bluuebunny/crossref_metadata_2025 huggingface dataset:
Remarkable Substituent Effects on the Activation Energy of Silylene Insertion into Silicon–Chlorine Bonds
Authors: Xu Zheng , Jin Juan , Li Zhifang , Qiu Huayu , Jiang Jianxiong , Lai Guoqiao , Kira Mitsuo
Published: August 2009

Insertion reactions of dimethylsilylene (Me2Si:) into the silicon–chlorine bond of various substituted chlorosilanes have been computationally studied by using DFT calculations with a 6‐31++G(d,p) basis set. All of the insertions investigated herein were exothermic (more than 40 kcal mol−1) and proceeded via three‐membered cyclic transition states (TS) with one substituent of a chlorosilane in the ring plane and two other substituents out of the plane. Among the two possible concerted insertion pathways, the pathway via a TS with a silylene lone‐pair orbital approaching a chlorosilane silicon atom was preferred. Important nucleophilic interactions of silylene lone‐pair orbitals with anti‐bonding σ orbitals of SiY (in plane) were supported by carrying out a natural bond orbital (NBO) analysis of the reaction. A radical pathway through the initial abstraction of chlorine from chlorosilane by the silylene cannot compete with the preferred concerted pathway. Systematic calculations for SiMe2 insertion into various chlorosilanes (YR2SiCl; Y (in‐plane substituent)=H, Me, NH2, OH, F, SiH3, PH2, SH and Cl; R (out‐of‐plane substituent)=H, Me, iPr and tBu) have revealed remarkable substituent effects on activation free energies (ΔG≠). In‐plane (Y) substituent effects were mostly electronic. Electron‐withdrawing substituents accelerate the insertion through enhanced nucleophilic interaction between silylene lone‐pair orbitals with the σ*(SiY) orbital at the TS. The ΔG≠ values correlate with the σI constants as a scale of the inductive effect of Y. Out‐of‐plane (R) substituent effects are mainly steric, and bulky substituents increase the activation free energy . Correlation of the ΔG≠ values with Taft’s steric substituent constants (Es) was observed. There was no significant difference in the out‐of‐plane substituent effects between the electron‐withdrawing Cl and the electron‐donating Me groups.
Gerührt oder geschüttelt? James‐Bond‐Cocktail
Authors: Eckelmann Jens , Lüning Ulrich
Published: August 2009

Ausgehend von Perfluorheptan, gesättigter wässriger Kaliumcarbonatlösung, Methanol, Toluol und geeigneten Farbstoffen wird eine zunächst dreiphasige Mischung hergestellt, die sich nach Schütteln – nicht nur Rühren – in vier Phasen trennt. Zugabe von Pentan kehrt die Reihenfolge zweier Phasen um. Die Zugabe der Komponenten erfolgt über einen neu entwickelten Weg, und die gewählte Art der Durchmischung verdeutlicht dem Zuschauer die Komplexität mehrphasiger Lösungen.
Wie Mäuse Gefahr wittern
Authors: Groß Michael
Published: August 2009

Säugetiere haben in ihren Nasen mindestens zwei Arten von Molekülsensoren. Die einen dienen dem Geruchssinn, und damit vor allem der Nahrungssuche, die anderen der Erkennung von Pheromonen von Artgenossen, und damit vor allem der sozialen und sexuellen Interaktion. Nun haben Forscher jedoch bei der Maus eine “dritte Nase” entdeckt, welche es den Nagern ermöglicht, Gefahrenquellen wie Krankheitserreger und kranke Artgenossen zu wittern.
Prognosis and prediction in a Facebook world
Authors: Stadler Walter M.
Published: August 2009

Nomograms are a useful tool for improving prognostics for individual patients and could have real benefits in terms of the number of patients exposed to toxic adjuvant therapy. However, it is far more important to develop and validate predictive markers.
Increase of intracellular Ca2+ by P2Y but not P2X receptors in cultured cortical multipolar neurons of the rat
Authors: Fischer Wolfgang , Nörenberg Wolfgang , Franke Heike , Schaefer Michael , Illes Peter
Published: August 2009

