bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome analysis of adipocyte lipid rafts reveals that gC1qR plays essential roles in adipogenesis and insulin signal transduction
Authors: Kim Ki‐Bum , Kim Bong‐Woo , Choo Hyo‐Jung , Kwon Young‐Chan , Ahn Byung‐Yoon , Choi Jong‐Soon , Lee Jae‐Seon , Ko Young‐Gyu 
Published: April 2009

AbstractSince insulin receptors and their downstream signaling molecules are organized in lipid rafts, proteomic analysis of adipocyte lipid rafts may provide new insights into the function of lipid rafts in adipogenesis and insulin signaling. To search for proteins involved in adipocyte differentiation and insulin signaling, we analyzed detergent‐resistant lipid raft proteins from 3T3‐L1 preadipocytes and adipocytes by 2‐DE. Eleven raft proteins were identified from adipocytes. One of the adipocyte‐specific proteins was globular C1q receptor (gC1qR), an acidic 32 kDa protein known as the receptor for the globular domain of complement C1q. The targeting of gC1qR into lipid rafts was significantly increased during adipogenesis, as determined by immunoblotting and immunofluorescence. Since the silencing of gC1qR by small RNA interference abolished adipogenesis and blocked insulin‐induced activation of insulin receptor, insulin receptor substrate‐1 (IRS‐1), Akt, and Erk1/2, we can conclude that gC1qR is an essential molecule involved in adipogenesis and insulin signaling.
Mistic: Cellular localization, solution behavior, polymerization, and fibril formation
Authors: Dvir Hay , Lundberg Matthew E. , Maji Samir K. , Riek Roland , Choe Senyon 
Published: April 2009

AbstractMistic represents a family of unique membrane‐associating proteins originally found in Bacillus subtilis (M110). As a fusion partner, it has been shown to assist overexpression of foreign integral membrane proteins in E. coli. We have expressed shorter Mistic homologs from other Bacillus species and surprisingly, unlike M110, found them abundant in the cytoplasm. These Mistic homologs including the corresponding shorter sequence (amino acids 27 through 110 of M110) exist as multimeric assemblies in solution in the absence of detergent. Crystals of Mistic from B. leicheniformis (M2) diffracted to 3.2 Å resolution, indicating that it exists as a multimer in the crystalline state as well. Moreover, we show that although M2 is mostly α‐helical, it tends to polymerize and form fibrils. Such oligomerization could potentially mask the charged surface of the monomeric Mistic to assist membrane integration.
Charge neutralization and collapse of the C‐terminal tail of alpha‐synuclein at low pH
Authors: McClendon Sebastian , Rospigliosi Carla C. , Eliezer David 
Published: April 2009

AbstractAlpha‐synuclein (αS) is the primary component of Lewy bodies, the pathological hallmark of Parkinson's Disease. Aggregation of αS is thought to proceed from a primarily disordered state with nascent secondary structure through intermediate conformations to oligomeric forms and finally to mature amyloid fibrils. Low pH conditions lead to conformational changes associated with increased αS fibril formation. Here we characterize these structural and dynamic changes using solution state NMR measurements of secondary chemical shifts, relaxation parameters, residual dipolar couplings, and paramagnetic relaxation enhancement. We find that the neutralization of negatively charged side‐chains eliminates electrostatic repulsion in the C‐terminal tail of αS and leads to a collapse of this region at low pH. Hydrophobic contacts between the compact C‐terminal tail and the NAC (non‐amyloid‐β component) region are maintained and may lead to the formation of a globular domain. Transient long‐range contacts between the C‐terminus of the protein and regions N‐terminal to the NAC region are also preserved. Thus, the release of long‐range contacts does not play a role in the increased aggregation of αS at low pH, which we instead attribute to the increased hydrophobicity of the protein.
Vector supersymmetry from OSp(3,2|2): Casimir operators
Authors: Casalbuoni R. , Elmetti F. , Gomis J. , Kamimura K. , Tamassia L. , Van Proeyen A. 
Published: April 2009

