bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitric Oxide Bioavailability in the Microcirculation: Insights from Mathematical Models
Authors: TSOUKIAS NIKOLAOS M. 
Published: July 2008

ABSTRACTOver the last 30 years nitric oxide (NO) has emerged as a key signaling molecule involved in a number of physiological functions, including in the regulation of microcirculatory tone. Despite significant scientific contributions, fundamental questions about NO's role in the microcirculation remain unanswered. Mathematical modeling can assist in investigations of microcirculatory NO physiology and address experimental limitations in quantifying vascular NO concentrations. The number of mathematical models investigating the fate of NO in the vasculature has increased over the last few years, and new models are continuously emerging, incorporating an increasing level of complexity and detail. Models investigate mechanisms that affect NO availability in health and disease. They examine the significance of NO release from nonendothelial sources, the effect of transient release, and the complex interaction of NO with other substances, such as heme‐containing proteins and reactive oxygen species. Models are utilized to test and generate hypotheses for the mechanisms that regulate NO‐dependent signaling in the microcirculation.
Chemokine Signaling to Lymphocyte Integrins Under Shear Flow
Authors: ALON RONEN , FEIGELSON SARA W. 
Published: July 2008

ABSTRACTThe arrest of lymphocytes at target vascular sites depends on the rapid activation of their integrins by specialized endothelial chemokines. For over a decade, the mechanisms by which these chemokines trigger initial integrin‐mediated adhesiveness and subsequent adhesion strengthening and crawling over endothelial surfaces have been dissected in vitro using flow chamber setups. These studies revealed that lymph node chemokines and subsets of inflammatory chemokines, collectively termed “arrest chemokines,” can trigger the fastest measurable inside‐out integrin activation events. Recent studies indicate that shear forces applied on lymphocytes are instrumental in these rapid activation processes. Different GTPases have been implicated in these activation processes. As these enzymes contribute to successive integrin activation and redistribution processes in both early and prolonged contacts there is a growing need to dissect in vitro and validate in vivo specific signaling routes involved in early and late integrin activation events controlling lymphocyte arrest and their subsequent crawling to sites of diapedesis. In this article, we present an overview of both early and recent shear‐flow studies of integrin activation in lymphocytes and discuss future perspectives of integrin activation research in vitro and in vivo.
The Cochlear Pericytes
Authors: SHI XIAORUI , HAN WEIJIU , YAMAMOTO HIROSHI , TANG WENXUE , LIN XI , XIU RUIJUAN , TRUNE DENNIS R. , NUTTALL ALFRED L. 
Published: July 2008

ABSTRACTObjectives: Cochlear pericytes are not well characterized. The aim of this study was to further advance the characterization of cochlear pericyte location and distribution, with particular focus on pericyte‐related proteins on the capillaries of the cochlear lateral wall that are functionally integral to structure, contraction, and gap junction transport. Materials and Methods: Cochlear pericytes were identified by the immunofluorescence labeling of pericyte marker proteins, including alpha–smooth muscle actin (α‐SMA), desmin, Thy‐1, tropomyosin, and NG2, and by morphological identification, using fluorescence, electron, and differential interference contrast microscopy. Results: Pericytes were predominately found in the capillary network of the cochlear lateral wall, with considerable morphological heterogeneity across different types of microvessels. For example, pericytes on the vessels of the spiral ligament (V/SL) strongly expressed a gap junction protein, connexin 40, and were positive for α‐SMA, tropomyosin, and desmin. In contrast, pericytes on the vessels of the stria vascularis (V/SV) were positive for desmin, and were negative for α‐SMA and tropomyosin. Conclusions: The capillary networks of the cochlear lateral wall comprise a rich population of pericytes. These pericytes are morphologically heterogeneous, with protein expression potentially indicative of function.
Systems Biology of Vascular Endothelial Growth Factors
Authors: GABHANN FEILIM MAC , POPEL ALEKSANDER S. 
Published: July 2008

