bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nephrin—signature molecule of the glomerular podocyte?
Authors: Welsh Gavin I , Saleem Moin A 
Published: October 2009

AbstractIn recent years there has been an explosion of interest in the glomerular podocyte, which plays a central role in control of glomerular filtration. A host of new molecules have been identified as playing essential roles in the maintenance of podocyte integrity in both humans and mouse models. Of all of these, arguably the most pivotal is nephrin, a transmembrane receptor molecule located at the specialized podocyte cell–cell junction, termed the slit diaphragm. Mutations in this gene cause the most severe form of congenital nephrotic syndrome, and many interacting proteins have now been described to form a large multiprotein complex with complex dynamics. There is little evidence of functional nephrin expression outside the glomerulus, and there are accumulating data that nephrin is essential for the unique properties of podocyte biology. Utilizing a powerful human cell culture model, comparing wild‐type with nephrin‐null podocytes, we can show that several crucial functional properties of podocytes depend on nephrin, including insulin responsiveness and cytoskeletal reorganization. Thus, it is reasoned that nephrin is a signature molecule required to define distinct podocyte characteristics. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The prolyl isomerase domain of PpiD fromEscherichia colishows a parvulin fold but is devoid of catalytic activity
Authors: Weininger Ulrich , Jakob Roman P. , Kovermann Michael , Balbach Jochen , Schmid Franz X. 
Published: October 2009

AbstractPpiD is a periplasmic folding helper protein ofEscherichia coli. It consists of an N‐terminal helix that anchors PpiD in the inner membrane near the SecYEG translocon, followed by three periplasmic domains. The second domain (residues 264–357) shows homology to parvulin‐like prolyl isomerases. This domain is a well folded, stable protein and follows a simple two‐state folding mechanism. In its solution structure, as determined by NMR spectroscopy, it resembles most closely the first parvulin domain of the SurA protein, which resides in the periplasm ofE. colias well. A previously reported prolyl isomerase activity of PpiD could not be reproduced when using improved protease‐free peptide assays or assays with refolding proteins as substrates. The parvulin domain of PpiD interacts, however, with a proline‐containing tetrapeptide, and the binding site, as identified by NMR resonance shift analysis, colocalized with the catalytic sites of other parvulins. In its structure, the parvulin domain of PpiD resembles most closely the inactive first parvulin domain of SurA, which is part of the chaperone unit of this protein and presumably involved in substrate recognition.
Enhanced red‐emitting railroad worm luciferase for bioassays and bioimaging
Authors: Li Xueyan , Nakajima Yoshihiro , Niwa Kazuki , Viviani Vadim R. , Ohmiya Yoshihiro 
Published: October 2009

AbstractA luciferase from the railroad worm (Phrixothrix hirtus) is the only red‐emitting bioluminescent enzyme in nature that is advantageous in multicolor luciferase assays and in bioluminescence imaging (BLI). However, it is not used widely in scientific or industrial applications because of its low activity and stability. By using site‐directed mutagenesis, we produced red‐emitting mutants with higher activity and better stability. Compared with the wild‐type (WT), the luminescent activities from extracts of cultured mammalian cells expressing mutant luciferase were 9.8‐fold in I212L/N351K, 8.4‐fold in I212L, and 7.8‐fold in I212L/S463R; and the cell‐based activities were 3.6‐fold in I212L/N351K and 3.4‐fold in N351K. The remaining activities after incubation at 37°C for 10 min were 50.0% for I212L/S463R, 31.8% for I212L, and 23.0% for I212L/N351K, but only 5.2% for WT. To demonstrate an application of I212L/N351K, cell‐based BLI was performed, and the luminescence signal was 3.6‐fold higher than in WT. These results indicate that the mutants might improve the practicability of this signaling in bioassays and BLI.
Surviving sin papeles in post‐Katrina New Orleans: an exploration of the challenges facing undocumented Latino immigrants in new and re‐emerging Latino destinations
Authors: Drever Anita I. , Blue Sarah A. 
Published: October 2009

