bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laser Spectroscopy
Authors: Inguscio Massimo , Rusciano Giulia , Sasso Antonio 
Published: March 2011

Abstract
Most of the actual knowledge of atomic and molecular structure derives from spectroscopic analysis of the radiation emitted when atoms or molecules are properly excited. The foundation of spectral analysis dates back to about 1860, with the work of Kirchhoff and Bunsen which argued that from the analysis of the emission by sample after a proper excitation it was possible to get information on the sample itself. Starting from this pioneering work, spectroscopic investigations have undergone an impressive evolution and applications have covered a wider a wider range. So far, besides fundamental physics, spectroscopic analysis are of direct importance in an increasing variety of applications in fields such asastrophysics, combusion, plasma physics, soft matter and, in recent years, bio‐medicine. In the following pages, the main techniques of laser spectroscopy are examined: starting from discovery of the hydrogen atom spectral series, the modern application of ultrasensitive spectroscopic techniques to sample constituted by only a few molecules (single molecule spectroscopy) are discussed. Of course, this contribution surely can not be exhaustive, and the reader is referred to more general treatments of the theory and practice of spectroscopy for a more detailed treatment.
Luteoviruses
Authors: Brault Véronique , Herrbach Etienne , Rodriguez‐Medina Caren 
Published: March 2011

Abstract

Luteoviruses, that is, members of the
Luteoviridae
family, are plant viruses that can infect a wide range of host plants, including many important crops such as cereals, cucurbits, legumes, potato, sugarbeet and sugar cane. Their icosahedral virions contain a single (+)
ribonucleic acid
genome in a capsid composed of two structural proteins. They are limited to phloem cells in host plants and are only transmitted by aphids in a circulative and nonpropagative mode with high specificity.

Growing data are accumulating on plant–luteovirus relationships and more particularly on the mechanism developed by the virus to overcome plant defence. The tight interaction between luteoviruses and their aphid vector has also been extensively studied. Information from these studies together with a better understanding of the epidemiology of luteoviruses will help to combat their detrimental effects on crops.

Key Concepts:

Luteoviruses have a highly compacted genome and use a diversity of translation mechanisms to express viral proteins.

Function of the viral gene products is known, but their plant and aphid partners have not been fully identified.

Luteoviruses are confined to phloem tissue, but the causes of their phloem restriction are not completely deciphered.

Luteoviruses circulate in the vector aphid's body, without any replication, by crossing the gut and the accessory salivary gland epithelia.

Epidemiology of luteoviruses reveals a high complexity of mutual ecological interactions between virus, plant and vector, influenced by multiple biotic and abiotic factors.

Control of luteoviral diseases includes cultural practices, insecticidal measures, natural and biotechnological plant resistance and epidemiology‐based forecasting systems.
Parainfluenza Viruses
Authors: Chambers Raychel , Takimoto Toru 
Published: March 2011

Abstract

Parainfluenza viruses are enveloped viruses that contain nonsegmented negative‐strand genomic
ribonucleic acid
(RNA). Replication of these viruses begins with entry by attachment and fusion, followed by genomic transcription and replication. Next, the

de novo

synthesised viral components are trafficked to assembly sites at the plasma membrane where newly formed virions bud out from the cell. These viruses are respiratory pathogens which act as the causative agents for croup, bronchiolitis and pneumonia. As a group, the parainfluenza viruses are second only to human respiratory syncytial virus as the cause of acute paediatric respiratory tract disease and are responsible for hundreds of thousands of additional U.S. hospitalisations per year. Despite their clinical importance, licensed vaccines or antiviral compounds for prevention or treatment of parainfluenza viruses are not currently available, making understanding the pathogenesis of these viruses critical for antiviral drug and vaccine development.

Key Concepts:

Parainfluenza viruses are enveloped, nonsegmented negative‐strand RNA viruses, which cause respiratory infections.

The structure of the virion consists of glycoprotein spikes protruding from a lipid envelope under which lies the matrix protein surrounding the viral nucleocapsid, consisting of viral RNA encapsidated by nucleoprotein and associated with the polymerase complex.