ABSTRACTSeveral cytokine families have roles in the development, maintenance, and remodeling of the microcirculation. Of these, the vascular endothelial growth factor (VEGF) family is one of the best studied and one of the most complex. Five VEGF ligand genes and five cell‐surface receptor genes are known in the human, and each of these may be transcribed as multiple splice isoforms to generate an extensive family of proteins, many of which are subject to further proteolytic processing. Using the VEGF family as an example, we describe the current knowledge of growth‐factor expression, processing, and transport in vivo. Experimental studies and computational simulations are being used to measure and predict the activity of these molecules, and we describe avenues of research that seek to fill the remaining gaps in our understanding of VEGF family behavior.
BioMAJ: a flexible framework for databanks synchronization and processing
Authors: Filangi Olivier , Beausse Yoann , Assi Anthony , Legrand Ludovic , Larré Jean-Marc , Martin Véronique , Collin Olivier , Caron Christophe , Leroy Hugues , Allouche David 
Published: July 2008

Abstract
Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks.
Availability: http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license.
Contact: biomaj@genouest.org
Back to the future: using landscape ecology to understand changing patterns of land use in Canada, and its effects on the sustainability of coastal ecosystems
Authors: Mercer Clarke Colleen S. L. , Roff John C. , Bard Shannon M. 
Published: July 2008

Abstract
Mercer Clarke, C. S. L., Roff, J. C., and Bard, S. M. 2008. Back to the future: using landscape ecology to understand changing patterns of land use in Canada, and its effects on the sustainability of coastal ecosystems. – ICES Journal of Marine Science, 65: 1534–1539. In Canada, concerns are mounting that the coastal environments may be more affected by human activities than is evidenced by current monitoring and assessment of environmental quality. Holistically orientated approaches to coastal management have concluded that indicators of coastal sustainability must include a wider array of factors that go beyond marine ecosystem health to include the health and well-being of coastal terrestrial environments and human communities. Research is needed to bridge the disciplinary and jurisdictional barriers that hamper better understanding of the relationships between terrestrial and marine ecosystems, and to help recognize the role of humans as both a contributing and an affected species in the coastal ecotone. Our examination of past and current knowledge of conditions along the Atlantic shore of Nova Scotia led us to challenge the predominant view that all is well along Canadian coasts. Using an interdisciplinary approach derived from landscape ecology, we examined international, national, and local efforts to assess management indicators against factors that gauge their relevance to marine- and land-development planning and management. We propose a new context for indicators, one that challenges scientists to provide decision-makers with information that can be used to drive social change, avoiding or mitigating human activities and sustaining coastal ecosystems.
Pollution fingerprints in eels as models for the chemical status of rivers
Authors: Belpaire C. , Goemans G. , Geeraerts C. , Quataert P. , Parmentier K. 
Published: July 2008

Abstract
Belpaire, C., Goemans, G., Geeraerts, C., Quataert, P., and Parmentier, K. 2008. Pollution fingerprints in eels as models for the chemical status of rivers. – ICES Journal of Marine Science, 65: 1483–1491. The 2006 EU Water Framework Directive (WFD) proposed the monitoring of a selection of priority substances in the aquatic phase, including lipophilic substances. However, there are strong arguments for measuring lipophilic substances in biota. Yellow eel is a good candidate because it is widespread, sedentary, and accumulates many lipophilic substances in its muscle tissue. Several authors have described the indicative value of measured concentrations, yet few studies have investigated to what extent the spectrum of contaminants present characterizes the local environmental pollution pressure. To evaluate the value of the pollution profile of an eel as a fingerprint of the chemical status of the local environment, two datasets were selected from the Flemish Eel Pollutant Network database. The pollution profiles in individual eels along a river (even at distances <5 km) proved to be significantly different. Analysis of pooled contaminant data from multiple sites and sampling years within rivers allows characterization of river-specific chemical pressures. These results highlight the usefulness of eels as bio-indicators for monitoring pollution with lipophilic chemicals, such as polychlorinated biphenyls and organochlorine pesticides, in rivers. As such, eels may be used effectively within the monitoring programme for a selection of priority substances referred to in the WFD.
First Report of Powdery Mildew of Chickpea (Cicer arietinum) Caused by Leveillula taurica in Washington State
Authors: Attanayake K. P. R. N. , Glawe D. A. , McPhee K. E. , Dugan F. M. , Chen W. 
Published: July 2008