AbstractThe literature on Latino migration to new and re‐emerging destinations has emphasised the advantages of settling outside gateway cities, especially with regard to employment and affordable housing, but less attention has been given to the challenges faced by Latinos in these areas of recent settlement, particularly by those who do not have legal permission to reside in the US. By examining the situation confronting undocumented Latino migrants in post‐Katrina New Orleans, we provide insight into some of their difficulties. Using data from a quantitative/qualitative survey of post‐Katrina Latino migrants conducted by the authors, this paper highlights the obstacles undocumented immigrants face in new and re‐emerging Latino destinations because of their limited access to (a) US financial institutions, (b) a social and economic safety net, and (c) public transportation or a driver's license. It argues further that these issues pose challenges not only for recent undocumented Latinos arrivals themselves, but for the wider communities in which they are living as well. Copyright © 2009 John Wiley & Sons, Ltd.
Worst‐case control policies for (terminal) linear–quadratic control problems under disturbances
Authors: Kostina E. , Kostyukova O. 
Published: October 2009

AbstractWe consider linear control systems under uncertainties. For such systems we solve the problem of constructing worst‐case feedback control policies that are allowed to be corrected at m fixed intermediate time moments. We propose two types of the approximative control policies. All of them guarantee that for all admissible uncertainties the terminal system state lies in a prescribed neighborhood of a given state x* at a given final moment, and the value of the cost function does not exceed a given estimate. It is shown that computation of the estimate for each policy is equivalent to solving a corresponding convex mathematical programming (MP) problem with m decision variables. Based on the solution of the MP problem, we derive simple explicit rules (which can be easily implemented on‐line) for constructing the corresponding control policy in the original control problem. Copyright © 2009 John Wiley & Sons, Ltd.
Constructions of sparse uniform hypergraphs with high chromatic number
Authors: Kostochka A.V. , Rödl V. 
Published: October 2009

AbstractA random construction gives new examples of simple hypergraphs with high chromatic number that have few edges and/or low maximum degree. In particular, for every integers k ≥ 2, r ≥ 2, and g ≥ 3, there exist r‐uniform non‐k‐colorable hypergraphs of girth at least g with maximum degree at most ⌈r kr‐1 lnk⌉. This is only 4r2 lnk times greater than the lower bound by Erdős and Lovász (Colloquia Math Soc János Bolyai 10 (1973), 609–627) that holds for all hypergraphs (without restrictions on girth). © 2009 Wiley Periodicals, Inc. Random Struct. Alg., 2010
Offline thresholds for Ramsey‐type games on random graphs
Authors: Krivelevich Michael , Spöhel Reto , Steger Angelika 
Published: October 2009

AbstractIn this article, we compare the offline versions of three Ramsey‐type one‐player games that have been studied in an online setting in previous work: the online Ramsey game, the balanced online Ramsey game, and the Achlioptas game. The goal in all games is to color the edges of the random graph Gn,m according to certain rules without creating a monochromatic copy of some fixed forbidden graph H. Although in general, the three online games have different thresholds, we prove that for most graphs H, the offline threshold for all three problems is m0(n) = n, where m2(H) ≔ maxH′⊆H(eH′ − 1)/(vH′ − 2). © 2009 Wiley Periodicals, Inc. Random Struct. Alg., 2010
Family sense‐making practices in science center conversations
Authors: Zimmerman Heather Toomey , Reeve Suzanne , Bell Philip 
Published: October 2009

AbstractIn this paper, we examine the interactional ways that families make meaning from biological exhibits during a visit to an interactive science center. To understand the museum visits from the perspectives of the families, we use ethnographic and discourse analytic methods, including pre‐ and postvisit interviews, videotaped observations of the museum visits, and coding and analysis of utterances from naturally occurring conversations. We employ an Everyday Expertise framework to understand how families use ideas and materials to make meaning from the scientific content presented in exhibits. We argue that individual and cognitive aspects of learning are fundamentally connected to the social and cultural aspects of learning; therefore, we analyze the intertwining role of individual cognitive resources, situated activities, and cultural toolkit resources that support learning interactions and processes. Findings indicate how families use a variety of knowledge types (epistemic resources) to make sense of exhibit content, how they make sense of biological content by transferring cultural epistemic resources from prior experiences, and how families use two types of scientific epistemic resources—biological facts and perceptual descriptions—as the primary means to make sense of biological exhibits. © 2009 Wiley Periodicals, Inc.Sci Ed94:478–505, 2010
Nanotechnology in the design of soft tissue scaffolds: innovations in structure and function
Authors: Ayres Chantal E. , Jha B. Shekhar , Sell Scott A. , Bowlin Gary L. , Simpson David G. 
Published: October 2009

