bluuebunny/crossref_metadata_2025_split huggingface dataset:
Roles for netrin signaling outside of axon guidance: A view from the worm
Authors: Ziel Joshua W. , Sherwood David R. 
Published: January 2010

AbstractThe Netrin family of extracellular ligands and their receptors were the first identified signaling pathway regulating axon guidance. Subsequent work across model systems has begun to reveal the interactions that take place downstream of Netrin reception to facilitate growth cone migration. Though intensely studied, many aspects of this signaling system remain unclear. Even less understood are the growing number of contexts in which Netrin signaling influences cells beyond axon guidance and even outside the nervous system. Genetic and cell‐biological studies in C. elegans have played an instrumental role in identifying critical functions for Netrin ligands in setting up specialized and potentially adhesive membrane‐associated domains within a broad range of cell types. Here we review recent literature implicating Netrin or its receptors in morphogenetic processes outside of growth cone regulation with a special focus on studies in C. elegans that suggest cell biological mechanisms for Netrin signaling. Developmental Dynamics 239:1296–1305, 2010. © 2010 Wiley‐Liss, Inc.
Movers and shakers or anchored: Caenorhabditis elegans nuclei achieve it with KASH/SUN
Authors: Zhou Kang , Hanna‐Rose Wendy 
Published: January 2010

AbstractThe invariant cell division patterns that characterize Caenorhabditis elegans development make it an ideal system to study the mechanisms that control nuclear movement and positioning. Forward genetic screens in this system allowed identification of the key molecular machinery for connecting the nucleus to the cytoskeleton; pairs of protein partners, consisting of a KASH domain protein and a SUN domain protein, bridge the nuclear envelope to connect the nucleus to cytoskeletal components. The C. elegans genome encodes several KASH/SUN pairs, and mutant phenotypes as well as tissue‐specific expression patterns suggest a diversity of functions. These functions include moving the nucleus but have been extended to effects on the chromosomes inside the nucleus as well. We review the impact of the C. elegans system in pioneering this field as well as the functions of these KASH/SUN protein pairs across spatial and temporal C. elegans development. Developmental Dynamics 239:1352–1364, 2010. © 2010 Wiley‐Liss, Inc.
C. elegans as a model organism to investigate molecular pathways involved with Parkinson's disease
Authors: Harrington Adam J. , Hamamichi Shusei , Caldwell Guy A. , Caldwell Kim A. 
Published: January 2010

AbstractParkinson's disease (PD) is an age‐related movement disorder resulting, in part, from selective loss of dopaminergic neurons. Both invertebrate and mammalian models have been developed to study the cellular mechanisms altered during disease progression; nevertheless there are limitations within each model. Mammalian models remain invaluable in studying PD, but are expensive and time consuming. Here, we review genetic and environmental factors associated with PD, and describe how the nematode roundworm, Caenorhabditis elegans, has been used as a model organism for studying various aspects of this neurodegenerative disease. Both genetic and chemical screens have been conducted in C. elegans to identify molecular pathways, proteins, and small molecules that can impact PD pathology. Lastly, we highlight future areas of investigation, in the context of emerging fields in biology, where the nematode can be exploited to provide mechanistic insights and potential strategies to accelerate the path toward possible therapeutic intervention for PD. Developmental Dynamics 239:1282–1295, 2010. © 2010 Wiley‐Liss, Inc.
Diphenoxido‐Bridged CoII and ZnII Complexes of Tripodal N2O2 Ligands: Stabilisation of MII‐Coordinated Phenoxyl Radical Species
Authors: Mukherjee Atasi , Lloret Francesc , Mukherjee Rabindranath 
Published: January 2010