In Oct. 2007, powdery mildew was found in chickpea fields in an experimental farm near Pullman, Whitman County, Washington. Although disease signs were observed on all chickpea cultivars in the fields, high incidence was seen only on cvs. Dwelley and Spanish White. To our knowledge this is the first record of powdery mildew caused by Leveillula taurica on chickpea in WA. The pathogen has also been reported from chickpea in California and elsewhere, e.g., Ethiopia, India, Iran, Morocco, Pakistan, Sudan, Turkey, and the former USSR. Accepted for publication 4 May 2008. Published 2 July 2008.
Identification ofPlasmodium falciparumRhopH3 protein peptides that specifically bind to erythrocytes and inhibit merozoite invasion
Authors: Pinzón Carlos Giovanni , Curtidor Hernando , Reyes Claudia , Méndez David , Patarroyo Manuel Elkin 
Published: July 2008

AbstractThe identification of sequences involved in binding to erythrocytes is an important step for understanding the molecular basis of merozoite–erythrocyte interactions that take place during invasion of thePlasmodium falciparummalaria parasite into host cells. Several molecules located in the apical organelles (micronemes, rhoptry, dense granules) of the invasive‐stage parasite are essential for erythrocyte recognition, invasion, and establishment of the nascent parasitophorous vacuole. Particularly, it has been demonstrated that rhoptry proteins play an important role in binding to erythrocyte surface receptors, among which is thePfRhopH3 protein, which triggers important immune responses in patients from endemic regions. It has also been reported that anti‐RhopH3 antibodies inhibit in vitro invasion of erythrocytes, further supporting its direct involvement in erythrocyte invasion processes. In this study,PfRhopH3 consecutive peptides were synthesized and tested in erythrocyte binding assays for identifying those regions mediating binding to erythrocytes. FourteenPfRhopH3 peptides presenting high specific binding activity were found, whose bindings were saturable and presented nanomolar dissociation constants. These high‐activity binding peptides (HABPs) were characterized by having α‐helical structural elements, as determined by circular dichroism, and having receptors of a possible sialic acid‐dependent and/or glycoprotein‐dependent nature, as evidenced in enzyme‐treated erythrocyte binding assays and further corroborated by cross‐linking assay results. Furthermore, these HABPs inhibited merozoite in vitro invasion of normal erythrocytes at 200 μM by up to 60% and 90%, suggesting that some RhopH3 protein regions are involved in theP. falciparumerythrocyte invasion.
Structural basis for the activation of FGFR by NCAM
Authors: Kochoyan Arthur , Poulsen Flemming M. , Berezin Vladimir , Bock Elisabeth , Kiselyov Vladislav V. 
Published: July 2008

AbstractThe fibroblast growth factor receptor (FGFR) can be activated through direct interaction with the neural cell adhesion molecule (NCAM). The extracellular part of the FGFR consists of three immunoglobulin‐like (Ig) modules, and that of the NCAM consists of five Ig and two fibronectin type III (F3) modules. NCAM–FGFR interactions are mediated by the third FGFR Ig module and the second NCAM F3 module. Using surface plasmon resonance and nuclear magnetic resonance analyses, the present study demonstrates that the second Ig module of FGFR also is involved in binding to the NCAM. The second Ig module residues involved in binding were identified and shown to be localized on the “opposite sides” of the module, indicating that when NCAMs are clustered (e.g., due to homophilic binding), high‐affinity FGFR binding sites may be formed by the neighboring NCAMs.
Efficient production of membrane‐integrated and detergent‐soluble G protein‐coupled receptors inEscherichia coli
Authors: Link A. James , Skretas Georgios , Strauch Eva‐Maria , Chari Nandini S. , Georgiou George 
Published: July 2008

