bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capturing Complex Protein Gradients on Biomimetic Hydrogels for Cell‐Based Assays
Authors: Cosson Steffen , Kobel Stefan A. , Lutolf Matthias P. 
Published: September 2009

AbstractA versatile strategy to rapidly immobilize complex gradients of virtually any desired protein on soft poly(ethylene glycol) (PEG) hydrogel surfaces that are reminiscent of natural extracellular matrices (ECM) is reported. A microfluidic chip is used to generate steady‐state gradients of biotinylated or Fc‐tagged fusion proteins that are captured and bound to the surface in less than 5 min by NeutrAvidin or ProteinA, displayed on the surface. The selectivity and orthogonality of the binding schemes enables the formation of parallel and orthogonal overlapping gradients of multiple proteins, which is not possible on conventional cell culture substrates. After patterning, the hydrogels are released from the microfluidic chip and used for cell culture. This novel platform is validated by conducting single‐cell migration experiments using time‐lapse microscopy. The orientation of cell migration, as well as the migration rate of primary human fibroblasts, depends on the concentration of an immobilized fibronectin fragment. This technique can be readily applied to other proteins to address a wealth of biological questions with different cell types.
Synthesis, characterization and hydroformylation activity of 7‐azaindolate‐bridged dinuclear rhodium(I)phosphines with pendant polar‐groups
Authors: Vasam Chandra Sekhar , Modem Sarangapani , Kankala Shravankumar , Budige Geeta , Vadde Ravinder 
Published: September 2009

AbstractNew dinuclear Rh(I)–Phosphines of the types [Rh(µ‐azi)(CO)(L)]2 (1,3–7) and [Rh(µ‐azi)(L)]2 (8) with pendant polar groups, and a chealated mononuclear compound [Rh(azi‐H)(CO)(L)] (2) (where azi = 7‐azaindolate, L = polar phosphine) were isolated from the reaction of [Rh(µ‐Cl)(CO)2]2 with 7‐azaindolate followed by some polar mono‐ and bis‐phosphines (L1–L8). A relationship between Δδ31P‐NMR and ν(CO) values was considered to define the impact of polar‐groups on σ‐donor properties of the phosphines. These compounds were evaluated as catalyst precursors in the hydroformylation of 1‐hexene and 1‐dodecene both in mono‐ and biphasic aqueous organic systems. While the biphasic hydroformylations (water + toluene) gave exclusively the aldehydes, the monophasic one (aqueous ethanol) showed propensity to form both aldehydes and alcohols. The influence of bimetallic cooperative effects, and σ‐donor and hydrophilic properties of the phosphines with pendant polar‐groups in enhancing the yields and selectivity of hydroformylation products was emphasized. In addition, when strong σ‐donor phosphine was used, the π‐acceptor nature of pyridine ring of 7‐azaindolate spacer was found to be a considerable factor in facilitating the facile cleavage of CO group during hydroformylation and in supplementing the cooperative effects. Copyright © 2009 John Wiley & Sons, Ltd.
Are we throwing histology out with the microscope? A look at histology from the physician's perspective
Authors: Pratt Rebecca L. 
Published: September 2009

AbstractA trend in medical schools across the United States is the refurbishing of histology laboratories with digital microscopy systems. Although such systems may reduce curricular time, they do not teach basic microscope skills, and students who learn solely with these systems may be less prepared for their practices or specialties, particularly in rural areas that may not be equipped with digital microscope technology. At the West Virginia School of Osteopathic Medicine (WVSOM), students are trained to practice in a wide variety of environments, especially rural areas. A research survey was conducted to gather information for evidence‐based decisions about histology education at WVSOM. The survey asked a range of questions concerning histology knowledge, tissue preparation, and microscopy. Responses did not differ significantly between physicians in urban versus rural practices. Ninety percent of physicians do not utilize digitized images, and only 50% have microscopes readily available. Regardless of the technology available, 90% feel that students must have microscope training and 88% of physicians feel that histology is important to the medical curriculum and use their histology knowledge often (weekly or daily) (66%). These results demonstrate that histology education should move toward a blending of traditional microscope and glass slides with computer‐based instructional technologies. Anat Sci Educ 2:205–209, 2009. © 2009 American Association of Anatomists.
Fungal incompatibility: Evolutionary origin in pathogen defense?
Authors: Paoletti Mathieu , Saupe Sven J. 
Published: September 2009