AbstractIn this paper we briefly review the main results obtained in [1], where some algebraic properties of the ‘vector supersymmetry’ (VSUSY) algebra have been studied. VSUSY is a graded extension of the Poincaré algebra in 4 dimensions with two central charges. We derive all independent Casimir operators of VSUSY and we find two distinct spin–related operators in the case of nonvanishing central charges. One is the analogue of superspin for VSUSY and the other is a new spin, called C–spin, whose value is fixed to 1/2. We also show that the VSUSY algebra and its Casimir operators can be derived by an Inönü‐Wigner contraction from OSp(3,2 |2). This paper is based on the talk given in Varna, Bulgaria, during the 4‐th EU RTN Workshop 2008.
Massive type IIA supergravity and E10
Authors: Henneaux M. , Jamsin E. , Kleinschmidt A. , Persson D. 
Published: April 2009

AbstractIn this talk we investigate the symmetry under E10 of Romans' massive type IIA supergravity. We show that the dynamics of a spinning particle in a non‐linear sigma model on the coset space E10/K(E10) reproduces the bosonic and fermionic dynamics of massive IIA supergravity, in the standard truncation. In particular, we identify Romans' mass with a generator of E10 that is beyond the realm of the generators of E10 considered in the eleven‐dimensional analysis, but using the same, underformed sigma model. As a consequence, this work provides a dynamical unification of the massless and massive versions of type IIA supergravitiy inside E10.
Spinning strings in AdS4 × CP3 and quantum corrections
Authors: Alday L.F. , Arutyunov G. , Bykov D. 
Published: April 2009

AbstractWe derive the one‐loop correction to the space‐time energy of a folded string in AdS4 × CP3 carrying spin S in AdS4 and angular momentum J in CP3 in the long string approximation. From this general result in the limit J log S we obtain the one‐loop correction to the cusp anomalous dimension which turns out to be –(5 log 2)/(2π). This value appears to be in conflict with the prediction from the recently conjectured all‐loop Bethe ansatz.
Targeting the conformational transitions of MDM2 and MDMX: Insights into key residues affecting p53 recognition
Authors: Carotti Andrea , Macchiarulo Antonio , Giacchè Nicola , Pellicciari Roberto 
Published: April 2009

AbstractThe oncogenic proteins MDM2 and MDMX have distinct and critical roles in the control of the activity of the p53 tumor suppressor protein. Recently, we have used spatial coarse graining simulations to analyze the conformational transitions manifest in the p53 recognition of MDM2 and MDMX. These conformational movements are different between MDM2 and MDMX and unveil the presence of conserved and nonconserved interactions in the p53 binding cleft that may be exploited in the design of selective and dual modulators of the oncogenic proteins. In this study, we investigate the conformational profiles of apo‐ and p53‐bound states of MDM2 and MDMX using molecular dynamic simulations along a time scale of 60 ns. The analysis of the trajectories is instrumental to discuss energetical and conformational aspects of p53 recognition and to point out specific key residues whose conformational shifts have crucial roles in affecting the apo‐ and p53‐bound states of MDM2 and MDMX. Among these, in particular, linear discriminant analyses identify diverse conformations of Y99/Y100 (MDMX/MDM2) as markers of the apo‐ and p53‐bound states of the oncogenic proteins. The results of this study shed further light on different p53 recognition in MDM2 and MDMX and may prove useful for the design and identification of new potent and selective synthetic modulators of p53‐MDM2/MDMX interactions. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Variability of the Northern Hemisphere polar stratospheric cloud potential: the role of North Pacific disturbances
Authors: Orsolini Yvan J. , Karpechko Alexey Yu. , Nikulin Grigory 
Published: April 2009

AbstractThe potential of the Arctic stratosphere to sustain the formation of Polar Stratospheric Clouds (PSCs) is a key factor in determining the amount of ozone destroyed each winter, and is often measured as a ‘PSC volume’. The latter quantity has been shown to closely follow a near‐linear compact relationship with winter‐averaged column ozone loss, and displays a high variability from monthly to decadal time‐scales. We examine the connection between meteorological conditions in the troposphere and the variability of lower polar stratospheric temperatures over the last four decades, and specifically, conditions leading to a high PSC volume. In addition to the well‐established connection between the North Atlantic Oscillation (NAO) and the polar vortex, we demonstrate the large influence of precursory disturbances over the North Pacific and the Far East, the region of maximum climatological upward wave activity flux. Namely, very high monthly PSC volume (in the top 12%) predominantly follows the development of positive tropospheric height anomalies over the Far East, which lead to a weakening of the background planetary wave trough, and lessened upward wave activity flux into the stratosphere. Precursory anomalies over the Far East are reminiscent of East Asian monsoon amplification episodes. Copyright © 2009 Royal Meteorological Society
Buoyancy reversal in cloud‐top mixing layers
Authors: Mellado Juan Pedro , Stevens Bjorn , Schmidt Heiko , Peters Norbert 
Published: April 2009