AbstractG protein‐coupled receptors (GPCRs) are notoriously difficult to express, particularly in microbial systems. Using GPCR fusions with the green fluorescent protein (GFP), we conducted studies to identify bacterial host effector genes that result in a general and significant enhancement in the amount of membrane‐integrated human GPCRs that can be produced inEscherichia coli. We show that coexpression of the membrane‐bound AAA+ protease FtsH greatly enhances the expression yield of four different class I GPCRs, irrespective of the presence of GFP. Using this new expression system, we produced 0.5 and 2 mg/L of detergent‐solubilized and purified full‐length central cannabinoid receptor (CB1) and bradykinin receptor 2 (BR2) in shake flask cultures, respectively, two proteins that had previously eluded expression in microbial systems.
Fatty acid synthesis and generation of glycerol-3-phosphate in brown adipose tissue from rats fed a cafeteria diet
Authors: Chaves Valéria E. , Frasson Danúbia , Martins-Santos Maria E.S. , Navegantes Luiz C.C. , Galban Victor D. , Garófalo Maria A.R. , Kettelhut Isis C. , Migliorini Renato H. 
Published: July 2008

In vivo fatty acid synthesis and the pathways of glycerol-3-phosphate (G3P) production were investigated in brown adipose tissue (BAT) from rats fed a cafeteria diet for 3 weeks. In spite of BAT activation, the diet promoted an increase in the carcass fatty acid content. Plasma insulin levels were markedly increased in cafeteria diet-fed rats. Two insulin-sensitive processes, in vivo fatty acid synthesis and in vivo glucose uptake (which was used to evaluate G3P generation via glycolysis) were increased in BAT from rats fed the cafeteria diet. Direct glycerol phosphorylation, evaluated by glycerokinase (GyK) activity and incorporation of [U-14C]glycerol into triacylglycerol (TAG)–glycerol, was also markedly increased in BAT from these rats. In contrast, the cafeteria diet induced a marked reduction of BAT glyceroneogenesis, evaluated by phosphoenolpyruvate carboxykinase-C activity and incorporation of [1-14C]pyruvate into TAG–glycerol. BAT denervation resulted in an approximately 50% reduction of GyK activity, but did not significantly affect BAT in vivo fatty acid synthesis, in vivo glucose uptake, or glyceroneogenesis. The data suggest that the supply of G3P for BAT TAG synthesis can be adjusted independently from the sympathetic nervous system and solely by reciprocal changes in the generation of G3P via glycolysis and via glyceroneogenesis, with no participation of direct phosphorylation of glycerol by GyK.
Pravastatin increases the expression of the tissue inhibitor of matrix metalloproteinase-1 and the oncogeneBaxin human aortic abdominal aneurysms
Authors: Mateos-Cáceres Petra J. , López-Farré Antonio J. , Morata Pilar C. , Ramos-Mozo Priscila , Macaya Carlos , Serrano Francisco J. , Moñux Guillermo 
Published: July 2008

The effect of pravastatin on matrix metalloproteinase-9 (MMP-9) and the level of tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2 was studied in explants of human abdominal aortic aneurysm (AAA) obtained from 13 patients. The effect of pravastatin on the apoptotic status of human AAA explants was also examined. Total MMP-9 content did not differ in human AAA explants incubated in vitro in the presence or absence of pravastatin (10−6mol/L) for 48 h. TIMP-1 levels were significantly increased in pravastatin-incubated AAA explants, but TIMP-2 production was not modified by pravastatin. Western blot experiments showed that, whereas Bax expression was increased in pravastatin-incubated AAA explants, the expression of Bcl-2 was not modified. On the other hand, the ratio of the expression of Bax to Bcl-2, an apoptotic index, was not modified by pravastatin. In the human AAA explants, the increase in Bax expression, but not the increase in TIMP-1 expression elicited by pravastatin, was reversed by l-mevalonate, a downstream HMG-CoA reductase metabolite, suggesting that the expression of Bax and TIMP-1 followed HMG-CoA reductase-dependent and -independent pathways, respectively. In conclusion, pravastatin increases both TIMP-1 and Bax expression in human AAA explants without changes in either MMP-9 activity or the apoptotic status.
Cache-oblivious databases
Authors: He Bingsheng , Luo Qiong 
Published: July 2008