Specific interactions between the two envelope glycoproteins HN and F are necessary for efficient virus infection.

Because the viral genome is negative‐stranded RNA, an intermediate step is required for production of progeny viral genomes.

Newly synthesised viral nucleocapsids are transported to the assembly site at the plasma membrane utilising the microtubule network.

Pathogenicity of parainfluenza viruses is highly dependent on the anti‐interferon activity of the viral accessory proteins.

Infectious virus can be created from a complementary deoxyribonucleic acid (cDNA) clone of the viral RNA genome, which is termed reverse genetics.

The development of vaccines against parainfluenza viruses currently include intranasally administered vaccines attenuated by cold‐passage, host range attenuation, chimeric vaccine constructs, or the introduction of attenuating mutations through the use of reverse genetics.
Cutin and Suberin
Authors: Li‐Beisson Yonghua 
Published: March 2011

Abstract

Cutin and suberin are cell‐wall associated glycerolipid polymers specific to plants. Cutin forms the framework of the cuticle sealing the aerial epidermis, whereas suberin is present in the periderm of barks and underground organs. Suberised walls are also found in root internal tissues. Barriers based on cutin and suberin restrict transport of water across cell walls and limit pathogen invasions. Chemical analysis shows that both polymers are polyesters composed mostly of C16‐C18 hydroxyacids, diacids and epoxyacids esterified to each other and to glycerol. Suberin, whose best known form is cork, usually differs from cutin by a higher content in C20‐C24 aliphatics and aromatics. In the last decade, the identification of

Arabidopsis

mutants affected in cutin or suberin content has allowed the identification of several proteins involved in polyester biosynthesis, including
acyltransferases
with unique specificities,
fatty acid hydroxylases
,
acyl‐CoA synthetases
,
fatty acid elongases
and an ABC transporter.

Key Concepts:

The epidermal cells and suberising cells have specialised enzymes that convert the common cellular fatty acids into the unique components of cutin and suberin, respectively.

Oxygenated fatty acid monomers are produced by fatty acid oxidases of the cytochrome P450 superfamily.

Acylglycerol dimers can be synthesised by special glycerol‐3‐phosphate acyltransferases.

Whether polymerisation of dimers and monomers occurs in intracellular compartments or in the cell walls is still unknown.

How cutin and suberin polymers are linked to the cell walls remains to be determined.

Cutin contributes to the formation of surface nanostructures in epidermis.
Bayes' Factors
Authors: Johnson Valen E 
Published: March 2011

AbstractBayes' factors play a pivotal role in Bayesian hypothesis testing, representing the factor through which the prior odds between competing hypotheses are transformed to the posterior odds between the hypotheses. Mathematically, Bayes' factors are defined as the ratio of the marginal probability assigned to the data by one hypothesis to the marginal probability assigned to data by the other hypothesis. In many parametric statistical tests, hypotheses are defined by the specification of prior densities on unknown parameters. In such cases, Bayes' factors represent the ratio of an averaged likelihood function, averaged with respect to the different prior densities assigned to the unknown parameter under each hypothesis. Inconsistencies in the limiting behaviour of Bayes' factors may arise when hypotheses are defined with respect to prior densities that have overlapping support.Key Concepts:Bayes' factors are used in Bayesian hypothesis tests and are the key factors through which experimental data determine the posterior probability assigned to scientific hypotheses.Bayes' factors represent the ratio of the probability assigned by competing hypotheses to a common set of data.Bayes' factors equal the posterior odds divided by the prior odds between hypotheses.The natural logarithm of a Bayes' factor is called the weight of evidence.
Brain Tumours
Authors: López Giselle Y , Cummings Thomas J , Bigner Darell D , McLendon Roger E 
Published: March 2011

