bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amplitude and recurrence time analysis of LP activity at Mount Etna, Italy
Authors: Cauchie Léna , Saccorotti Gilberto , Bean Christopher J. 
Published: August 2015

AbstractThe aim of this work is to improve our understanding of the long‐period (LP) source mechanism at Mount Etna (Italy) through a statistical analysis of detailed LP catalogues. The behavior of LP activity is compared with the empirical laws governing earthquake recurrence, in order to investigate whether any relationships exist between these two apparently different earthquake classes. We analyzed a family of 8894 events detected during a temporary experiment in August 2005. For that time interval, the LP activity is sustained in time and the volcano did not exhibit any evident sign of unrest. The completeness threshold of the catalogue is established through a detection test based on synthetic waveforms. The retrieved amplitude distribution differs significantly from the Gutenberg‐Richter law, and the interevent times distribution does not follow the typical γ law, expected for tectonic activity. In order to compare these results with a catalogue for which the source mechanism is well established, we applied the same procedure to a data set from Stromboli Volcano, where recurrent LP activity is closely related to very‐long‐period pulses, in turn associated with the summit explosions. Our results indicate that the two catalogues exhibit similar behavior in terms of amplitude and interevent time distributions. This suggests that the Etna's LP signals are most likely driven by stress changes caused by an intermittent degassing process occurring at depth, similar to that which drives the summit explosions at Stromboli Volcano.
Zonal jets in equilibrating baroclinic instability on the polar beta‐plane: Experiments with altimetry
Authors: Matulka A. M. , Afanasyev Y. D. 
Published: August 2015

AbstractResults from the laboratory experiments on the evolution of baroclinically unstable flows generated in a rotating tank with topographic β‐effect are presented. We study zonal jets of alternating direction which occur in these flows. The primary system we model includes lighter fluid in the South and heavier fluid in the North with resulting slow meridional circulation and fast mean zonal motion. In a two‐layer system, the velocity shear between the layers results in baroclinic instability which equilibrates with time and, due to interaction with β‐effect generates zonal jets. This system is archetypal for various geophysical systems including the general circulation and jet streams in the Earth's atmosphere, the Antarctic Circumpolar Current, or the areas in the vicinity of western boundary currents where baroclinic instability and multiple zonal jets are observed. The gradient of the surface elevation and the thickness of the upper layer are measured in the experiments using the Altimetric Imaging Velocimetry and the Optical Thickness Velocimetry techniques, respectively. Barotropic and baroclinic velocity fields are then derived from the measured quantities. The results demonstrate that the zonal jets are driven by “eddy forcing” due to continuously created baroclinic perturbations. The flow is baroclinic to a significant degree and the jets are “surface intensified.” The meridional wavelength of the jets varies linearly with the baroclinic radius of deformation and is also in a good agreement with a modified Rhines scale. This suggests a linear dependence of the perturbation velocity in the equilibrated baroclinically unstable flow on the β‐parameter.
Study of the wind velocity‐layered structure in the stratosphere, mesosphere, and lower thermosphere by using infrasound probing of the atmosphere
Authors: Chunchuzov I. , Kulichkov S. , Perepelkin V. , Popov O. , Firstov P. , Assink J. D. , Marchetti E. 
Published: August 2015