AbstractIn fungi, cell fusion between genetically unlike individuals triggers a cell death reaction known as the incompatibility reaction. In Podospora anserina, the genes controlling this process belong to a gene family encoding STAND proteins with an N‐terminal cell death effector domain, a central NACHT domain and a C‐terminal WD‐repeat domain. These incompatibility genes are extremely polymorphic, subject to positive Darwinian selection and display a remarkable genetic plasticity allowing for constant diversification of the WD‐repeat domain responsible for recognition of non‐self. Remarkably, the architecture of these proteins is related to pathogen‐recognition receptors ensuring innate immunity in plants and animals. Here, we hypothesize that these P. anserina incompatibility genes could be components of a yet‐unidentified innate immune system of fungi. As already proposed in the case of plant hybrid necrosis or graft rejection in mammals, incompatibility could be a by‐product of pathogen‐driven divergence in host defense genes.
Stripe formation in the early fly embryo: principles, models, and networks
Authors: Papatsenko Dmitri 
Published: September 2009

AbstractEarly development of animal embryos begins from spatially distributed products of gene expression, i.e., gradients. While maternal and early zygotic genes form broad and/or terminal gradients, their direct targets appear later on as relatively narrow stripes, which foreshadow presumptive germ layers or future segments. Evidently, stripe expression of the zygotic genes is among the key mechanisms of embryo patterning. In this paper, known qualitative and quantitative models for the stripe formation are considered on the example of early embryogenesis of Drosophila. The current model analysis emphasizes the role of spatial information flow in development. Discussion is given on frequent network motifs, pointing to spatial stripe formation solutions.
Intrinsic amino acid side‐chain hydrophilicity/hydrophobicity coefficients determined by reversed‐phase high‐performance liquid chromatography of model peptides: Comparison with other hydrophilicity/hydrophobicity scales
Authors: Mant Colin T. , Kovacs James M. , Kim Hyun‐Min , Pollock David D. , Hodges Robert S. 
Published: September 2009

AbstractAn accurate determination of the intrinsic hydrophilicity/hydrophobicity of amino acid side‐chains in peptides and proteins is fundamental in understanding many area of research, including protein folding and stability, peptide and protein function, protein–protein interactions and peptide/protein oligomerization, as well as the design of protocols for purification and characterization of peptides and proteins. Our definition of intrinsic hydrophilicity/hydrophobicity of side‐chains is the maximum possible hydrophilicity/hydrophobicity of side‐chains in the absence of any nearest‐neighbor effects and/or any conformational effects of the polypeptide chain that prevent full expression of side‐chain hydrophilicity/hydrophobicity. In this review, we have compared an experimentally derived intrinsic side‐chain hydrophilicity/hydrophobicity scale generated from RP‐HPLC retention behavior of de novo designed synthetic model peptides at pH 2 and pH 7 with other RP‐HPLC‐derived scales, as well as scales generated from classic experimental and calculation‐based methods of octanol/water partitioning of Nα‐acetyl‐amino‐acid amides or free energy of transfer of free amino acids. Generally poor correlation was found with previous RP‐HPLC‐derived scales, likely due to the random nature of the peptide mixtures in terms of varying peptide size, conformation and frequency of particular amino acids. In addition, generally poor correlation with the classical approaches served to underline the importance of the presence of a polypeptide backbone when generating intrinsic values. We have shown that the intrinsic scale determined here is in full agreement with the structural characteristics of amino acid side‐chains. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 573–595, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Simultaneous quantification of oleuropein and its metabolites in rat plasma by liquid chromatography electrospray ionization tandem mass spectrometry
Authors: Bazoti Fotini N. , Gikas Evangelos , Tsarbopoulos Anthony 
Published: September 2009