AbstractBrain tumour genetics allow for improved classification and development of therapeutic options for certain primary brain tumours. Tumours with specific genetic alterations and molecular profiles are also associated with certain inherited familial cancer syndromes, including Li–Fraumeni syndrome, neurofibromatosis and tuberous sclerosis. Recent advances in genetic profiling, from karyotype analyses to fluorescencein situhybridisation (FISH) to genome‐wide sequencing have greatly improved the understanding of the genetic basis for these tumours. Karyotype analyses rapidly identified loss of chromosome arms 1p and 19q as the most common genetic abnormality in oligodendrogliomas. Digital karyotyping identifiedOTX2in medulloblastomas, and further studies revealed its frequent overexpression in anaplastic medulloblastomas. Recently, genome‐wide sequencing identified three key pathways as mutated in the majority of glioblastomas, namely, thep53, retinoblastoma and receptortyrosine kinasepathways. Further analysis may prove key to identifying likely therapeutic targets.Key Concepts:The most common primary malignant brain tumour of adults is glioblastoma, a grade IV astrocytoma with an average survival of approximately 1 year following diagnosis.Recent genome‐wide expression analyses have identified distinct expression patterns in glioblastoma patients which predict survival and may eventually be used to target therapies.Three key pathways altered in the majority of astrocytomas include the receptor tyrosine kinase, p53 and retinoblastoma signalling pathways.Epidermal growth factor receptor (EGFR) is overexpressed in the majority of glioblastomas and is frequently mutated to a constitutively active variant, EGFRvIII.Mutations in IDH1 or IDH2 are the most common abnormality in both oligodendrogliomas and progressive astrocytomas, occurring in 60–90% of tumours.The most characteristic chromosomal abnormality in oligodendrogliomas is complete allelic losses of chromosome 1p and 19q.Gene expression microarray data has made possible the classification of medulloblastomas into subgroups based on expression of Sonic hedgehog pathway, Wnt pathway, neuronal differentiation or photoreceptor gene expression patterns.The most common specific chromosomal abnormality in medulloblastomas is loss of 17p, which is often associated with gain of 17q.
Origin and Evolution of Insect Metamorphosis
Authors: Belles Xavier 
Published: March 2011

AbstractInsect metamorphosis can be classified into three modalities: ametabolan (no changes), hemimetabolan (progressive changes) and holometabolan (dramatical changes at the end of the cycle). The metamorphic changes are mainly regulated by two hormones: the moulting hormone, which promotes the moults, and the juvenile hormone (JH), which represses the transformation into the adult. The action of these two hormones is mediated by a number of transcription factors, and the molecular mechanisms regulating the expression of these and of the corresponding target genes are finally refined by the action of microribonucleic acids. Among the different transcription factors involved, those of the Broad‐Complex group are especially interesting because they have a differential expression and JH dependency in holometabolans and hemimetabolans. Holometabolan metamorphosis probably evolved from hemimetabolan ancestors, although the mechanisms underlying such a transition are still obscure.Key Concepts:Insect metamorphosis can be classified into three modalities: ametabolan, hemimetabolan and holometabolan.The main hormones involved in the regulation of insect metamorphosis are the moulting hormone and the juvenile hormone.The molecular mechanisms underlying the action of the moulting hormone are reasonably well known, but those related to juvenile hormone are much less understood.Broad‐Complex transcription factors are involved in the transduction of both, the moulting hormone and the juvenile hormone, but have a differential expression and juvenile hormone dependency in holometabolans and hemimetabolans.Fossil record and phylogenetic reconstructions suggest that hemimetaboly evolved from ametabolan ancestors, whereas holometaboly derived from hemimetaboly.Mechanisms underlying the evolutionary transitions from ametaboly to hemimetaboly and to holometaboly are still obscure and under debate.
Hogben, Lancelot
Authors: Tabery James 
Published: March 2011

AbstractLancelot Hogben, although less famous than contemporaries such as RA Fisher, Julian Huxley and JBS Haldane, left a lasting impression on twentieth‐ and twenty‐first‐century biology. Hogben's extensive background in experimental biology led him to introduce theinterdependence of nature and nurtureas a concept and tool for critiquing eugenic attempts to partition nature and nurture. This attention to the interdependence of nature and nurture can be traced into modern scientific practice (in research on gene–environment interaction, phenotypic plasticity and developmental systems theory) as well as modern scientific debate (in disputes over the limits of the human genome project, the heritability wars and the geneticisation of complex human traits).
Ultraviolet/Visible Light Detection and Ranging Applications in Air Monitoring
Authors: Wolf J.‐P. 
Published: March 2011