AbstractThe wind velocity structure in the upper stratosphere, mesosphere, and lower thermosphere (MLT) is studied with the recently developed method of infrasound probing of the atmosphere. The method is based on the effect of infrasound scattering from highly anisotropic wind velocity and temperature inhomogeneities in the middle and upper atmosphere. The scattered infrasound field propagates in the acoustic shadow zones, where it is detected by microbarometers. The vertical profiles of the wind velocity fluctuations in the upper stratosphere (30–52 km) and MLT (90–140 km) are retrieved from the waveforms and travel times of the infrasound signals generated by explosive sources such as volcanoes and surface explosions. The fine‐scale wind‐layered structure in these layers was poorly observed until present time by other remote sensing methods, including radars and satellites. It is found that the MLT atmospheric layer (90–102 km) can contain extremely high vertical gradients of the wind velocity, up to 10 m/s per 100 m. The effect of a fine‐scale wind velocity structure on the waveforms of infrasound signals is studied. The vertical wave number spectra of the retrieved wind velocity fluctuations are obtained for the upper stratosphere. Despite the difference in the locations of the explosive sources all the obtained spectra show the existence of high vertical wave number spectral tail with a −3 power law decay. The obtained spectral characteristics of the wind fluctuations are necessary for improvement of gravity wave drag parameterizations for numerical weather forecast.
Aerosol‐induced mechanisms for cumulus congestus growth
Authors: Sheffield Amanda M. , Saleeby Stephen M. , van den Heever Susan C. 
Published: August 2015

AbstractTropical convection has been observed to contain three cloud modes, the middle of which is cumulus congestus clouds. Congestus clouds act to moisten the tropical atmosphere, may be mixed‐phase, and on occasion surpass the freezing level inversion from where they may develop into deeper convection. This study investigates the impacts of enhanced aerosol concentrations on the growth of congestus clouds produced in idealized cloud‐resolving model simulations run under a state of radiative convective equilibrium (RCE). High‐resolution, long‐duration simulations were completed using the Regional Atmospheric Modeling System (RAMS). Aerosol concentrations between 2 and 4 km above ground level were varied from clean to polluted conditions in order to represent the advection of Saharan dust over the Atlantic Ocean. The congestus populations within each aerosol simulation are statistically analyzed using 10 days of model output after the simulation reaches RCE. Results indicate that congestus in more polluted conditions produce greater amounts of cloud water and ice mass, enhanced updraft strengths, and an increase in the number of congestus cloud tops that extend above the freezing level. Enhanced vapor depositional growth on the populations of more numerous, smaller cloud droplets in the polluted conditions, and the subsequent increase in latent heat release in the warm phase regions of the cloud, is found to be important factors in convective invigoration of these cloud systems. Aerosol feedbacks associated with cold pools and condensate loading also influence the updraft strength and act in opposition to the warm phase invigoration processes.
Joint assimilation of eddy covariance flux measurements and FAPAR products over temperate forests within a process‐oriented biosphere model
Authors: Bacour C. , Peylin P. , MacBean N. , Rayner P. J. , Delage F. , Chevallier F. , Weiss M. , Demarty J. , Santaren D. , Baret F. , Berveiller D. , Dufrêne E. , Prunet P. 
Published: August 2015

AbstractWe investigate the benefits of assimilating in situ and satellite data of the fraction of photosynthetically active radiation (FAPAR) relative to eddy covariance flux measurements for the optimization of parameters of the ORCHIDEE (Organizing Carbon and Hydrology in Dynamic Ecosystem) biosphere model. We focus on model parameters related to carbon fixation, respiration, and phenology. The study relies on two sites—Fontainebleau (deciduous broadleaf forest) and Puechabon (Mediterranean broadleaf evergreen forest)—where measurements of net carbon exchange (NEE) and latent heat (LE) fluxes are available at the same time as FAPAR products derived from ground measurements or derived from spaceborne observations at high (SPOT (Satellite Pour l′Observation de la Terre)) and medium (MERIS (MEdium Resolution Imaging Spectrometer)) spatial resolutions. We compare the different FAPAR products, analyze their consistency with the in situ fluxes, and then evaluate the potential benefits of jointly assimilating flux and FAPAR data. The assimilation of FAPAR data leads to a degradation of the model‐data agreement with respect to NEE at the two sites. It is caused by the change in leaf area required to fit the magnitude of the various FAPAR products. Assimilating daily NEE and LE fluxes, however, has a marginal impact on the simulated FAPAR. The results suggest that the main advantage of including FAPAR data is the ability to constrain the timing of leaf onset and senescence for deciduous ecosystems, which is best achieved by normalizing FAPAR time series. The joint assimilation of flux and FAPAR data leads to a model‐data improvement across all variables similar to when each data stream is used independently, corresponding, however, to different and likely improved parameter values.
Bacteriophage
T4
Authors: Mathews Christopher K 
Published: August 2015