Cache-oblivious techniques, proposed in the theory community, have optimal asymptotic bounds on the amount of data transferred between any two adjacent levels of an arbitrary memory hierarchy. Moreover, this optimal performance is achieved without any hardware platform specific tuning. These properties are highly attractive to autonomous databases, especially because the hardware architectures are becoming increasingly complex and diverse.
In this article, we present our design, implementation, and evaluation of the first cache-oblivious in-memory query processor, EaseDB. Moreover, we discuss the inherent limitations of the cache-oblivious approach as well as the opportunities given by the upcoming hardware architectures. Specifically, a cache-oblivious technique usually requires sophisticated algorithm design to achieve a comparable performance to its cache-conscious counterpart. Nevertheless, this development-time effort is compensated by the automaticity of performance achievement and the reduced ownership cost. Furthermore, this automaticity enables cache-oblivious techniques to outperform their cache-conscious counterparts in multi-threading processors.
Quasi-inverses of schema mappings
Authors: Fagin Ronald , Kolaitis Phokion G. , Popa Lucian , Tan Wang-Chiew 
Published: July 2008

Schema mappings are high-level specifications that describe the relationship between two database schemas. Two operators on schema mappings, namely the composition operator and the inverse operator, are regarded as especially important. Progress on the study of the inverse operator was not made until very recently, as even finding the exact semantics of this operator turned out to be a fairly delicate task. Furthermore, this notion is rather restrictive, since it is rare that a schema mapping possesses an inverse.
In this article, we introduce and study the notion of a quasi-inverse of a schema mapping. This notion is a principled relaxation of the notion of an inverse of a schema mapping; intuitively, it is obtained from the notion of an inverse by not differentiating between instances that are equivalent for data-exchange purposes. For schema mappings specified by source-to-target tuple-generating dependencies (s-t tgds), we give a necessary and sufficient combinatorial condition for the existence of a quasi-inverse, and then use this condition to obtain both positive and negative results about the existence of quasi-inverses. In particular, we show that every LAV (local-as-view) schema mapping has a quasi-inverse, but that there are schema mappings specified by full s-t tgds that have no quasi-inverse. After this, we study the language needed to express quasi-inverses of schema mappings specified by s-t tgds, and we obtain a complete characterization. We also characterize the language needed to express inverses of schema mappings, and thereby solve a problem left open in the earlier study of the inverse operator. Finally, we show that quasi-inverses can be used in many cases to recover the data that was exported by the original schema mapping when performing data exchange.
Bound analysis of closed queueing networks with workload burstiness
Authors: Casale Giuliano , Mi Ningfang , Smirni Evgenia 
Published: July 2008

Burstiness and temporal dependence in service processes are often found in multi-tier architectures and storage devices and must be captured accurately in capacity planning models as these features are responsible of significant performance degradations. However, existing models and approximations for networks of first-come first-served (FCFS) queues with general independent (GI) service are unable to predict performance of systems with temporal dependence in workloads.
To overcome this difficulty, we define and study a class of closed queueing networks where service times are represented by Markovian Arrival Processes (MAPs), a class of point processes that can model general distributions, but also temporal dependent features such as burstiness in service times. We call these models MAP queueing networks. We introduce provable upper and lower bounds for arbitrary performance indexes (e.g., throughput, response time, utilization) that we call Linear Reduction (LR) bounds. Numerical experiments indicate that LR bounds achieve a mean accuracy error of 2 percent.
The result promotes LR bounds as a versatile and reliable bounding methodology of the performance of modern computer systems.