AbstractRecent progress in light detection and ranging (LIDAR) and differential absorption light detection and ranging (DIAL) technology has allowed three‐dimensional (3‐D) mappings of concentrations of air pollutants to be obtained at the highest sensitivity (parts per billion) and over large distances (several kilometers). It is now possible to monitor on‐line spatial distributions of nitrogen oxides, sulfur dioxide, ozone, benzene, toluene, and aerosols. With the advent of tunable solid‐state laser systems, such as vibronic lasers and optical parametric oscillators (OPOs), LIDAR systems have furthermore reached industrial standards in terms of reliability and ease of operation. An overview of results and capabilities of “all‐solid‐state” LIDAR/DIAL systems is presented. The examples of application include detailed urban studies performed in large cities (e.g. Berlin, Leipzig, Lyon, Paris, Stuttgart, Geneva, Athens, and Seville), with special attention to smog formation processes and tropospheric ozone generation. Industrial applications are also numerous, such as site monitoring, identification of diffuse emissions, and evaluation of the impact of new emitters through plume dispersion studies. The use of LIDAR systems for validating numerical models is also discussed, along with intercomparison with standard analyzers and related certification issues. The last section is dedicated to a new class of LIDAR systems, based on femtosecond lasers, which not only allow multicomponent analysis but also possible weather modulation.
Electron Paramagnetic Resonance Imaging
Authors: Eaton Gareth R. , Eaton Sandra S. 
Published: March 2011

AbstractUnpaired electrons can be measured by their absorption of electromagnetic radiation when the energy level separations established by a magnetic field match the energy of the incident electromagnetic radiation (usually microwave or radio frequency). The measurement method is called electron paramagnetic resonance (EPR). The EPR methodology can be continuous‐wave (CW), pulsed, or rapid‐scan EPR. Since the paramagnetic species are commonly not uniformly distributed in the material studied, the spatial distribution can be discerned by performing the EPR measurement in a magnetic‐field gradient, such that different parts of the sample resonate at different strengths of the applied magnetic field. Performing EPR in a gradient field and then constructing a spatial image from the acquired EPR spectra is called EPR imaging, sometimes abbreviated to EPRI. The method is analogous to MRI, but with several differences in implementation due to differences in spectral line widths, relaxation times, and unpaired spin concentrations. The goal of EPRI is to determine why the spins are where they are. Applications are as diverse as understanding physiology, measuring O2concentration in tumors, and determining the distribution of radiation‐induced defect centers in solid materials.
Matrix‐assisted Laser Desorption/Ionization Mass Spectrometry of Polymers
Authors: Pasch Harald , Alpheus Mautjana Nare 
Published: March 2011

AbstractMatrix‐assisted laser desorption/ionization mass spectrometry (MALDI MS) has proved to be one of the best methods for identification and determination of the number of monomer units of simple polymers, including their end‐groups. However, most man‐made polymers are complex materials with numerous macromolecules (oligomers) of different chain lengths and different chemical compositions in one sample. Since MALDI MS primarily produces singly charged ions of each molecule in the sample, its mass spectra are easy to interpret and therefore useful for polymer characterization. Different oligomers of interesting polymers can be isolated in tandem mass spectrometry (MS/MS) for analysis of their monomer sequence to relate properties of the polymer to its molecular structure. Furthermore, the polymerization mechanism responsible for a given polymer can often be deduced from the oligomer structure. MALDI MS‐based methods have been used for the determination of molar mass distributions of complex polymers. However, to obtain meaningful data, proper understanding of polymer complexity as well as good insight of MALDI MS instrumentation and sample preparation protocol is necessary. Since the introduction of MALDI, different types of mass analyzers have been used. Each type has its advantages while other mass analyzers are simply not suitable for MALDI or for the targeted mass range.
Generation of Spatio‐Temporally Controlled Targeted Somatic Mutations in the Mouse
Authors: Metzger Daniel , Chambon Pierre 
Published: March 2011

