bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small‐angle Scattering of Neutrons and X‐rays
Authors: Chow John YH , Trewhella Jill 
Published: January 2010

Abstract

Small‐angle scattering of X‐rays and neutrons is used to study the structures of biological macromolecules in solution. Where the components of biomolecular complexes have different scattering densities, scattering data provide structural information on the individual components and their relative dispositions. One can therefore gain insights into protein–protein and protein–
deoxyribonucleic acid
(DNA) or ribonucleic acid (RNA) interactions within functional complexes. Although scattering data are inherently low resolution and limited in information content due to the random orientations of the scattering molecules, recent applications that use data from complementary methods have facilitated the interpretation of scattering data in terms of detailed models. Advances in computational methods and user interfaces have enabled nonspecialists to use the technique to advance our understanding of biomolecular systems. The increasing availability of synchrotron facilities has also enabled advances in studies of time‐dependent changes in protein structure and the development of high‐throughput approaches.

Key concepts:

Small‐angle scattering provides information on the shapes of biological macromolecules in solution.

Neutron contrast variation reveals the structures and disposition of the components within biomolecular complexes and assemblies.

Proteins and polynucleotides naturally have different scattering densities for X‐rays and neutrons and can therefore be distinguished in a scattering experiment.

Protein deuteration combined with systematic variation in solvent detueration can provide enhanced contrast variation capability for protein complexes.

Small‐angle solution scattering data complements the higher resolution structural data from crystallography and NMR.

Small‐angle scattering improves solution structure determination by providing information on long‐range distances that complements the predominantly short‐range distance information obtained by NMR.

Solution scattering data complements high‐resolution crystallography by providing insights into conformational dynamics that are observed as a result of ligand binding or other changes in biological state.

Synchrotron X‐ray sources enable time‐resolved solution scattering experiments to probe conformational dynamics in proteins and DNA or RNA.

Structural characterization by small‐angle scattering requires highly pure, monodisperse identical particles in solution.
Nuclear Receptor Genes: Evolution
Authors: Sáez Pablo J , Lange Soledad , Pérez‐Acle Tomas , Owen Gareth I 
Published: January 2010

Abstract

Nuclear receptor superfamily members are metazoan innovations which are present in all living metazoan phyla. These genes, presumably originating from a common ancestor in an extinct phylum that predates the sponge (Porifera), has evolved, and is still evolving, to mediate nearly every facet of metazoan life. Representatives of all six classical nuclear receptor superfamily members were present before the protostome–deuterostome split, more than 700 million years ago. Nuclear receptor sequence and structure diversification to accommodate ligand binding has occurred numerous times, with the earliest report of steroid‐hormone binding occurring in the Annelid and of retinoic acid in the lower metazoan phylum Cnidaria. During the Cambrian period a quadruplication of the genome leading to jawed vertebrates gave rise to many of the nuclear receptor paralogues present today.

Key Concepts:

The evolutionary origins and diversification of the nuclear receptor superfamily gene structure in the Metazoa.

Nuclear receptors are unique to the metazoan kingdom.

Members of the nuclear receptor superfamily are present in all extant phyla of metazoans.

Representatives of six classical nuclear receptor superfamily members were present before the proteosome–deutrosome division more than 700 million years ago.

During the Cambrian period a quadruplication of the genome giving rise to jawed vertebrates occurred producing many of the nuclear receptor paralogues present today.
Avirulence Genes
Authors: Rouxel Thierry , Balesdent Marie‐Hélène 
Published: January 2010

Abstract

In gene‐for‐gene systems, resistance of a plant to a pathogen is due to the ‘recognition’ by plant surveillance system (i.e. plant resistance gene product) of a pathogen avirulence determinant encoded by an avirulence gene to eventually result in triggering of plant immunity. Avirulence proteins (or products) actually are effectors involved in pathogenicity. In viruses, virtually all the proteins can behave as avirulence determinants. In all other cases, avirulence genes are extremely diverse, being often species or isolate/strain‐specific and rarely have matches in sequence databases. They often are specifically expressed or strongly over‐expressed during plant–pathogen interaction and the encoded proteins show the presence of secretion signals and translocation signals (e.g. the Type III secretion signal for bacteria). Avirulence genes seem to be submitted to high‐speed diversifying selection allowing the pathogen to diversify its effector repertoire and rapidly escape recognition by the plant resistance gene.