Abstract

Bacteriophage
T4
and its host bacterium,
Escherichia coli
, can be considered among the earliest model organisms – biological systems that attract large numbers of investigators who, because of technical or conceptual advantages of the system, use the system to investigate processes and mechanisms of general significance in biology. Beginning in the mid‐twentieth century, studies focused on bacteriophage
T4
revealed essential features of the molecular nature of genes and genomes, mechanism and fidelity of
DNA
replication, genetic recombination,
DNA
repair, control of gene expression, genome organisation, assembly of complex macromolecular structures and pre‐emption of cell metabolism by virus infection. Although much of the molecular biology research community has moved on to eukaryotic model organisms, such as yeast, nematode worms, fruitflies, the plant
Arabidopsis
, zebrafish and mice, bacteriophage
T4
still presents the best opportunities for understanding at the molecular level
DNA
replication and recombination, and macromolecular assembly. In addition,
T4
and related phages are being used in investigations of bacteriophage therapy. Finally, recent analyses of
DNA
packaging and morphogenesis have suggested applications of
T4
as a gene delivery vehicle.

Key Concepts

Bacteriophage T4 presents numerous technical advantages as a model for studying virus reproduction or gene organisation and expression.

Bacteriophage T4 is representative of a large group of closely related phages found in varied environments worldwide.

Bacteriophage T4 is a virulent phage, which always lyses and kills its host bacterium.

The T4 virion has a complex multiprotein structure with a contractile tail that serves both for adsorption to host cells and for intracellular delivery of the viral genome.

Bacteriophage T4 contains a large, linear double‐stranded DNA genome, with chemical modifications of its cytosine residues.

The T4 genome is circularly permuted and terminally redundant with respect to base sequence; these features protect against information loss during replication of a linear DNA.

The T4 genome encodes numerous enzymes, used to support replication of the viral genome and to synthesise deoxyribonucleotides to support the enormous rate of DNA accumulation in infected cells.

T4 uses host cell RNA polymerase for transcription of its own genes, but it modifies the bacterial enzyme, both to prevent its transcription of bacterial genes after infection and to contribute towards a timed viral gene transcription program.

T4 morphogenesis involves separate subassembly pathways for viral heads, tails, tail baseplates and fibres, with the substructures assembling spontaneously.
T
‐Cell Receptors
Authors: Schoettle Louis N , Poindexter Morgan E , Blattman Joseph N 
Published: August 2015

Abstract

In order to combat a wide array of pathogens, the immune system must be able to generate cells with the ability to recognise virtually any pathogen while at the same time balancing this diversity with the maintenance of sufficient numbers of cells specific for each pathogen in order to mount an effective response. T cells, which are important for both the direct elimination of infected cells as well as providing support for other immune responses to pathogens, generate immunologic diversity by imprecise joining of gene segments to generate either α/β or γ/δ heterodimeric receptors during development. Although the potential diversity of rearranged T‐cell receptors (
TCR
) is many orders of magnitude greater than the number of T cells in any given individual, highly regulated steps in development, as well as restrictions in the specificity of
TCR
, facilitate the generation of sufficient numbers of T cells with each
TCR
to ensure efficacy in pathogen control.

Key Concepts

The T‐cell repertoire must balance diversity of antigen recognition with sufficient numbers of each specificity to elicit protection.

T cells may express either αβ or γδ T‐cell receptors, which have different roles in immunity.

T‐cell receptor diversity arises mainly through the process of somatic recombination.

