bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linear Polynuclear Helicates as a Link between Discrete Supramolecular Complexes and Programmed Infinite Polymetallic Chains
Authors: Dalla‐Favera Natalia , Hamacek Josef , Borkovec Michal , Jeannerat Damien , Gumy Frédéric , Bünzli Jean‐Claude G. , Ercolani Gianfranco , Piguet Claude 
Published: February 2008

AbstractThe contribution of the solvation energies to the assembly of polynuclear helicates reduces the free energy of intermetallic repulsion, ΔEMM, in condensed phase to such an extent that stable D3‐symmetrical tetranuclear lanthanide‐containing triple‐stranded helicates [Ln4(L4)3]12+ are quantitatively produced at millimolar concentrations, despite the twelve positive charge borne by these complexes. A detailed modelling of the formation constants using statistical factors, adapted to self‐assembly processes involving intra‐ and intermolecular connections, provides a set of five microscopic parameters, which can be successfully used for rationalizing the stepwise generation of linear bi‐, tri‐ and tetranuclear analogues. Photophysical studies of [Eu4(L4)3]12+ confirm the existence of two different binding sites producing differentiated metal‐centred emission at low temperature, which transforms into single site luminescence at room temperature because of intramolecular energy funelling processes.
Supramolecular Assemblies of Tripodal Porphyrin Hosts and C60
Authors: Tong Lok H. , Wietor Jean‐Luc , Clegg William , Raithby Paul R. , Pascu Sofia I. , Sanders Jeremy K. M. 
Published: February 2008

AbstractThe self‐assembly of two tripodal porphyrin hosts in the presence of C60, in the solid state, has been studied using synchrotron X‐ray crystallography, and in solution by using1H NMR and fluorescence spectroscopies. The binding affinities, stoichiometries and geometries strongly depend on the size of the porphyrin host. Intramolecular and/or intermolecular porphyrin–fullerene interactions are observed in the co‐crystallites and in each case, the trimer exhibits a “tweezers‐like” structural motif. The solid‐state structures of the trimer‐fullerene co‐crystallites reveal close fullerene–porphyrin and fullerene–fullerene contacts.
Self‐Assembled Structures in Organogels of Amphiphilic Diblock Codendrimers
Authors: Yang Miao , Zhang Zijian , Yuan Fei , Wang Wei , Hess Sandra , Lienkamp Karen , Lieberwirth Ingo , Wegner Gerhard 
Published: February 2008

AbstractAmphiphilic diblock codendrimers consisting of dendrons of hydroxyl‐containing poly(methallyl dichloride) (PMDC) and long alkyl‐containing poly(urethane amide) (PUA) were synthesized in different generations. These codendrimers were found to self‐assemble into ribbonlike aggregates in organic solvent and further formed three‐dimensional networks and behaved macroscopically as gels. The width of the self‐assembled ribbons decreases with the generation of both dendritic blocks. Multiple intermolecular hydrogen bonds between amide and hydroxyl groups were found to be the main driving force to form these self‐assembled gels.
Towards high‐throughput single cell/clone cultivation and analysis
Authors: Lindström Sara , Larsson Rolf , Andersson Svahn Helene 
Published: February 2008