Key concepts

Effectors
of plant pathogens are pathogen molecules that manipulate host cell structure and function thereby facilitating infection.

Effectors often contribute quantitatively to pathogen aggressiveness and are dispensable for the pathogen life cycle.

In the course of plant–pathogen co‐evolution, plants have evolved receptors that detect pathogen effectors (or the effect of the effectors on a plant target) and activate defence responses.

The effectors specifically recognized by ‘matching’ resistance proteins (termed R proteins) are termed
avirulence (AVR) proteins
.

This forms the basis of the
gene‐for‐gene
concept, genetically demonstrated by Flor between 1942 and 1955 and stating that plants producing a specific
R
gene product are resistant towards a pathogen that produces the corresponding
Avr
gene product whereas whenever one of the genes or both are lacking the plant is susceptible and disease ensues.

In wild plant and pathogen populations, avirulence and resistance are discontinuous traits, only present in part of the population. Thus resistance will be applied against only part of the pathogen population (harbouring the corresponding Avr allele) and pathogen will only be avirulent towards part of the plant population (harbouring the matching resistance gene).

All plant pathogens from viruses to nematodes, but also some pests like aphids produce avirulence proteins.

When submitted to resistant populations of plants, pathogens can alter or delete their avirulence proteins to avoid defence elicitation, at risk of a
fitness cost
associated with loss‐of‐function of those effectors.
Calcium Imaging in Neuroscience
Authors: Neubauer Florian B , MacLean Jason N 
Published: January 2010

Abstract

Calcium imaging uses fluorescent indicator molecules to monitor changes of intracellular free calcium concentrations. Calcium imaging is employed to examine electrically excitable tissues such as muscle and neuronal tissue (including glia) where membrane‐related electrical activity is tightly coupled to significant calcium movements into or within cells. In the context of neuroscience research, calcium imaging can be applied at many scales, ranging from a single part of a single neuron to populations of many interconnected neurons. The ability to move between different scales of resolution is a major advantage of calcium imaging, making this technique an important tool for enhancing our understanding of the brain.

Key concepts

Brain researchers use calcium imaging to monitor electrical activity in neurons.

Calcium can be imaged at many scales: from the subcellular to entire brain regions.

Calcium imaging can use different dyes and optical methods.
Molecular Phylogenetic Analyses in Court Trials
Authors: González‐Candelas Fernando 
Published: January 2010

AbstractMolecular phylogenetics allows reconstructing of the genealogy and evolutionary history of organisms from information on their nucleotide or amino acid sequences. When sequences are derived from very fast evolving organisms, such asribonucleic acid(RNA) viruses, changes accumulate in a few days or weeks, thus allowing the reconstruction of very recent evolutionary events in the history of these populations. One such event is the transmission of one of these viruses, for instancehuman immunodeficiency virus(HIV) orhepatitis C virus(HCV), from an infected person to another. This occasionally results in a legal demand seeking for compensation and/or punishment for the transmitter. Hence, expert testimony is sought in court to determine whether the viruses isolated from the source and the infected patients actually share a common origin or not. Molecular phylogenetics and statistical inference methods are used to translate scientific testimony into expert evaluation of the evidence for the court.Key concepts:Fast evolving organisms, such as RNA viruses, can accumulate changes in their genome sequence in a few days or weeks.Changes in nucleotide sequences can be used to track the evolutionary history of organisms sharing a common ancestor.The last common ancestor (LCA) of a set of sequences represents the last sequence before the corresponding lineage split in two or more separate lines of descent.During a transmission event, a portion of the microorganisms in the source is passed onto the recipient(s).Phylogenetic analysis can be used to ascertain when two or more sequences shared an LCA as well as some of its features.Sequences derived from a transmission event will share a more recent LCA than those obtained from unrelated sources.The analysis of LCA can be used to provide expert testimony in courts on the source of an infection.Under special conditions, it is also possible to ascertain the direction of the transmission and an approximate time for it.Phylogenetic analysis is a very powerful and reliable methodology whose use for resolving transmission cases has been validated by courts in many countries.
Membrane Insertion of Tail‐anchored Proteins
Authors: Schuldiner Maya , Schwappach Blanche , Weissman Jonathan S 
Published: January 2010