Somatic recombination, the process of reorganisation of T‐cell receptor genes, is a highly ordered and regulated process.

T‐cell development includes checkpoints to ensure both self‐MHC restriction and negative selection to remove any autoreactive T cells.

T‐cell receptors recognise processed antigen displayed on self‐MHC complexes presented by antigen‐presenting cells.

T‐cell receptors signal intracellularly through the CD3 signalling complex.

TCR:pMHC activation with appropriate costimulation results in differentiation of effector T cells .
Hypersensitivity:TLymphocyte Mediated (TypeIV)
Authors: Hwang Shen‐An , Actor Jeffrey K 
Published: August 2015

AbstractFive types of hypersensitivity reactions have been described: types I,II,IIIand V depend on antigen antibody interactions and have been termed ‘immediate’ and typeIVreactions depend on interaction of antigen with T lymphocytes and has been called ‘delayed‐type hypersensitivity’, orDTH. TheDTHreaction involves cellular activation of T helper cells (CD4+) and/or cytotoxic T cells (CD8+CTLs). Subsequent cytokine secretion gives rise to distinct pathologies. In many cases, sustained release of antigen and continued activation of sensitized T lymphocytes result in amplification of responses that provoke excessive immune activation. These events are the basis for development of a broad range of inflammatory pathologies that include erythema and oedema, granuloma formation, extended development of fibrosis, and tissue necrosis.Key ConceptsType IV hypersensitivity (also calleddelayed‐type hypersensitivity, DTH) represents immune reactivity where T lymphocytes have had prior encounter with antigen.It is termed ‘delayed‐type’ hypersensitivity because the reaction usually manifests 12–24 h post antigen exposure.DTH responses can manifest from contact with allergens or infectious agents, giving rise to localised inflammation, erythema and oedema.The classical manifestations of DTH are defined as cutaneous (contact), tuberculin or granulomatous hypersensitivity. Broader classification now includes subdivision based on dominant effector activity and defined elicited pathology.DTH evolved as a protective host mechanism to combat pathogens; however, excessive DTH responses can lead to immunopathology, exhibited by granuloma formation, fibrosis or even tissue necrosis.DTH reactions are prominent in autoimmune diseases, and have also been demonstrated to play a role in the response to transplantation of tissue from a genetically different donor (allogeneic transplantation).
Video Microscopy
Authors: Hinchcliffe Edward H 
Published: August 2015

Abstract

Video microscopy represents the first form of electronic imaging in light microscopy, and heralded the use of sophisticated fluorescence imaging techniques. However, today video microscopy – based on phase or differential interference optics – is considered to be an outdated technology. Rather than being yesterday's technology, a simple video microscope is a powerful tool for imaging cellular dynamics, and can easily be used to monitor cell cycle progression. Because the nonfluorescence imaging modes require significantly less light throughput, the video microscope is particularly suited for long‐term experiments, where photodamage can be a limiting factor. The video microscope is also an economical instrument that complements more sophisticated fluorescence‐based imaging systems, such as confocals, wide‐field deconvolution microscopes and super‐resolution microscopes. Here, I discuss a brief history of video microscopy, define some popular uses for the technology and discuss the selection of components for building a simple, yet functioning video microscopy system.

Key Concepts

Video microscopy represents the first electronic imaging system.

Simple video microscopes are an economical choice for live‐cell imaging.

System design requires selecting appropriate microscopes and illumination sources to allow long‐term imaging.

Live‐cell imaging requires control of temperature and pH.