AbstractIn order to better understand cellular processes and behavior, a controlled way of studying high numbers of single cells and their clone formation is greatly needed. Numerous ways of ordering single cells into arrays have previously been described, but platforms in which each cell/clone can be addressed to an exact position in the microplate, cultivated for weeks and treated separately in a high‐throughput manner have until now been missing. Here, a novel microplate developed for high‐throughput single cell/clone cultivation and analysis is presented. Rapid single cell seeding into microwells, using conventional flow cytometry, allows several thousands of single cells to be cultivated, short‐term (72 h) or long‐term (10–14 days), and analyzed individually. By controlled sorting of individual cells to predefined locations in the microplate, analysis of single cell heterogeneity and clonogenic properties related to drug sensitivity can be accomplished. Additionally, the platform requires remarkably low number of cells, a major advantage when screening limited amounts of patient cell samples. By seeding single cells into the microplate it is possible to analyze the cells for over 14 generations, ending up with more than 10 000 cells in each well. Described here is a proof‐of‐concept on compartmentalization and cultivation of thousands of individual cells enabling heterogeneity analysis of various cells/clones and their response to different drugs.
Prolyl endopeptidase is revealed following SILAC analysis to be a novel mediator of human microglial and THP‐1 cell neurotoxicity
Authors: Klegeris Andis , Li Jane , Bammler Theo K. , Jin Jinghua , Zhu David , Kashima Daniel T. , Pan Sheng , Hashioka Sadayuki , Maguire John , Mcgeer Patrick L. , ZHANG JING 
Published: February 2008

AbstractReactive microglial cells may exacerbate the pathology in some neurodegenerative disorders. Supernatants of stimulated human microglial cells, or their surrogate THP‐1 cells, are lethal to cultured human neuroblastoma SH‐SY5Y cells. To explore this neurotoxicity, we examined the spectrum of proteins generated by THP‐1 cells using the technique of stable isotope labeling by amino acids in cell culture (SILAC). Unstimulated cells were grown in medium with light L‐[12C6] arginine while cells stimulated by lipopolysaccharide (LPS) plus interferon‐γ (IFN‐γ) were grown in medium with heavy L‐[13C6] arginine. Proteins isolated from the media were digested with trypsin, and relative concentrations of generated peptides determined by mass spectrometry. More than 1,500 proteins or putative proteins were identified. Of these, 174 were increased and 189 decreased by more than twofold in the stimulated cell supernatant. We selected one upregulated protein, prolyl endopeptidase (PEP), for further investigation of its potential contribution to neurotoxicity. We first confirmed its upregulation by comparing its enzymatic activity in stimulated and unstimulated cell supernatants. We then evaluated two specific PEP inhibitors, Boc‐Asn‐Phe‐Pro‐aldehyde and Z‐Pro‐Pro‐aldehyde‐dimethyl acetal, for their potential to reduce toxicity of stimulated THP‐1 cell and human microglia supernatants towards SH‐SY5Y cells. We found both to be partially protective in a concentration‐dependent manner. Inhibition of PEP may be a therapeutic approach to neurodegenerative disorders including Alzheimer and Parkinson diseases. © 2008 Wiley‐Liss, Inc.
Calcium/calcineurin signaling in primary cortical astrocyte cultures: Rcan1‐4 and cyclooxygenase‐2 as NFAT target genes
Authors: Canellada Andrea , Ramirez Belén G. , Minami Takashi , Redondo Juan Miguel , Cano Eva 
Published: February 2008

AbstractThe calcineurin/nuclear factor of activated T cells (NFAT) signaling pathway mediates important cell responses to calcium, but its activity and function in astrocytes have remained unclear. We show that primary cortical astrocyte cultures express the regulatory and catalytic subunits of the phosphatase calcineurin as well as the calcium‐regulated NFAT family members (NFATc1, c2, c3, and c4). NFATs are activated by calcium‐mobilizing agents in astrocytes, and this activation is blocked by the calcineurin inhibitor cyclosporine A. Microarray screening identified cyclooxygenase‐2 (Cox‐2), which is implicated in brain injury, and Rcan 1‐4, an endogenous calcineurin inhibitor, as genes up‐regulated by calcineurin‐dependent calcium signals in astrocytes. Mobilization of intracellular calcium with ionophore potently augments the promoter activity and mRNA and protein expression of Rcan 1‐4 and Cox‐2 induced by combined treatment with phorbol esters. Moreover, Rcan 1‐4 expression is efficiently induced by calcium mobilization alone. For both the genes, the calcium signal component is dependent on calcineurin and is replicated by exogenous expression of a constitutively active NFAT, strongly suggesting that the calcium‐induced gene activation is mediated by NFATs. Finally, we report that calcineurin‐dependent expression of Cox‐2 and Rcan 1‐4 is induced by physiological calcium mobilizing agents, such as thrombin, agonists of purinergic and glutamate receptors, and L‐type voltage‐gated calcium channels. These findings provide insights into calcium‐initiated gene transcription in astrocytes, and have implications for the regulation of calcium responses in astrocytes. © 2008 Wiley‐Liss, Inc.
Mechanisms of ATP‐ and glutamate‐mediated calcium signaling in white matter astrocytes
Authors: Hamilton Nicola , Vayro Steven , Kirchhoff Frank , Verkhratsky Alexej , Robbins Jon , Gorecki Dariuz C. , Butt Arthur M. 
Published: February 2008