AbstractTail‐anchored (TA) proteins are a special class of transmembrane proteins, which harbour only a single hydrophobic segment adjacent to their mostC‐terminus. This anchor must be inserted into membranes posttranslationally to allow for their correct cellular localization. Although TA proteins have essential cellular roles such as signal transduction, apoptosis and vesicle fusion, their biogenesis route has for many years remained unknown. Recently, several advances have created a new understanding of the TA protein insertion machinery. Uncovering the machinery responsible for the biogenesis of TA proteins should further our ability to understand a wide variety of diseases such as forms of cancer caused by activation of the TA protein oncogeneBCL2.Key concepts:Tail‐anchored proteins haveC‐terminal hydrophobic domains.Tail‐anchored proteins are inserted posttranslationally into the membrane.The GET complex inserts tail‐anchored proteins into the endoplasmic reticulum membrane in yeast.The TRC complex chaperones tail‐anchored proteins into membranes in humans.
Neuroimaging
Authors: Schweitzer Julie 
Published: January 2010

Abstract
Neuroimaging is the use of techniques to map the location of structural and functional regions within the living brain. It is used extensively in clinical practice to identify abnormalities, such as testing for brain tumors, stroke, and other neurological conditions. It is also increasingly used as a diagnostic tool on a finer scale for metabolic diseases and lesions, including differentiation of neurological disorders (e.g., Alzheimer's Disease versus frontotemporal dementia). Structural neuroimaging techniques generate anatomic images relating to the volume, position, and shape of a structure, whereas functional neuroimaging produces data relating to activities to the active processing of the brain, either in a “resting” state or a response to external stimulus. Functional imaging is also used to assess chemical composition and neuroreceptor characteristics. Structural neuroimaging is more likely to be used clinically, while functional neuroimaging is primarily associated with research endeavors.
Artificial Vision
Authors: Chen S. C. , Hallum L. E. , Wong Y. T. , Dommel N. , Byrnes‐Preston P. J. , Suaning G. J. , Lovell N. H. 
Published: January 2010

Abstract
“Artificial vision” or “prosthetic vision,” in the therapeutic sense, refers to the restoration of some degree of visual perception to the profoundly blind. In nearly all instances, such therapeutic devices are based on electrically exciting the remaining functional neural tissue within the visual pathway, which replaces the intrinsic signals that can no longer be effectively elicited because of the underlying pathology or trauma. The therapeutic device for restoring vision is generally called a “vision prosthesis.”
Although a variety of approaches for a vision prosthesis design are available, a typical system usually would constitute a light sensing component (e.g., a video camera) to replace the photosensitive elements related to light transduction, an image processing unit to replace the signal processing in the visual system bypassed by the prosthesis, electronic circuitry to generate electrical stimulus waveforms to elicit perceptions of light artificially, and stimulating electrodes placed in close proximity to the target neural tissue to deliver the electric charge. Furthermore, the implanted portion of the system has to be encapsulated properly to ensure longevity and biocompatibility.
At the time of writing, no commercially available product was available to provide artificial vision. However, several major research groups are working toward developing such a therapeutic device. Simple prototypes have been tested successfully in acute and chronic animal trials and more recently in small‐scale human trials. Psychophysical studies show that, despite the limited functionality of these prototypes, the recipients can successfully execute some simple visually guided tasks.
Optimization of physico‐mechanical properties of silica‐filled NR/SBR compounds
Authors: Salimi D. , Khorasani S. Nouri , Abadchi M. Rezaei , Veshare S. Jahanbani 
Published: January 2010