AbstractThree new tripodal ligands with an N2O2 donor set, namely2‐tert‐butyl‐6‐({(2‐hydroxybenzyl)[2‐(2‐pyridyl)ethyl]amino}methyl)‐4‐methylphenol (H2L1), 2‐tert‐butyl‐6‐({(2‐hydroxybenzyl)[2‐(2‐pyridyl)ethyl]amino}methyl)‐4‐methoxyphenol (H2L2) and 2‐tert‐butyl‐6‐({[2‐(dimethylamino)ethyl](2‐hydroxybenzyl)amino}methyl)‐4‐methoxyphenol (H2L3) have been synthesised. Treatment of the ligands with Co(CH3CO2)2·4H2O or [Zn(H2O)6][ClO4]2 in the presence of Et3N provides the corresponding CoII and ZnII complexes of composition [MII2(L1)2] [M = Co (1) (single‐crystals are a solvate with the composition [CoII2(L1)2]·2CHCl3, i.e. 1·2CHCl3); M = Zn (2)], [MII2(L2)2] [M = Co (3); Zn (4)] and [CoII2(L3)2] (5). Crystallographic analyses reveal that the complexes have closely similar diphenoxido‐bridged structures. Each metal centre assumes MIIN2O3 coordination. The geometry around each metal ion in 1·2CHCl3 (τ = 0.76), 2 (τ = 0.77), 3 (τ = 0.74), 4 (τ = 0.76) and 5 [one CoII (τ = 0.49) and the other CoII (τ = 0.63)] is intermediate between ideal square‐pyramidal (τ = 0) and trigonal‐bipyramidal (τ = 1). Temperature‐dependent magnetic studies reveal weak intramolecular antiferromagnetic exchange couplings for all the three CoII complexes(–J = 1.84, 1.32 and 5.70 cm–1 for 1, 3 and 5, respectively). Spectroscopic properties of the complexes have also been investigated. Cyclic voltammetric (CV) measurements of 1 and 2 show an irreversible oxidative response at Epa (anodic peak potential) in the range 0.60–0.75 V relative to the SCE (saturated calomel electrode), whereas two successive quasi‐reversible oxidative responses can be observed for 3–5 at E1/2 values in the range 0.40–0.53 V relative to the SCE. Oxidative responses are due to the formation of MII‐coordinated phenoxyl radical species. The metal‐coordinated phenoxyl radical species, generated by two‐electron coulometric oxidation of 3–5, were characterised by CV and by adsorption and EPR spectroscopy. The stability of such species was determined by measuring the decay constant (absorption spectroscopy), which reveals that the phenoxyl radical species of 5 is more stable than that of 3 and 4. EPR spectroscopic studies (120 K) of coulometrically generated two‐electron oxidised species of 4 in CH2Cl2 (containing 0.1 M TBAP) at 298 K reveal a combination of an isotropic S = ${1 \over 2}$ signal at g = 2 [(phenolato)(phenoxyl radical)‐coordinated dizinc(II) complex] and a spin‐triplet resonance (S = 1) that gives rise to the symmetric split‐line pattern [bis(phenoxyl radical)‐cordinated dizinc(II) complex]. To pinpoint the site of oxidation (metal‐ or ligand‐centred) in each case, DFT calculations were performed at the B3LYP level of theory.
Bioconjugates of 1′‐Aminoferrocene‐1‐carboxylic Acid with (S)‐3‐Amino‐2‐methylpropanoic Acid and L‐Alanine
Authors: Semenčić Mojca Čakić , Heinze Katja , Förster Christoph , Rapić Vladimir 
Published: January 2010

AbstractFormal CH2 insertion in bioconjugates composed of 1′‐aminoferrocene‐1‐carboxylic acid (Fca) and alanine Boc‐Ala‐Fca‐Ala‐OCH3 gives Fca bioconjugates with the β‐amino acid (S)‐3‐amino‐2‐methylpropanoic acid (Aib). The novel homologous conjugates of ferrocene were fully characterized by spectroscopic and analytical methods. NMR, CD and IR spectroscopy in concert with DFT calculations suggest that the formal “L‐Ala–to–(S)‐β‐Aib mutations” can exert ferrocene helix inversion due to the different stereogenic carbon atoms of L‐Ala and (S)‐β‐Aib. Furthermore, the mutation (de‐)stabilizes the conserved secondary structure with two intramolecular hydrogen bonds, depending on the “mutation site”. The systematic work presented provides a firm basis for understanding the factors that determine folding in bioconjugates of ferrocene and β‐amino acids and will guide the rational design of metallocene peptidomimetics incorporating β‐amino acids.
Digital quantification of gene expression using emulsion PCR
Authors: Shi Xiaolong , Tang Chao , Wang Wei , Zhou Dequan , Lu Zuhong 
Published: January 2010