AbstractA theoretical and numerical small‐scale study of the evaporative cooling phenomenon that might appear in the stratocumulus‐topped boundary layers is presented. An ideal configuration of a cloud‐top mixing layer is considered as defined by two non‐turbulent horizontal layers, stably stratified and with buoyancy reversal within a certain range of mixture fractions due to the evaporative cooling. Linear stability analysis of the shear‐free configuration is employed to provide a new interpretation of the buoyancy reversal parameter, namely in terms of a time‐scale ratio between the stable and the unstable modes of the system. An incompressible high‐order numerical algorithm to perform direct numerical simulation of the configuration is described and two‐dimensional simulations of single‐mode perturbations are presented. These simulations confirm the role of the different parameters identified in the linear stability analysis and show that convoluted flow patterns can be generated by the evaporative cooling even for the low levels of buoyancy reversal found in stratocumulus clouds. They also show that there is no enhancement of turbulent entrainment of upper‐layer fluid in the shear‐free configuration, and turbulent mixing enhancement by the evaporative cooling is restricted to the lower layer. Copyright © 2009 Royal Meteorological Society
Consensus QSAR Modeling of Phosphor‐Containing Chiral AChE Inhibitors
Authors: Kuz'min Victor E. , Muratov Eugene N. , Artemenko Anatoly G. , Varlamova Ekaterina V. , Gorb Leonid , Wang Jing , Leszczynski Jerzy 
Published: April 2009

AbstractIn this article the Hierarchical QSAR technology (HiT QSAR) has been used for consensus QSAR modeling of Acetylcholinesterase (AChE) inhibition by various organophosphate compounds. Simplex representation of molecular structure (SiRMS) and Lattice model (LM) QSAR approaches have been used for descriptors' generation. Statistical models have been obtained by partial least squares (PLS) method. Various chiral organophosphates represented by their (R)‐ and (S)‐isomers, racemic mixtures and achiral structures have been investigated. Successful consensus model (R2=0.978) based on fourteen best QSAR models obtained using different QSAR approaches and training sets for several levels and methods of molecular structure representation (2.5D, double 2.5D, and 3D) has been used for the prediction of AChE inhibition of new compounds. In order to avoid chance correlations 1000 rounds of Y‐scrambling were performed for each selected model. Leverage and ellipsoid Applicability domain (DA) approaches have been used for additional estimation of the quality of prognosis. Molecular fragments enhancing and interfering with inhibitory activity have been determined. It was revealed that atom's individuality and stereochemistry of chiral surroundings of the asymmetric atom of phosphorus play a vital role in AChE inhibition. Thus, (R)‐isomers are always less active than the (S) isomers and the racemate. HiT QSAR proves to be a powerful tool for investigation of activity of stereo selective interactions and can be used in such subsequent studies.
3D‐QSAR Study of Pyridine Derivates as IKK‐2 Inhibitors
Authors: Sala Esther , Guasch Laura , Vaqué Montserrat , Mateo‐Sanz Josep Maria , Blay Mayte , Bladé Cinta , Garcia‐Vallvé Santiago , Pujadas Gerard 
Published: April 2009