AbstractEngineered scaffolds function to supplement or replace injured, missing, or compromised tissue or organs. The current direction in this research area is to create scaffolds that mimic the structure and function of the native extracellular matrix (ECM). It is believed that the fabrication of a scaffold that has both structural integrity and allows for normal cellular function and interaction will bring scaffolds closer to clinical relevance. Nanotechnology innovations have aided in the development of techniques for the production of nanofiber scaffolds. The three major processing techniques, self‐assembly, phase separation, and electrospinning, produce fibers that rival the size of those found in the native ECM. However, the simplicity, versatility, and scalability of electrospinning make it an attractive processing method that can be used to reproduce aspects of the complexity that characterizes the native ECM. Novel electrospinning strategies include alterations of scaffold composition and architecture, along with the addition and encapsulation of cells, pharmaceuticals and growth factors within the scaffold. This article reviews the major nanofiber fabrication technologies as well as delves into recent significant contributions to the conception of a meaningful and practical electrospun scaffold. WIREs Nanomed Nanobiotechnol 2010 2 20–34This article is categorized under:

Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement
Probing dynamic fluorescence properties of single and clustered quantum dots toward quantitative biomedical imaging of cells
Authors: Kang Hyeong‐Gon , Tokumasu Fuyuki , Clarke Matthew , Zhou Zhenping , Tang Jianyong , Nguyen Tinh , Hwang Jeeseong 
Published: October 2009

AbstractWe present results on the dynamic fluorescence properties of bioconjugated nanocrystals or quantum dots (QDs) in different chemical and physical environments. A variety of QD samples was prepared and compared: isolated individual QDs, QD aggregates, and QDs conjugated to other nanoscale materials, such as single‐wall carbon nanotubes (SWCNTs) and human erythrocyte plasma membrane proteins. We discuss plausible scenarios to explain the results obtained for the fluorescence characteristics of QDs in these samples, especially for the excitation time‐dependent fluorescence emission from clustered QDs. We also qualitatively demonstrate enhanced fluorescence emission signals from clustered QDs and deduce that the band 3 membrane proteins in erythrocytes are clustered. This approach is promising for the development of QD‐based quantitative molecular imaging techniques for biomedical studies involving biomolecule clustering. WIREs Nanomed Nanobiotechnol 2010 2 48–58This article is categorized under:

Diagnostic Tools > In Vitro Nanoparticle-Based Sensing
Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
Modeling breast biomechanics for multi‐modal image analysis—successes and challenges
Authors: Rajagopal Vijay , Nielsen Poul M. F. , Nash Martyn P. 
Published: October 2009

AbstractBiomechanical modeling of the breast is a burgeoning research field that has potential uses across a wide range of healthcare applications. This review describes recent developments regarding multi‐modal breast image analysis, and outlines some of the key challenges that researchers face in introducing the models into the clinical arena. Deformable breast models have demonstrated capabilities across a wide range of breast cancer diagnoses and treatments. Specific applications include magnetic resonance (MR) image guided surgery, registration of x‐ray and MR images, and breast reduction/augmentation surgery planning. Challenges lie in improving the fidelity of these models, which are presently simplistic and use many unverified parameters. Specific challenges include characterization of individual‐specific mechanical properties of breast tissues, precise representation of loading and boundary constraints during different clinical procedures, and validation of modeling techniques used to represent key mechanical aspects such as the suspensory Cooper's ligaments. Scientists must also work towards translating their research tools into the clinical setting by developing efficient tools with user‐friendly interactivity. Widespread adoption of such techniques has the potential to significantly reduce the numbers of misdiagnosed breast cancers and enhance surgical planning for patient treatment. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Laboratory Methods and Technologies > Imaging
Models of Systems Properties and Processes > Mechanistic Models
Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models
DNA methylation and gene expression
Authors: Siegfried Zahava , Simon Itamar 
Published: October 2009