AbstractHere we describe a single‐molecule quantitative assay of mRNA levels based on mRNA mediate‐ligation and BEAMing (beads, emulsion, amplification, and magnetics) technique, which allows accurate and parallel measurement of multiple genes from a small amount of cells. In this method, a pair of oligos complementary target mRNA was used to probe transcripts for each gene of interest. The ligated products of oligos pair were clonally amplified on beads in millions of parallel compartmentalized droplets in a water‐in‐oil emulsion. The levels of each transcript within a sample were measured by counting the number of the correspondingly amplified beads which were immobilized on a glass surface. To demonstrate its utility, this method has been applied to the quantitation of the mRNA levels for two transcription factors, Klf4 and Sox5, and a housekeeping gene, Gapdh, in human leukemia K562 cells before and after induction with phorbol 12‐myristate 13‐acetate. Interestingly, we found a significant downregulation of the mRNA level of Sox5 after phorbol 12‐myristate 13‐acetate treatment. The mRNA mediate‐ligation and BEAMing technique provides an accurate and sensitive way to quantify the amount of multiple specific mRNA in a very small number of cells, which may be valuable in the studies requiring precise and parallel quantization of multiple mRNA in the defined cell populations.
Preparative divergent flow IEF without carrier ampholytes for separation of complex biological samples
Authors: Stastna Miroslava , Slais Karel 
Published: January 2010

AbstractEfficient separation method is a crucial part of the process in which components of highly complex biological sample are identified and characterized. Based on the principles of recently newly established electrophoretic method called divergent flow IEF (DF IEF), we have tested the DF IEF instrument which is able to operate without the use of background carrier ampholytes. We have verified that during separation and focusing of sample consisting of high numbers of proteins (yeast lysate and wheat flour extract), the pH gradient of preparative DF IEF can be created by autofocusing of the sample components themselves without any addition of carrier ampholytes. In DF IEF, the proteins are separated, desalted and concentrated in one step. The fractions of yeast lysate sample, collected at the DF IEF output and subjected to gel IEF, contained the zones of proteins gradually covering the pI values from 3.7 to 8.5. In our experimental arrangement, the highest number of proteins has been found in fractions with pI values around 5.3 as detected by polyacrylamide gel IEF with CBB staining. During DF IEF, the selected protein bands have been concentrated up to 16.8‐fold.
SDS‐PAGE and two‐dimensional maps in a radial gel format
Authors: Millioni Renato , Miuzzo Manuela , Antonioli Paolo , Sbrignadello Stefano , Iori Elisabetta , Dosselli Ryan , Puricelli Lucia , Kolbe Markus , Tessari Paolo , Righetti Pier Giorgio 
Published: January 2010

AbstractA novel method for performing 2‐D map analysis is here reported, consisting in a modification of the second dimension run, which is performed not in a conventional square‐ or rectangular‐size gel, but in a radial surface. This has the advantage of permitting resolution of closely adjacent bands, representing strings of isoforms of similar or identical mass but of closely spaced isoelectric points. When used in a mono‐dimensional, SDS‐PAGE format, this system allows the simultaneous running of 62 sample tracks. Examples are given of separation of plasma and urinary proteins.
ACE applied to the quantitative characterization of benzo‐18‐crown‐6‐ether binding with alkali metal ions in a methanol–water solvent system
Authors: Ehala Sille , Makrlík Emanuel , Toman Petr , Kašička Václav 
Published: January 2010