AbstractIkB kinase β (IKK‐2) is a serine‐threonine protein kinase that is critically involved in activating the transcription factor NF‐κβ in response to various inflammatory stimuli (hence, the interest in synthesizing molecules that can inhibit IKK‐2). Some pyridine derivates have been shown to be among the most potent IKK‐2 inhibitors known at present. This study reports how pyridine derivates have been used to develop a 3D‐QSAR model for rationalizing results from previous structure‐activity relationship studies on IKK‐2 inhibition by these molecules; and predicting the IC50 of other pyridine‐derivate IKK‐2 inhibitors whose activity is unknown. Therefore, 3D‐QSAR models were built with PHASE and a training set of 21 molecules with IC50 values that span five orders of magnitude (ranging from 0.004 to more than 20 μM) and in which each order of magnitude had from two to seven molecules. The resulting models were validated with a test set made up of 16 molecules of known IC50. Only 3 out of 1245 3D‐QSAR models had statistical parameter values in the following ranges: a) R2, Q2 and r‐Pearson value≥0.8000; b) RMSE/SD in the [0.90–1.05] interval; c) Q2/R2≈1; and d) P<0.05 (statistical significance). Moreover, a second test set (consisting of 63 molecules whose activity has been reported in the form of the IC50 interval to which it belongs) was used for selecting which of the three remaining 3D‐QSAR models makes the best predictions. The best 3D‐QSAR model obtained is associated with a pharmacophore that contains all the characteristics that previous structural‐activity studies have reported to be essential if IKK‐2 is to be inhibited by these ligands. Therefore, it is concluded that this 3D‐QSAR model can be used to reliably predict how other pyridine derivates inhibit IKK‐2.
Pharmacophore Model of Cruzain Inhibitors
Authors: Malvezzi Alberto , de Rezende Leandro , Amaral Antonia T.‐do 
Published: April 2009

AbstractChagas disease, caused by the protozoan Trypanosoma cruzi, is one of the most serious amongst the so‐called neglected diseases in Latin America, specially in Brazil. So far there has been no effective treatment for the chronic phase of this disease. Cruzain is a major cysteine protease of T. cruzi and it is recognized as a valid target for Chagas disease chemotherapy. The mechanism of cruzain action is associated with the nucleophilic attack of an activated sulfur atom towards electrophilic groups. In this report, features of a putative pharmacophore model of the enzyme, developed as a virtual screening tool for the selection of potential cruzain inhibitors, are described. The final proposed model was applied to the ZINC v.7 database and afterwards experimentally validated by an enzymatic inhibition assay. One of the compounds selected by the model showed cruzain inhibition in the low micromolar range.
Score test for age at onset genetic linkage analysis in selected sibling pairs
Authors: Callegaro A. , van Houwelingen H. C. , Houwing‐Duistermaat J. J. 
Published: April 2009

AbstractA new score statistic is derived, which uses information from registries (age‐specific incidences) and family studies (sib–sib marginal correlation) to weight affected sibling pairs according to their age at onset. Age at onset of sibling pairs is modelled by a gamma frailty model. From this model we derive a bivariate survival function, which depends on the marginal survival and on the marginal correlation. The score statistic for linkage is a classical nonparametric linkage (NPL) statistic where the identical by descent sharing is weighted by a particular function of the age at onset data. Since the statistic is based on survival models, it can also be applied to discordant and healthy sibling pairs. Simulation studies show that the proposed method is robust and more powerful than standard NPL methods. As illustration we apply the new score statistic to data from a breast cancer study. Copyright © 2009 John Wiley & Sons, Ltd.
Interobserver repeatability of three‐ and four‐dimensional transperineal ultrasound assessment of pelvic floor muscle anatomy and function
Authors: Majida M. , Brækken I. H. , Umek W. , Bø K. , Šaltytė Benth J. , Ellstrøm Engh M. 
Published: April 2009

AbstractObjectiveTo evaluate the interobserver repeatability of measurement of the pubovisceral muscle and levator hiatus, and the position of related organs, during rest, muscle contraction and Valsalva maneuver using three‐ and four‐dimensional (3D and 4D) transperineal ultrasound.MethodsSeventeen women were included in the study. The position and dimensions of the pubovisceral muscle and levator hiatus in patients at rest and during contraction and Valsalva were determined from stored 3D and 4D ultrasound volumes. Analyses were conducted offline by two observers blinded to the clinical data and to each others' measurements.ResultsMeasurements of levator hiatal dimensions at rest demonstrated intraclass correlation coefficient (ICC) values of 0.92 to 0.96. The ICC values for pubovisceral muscle thickness at rest varied between good and very good (ICC, 0.61–0.93), regardless of plane. During contraction, the ICC values for all measured parameters were very good, varying between 0.61 and 0.92. Measurement of the transverse diameter of the levator hiatus during the Valsalva maneuver showed good reliability (ICC, 0.86), but assessment of the anterior and posterior borders of the levator hiatus was only possible in 29% of cases.Conclusions3D and 4D transperineal ultrasound measurement of the pubovisceral muscle and levator hiatus is reliable in women with no or minor symptoms of prolapse at rest and during contraction. The technique for recording during the Valsalva maneuver requires improvement if it is to be useful in the diagnosis of pelvic organ prolapse. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Analysis and comparison of scheduling techniques for a BWA OFDMA mobile system
Authors: Tarchi Daniele , Fantacci Romano , Bonciani Emanuele 
Published: April 2009