Software selection to capture movies, control the imaging system and present the data is important.
Actin Reorganisation in Nerve Morphogenesis
Authors: Singh Ajeet P , Rodrigues Veronica , VijayRaghavan Krishnaswamy 
Published: August 2015

Abstract

Anatomists over centuries have described nerve cells which are notable for their diversity of architectures ranging from rather simple cells to highly complex and beautiful shapes. The soma of most neurons has two types of projections – dendrites, which receive inputs from the environment or other nerve cells, and axons, which specialise in information transfer. The correct shape of a neuron and its connectivity which forms the basis of a functional circuit is crucial for the normal physiology of an animal. Defects in neuronal morphogenesis have been shown to be the cause of several neurological diseases. In this article, we focus on a key molecule – actin, a component of the cytoskeleton – that forms the basis of cell shape and growth. We discuss how signals from within the cells and from its developmental milieu influence the organisation of actin which in turn impacts on the shape and function of a nerve cell.

Key Concepts

Actin is enriched in areas of neurons which undergo rapid changes in shape.

Actin dynamics is regulated by multiple upstream signals and intracellular effectors.

Local destabilisation of the actin cytoskeleton is a key downstream event during selection of an axon.

Actin dynamics in the growth cone regulates filopodial extension/retraction.

Actin cytoskeleton is highly dynamic in dendritic spines.

Neuronal activity‐dependent spine enlargement is correlated with a shift in F‐/G‐actin equilibrium towards F‐actin.

Rho GTPases are major intracellular regulators of actin dynamics.
Horizontal Gene Transfer in Evolution
Authors: Boto Luis 
Published: August 2015

Abstract

The concept of horizontal or lateral gene transfer (the non‐genealogical transmission of genetic material between organisms) was introduced in 1990s to explain the observed incongruence in phylogenetic reconstructions using different genes. Today, horizontal gene transfer is accepted as an important force modulating evolution of Bacteria, Archaea and unicellular eukaryotes, and evidence is rising for their role in the evolution of pluricellular eukaryotes (fungi, plants and animals). The realisation that horizontal gene transfer plays an important role in evolution of both, prokaryotes and eukaryotes, put in question the metaphor of the tree of life and the traditional view of evolution as a slow process. A more pluralistic approach to evolution is emerging that encompasses different evolutionary mechanisms operating at different levels of complexity.

Key Concepts

Horizontal gene transfer is the non‐genealogical transmission of genetic material between different organisms.

Horizontal gene transfer has become a part of evolutionary thinking over the past 25 years.

Horizontal gene transfer plays an important role in prokaryotic evolution.

Horizontal gene transfer also modulates evolution of unicellular eukaryotes.

Increasing evidence support the role of horizontal gene transfer in evolution of pluricellular eukaryotes.

Horizontal gene transfer challenges the tree of life metaphor.

Horizontal gene transfer challenges the traditional view of evolution as a slow process.

A pluralistic approach to evolution is needed.
Neurobiology of Itch (Pruritus)
Authors: Akiyama Tasuku , Mochizuki Hideki , Carstens E 
Published: August 2015

Abstract

Itch is often defined as an ‘unpleasant sensation that provokes the desire to scratch’. Recent studies have provided novel insights into the molecular mechanisms underlying itch‐selective signalling pathways from the periphery to the central nervous system. Chronic itch is often associated with inflammatory skin diseases such as atopic dermatitis, psoriasis or contact dermatitis, as well as systemic diseases such as renal, cholestatic, hematologic or endocrine pruritus or pruritus related to malignancy, and reduces quality of life. Chronic itch is thought to involve the sensitisation of itch‐signalling pathways, the molecular and cellular processes of which we are just starting to uncover. This review article describes recent findings regarding the basic mechanisms of itch transmission from the skin to the brain. We further describe the neuronal changes that occur both peripherally and centrally under conditions of chronic itch.

Key Concepts

There are a variety of endogenous pruritogens and external itch stimuli.

Itch transducing channels include TRPV1, TRPA1 and Nav1.7.

Spinal excitatory and inhibitory interneurons process itch information.

Descending noradrenergic and serotonergic systems modulate spinal itch transmission.

Sensitisation occurs in both peripheral and central nervous system under conditions of chronic itch.

NK1‐expressing spinal neurons play a major role in itch sensitisation.