AbstractOleuropein (OE) is the cardinal bioactive compound derived from Olea europaea and possesses numerous beneficial properties for human health. However, despite the plethora of analytical methods that have studied the biological fate of olive oil‐derived bioactive compounds, no validated methodology has been published to date for the simultaneous determination of OE, along with all its major metabolites. In this study, a liquid chromatography‐electrospray ionization‐tandem mass spectrometry (LC‐ESI MS/MS) method has been developed and validated for the quantification of OE, simultaneously with its main metabolites hydroxytyrosol, 2‐(3,4‐dihydroxyphenyl)acetic acid, 4‐(2‐hydroxyethyl)‐2‐methoxy‐phenol or homovanillyl alcohol, 2‐(4‐hydroxy‐3‐methoxyphenyl)acetic acid or homovanillic acid, and elenolic acid in rat plasma matrix. Samples were analyzed by LC‐ESI MS/MS prior to and after enzymatic treatment. A solid‐phase extraction step with high mean recovery for all compounds was performed as sample pretreatment. Calibration curves were linear for all bioactive compounds over the range studied, while the method exhibited good accuracy, intra‐ and inter‐day precision. The limit of detection was in the picogram range (per milliliterof plasma) for HT and OE and in the nanogram range (per milliliter of plasma) for the other analytes, and the method was simple and rapid. The developed methodology was successfully applied for the simultaneous quantification of OE and its aforementioned metabolites in rat plasma samples, thus demonstrating its suitability for pharmacokinetics, as well as bioavailability and metabolism studies. Copyright © 2009 John Wiley & Sons, Ltd.
Sensitivity enhancement and matrix effect evaluation during summation of multiple transition pairs—case studies of clopidogrel and ramiprilat
Authors: Manjunath Swamy J. , Kamath Narendra , Radha Shekar Anil Kumar , Srinivas Nuggehally R. , Kristjansson Fjalar 
Published: September 2009

AbstractSensitivity enhancement via summation of multiple MRM transition pairs is gaining popularity in tandem mass spectrometric assays. Numerous validation experiments describing the assays for two model substrates, clopidogrel and ramiprilat, were performed. The quantitation of clopidogrel was achieved by the summation of transition pairs m/z 322.2 to m/z 212.0 and m/z 322.2 to m/z 184.0, while that of ramiprilat was achieved by the summation of transition pairs m/z 389.2 to m/z 206.1 and m/z 389.2 to m/z156.1. The use of summation approach achieved sensitivities of >2 fold for both compounds as compared with the reported single MRM transition pair assays. The validation experiments addressed some important assay development issues, such as: (a) lack of impact of matrix effect; (b) unequivocal verification of the percentage contribution of each MRM transition pair towards sensitivity; (c) sensitivity enhancement factor achieved by summation approach of MRM transition pairs; and (d) accurate prediction of quality control samples using summation approach vs a single MRM transition pair. In summary, the appropriateness of using two MRM transition pairs for quantitation was demonstrated for both clopidogrel and ramiprilat. Additionally, pharmacokinetic application of the MRM transition pair assays using a summation approach was established for the two compounds. Copyright © 2009 John Wiley & Sons, Ltd.
Determination of asperosaponin VI in rat plasma by HPLC‐ESI‐MS and its application to preliminary pharmacokinetic studies
Authors: Li Kai , Ding Li , Yang Zhong‐Lin , Liu E‐Hu , Qi Lian‐Wen , Li Ping , Hu Yu‐Zhu 
Published: September 2009

AbstractAsperosaponin VI (also named akebia saponin D) is a typical bioactive triterpenoid saponin isolated from the rhizome of Dipsacus asper Wall (Dipsacaceae). In this work, a sensitive high‐performance liquid chromatography–electrospray ionization–mass spectrometry (HPLC‐ESI‐MS) assay has been established for determination of asperosaponin VI in rat plasma. With losartan as the internal standard (IS), plasma samples were prepared by protein precipitation with methanol. Chromatographic separation was performed on a C18 column with a mobile phase of 10 mm ammonium acetate buffer containing 0.05% formic acid–methanol (32 : 68, v/v). The analysis was performed on an ESI in the selected ion monitoring mode using target ions at m/z 951.4 for asperosaponin VI and m/z 423.2 for the IS. The calibration curve was linear over the range 3–1000 ng/mL and the lower limit of quantification was 3.0 ng/mL. The intra‐ and inter‐assay variability values were less than 9.5 and 7.8%, respectively. The accuracies determined at the concentrations of 3.0, 100.0, 300.0 and 1000 ng/mL for asperosaponin VI were within ±15.0%. The validated method was successfully applied to a pharmacokinetic study in rats after oral administration of asperosaponin VI. Copyright © 2009 John Wiley & Sons, Ltd.
Lignin/Tannin‐Abtrennung aus Lignocellulosen
Authors: Unkelbach G. , Pindel E. , Schweppe R. 
Published: September 2009

