, respectively, by the year 2020. Assuming that this power is generated entirely by wind and that a single wind turbine can generate up to 10 MW, at least 3,900 offshore turbines would be required by these two states alone to achieve this goal. A popular turbine construction method known as “pile driving” involves the use of hammering a steel cylinder (a “monopile”) into the seabed. A concern has arisen for the possible effect on mammals (Southall et al. 2007) and fish (Popper and Hastings 2009) of the sound produced by the succession of hammer impacts required to sink the pile to its required depth (tens of meters)
Assessment of cumulative sound exposure levels for marine piling events

This article was published in the journal, Advances in Experimental Medicine and Biology [© Springer]. The definitive version is available at: http://www.springerlink.com/content/p0286wv2j2v551l7/The installation of offshore wind farms in European waters and the scale of the planned activity have led to concern over the generation of noise and its potential impact on marine life. Much of this concern is centered around the noise generated by pile driving, which is used for the installation of the turbine foundations, and its potential impact on marine life (Thomsen et al. 2006). The noise generated by pile driving has the potential to cause injury, induce temporary or permanent hearing loss, and evoke avoidance reactions. One injury criterion for marine mammals is defined as the onset of auditory permanent threshold shift (PTS) (Southall et al. 2007), which is governed by either an instantaneous peak pressure or an integrated sound exposure level. The latter is the total noise energy to which the mammal is exposed during a given duration that, for a pile-driving source, would be either the duration of the piling or the time over which the mammal is in auditory range and is known as sound exposure level (SEL). In this case, cumulative exposure can be a useful parameter. This paper considers a summation of the SELs to which the animal is exposed during the entire piling sequence
Measurement of underwater noise arising from marine aggregate operations

This article was published in the journal, Advances in Experimental Medicine and Biology [© Springer]. The definitive version is available at: http://www.springerlink.com/content/t3j662634u652573/As of 2009, there were 75 licensed areas within UK waters for marine aggregate extraction, with dredging activity taking place at any given point in time. In 2008, the dredged area totaled 137.9 km2, extracting 21.24 million tons of sand and gravel for the building and construction industry. There is concern that the extraction of marine aggregate has the potential to generate noise levels that could have a negative impact on marine species in or around the dredging area. Although this paper deals only with the underwater noise generated and the potential impact it might have, there are many ways in which dredging can have an impact on marine life. For marine aggregate extraction, the type of dredger used is a trailing suction hopper dredger (TSHD). This type of dredger lowers a drag head and suction pipe to the sea floor, in water depths of up to 50 m, to extract the sand or gravel, depositing it in a hopper on the vessel. The vessel will often screen the dredged material for granular size and return the unwanted material and water over the side of the vessel. Such an operation can take from as little as 3 h to up to 12 h, concentrated in a relatively small area. The vessels usually dredge in tight lanes, usually less than 2 km in length and up to 100 m in width
The Large Magellanic Cloud: A power spectral analysis of Spitzer images

We present a power spectral analysis of Spitzer images of the Large
Magellanic Cloud. The power spectra of the FIR emission show two different
power laws. At larger scales (kpc) the slope is ~ -1.6, while at smaller ones
(tens to few hundreds of parsecs) the slope is steeper, with a value ~ -2.9.
The break occurs at a scale around 100-200 pc. We interpret this break as the
scale height of the dust disk of the LMC. We perform high resolution
simulations with and without stellar feedback. Our AMR hydrodynamic simulations
of model galaxies using the LMC mass and rotation curve, confirm that they have
similar two-component power-laws for projected density and that the break does
indeed occur at the disk thickness. Power spectral analysis of velocities
betrays a single power law for in-plane components. The vertical component of
the velocity shows a flat behavior for large structures and a power law similar
to the in-plane velocities at small scales. The motions are highly anisotropic
at large scales, with in-plane velocities being much more important than
vertical ones. In contrast, at small scales, the motions become more isotropic.Comment: 8 pages, 4 figures, talk presented at "Galaxies and their Masks",
  celebrating Ken Freeman's 70-th birthday, Sossusvlei, Namibia, April 2010. To
  be published by Springer, New York, editors D.L. Block, K.C. Freeman, & I.
  Puerar
Super star clusters and Supernovae in interacting LIRGs unmasked by NIR
  adaptive optics

We report on an on-going near-IR adaptive optics survey targeting interacting
luminous IR galaxies. High-spatial resolution NIR data are crucial to enable
interpretation of kinematic, dynamical and star formation (SF) properties of
these very dusty objects. Whole progenitor nuclei in the interactions can be
missed if only optical HST imaging is used. Here we specifically present the
latest results regarding core-collapse supernovae found within the highly
extincted nuclear regions of these galaxies. Direct detection and study of such
highly obscured CCSNe is crucial for revising the optically-derived SN rates
used for providing an independent measurement of the SF history of the
Universe. We also present thus-far the first NIR luminosity functions of super
star cluster (SSC) candidates. The LFs can then be used to constrain the
formation and evolution of SSCs via constraints based on initial mass functions
and cluster disruption models.Comment: 6 pages. To appear in proceedings of 'Galaxies and their Masks'
  (Namibia, April 2010), published by Springer, New York, eds. D.L. Block, K.C.
  Freeman, I. Puerar
Structure, mass and stability of galactic disks