AbstractIn the last few years the wireless metropolitan area networks (WMANs) have increased their popularity and attracted the interest of important research groups all over the world; as a consequence, several standards have been proposed. Among them, the IEEE 802.16 (WiMAX) is one of the most promising standard to carry out a full‐service broadband wireless network in an urban and suburban area. This standard provides high data rate within a wide coverage area with low implementation costs, possibility of multi‐traffic communications, and different network topologies. This paper deals with the analysis and performance comparison of different scheduling techniques for WiMAX networks for allowing quality of service (QoS) differentiation when different types of applications have to be supported and achieving a fair distribution of resource among users. In particular, the focus here is on the resource allocation problem for the case of mobile stations (MSs) active in an urban environment. The proposed scheduling algorithms exploit the orthogonal frequency division multiple access (OFDMA) scheme with adaptive modulation techniques in order to achieve a better network behavior. The performance of the proposed approaches will be derived here by means of theoretical analysis and computer simulations. Copyright © 2009 John Wiley & Sons, Ltd.
Adenosine‐to‐inosine RNA editing
Authors: Zinshteyn Boris , Nishikura Kazuko 
Published: April 2009

AbstractRibonucleic acid (RNA) editing is a mechanism that generates RNA and protein diversity, which is not directly encoded in the genome. The most common type of RNA editing in vertebrates is the conversion of adenosine to inosine in double‐stranded RNA which occurs in the higher eukaryotes. This editing is carried out by the family of adenosine deaminase acting on RNA (ADAR) proteins. The most‐studied substrates of ADAR proteins undergo editing which is very consistent, highly conserved, and functionally important. However, editing causes changes in protein‐coding regions only at a small proportion of all editing sites. The vast majority of editing sites are in noncoding sequences. This includes microRNAs, as well as the introns and 3′ untranslated regions of messenger RNAs, which play important roles in the RNA‐mediated regulation of gene expression. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Biological Mechanisms > Regulatory Biology
Laboratory Methods and Technologies > RNA Methods
Chronic lung diseases
Authors: Wu Wei , Kaminski Naftali 
Published: April 2009

AbstractChronic lung diseases often have high morbidity and mortality rate and have posed a serious threat to human health. The incidence of many chronic lung diseases such as asthma has been on the rise in the past decade, which causes serious economic burden. Despite many efforts which employed traditional experimental approaches to elucidate the mechanisms of the diseases have been made, little is known about the pathogenesis of complex lung diseases. Systems biology approaches which aim to integrate and analyze information gathered from multiple sources offer a great opportunity to examine complex human diseases from a new angle. Many attempts have been made using high‐throughput technologies such as microarrays to study chronic lung diseases; although compared with the full‐fledged systems biology approach, research strategies employed in most of these investigations still have much room to improve, promising findings have already emerged from these efforts, which demonstrates the potential of implementing systems biology in pulmonary biomedical research. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Physiology > Mammalian Physiology in Health and Disease
Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology
Authors: Ben‐Tabou de‐Leon Smadar , Davidson Eric H. 
Published: April 2009

AbstractGene regulatory networks (GRNs) for development underlie cell fate specification and differentiation. Network topology, logic, and dynamics can be obtained by thorough experimental analysis. Our understanding of the GRN controlling endomesoderm specification in the sea urchin embryo has attained an advanced level such that it explains developmental phenomenology. Here we review how the network explains the mechanisms utilized in development to control the formation of dynamic expression patterns of transcription factors and signaling molecules. The network represents the genomic program controlling timely activation of specification and differentiation genes in the correct embryonic lineages. It can also be used to study evolution of body plans. We demonstrate how comparing the sea urchin GRN to that of the sea star and to that of later developmental stages in the sea urchin, reveals mechanisms underlying the origin of evolutionary novelty. The experimentally based GRN for endomesoderm specification in the sea urchin embryo provides unique insights into the system level properties of cell fate specification and its evolution. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Physiology > Physiology of Model Organisms