AbstractACE was applied to the quantitative evaluation of noncovalent binding interactions between benzo‐18‐crown‐6‐ether (B18C6) and several alkali metal ions, Li+, Na+, K+, Rb+ and Cs+, in a mixed binary solvent system, methanol–water (50/50 v/v). The apparent binding (stability) constants (Kb) of B18C6–alkali metal ion complexes in the hydro‐organic medium above were determined from the dependence of the effective electrophoretic mobility of B18C6 on the concentration of alkali metal ions in the BGE using a nonlinear regression analysis. Before regression analysis, the mobilities measured by ACE at ambient temperature and variable ionic strength of the BGE were corrected by a new procedure to the reference temperature, 25°C, and the constant ionic strength, 10 mM. In the 50% v/v methanol–water solvent system, like in pure methanol, B18C6 formed the strongest complex with potassium ion (log Kb=2.89±0.17), the weakest complex with cesium ion (log Kb=2.04±0.20), and no complexation was observed between B18C6 and the lithium ion. In the mixed methanol–water solvent system, the binding constants of the complexes above were found to be about two orders lower than in methanol and about one order higher than in water.
Uniform hazard versus uniform risk bases for performance‐based earthquake engineering of light‐frame wood construction
Authors: Li Yue , Yin Yuejun , Ellingwood Bruce R. , Bulleit William M. 
Published: January 2010

AbstractThis paper investigates the implications of designing for uniform hazard versus uniform risk for light‐frame wood residential construction subjected to earthquakes in the United States. Using simple structural models of one‐story residences with typical lateral force‐resisting systems (shear walls) found in buildings in western, eastern and central regions of the United States as illustrations, the seismic demands are determined using nonlinear dynamic time‐history analyses, whereas the collapse capacities are determined using incremental dynamic analyses. The probabilities of collapse, conditioned on the occurrence of the maximum considered earthquakes and design earthquakes stipulated in ASCE Standard 7‐05, and the collapse margins of these typical residential structures are compared for typical construction practices in different regions in the United States. The calculated collapse inter‐story drifts are compared with the limits stipulated in FEMA 356/ASCE Standard 41‐06 and observed in the recent experimental testing. The results of this study provide insights into residential building risk assessment and the relation between building seismic performance implied by the current earthquake‐resistant design and construction practices and performance levels in performance‐based engineering of light‐frame wood construction being considered by the SEI/ASCE committee on reliability‐based design of wood structures. Further code developments are necessary to achieve the goal of uniform risk in earthquake‐resistant residential construction. Copyright © 2010 John Wiley & Sons, Ltd.
Dynamic interactions of life and its landscape: feedbacks at the interface of geomorphology and ecology
Authors: Reinhardt Liam , Jerolmack Douglas , Cardinale Brad J. , Vanacker Veerle , Wright Justin 
Published: January 2010

AbstractThere appears to be no single axis of causality between life and its landscape, but rather, each exerts a simultaneous influence on the other over a wide range of temporal and spatial scales. These influences occur through feedbacks of differing strength and importance with co‐evolution representing the tightest coupling between biological and geomorphological systems. The ongoing failure to incorporate these dynamic bio‐physical interactions with human activity in landscape studies limits our ability to predict the response of landscapes to human disturbance and climate change. This limitation is a direct result of the poor communication between the ecological and geomorphological communities and consequent paucity of interdisciplinary research. Recognition of this failure led to the organization of the Meeting of Young Researchers in Earth Science (MYRES) III, titled ‘Dynamic Interactions of Life and its Landscape’. This paper synthesizes and expands upon key issues and findings from that meeting, to help chart a course for future collaboration among Earth surface scientists and ecologists: it represents the consensus view of a competitively selected group of 77 early‐career researchers. Two broad themes that serve to focus and motivate future research are identified: (1) co‐evolution of landforms and biological communities; and (2) humans as modifiers of the landscape (through direct and indirect actions). Also outlined are the state of the art in analytical, experimental and modelling techniques in ecological and geomorphological research, and novel new research avenues that combine these techniques are suggested. It is hoped that this paper will serve as an interdisciplinary reference for geomorphologists and ecologists looking to learn more about the other field. Copyright © 2010 John Wiley & Sons, Ltd.
Reduced functional coupling in the default‐mode network during self‐referential processing
Authors: van Buuren Mariët , Gladwin Thomas E. , Zandbelt Bram B. , Kahn René S. , Vink Matthijs 
Published: January 2010