AbstractMethylation of cytosines is the key epigenetic modification of DNA in eukaryotes and is associated with a repressed chromatin state and inhibition of gene expression. The methylation pattern in mammalian genomes is bimodal, with most of the genomes methylated except for short DNA stretches called CpG islands (CGIs), which are generally protected from methylation. Recent technical advances have made it possible to map DNA methylation patterns on a large scale. Several genomic studies have made significant progress in unraveling the intricate relationships between DNA methylation, chromatin structure, and gene expression. What is emerging is a more dynamic and complex association between DNA methylation and expression than previously known. Here we highlight several recent genomic studies with an emphasis on what new information is gained from these studies and what conclusions can be reached about the role of DNA methylation in controlling gene expression. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Biological Mechanisms > Regulatory Biology
Monodentate Coordination of 4,4′‐Bipyridine Leading to a Supramolecular Network – Synthesis and Crystal Structure of [H2bpp][{Cu(Hbpy)2}{α‐HP2W18O62}]·4H2O
Authors: Li Jia , Wang Da‐Peng , Chen Ya‐Guang , Zhang Chun‐Jing 
Published: October 2009

AbstractThe new supramolecular compound [H2bpp][{Cu(Hbpy)2}{α‐HP2W18O62}]·4H2O (1) (bpy = 4,4′‐bipyridine, bpp = 1,3‐bis(4‐pyridyl)propane) was synthesized hydrothermally and characterized byelemental analysis, IR spectroscopy, thermogravimetric analysis and single‐crystal X‐ray diffraction. In compound 1, the cationic fragment [Cu(Hbpy)2]+ connects to the Dawson anion through a coordinating Cu←O bond, and the copper atom is coordinated by another polyoxoanion through a weak covalent bond with a Cu1–O26 distance of 2.879(2) Å, forming a polymeric chain. The bpy ligand in [Cu(Hbpy)2]+ adopts a monodentate coordination mode, the other nitrogen atom of the bpy ligand is protonated. The protonated Hbpy+ acts as hydrogen‐bond donor and constructs a two‐dimensional double‐sheet supramolecular network involving the one‐dimensional chains through the hydrogen bonds. The H2bpp2+ ion connects twoα‐HP2W18O626– clusters from two supramolecular networks through hydrogen bonds and creates a three‐dimensional supramolecular architecture. The thermal decomposition of 1 happens over a wide temperature range (450–800 °C), which indicates that it might include complicated oxidation–reduction processes.
Intramolekulare Ringerweiterung eines 2‐Lithium‐anilido‐2‐fluoro‐1,3‐diaza‐2‐silacyclopentens zum 1,3,5‐Triaza‐7‐bora‐2‐silacyclohepten – Experimentelle und Quantenchemische Ergebnisse
Authors: Abraham Sascha , Schmatz Stefan , Klingebiel Uwe , Fischer Andreas 
Published: October 2009

AbstractThe reaction between the lithiated 2‐diisopropylanilino‐2‐fluoro‐1,3‐diaza‐2‐silacyclopentene, (HCNCMe3)2SiFNLi(2,6‐Me2CH)2C6H3 (I), and BF3·OEt2 in THF afforded in an unknown, intramolecular ring expansion the seven‐membered 1,3,4‐triaza‐7‐bora‐2‐silacycloheptene, (HCNCMe3)2(SiF2)BFN‐2,6‐(Me2CH)2C6H3 (1). Starting with the BF2‐substituted compound A, quantum‐chemical calculations on the thermal isomeration process revealed a two‐step reaction mechanism: First, the bicyclic compound C is formed via transition state TS1, and second, a 1,3‐fluoride ion migration occurs in the seven‐membered transition state TS2 from a BF2‐ to a SiF‐unit. The reaction mechanism and the structures of the transition states are discussed in detail.
There are big gaps in our knowledge, and thus approach, to zoo animal welfare: a case for evidence‐based zoo animal management
Authors: Melfi V. A. 
Published: October 2009