AbstractDie vorliegende Arbeit beschreibt die Anwendung eines modifizierten Organosolv‐Verfahrens zum Aufschluss von Fichtenrinde. Ziel war die Optimierung des Aufschlusses und der Hydrolyse der Hemicellulosen und die Maximierung der Ausbeute an wasserunlöslichem Tannin. Die Versuche wurden in zwei verschiedenen Batch‐Autoklaven (100 mL, 13 L) im Temperaturbereich von 120–180 °C bei Verweilzeiten zwischen 30 und 90 min durchgeführt. Weiterhin wurde der Einfluss des Verhältnisses von Aufschlussmittel zu Biomasse und der Zusammensetzung des Aufschlussmittels auf die genannten Zielgrößen untersucht. Die Ergebnisse wurden mithilfe einer Statistiksoftware ausgewertet und die optimalen Prozessparameter ermittelt. Anhand dieser Ergebnisse wurde ein Konzept für eine kontinuierliche Prozessführung entwickelt.
The cytologic features of NUT midline carcinoma
Authors: Bellizzi Andrew M. , Bruzzi Cynthia , French Christopher A. , Stelow Edward B. 
Published: September 2009

AbstractBACKGROUND:Nuclear protein in testis (NUT) midline carcinoma (NMC) represents an aggressive, high‐grade carcinoma typically involving the upper aerodigestive tract or mediastinum. Although the tumor was originally noted in young persons, we have subsequently identified 5 adult cases. To our knowledge, the cytology of NMC has not been systematically described.METHODS:We recently published a series of NMCs identified by fluorescent in situ hybridization for characteristic NUT rearrangement. Three of these patients had undergone fine‐needle aspiration. Patient age, sex, primary tumor location, and aspiration site were noted. Cases were assessed for the following: cellularity, architecture, cytoplasm, cell size, nuclear contours, nucleoli, chromatin, anisonucleosis/cytosis, mitotic activity, background, and nuclear crush.RESULTS:The 3 cases occurred in 2 women and 1 man, ages 31‐79 years. Primaries involved the sinonasal tract (2) and larynx. Aspirates were of right neck masses (2) and supraclavicular lymph node. Smears were highly cellular and generally noncohesive. Cytoplasm was scant/delicate, although occasional cells with denser cytoplasm were noted in 1 case. Cells were 2‐3 times the diameter of a small lymphocyte with irregular nuclear contours, discrete nucleoli, and fine/granular to vesicular chromatin. Anisonucleosis/cytosis was slight to moderate. Mitotic figures were noted in each case. The background contained naked nuclei and karyorrhectic debris; nuclear crush was noted.CONCLUSIONS:NMCs exhibit cytologic features of a poorly differentiated or undifferentiated carcinoma. Although reports mention squamous differentiation as a histologic feature, it is typically focal, and overt squamous differentiation was not identified in our cases. Given morphologic overlap with other high‐grade carcinomas, diagnosis requires a high index of suspicion. Cancer (Cancer Cytopathol) 2009. © 2009 American Cancer Society.
The Collaboratory for the Study of Earthquake Predictability perspective on computational earthquake science
Authors: Zechar J. Douglas , Schorlemmer Danijel , Liukis Maria , Yu John , Euchner Fabian , Maechling Philip J. , Jordan Thomas H. 
Published: September 2009

AbstractThe Collaboratory for the Study of Earthquake Predictability (CSEP) aims to advance earthquake research by rigorous testing of earthquake forecast hypotheses. As in other disciplines, such hypothesis testing requires carefully designed experiments that meet certain requirements: they should be reproducible, fully transparent, and conducted within a controlled environment. CSEP has begun building infrastructure for conducting such rigorous earthquake forecasting experiments. Because past earthquake prediction experiments often have been controversial, CSEP testing centers—the secure, controlled computational environments within which experiments are conducted—have been designed to address particular issues related to transparency and exact reproducibility. Moreover, CSEP fosters collaboration among scientists developing earthquake forecast models, and the testing center concept allows multiple concurrent predictability experiments. In this paper, we share our perspective on computational earthquake science by presenting the design principles, organizational structure, and implementation details of CSEP testing centers. We describe ongoing forecast experiments in different testing regions and some of the implementation challenges encountered. We also describe the collaboration tools used for multinational software development and regional presentation websites. The need for common data exchange formats is discussed, as are potential avenues of future research within CSEP testing centers. Copyright © 2009 John Wiley & Sons, Ltd.
Effects of impurity ions on solubility and metastable zone width of phosphoric acid
Authors: Ma Yong , Zhu Jiawen , Ren Hongrui , Chen Kui 
Published: September 2009