AbstractIn this extended study, the effect of silica reinforcement on natural rubber (NR) and NR/styrene–butadiene rubber (SBR) compounds was studied. The silica surfaces were treated with bis(3‐triethoxysilylpropyl)‐tetrasulfide, which is a silane‐coupling agent, to chemically bond the silica to the rubber. Optimum levels of silane were determined according to the silica loading in NR compounds. Results in NR/SBR compounded with optimum levels of silane show that the cure time decreases with increasing NR content. Also, the tensile properties of the NR/SBR blends decrease with increasing SBR content. This study further confirmed that filler materials affect the physical and mechanical properties of these blends. © 2010 Wiley Periodicals, Inc. Adv Polym Techn 28:224–232, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/adv.20169
CFD simulations of hydrodynamic/thermal coupling phenomena in a bubble column with internals
Authors: Laborde‐Boutet Cédric , Larachi Faiçal , Dromard Nicolas , Delsart Olivier , Béliard Pierre‐Emmanuel , Schweich Daniel 
Published: January 2010

AbstractCFD simulations have been carried out in a full three‐dimensional, unsteady, Eulerian framework to simulate hydrodynamic/thermal coupling in a bubble column with internals. A first part of the study, dedicated to the hydrodynamic/thermal coupling in liquid single‐phase flows, showed that assuming constant wall temperature on the internals constitutes a reasonable approximation in lieu of comprehensive simulations encompassing shell flow and coolant flow together. A second part dealing with the hydrodynamics of gas–liquid flows in a bubble column with internals showed that a RNG k–ε turbulence model formulation accounting for gas‐induced turbulence was a relevant choice. The last part used these conclusions to build a hydrodynamic/thermal coupling model of a gas–liquid flow in a bubble column with internals. With a per‐phase RNG k–ε turbulence model and assuming constant wall temperature, it was possible to simulate heat transfer phenomena consistent with experimentally measured heat transfer coefficients. © 2010 American Institute of Chemical Engineers AIChE J, 2010
Laser heating of moving solid: Influence of workpiece speed on melt size
Authors: Shuja Shahzade Z. , Yilbas Bekir S. , Momin Omeir 
Published: January 2010

AbstractLaser heating of a moving solid is considered and phase change in the irradiated region is modeled. Three‐dimensional heating situation is considered in the analysis and phase change is modeled using the enthalpy‐porosity technique. Temperature field and melt zone are predicted for different workpiece velocities. The predictions are compared with the experimental results. It is found that the maximum temperature in the irradiated region and the size of heat affected zone increase significantly at low workpiece speeds. The prediction of melt depth agrees well with the experimental results. © 2010 American Institute of Chemical Engineers AIChE J, 2010
Brief communication: Transportation and trauma: Dog‐sledding and vertebral compression in Alaskan Eskimos
Authors: Legge Scott S. 
Published: January 2010

AbstractVertebral compression, as evidenced by compression of the centrum, was observed within two Native Alaskan skeletal samples. Information was collected from 1,071 and 656 vertebrae from Golovin Bay and Nunivak Island, Alaska, respectively. In addition, patterns of compression related vertebral change in each collection were characterized by sex and location within the vertebral column. The overall frequencies of vertebral compression were 3.6% (n = 721) at Golovin Bay and 1.7% (n = 403) at Nunivak Island for all observable thoracic and lumbar vertebrae (T1–L5). There was no statistically significant difference in the occurrence of compression among adults between these two collections. When examining the thoracic and lumbar vertebral segments by sex, females at Golovin Bay (4.5%; n = 442) exhibited a significantly higher frequency of vertebral compression than females at Nunivak (1.0%; n = 203). However, this difference in occurrence of compression could be accounted for by the age distributions of the two samples. No difference was noted between the males of the two collections. Compression frequencies in both samples are discussed in relation to the modes of transportation historically utilized by each community. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.
Host intrinsic determinants and potential consequences of parasite infection in free‐ranging red‐fronted lemurs (Eulemur fulvus rufus)
Authors: Clough Dagmar , Heistermann Michael , Kappeler Peter M. 
Published: January 2010