AbstractThere are gaps in knowledge that hinder our ability within zoos to provide good animal welfare. This does not mean that zoos cannot or do not provide good welfare, only that currently this goal is hindered. Three reasons for these gaps are identified as: (1) there is an emphasis on the identification and monitoring of indicators that represent poor welfare and it is assumed that an absence of poor welfare equates to good welfare. This assumption is overly simplistic and potentially erroneous; (2) our understanding of how housing and husbandry (H&H) affects animals is limited to a small set of variables determined mostly by our anthropogenic sensitivities. Thus, we place more value on captive environmental variables like space and companionship, ignoring other factors that may have a greater impact on welfare, like climate; (3) finally, whether intentional or not, our knowledge and efforts to improve zoo animal welfare are biased to very few taxa. Most attention has been focused on mammals, notably primates, large cats, bears, and elephants, to the exclusion of the other numerous species about which very little is known. Unfortunately, the extent to which these gaps limit our ability to provide zoo animals with good welfare is exacerbated by our over reliance on using myth and tradition to determine zoo animal management. I suggest that we can fill these gaps in our knowledge and improve our ability to provide zoo animals with good welfare through the adoption of an evidence‐based zoo animal management framework. This approach uses evidence gathered from different sources as a basis for making any management decisions, as good quality evidence increases the likelihood that these decisions result in good zoo animal welfare. Zoo Biol 28:574–588, 2009. © 2009 Wiley‐Liss, Inc.
Isorhizochalin: a Minor Unprecedented Bipolar Sphingolipid of Stereodivergent Biogenesis from the Rhizochalina incrustata
Authors: Makarieva Tatyana N. , Zakharenko Alexander M. , Dmitrenok Pavel S. , Guzii Alla G. , Denisenko Vladimir A. , Savina Alexandra S. , Dalisay Doralyn S. , Molinski Tadeusz F. , Stonik Valentin A. 
Published: October 2009

AbstractIsorhizochalin (1) was isolated as its peracetate from the EtOH extract of the sponge Rhizochalina incrustata. Its structure and absolute stereochemistry were elucidated as (2S,3R,26R,27R)‐2,27‐diamino‐3‐O‐β‐d‐galactopyranosyl‐oxy‐26‐hydroxyoctacosan‐18‐one by extensive NMR, MS studies, chemical transformations, including micromolar‐scale Baeyer–Villiger oxidation, and by analysis of CD spectra of isorhizochalinin perbenzoate (2b). Isorhizochalin is an unprecedented C‐2 epimer of rhizochalin having an erythro configuration at the glycosylated 2‐amino‐3‐alkanol α‐terminus in contrast with a canonical threo configuration for other representatives of this structural group. Probable biogenesis of 1 is discussed in the context of known sphingolipid biosynthesis beginning with condensation of alanine with a fatty acyl CoA thioester. The aglycone, isorhizochalinin (2a), shows cytotoxicity against human leukemia HL‐60 and THP‐1 cells with IC50 values of 2.90 and 2.20 μM, respectively.
Do illness perceptions predict pain‐related disability and mood in chronic orofacial pain patients? A 6‐month follow‐up study
Authors: Galli Ursula , Ettlin Dominik A. , Palla Sandro , Ehlert Ulrike , Gaab Jens 
Published: October 2009

AbstractIn our study, we investigated the predictive value of illness beliefs as measured by the revised illness perception questionnaire (IPQ‐R) in the context of other clinical predictors in patients with chronic orofacial pain over a 6‐month follow‐up period. Consecutive patients (152) referred to the interdisciplinary orofacial pain service at the Centre for Dental and Oral Medicine and Cranio‐Maxillofacial Surgery, University of Zurich received questionnaires to assess pain and pain‐related disability, anxiety, depression as well as physical and mental quality of life at three time points: prior to treatment, 3 and 6 months after beginning of treatment. Results: significant improvement was found over time for all outcome measures except mental quality of life. Results of the regression analysis indicated that believing pain could have serious consequences on one's life (IPQ subscale consequences) is one of the most important predictors for treatment outcome. The belief in low personal control and in a chronic timeline is also shown to be predictive for outcome, though explaining a smaller proportion of variance. These results provided evidence that beliefs about pain are important predictors for treatment outcome even when controlled for pain and mood. They therefore need to be considered in the management of patients with chronic orofacial pain. Assessing patients’ illness beliefs can provide essential information on these important psychological determinants of adjustment to chronic pain and may be specific targets for individualised treatment approaches.