AbstractNeurotransmitters released at synapses mediate Ca2+ signaling in astrocytes in CNS grey matter. Here, we show that ATP and glutamate evoke these Ca2+ signals in white matter astrocytes of the mouse optic nerve, a tract that contains neither neuronal cell bodies nor synapses. We further demonstrate that action potentials along white matter axons trigger the release of ATP and the intercellular propagation of astroglial Ca2+ signals. These mechanisms were studied in astrocytes in intact optic nerves isolated from transgenic mice expressing enhanced green fluorescent protein (EGFP) under control of the human glial fibrillary acidic protein promoter (GFAP) by Fura‐2 ratiometric Ca2+ imaging. ATP evoked astroglial Ca2+ signals predominantly via metabotropic P2Y1 and ionotropic P2X7 purinoceptors. Glutamate acted on both AMPA‐ and NMDA‐type receptors, as well as on group I mGlu receptors to induce an increase in astroglial [Ca2+]i. The direct Ca2+ signal evoked by glutamate was small, and the main action of glutamate was to trigger the release of the “gliotransmitter” ATP by a mechanism involving P2X7 receptors; propagation of the glutamate‐mediated Ca2+ signal was significantly reduced in P2X7 knock‐out mice. Furthermore, axonal action potentials and mechanical stimulation of astrocytes both induced the release of ATP, to propagate Ca2+ signals in astrocytes and neighboring EGFP‐negative glia. Our data provide a model of multiphase axon–glial signaling in the optic nerve as follows: action potentials trigger axonal release of ATP, which evokes further release of ATP from astrocytes, and this acts by amplifying the initiating signal and by transmitting an intercellular Ca2+ wave to neighboring glia. © 2008 Wiley‐Liss, Inc.
Astrocytes, but not olfactory ensheathing cells or Schwann cells, promote myelination of CNS axons in vitro
Authors: Sorensen Annette , Moffat Keith , Thomson Christine , Barnett Susan C. 
Published: February 2008

AbstractWe have examined the interaction between olfactory ensheathing cells (OECs), Schwann cells (SC), oligodendrocytes, and CNS axons using cultures generated from embryonic rat spinal cord. Oligodendrocyte process extension and myelination in these cultures was poor if the cells were plated on OECs or SCs. Myelin internodes and nodes of Ranvier formed frequently if these cultures were plated onto monolayers of neurosphere‐derived astrocytes (NsAs). In the myelinated fibers generated on NsAs, Nav channels, caspr, and neurofascin molecules were correctly assembled at the nodes of Ranvier. The density of neurites, survival, and antigenic differentiation of oligodendrocytes was similar on OEC and NsAs monolayers. However, on OEC monolayers, despite a transient increase in the number of endogenous oligodendrocytes, there was a decrease in oligodendrocyte process extension and axonal ensheathment when compared with cultures plated on NsAs monolayers. To determine if these changes were due to axonal or glial factors, spinal cord oligodendrocytes were plated onto monolayers of OECs, NsAs, and poly‐L‐lysine in the absence of neurons. In these cultures, process extension and myelin‐like membrane formation by oligodendrocytes was improved on monolayers of OEC. This suggests that inhibition of process extension is mediated via cross‐talk between OECs and neurites. In cultures containing axons plated on OEC monolayers, oligodendrocyte process formation, axonal ensheathment, and myelination occurred albeit lower if the cultures were supplemented with NsAs conditioned medium. These data suggest OECs can permit neurite extension and oligodendrocyte proliferation, but lack secreted factor(s) and possible cell–cell contact that is necessary for oligodendrocyte process extension and myelination. © 2008 Wiley‐Liss, Inc.
Seasonal forecast of cooling water problems in the River Rhine
Authors: Rutten Martine , van de Giesen Nick , Baptist Martin , Icke Joost , Uijttewaal Wim 
Published: February 2008