AbstractThe generation of ligand‐activated site‐specific Cre recombinases has led to the development of cell type–specific temporally controlled targeted somatic mutagenesis in the mouse. We illustrate this technique using K14‐Cre‐ERT2 transgenic mice that express the tamoxifen (tam)‐activatable Cre‐ERT2 recombinase in epidermal basal keratinocytes to induce mutations in epidermal keratinocytes of adult mice. Our highly reproducible technique, based on induction of Cre‐ERT2 recombinase activity by tamoxifen administration at low doses (once daily 100‐µg intraperitoneal injection for 5 days), has allowed the generation of site‐directed somatic mutations of numerous genes in mouse epidermal keratinocytes, and several mouse models of human diseases. The present step‐by‐step protocol describes how to introduce temporally controlled targeted mutations in epidermal keratinocytes of adult mice. Curr. Protoc. Mouse Biol. 1:55‐70. © 2011 by John Wiley & Sons, Inc.
Imaging Cancer in Mice by PET, CT, and Combined PET‐CT
Authors: Mulero Francisca , Donate Luis E. , Serrano Manuel 
Published: March 2011

AbstractThe possibility of imaging tumors in live mice has opened new opportunities for cancer research, particularly regarding the ability to perform longitudinal studies in combination with a therapeutic intervention. Here, we detail methods to optimize visualization of murine tumors by positron emission tomography (PET), computed tomography (CT), and combined PET‐CT. Curr. Protoc. Mouse Biol. 1:85‐103. © 2011 by John Wiley & Sons, Inc.
Ethical Considerations in Mouse Experiments
Authors: Baertschi Bernard , Gyger Marcel 
Published: March 2011

AbstractMice count morally because they can be harmed. This raises a moral issue in animal experimentation. Three main ethical attitudes towards animals are reviewed here. The Kantian view denies moral value to animals because they lack reason. The second view, by Singer, considers animals as sentient creatures (i.e., able to suffer). Finally, Regan considers that animals are subjects of their own life; they are autonomous and therefore have moral rights. Singer is a reformist and allows animal experimentation under certain conditions. Regan is abolitionist, saying that animals have moral rights that cannot be negotiated. Current animal protection legislation strives to put in balance the human and animal interests to decide whether an animal experiment is morally justified or not. An ethical evaluation process is conducted based on the harm‐benefit assessment of the experiment. The researcher has to implement the 3Rs (Replacement, Reduction, Refinement) to minimize the harms to the animals and make sure that the outcomes are scientifically significant and that the quality of the science is high, in order to maximize benefits to humans and animals. Curr. Protoc. Mouse Biol. 1:155‐167. © 2011 by John Wiley & Sons, Inc.
High‐Resolution Patterning of Various Large‐Area, Highly Ordered Structural Motifs by Directional Photofluidization Lithography: Sub‐30‐nm Line, Ellipsoid, Rectangle, and Circle Arrays
Authors: Lee Seungwoo , Kang Hong Suk , Park Jung‐Ki 
Published: March 2011

AbstractA major challenge in nanolithography is to overcome the resolution limit of conventional patterning methods. Herein, we demonstrate a simple and convenient approach to generate sub‐30‐nm various structural motifs with precisely controlled sizes, shapes, and orientations. The proposed method, the “directional photofluidization” of an azopolymer, follows the same philosophy as a path‐changing approach, for example, thermal‐reflow of polymer arrays, in that post‐treatment simultaneously leads to a reduction of the feature sizes and line‐edge roughness (LER) of nanostructures. However, in contrast to thermal‐induced isotropic reflow, directional photofluidization provides unprecedented flexibility to control the structural features, because the direction of photofluidization can be arbitrary controlled according to the light polarization. Furthermore, this approach offers good control of the final features due to a gradual reduction in the rate of photofluidization during light irradiation. More importantly, the photofluidic behavior of the azopolymer significantly reduces the LER, and thus it can improve the quality of nanostructures. Finally, the far‐field process of directional photofluidization enables hierarchical nanofabrication, in contrast to mechanical contact fabrication, because the patterned light can reconfigure the polymer arrays selectively. Our approach is potentially advantageous for the fabrication of various structural motifs with well‐controlled dimensions on the nanoscale and with minimized LER.