AbstractParasites and infectious diseases represent ecological forces shaping animal social evolution. Although empirical studies supporting this link abound in various vertebrate orders, both the study of the dynamics and impact of parasite infections and infectious diseases in strepsirrhine primates have received little empirical attention. We conducted a longitudinal parasitological study on four groups of wild red‐fronted lemurs (Eulemur fulvus rufus) at Kirindy Forest, Madagascar, during two field seasons in consecutive years to investigate i) the degree of gastrointestinal parasite infection on population and individual levels and ii) factors potentially determining individual infection risk. Using a comprehensive dataset with multiple individually assignable parasite samples as well as information on age, sex, group size, social rank, and endocrine status (fecal androgen and glucocorticoid), we examined parasite infection patterns and host traits that may affect individual infection risk. In addition, we examined whether parasite infection affects mating and reproductive success. Our results indicated high variability in parasite infection on individual and population levels. Time of year and group size was important determinants of variability in parasite infection. Variation in hormone levels was also associated with parasite species richness and parasite infection intensity. Differences in parasite infection between years indicate a potential immune‐enhancing function of steroid hormones on nematode infections, which has not been reported before from other vertebrates studied under natural conditions. Male mating and reproductive success were not correlated to any measure of parasite infection, which suggests a nonfunctional role of the parasites we examined in primate sexual selection. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.
Chitosan modified MMT‐poly(AMPS) nanocomposite hydrogel: Heating effect on swelling and rheological behavior
Authors: Kabiri K. , Mirzadeh H. , Zohuriaan‐Mehr M. J. 
Published: January 2010

AbstractVulnerability of hydrogels against thermal circumstances may be substantially eliminated via incorporating nanoclay to prepare nanocomposite hydrogels. In this research, chitosan‐intercalated montmorillonite (ChitoMMT) was used as a bionanoclay to yield novel nanocomposite hydrogels based on 2‐acrylamido‐2‐methylpropanesulfonic acid. The bionanoclay is suitable especially for preparing biomaterials used in biomedical, food, and pharmaceutical applications, unlike conventional commercial nanoclays (alkyl ammonium‐intercalated MMT) which are not appropriate for bio‐applications due to toxicity of the intercalant particularly where the clay content is high. Two different crosslinkers (i.e., methylene bisacrylamide, and polyethyleneglycol dimethacrylate) were employed to synthesize the nanocomposites. The variations in swelling, rheological and thermal properties of the hydrogels were essentially attributed to thermally induced crosslink cleavage/formation depending upon the crosslinker nature. The nanocomposites comprised superior thermal properties in comparison with the clay‐free hydrogel counterpart. They can preserve substantially their swelling ability for longer heating periods. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Influence of polyfunctional monomer on melt strength and rheology of long‐chain branched polypropylene by reactive extrusion
Authors: Su Feng‐Hua , Huang Han‐Xiong 
Published: January 2010

AbstractLong chain branching (LCB) were added to linear polypropylene (PP) using reactive extrusion in the presence of selected polyfunctional monomers (PFMs) and a peroxide of dibenzoyl peroxide (BPO). Fourier Transformed Infrared spectra (FTIR) directly confirmed the grafting reaction occurred during the reactive extrusion process. Various rheological plots including viscosity curve, storage modulus, Cole‐Cole plot, and Van‐Gurp plots, confirmed that the LCB structure were introduced into modified PPs skeleton after modification. In comparison with linear PP, the branched samples exhibited higher melt strength, lower melt flow index, and the enhancement of crystallization temperature. The LCB level in modified PPs and their melt strength were affected by the type of PFM used and could be controlled by the PFM properties and structure. PFMs with lower boiling points, such as 1, 4‐butanediol diacrylate (BDDA), could not produce LCB structure in modified PP skeleton. The shorter molecular chain bifunctional monomers, such as 1,6‐hexanediol diacrylate (HDDA), favored the branching reaction if their boiling points were above the highest extrusion temperature. And some polar groups, such as hydroxyl, in the molecule of PFM were harmful to the branching reaction, which might be attributed to the harm of the polarity of groups to the dispersion of PFM in PP matrix. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010