AbstractCooling water scarcity in the River Rhine due to low flows during summer and high water temperatures may endanger power supply in the Netherlands and Germany. This research addresses the feasibility of early warning for cooling water problems on a seasonal timescale using large‐scale oceanic and atmospheric patterns as predictors. The correlation strength, stability as well as probabilistic skill of possible teleconnections were assessed. The strongest teleconnection was found between January North Atlantic Oscillation (NAO) and August water temperatures. The evaluated teleconnections between NAO and El Niño Southern Oscillation (ENSO) and discharge do not increase skill compared to only using information on discharge itself in the winter and spring months. In pseudo‐operational context model results were shown to be very sensitive to the choice of predictor selection criteria significance and stability. Though for some responses statistically significant forecasts were found, discussion and research with stakeholders about handling risk levels and probabilistic forecasts would be required to assess the practical significance of the forecasts. Copyright © 2008 John Wiley & Sons, Ltd.
Spectral imaging for precise surgical intervention in Hirschsprung's Disease
Authors: Frykman Philip K. , Lindsley Erik H. , Gaon Mark , Farkas Daniel L. 
Published: February 2008

AbstractWe used advanced spectral imaging for intrasurgical decision making in a preclinical study, on a mouse model of Hirschsprung's Disease. Our imaging device sampled areas from normal and abnormal (aganglionic) colon in these animals. Spectral segmentation and classification of the resulting images showed a clear distinction between the normal and aganglionic regions, as confirmed by pathological analysis and use of mutant mice. We developed a simple algorithm that could distinguish normal from aganglionic colon with high spatial resolution and reproducibility, and the following statistics: sensitivity = 97%, specificity = 94%, positive predictive value = 92%, negative predictive value = 98%. These studies showed translational proof of concept that spectral imaging could be used during operations, in real time, to help surgeons precisely distinguish normal from abnormal tissue without requiring traditional biopsy. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Refractory thyrotoxicosis induced by iodinated contrast agents treated with therapeutic plasma exchange. A case report
Authors: Pasimeni G. , Caroli F. , Spriano G. , Antonini M. , Baldelli R. , Appetecchia M. 
Published: February 2008

AbstractExcess free iodide in the blood (ingested or injected) may cause thyrotoxicosis in patients at risk. Iodinated contrast solutions contain small amounts of free iodide and may be of significance for patients affected by Graves' disease, multinodular goiter or living in areas of iodine deficiency. Herein, we report a 57 elderly woman with a clinical history of multinodular goiter presented with a thyrotoxicosis induced by an iodinate contrast agent used during computed tomography scan. Because of the patient's resistance to conventional antithyroid drugs, she was treated with therapeutic plasma exchange (TPE). TPE is used in the treatment of several immunologic and nonimmunologic disorders. Temporary improvement after TPE in cases with thyrotoxicosis has been reported. In our patient's case, we observed an improvement in the thyroid hormone laboratory values as well as clinical findings. TPE can be an addition treatment when standard therapies for thyrotoxicosis fail providing the clinician with an adjuvant tool for rapid preparation of such a patient for thyroidectomy surgery. J. Clin. Apheresis, 2008. © 2008 Wiley‐Liss, Inc.
Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments
Authors: Pilmé Julien , Piquemal Jean‐Philip 
Published: February 2008