AbstractActivity within the default‐mode network (DMN) is thought to be related to self‐referential processing, such as thinking about one's preferences or personality traits. Although the DMN is generally considered to function as a network, evidence is starting to accumulate that suggests that areas of the DMN are each specialized for different subfunctions of self‐referential processing. Here, we address the issue of functional specialization by investigating changes in coupling between areas of the DMN during self‐referential processing. To this aim, brain activity was assessed during a task in which subjects had to indicate whether a trait adjective described their own personality (self‐referential, Self condition), that of another person (other‐referential, Other condition), or whether the trait was socially desirable (nonreferential, Control condition). To exclude confounding effects of cardiorespiratory processes on activity and functional coupling, we corrected the fMRI signal for these effects. Activity within areas of the DMN was found to be modulated by self‐referential processing. More specifically, during the Self condition compared to the Other and Control condition, activity within the dorsal medial prefrontal cortex, ventral medial prefrontal cortex, and posterior cingulate cortex was increased. Moreover, coupling between areas of the DMN was reduced during the Self condition compared to the Other and Control condition, while coupling between regions of the DMN and regions outside the network was increased. As such, these results provide an indication for functional specialization within the DMN and support the notion that each area of the DMN is involved in different subfunctions of self‐referential processing. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.
Atlas‐based segmentation of developing tissues in the human brain with quantitative validation in young fetuses
Authors: Habas Piotr A. , Kim Kio , Rousseau Francois , Glenn Orit A. , Barkovich A. James , Studholme Colin 
Published: January 2010

AbstractImaging of the human fetus using magnetic resonance (MR) is an essential tool for quantitative studies of normal as well as abnormal brain development in utero. However, because of fundamental differences in tissue types, tissue properties and tissue distribution between the fetal and adult brain, automated tissue segmentation techniques developed for adult brain anatomy are unsuitable for this data. In this paper, we describe methodology for automatic atlas‐based segmentation of individual tissue types in motion‐corrected 3D volumes reconstructed from clinical MR scans of the fetal brain. To generate anatomically correct automatic segmentations, we create a set of accurate manual delineations and build an in utero 3D statistical atlas of tissue distribution incorporating developing gray and white matter as well as transient tissue types such as the germinal matrix. The probabilistic atlas is associated with an unbiased average shape and intensity template for registration of new subject images to the space of the atlas. Quantitative whole brain 3D validation of tissue labeling performed on a set of 14 fetal MR scans (20.57–22.86 weeks gestational age) demonstrates that this atlas‐based EM segmentation approach achieves consistently high DSC performance for the main tissue types in the fetal brain. This work indicates that reliable measures of brain development can be automatically derived from clinical MR imaging and opens up possibility of further 3D volumetric and morphometric studies with multiple fetal subjects. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.
Neural representation of abstract and concrete concepts: A meta‐analysis of neuroimaging studies
Authors: Wang Jing , Conder Julie A. , Blitzer David N. , Shinkareva Svetlana V. 
Published: January 2010

AbstractA number of studies have investigated differences in neural correlates of abstract and concrete concepts with disagreement across results. A quantitative, coordinate‐based meta‐analysis combined data from 303 participants across 19 functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) studies to identify the differences in neural representation of abstract and concrete concepts. Studies that reported peak activations in standard space in contrast of abstract > concrete or concrete > abstract concepts at a whole brain level in healthy adults were included in this meta‐analysis. Multilevel kernel density analysis (MKDA) was performed to identify the proportion of activated contrasts weighted by sample size and analysis type (fixed or random effects). Meta‐analysis results indicated consistent and meaningful differences in neural representation for abstract and concrete concepts. Abstract concepts elicit greater activity in the inferior frontal gyrus and middle temporal gyrus compared to concrete concepts, while concrete concepts elicit greater activity in the posterior cingulate, precuneus, fusiform gyrus, and parahippocampal gyrus compared to abstract concepts. These results suggest greater engagement of the verbal system for processing of abstract concepts and greater engagement of the perceptual system for processing of concrete concepts, likely via mental imagery. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.