AbstractEffects of two typical impurity ions as Fe2+ and SO42– in phosphoric acid on solubility and metastable zone width (MZW) had been studied. It was shown that polythermal method was suitable for solubility measurement in this study. The solubility experimental data was correlated with a polynomial equation. Being compared with Fe2+, SO42– had a greater impact on the phosphoric acid solubility; and the variation in phosphoric acid MZW was just opposite. Phosphoric acid apparent secondary nucleation order was calculated to be 3.50 by means of modified regression method. And also the influence of impurity ions on apparent secondary nucleation order was investigated in this paper. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Strain accommodation and interfacial structure of AlN interlayers in GaN
Authors: Dimitrakopulos G. P. , Kalesaki E. , Komninou Ph. , Kehagias Th. , Kioseoglou J. , Karakostas Th. 
Published: September 2009

AbstractThe strain accommodation mechanisms at AlN interlayers in GaN, grown by radio‐frequency plasma assisted molecular beam epitaxy, are studied using transmission electron microscopy techniques and atomistic modelling. Interlayers of various thicknesses grown within GaN epilayers deposited on both sapphire and silicon substrates have been employed. Interlayers of thickness below 6 nm do not exhibit line defects although local roughness of the upper interlayer interface is observed as a result of the Al adatom kinetics and higher interfacial energy compared to the lower interface. Above 6 nm, introduction of a‐type misfit and threading dislocations constitutes the principal relaxation mechanism. Due to strain partitioning between AlN and GaN, threading dislocations adopt inclined zig‐zag lines thus contributing to the relief of alternating compressive‐tensile elastic strain across the AlN/GaN heterostructure. The observed dislocation configurations are consistent with a model of independent motion by climb or ancillary glide in response to their localized three‐dimensional strain environment. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth and characterization of large La1‐xPbxMnO3+δ (x=0.32–0.35) crystals
Authors: Milenov T. I. , Rafailov P. M. , Abrashev M. V. , Nikolova R. P. , Titorenkova R. , Gospodinov M. M. 
Published: September 2009

AbstractLarge crystals of La0.63Pb0.37Mn O3+δ with small La(Pb)‐ deficiency of about 0.005‐0.01 at.% were grown by high temperature solution growth method. The structure of the grown crystals was determined as rhombohedral with R‐3 space group by single‐crystal X‐ray diffractometry. The surface morphology of the crystals and the exact chemical composition was examined by scanning electron microscopy and energy dispersive X‐ray analysis methods, respectively. The IR‐transmission spectrum reveals the presence of Mn3+O6‐ and Mn4+O6‐ octahedra in the lattice of La0.63Pb0.37Mn O3+δ crystals. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Delayed dopaminergic neuron differentiation in Lrp6 mutant mice
Authors: Castelo‐Branco Gonçalo , Andersson Emma R. , Minina Eleonora , Sousa Kyle M. , Ribeiro Diogo , Kokubu Chikara , Imai Kenji , Prakash Nilima , Wurst Wolfgang , Arenas Ernest 
Published: September 2009

AbstractWnts are known to bind and activate multiple membrane receptors/coreceptors and to regulate dopaminergic (DA) neuron development and ventral midbrain (VM) morphogenesis. The low density lipoprotein receptor–related protein (Lrp6) is a Wnt co‐receptor, yet it remains unclear whether Lrp6 is required for DA neuron development or VM morphogenesis. Lrp6 is expressed ubiquitously in the developing VM. In this study, we show that Lrp6−/− mice exhibit normal patterning, proliferation and cell death in the VM, but display a delay in the onset of DA precursor differentiation. A transient 50% reduction in tyrosine hydroxylase–positive DA neurons and in the expression of DA markers such as Nurr1 and Pitx3, as well as a defect in midbrain morphogenesis was detected in the mutant embryos at embryonic day 11.5. Our results, therefore, suggest a role for Lrp6 in the onset of DA neuron development in the VM as well as a role in midbrain morphogenesis. Developmental Dynamics 239:211–221, 2010. © 2009 Wiley‐Liss, Inc.