AbstractWe propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function (ELF). As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the ELF partition (DEMEP) allows computing of local moments located at non atomic centers such as lone pairs, σ bonds and π systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a π character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the CO bond has been revisited for several typical systems by means of the DEMEP analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the CuCO complex and to a weak intramolecular N|‐‐‐CO interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the CO bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
The minimized dead‐end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
Authors: Georgiev Ivelin , Lilien Ryan H. , Donald Bruce R. 
Published: February 2008

AbstractOne of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly‐observed low‐energy side‐chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead‐end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy‐minimized) and is thus referred to as the rigid‐GMEC. As a postprocessing step, the conformations that survive DEE may be energy‐minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid‐rotamer energies may subsequently minimize to a lower energy than the rigid‐GMEC. That is, the rigid‐GMEC and the conformation with the lowest energy among all energy‐minimized conformations (the minimized‐GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid‐GMEC, it makes no guarantees regarding the identification of the minimized‐GMEC. In this paper we derive a novel, provable, and efficient DEE‐like algorithm, called minimized‐DEE (MinDEE), that guarantees that rotamers belonging to the minimized‐GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized‐GMEC, but also as a filter in an ensemble‐based scoring and search algorithm for protein redesign that exploits energy‐minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized‐DEE algorithm is applicable in protein redesign, protein‐ligand binding prediction, and computer‐aided drug design. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Prediction of protein structural class using novel evolutionary collocation‐based sequence representation
Authors: Chen Ke , Kurgan Lukasz A. , Ruan Jishou 
Published: February 2008

AbstractKnowledge of structural classes is useful in understanding of folding patterns in proteins. Although existing structural class prediction methods applied virtually all state‐of‐the‐art classifiers, many of them use a relatively simple protein sequence representation that often includes amino acid (AA) composition. To this end, we propose a novel sequence representation that incorporates evolutionary information encoded using PSI‐BLAST profile‐based collocation of AA pairs. We used six benchmark datasets and five representative classifiers to quantify and compare the quality of the structural class prediction with the proposed representation. The best, classifier support vector machine achieved 61–96% accuracy on the six datasets. These predictions were comprehensively compared with a wide range of recently proposed methods for prediction of structural classes. Our comprehensive comparison shows superiority of the proposed representation, which results in error rate reductions that range between 14% and 26% when compared with predictions of the best‐performing, previously published classifiers on the considered datasets. The study also shows that, for the benchmark dataset that includes sequences characterized by low identity (i.e., 25%, 30%, and 40%), the prediction accuracies are 20–35% lower than for the other three datasets that include sequences with a higher degree of similarity. In conclusion, the proposed representation is shown to substantially improve the accuracy of the structural class prediction. A web server that implements the presented prediction method is freely available at http://biomine.ece.ualberta.ca/Structural_Class/SCEC.html. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
A novel strategy to determine protein structures using exclusively residual dipolar coupling
Authors: Rathinavelan Thenmalarchelvi , Im Wonpil 
Published: February 2008

AbstractRecent advances in NMR techniques to measure anisotropic spin interactions such as residual dipolar coupling (RDC) have provided better insights into protein structure as well as dynamics. Exploitation of RDC, however, still remains challenging because its successful application requires a reasonable starting model. Using the singular value decomposition method, we have recently developed an RDC restraint potential to optimally extract orientational information from RDC without the prerequisite of any structural information. In the present study, its efficacy is further illustrated by folding a β‐hairpin and α‐helix of protein G from extended conformations with RDC restraints alone by employing the replica exchange torsion angle molecular dynamics (REX‐TAMD) technique. Subsequently, the entire structure of protein G has been determined accurately using the developed fragment superposition method (FRAGSUM). In FRAGSUM, each overlapping fragments (10 amino acids long) is first folded individually by REX‐TAMD, and then the common amino acids are superimposed to determine the entire structure. Because FRAGSUM does not require any additional information besides RDC, it offers a new strategy for de novo structure determination using exclusively RDC. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008