In this review I concentrate on three areas related to structure of disks in
spiral galaxies. First I will review the work on structure, kinematics and
dynamics of stellar disks. Next I will review the progress in the area of
flaring of HI layers. These subjects are relevant for the presence of dark
matter and lead to the conclusion that disk are in general not `maximal', have
lower M/L ratios than previously suspected and are locally stable w.r.t.
Toomre's Q criterion for local stability. I will end with a few words on
`truncations' in stellar disks.Comment: Invited review at "Galaxies and their Masks" for Ken Freeman's 70-th
  birthday, Sossusvlei, Namibia, April 2010. A version with high-res. figures
  is available at
  http://www.astro.rug.nl/~vdkruit/jea3/homepage/Namibiachapter.pd
The complex interplay of dust and star light in spiral galaxy discs

Interstellar dust grains efficiently absorb and scatter UV and optical
radiation in galaxies, and therefore can significantly affect the apparent
structure of spiral galaxies. We discuss the effect of dust attenuation on the
observed structural properties of bulges and discs. We also present some first
results on modelling the dust content of edge-on spiral galaxies using both
optical and Herschel far-infrared data. Both of these results demonstrate the
complex interplay of dust and star light in spiral galaxies.Comment: 6 pages, 2 figures, to appear in "Galaxies and their Masks", eds. D.
  L. Block, K. C. Freeman & I. Puerari, Springer (New York
Rings and bars: unmasking secular evolution of galaxies

Secular evolution gradually shapes galaxies by internal processes, in
contrast to early cosmological evolution which is more rapid. An important
driver of secular evolution is the flow of gas from the disk into the central
regions, often under the influence of a bar. In this paper, we review several
new observational results on bars and nuclear rings in galaxies. They show that
these components are intimately linked to each other, and to the properties of
their host galaxy. We briefly discuss how upcoming observations, e.g., imaging
from the Spitzer Survey of Stellar Structure in Galaxies (S4G), will lead to
significant further advances in this area of research.Comment: Invited review at "Galaxies and their Masks", celebrating Ken
  Freeman's 70-th birthday, Sossusvlei, Namibia, April 2010. To be published by
  Springer, New York, editors D.L. Block, K.C. Freeman, & I. Puerari; minor
  change
The outer halos of elliptical galaxies

Recent progress is summarized on the determination of the density
distributions of stars and dark matter, stellar kinematics, and stellar
population properties, in the extended, low surface brightness halo regions of
elliptical galaxies. With integral field absorption spectroscopy and with
planetary nebulae as tracers, velocity dispersion and rotation profiles have
been followed to ~4 and ~5-8 effective radii, respectively, and in M87 to the
outer edge at ~150 kpc. The results are generally consistent with the known
dichotomy of elliptical galaxy types, but some galaxies show more complex
rotation profiles in their halos and there is a higher incidence of
misalignments, indicating triaxiality. Dynamical models have shown a range of
slopes for the total mass profiles, and that the inner dark matter densities in
ellipticals are higher than in spiral galaxies, indicating earlier assembly
redshifts. Analysis of the hot X-ray emitting gas in X-ray bright ellipticals
and comparison with dynamical mass determinations indicates that non-thermal
components to the pressure may be important in the inner ~10 kpc, and that the
properties of these systems are closely related to their group environments.
First results on the outer halo stellar population properties do not yet give a
clear picture. In the halo of one bright galaxy, lower [alpha/Fe] abundances
indicate longer star formation histories pointing towards late accretion of the
halo. This is consistent with independent evidence for on-going accretion, and
suggests a connection to the observed size evolution of elliptical galaxies
with redshift.Comment: 8 pages. Invited review to appear in the proceedings of "Galaxies and
  their Masks" eds. Block, D.L., Freeman, K.C. & Puerari, I., 2010, Springer
  (New York
Dark haloes as seen with gravitational lensing

Dark matter is an important ingredient of galaxies, as was recognised early
on by Ken Freeman himself! Evidence for dark matter halos is still indirect,
based on analysing motions of tracers such as gas and stars. In a sense the
visible galaxy is the mask through which we can study the dark matter. Light
rays are also sensitive to gravitational fields, and dark haloes cause
observable gravitational lensing effects. There are three regimes: microlensing
(which probes the clumpiness of dark matter haloes), strong lensing (sensitive
to the inner mass distribution) and weak lensing (which can probe haloes out to
100s of kpc from the center). This review will concentrate on weak lensing, and
describe a new survey, the Kilo-Degree Survey (KiDS) that is designed to study
galaxy halo masses, extents and shapes as a function of environment, galaxy
type and redshift.Comment: To appear in 'Galaxies and their Masks' (Namibia, April 2010), eds.
  Block, D.L., Freeman, K.C. & Puerari, I., 2010, Springer (New York
Diffuse light and galaxy interactions in the core of nearby clusters

The kinematics of the diffuse light in the densest regions of the nearby
clusters can be unmasked using the planetary nebulae (PNs) as probes of the
stellar motions. The position-velocity diagrams around the brightest cluster
galaxies (BCGs) identify the relative contributions from the outer halos and
the intracluster light (ICL), defined as the light radiated by the stars
floating in the cluster potential. The kinematics of the ICL can then be used
to asses the dynamical status of the nearby cluster cores and to infer their
formation histories. The cores of the Virgo and Coma are observed to be far
from equilibrium, with mergers currently on-going, while the ICL properties in
the Fornax and Hydra clusters show the presence of sub-components being
accreted in their cores, but superposed to an otherwise relaxed population of
stars. Finally the comparison of the observed ICL properties with those
predicted from Lambda-CDM simulations indicates a qualitative agreement and
provides insights on the ICL formation. Both observations and simulations
indicate that BCG halos and ICL are physically distinct components, with the
``hotter" ICL dominating at large radial distances from the BCGs halos as the
latter become progressively fainter.Comment: 14 pages, 5 figures. Invited review to appear in the proceedings of
  "Galaxies and their masks" eds. Block, D.L., Freeman, K.C. and Puerari, I.,
  2010, Springer (New York