The expression and functionality of P2X/P2Y receptor subtypes in multipolar nonpyramidal neurons of mixed cortical cell cultures were investigated by means of immunocytochemistry and fura‐2 microfluorimetry. The morphological studies revealed that most of the neurons are immunoreactive for GABA and express a range of P2X/P2Y receptors, predominantly of the P2X2,4,6 and P2Y1,2 subtypes. P2X1 and P2X7 receptor immunoreactivity (IR) was found on thin axon‐like processes and presynaptic structures, respectively. Application of ATP caused a small concentration‐dependent increase in intracellular Ca2+ concentration ([Ca2+]i) in most investigated neurons, whereas only about the half of these cells responded to 2′,3′‐O‐(benzoyl‐4‐benzoyl)‐ATP (BzATP), ADPβS, 2MeSADP, or 2‐MeSATP and even fewer cells to UTP. In contrast, α,β‐meATP, UDP, and UDP‐glucose failed to produce any [Ca2+]i signaling. The response to ATP itself was inhibited by pyridoxal‐5′‐phosphate‐6‐azophenyl‐2′,4′‐disulfonic acid (PPADS), Reactive Blue 2, 2′‐deoxy‐N6‐methyl adenosine 3′,5′‐diphosphate (MRS2179), and suramin (300 μM) as well as by a cyclopiazonic acid‐induced depletion of intracellular Ca2+ stores. A Ca2+‐free external medium tended to decrease the ATP‐induced [Ca2+]i transients, although this action did not reach statistical significance. Various blockers of voltage‐sensitive Ca2+ channels and the gap junction inhibitor carbenoxolone did not interfere with the effect of ATP, whereas a combination of the ionotropic glutamate receptor antagonists D(–)‐2‐amino‐5‐phosphonopentanoic acid (AP5) and 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione disodium (CNQX) decreased it. Cross‐desensitization experiments between ADPβS or UTP and ATP suggested that ATP acts on the one hand via P2Y1,2 receptors and on the other hand by additional signaling mechanisms. These mechanisms may involve the release of glutamate (which in consequence activates ionotropic glutamate receptors) and the entry of Ca2+ via store‐operated Ca2+ channels. Evidence for the presence of functional P2X receptors, in particular P2X7, remains elusive. J. Comp. Neurol. 516:343–359, 2009. © 2009 Wiley‐Liss, Inc.
Comparison of color vision models based on spectral color representation
Authors: Jetsu Tuija , Heikkinen Ville , Pogosova Anahit , Jaaskelainen Timo , Parkkinen Jussi
Published: August 2009

Recent break‐throughs in retinal imaging have raised new questions for color vision research, and the existing color vision models should be re‐evaluated. Many color vision models are based on an assumption that there are no differences in the detection phase, neither in the spatial configuration nor in the spectral sensitivities of cells. In this article, we have run experiments with four different color vision models. This evaluation gives us more knowledge about the essential properties of the models. We show how the tested color vision models are able to replicate the behaviour of human color vision by evaluating their performance in Farnsworth‐Munsell 100‐Hue color vision test. Also, the wavelength discrimination power of each model is presented and the properties of color spaces spanned by models are examined using samples from Munsell Book of Color. Our experiments show that there are large differences in the properties of different models. © 2009 Wiley Periodicals, Inc. Col Res Appl, 34, 341–350, 2009
Analyzing the metrics of the perceptual space in a new multistage physiological colour vision model
Authors: Chorro Elísabet , Martínez‐Verdú Francisco Miguel , de Fez Dolores , Capilla Pascual , Luque Maria José
Published: August 2009

In this work, the metric of a new multistage colour vision model, ATTD05, is assessed and a new colour difference formula is suggested. Firstly, the uniformity of the ATTD05 colour space was compared with that of CIECAM02 for some Munsell samples, because if the model yields a uniform perceptual space, we will be able to implement a colour difference formula as a Euclidian distance between two points. Secondly, we developed a new space based on the perceptual descriptors of the model: brightness, hue, colourfulness, and saturation. After that, we calculated the free parameters of the space that better fit the measured and experimental data of two datasets (small‐magnitude and large‐magnitude colour differences), by minimizing the performance factor (PF/3). Finally, we compare colour differences calculated for ATTD05 and for other models. The PF/3 and the STRESS parameters were used to decide which model predicts better perceptual differences and, therefore, which model was the more uniform. © 2009 Wiley Periodicals, Inc. Col Res Appl, 34, 359–366, 2009
Statistically q‐deformed and tau‐deformed systems
Authors: Badescu Viorel , Landsberg Peter
Published: August 2009

Two classes of statistically deformed systems are known in literature. They are, respectively, the q‐deformed systems (Lavagno and Narayana Swamy, Phys Rev E 2002, 65, 036101) and the κ‐deformed systems (Kaniadakis and Scarfone, Physica A 2002, 305, 69). In this article, a new class, i.e., the tau‐deformed systems, is introduced. For each of these systems, a consistent thermodynamics may be developed. A summary of the main similarities between the thermodynamic properties of q‐deformed and tau‐deformed systems is presented. The deformation outlined in this article is radically different from the nonextensive Tsallis statistics, where the structure of the entropy is rather arbitrary deformed via the logarithmic function. In contrast, the theory of tau‐deformed systems is developed on a purely physical basis. However, one finally shows that the tau‐systems may be described by using a new form of deformed logarithmic function. © 2009 Wiley Periodicals, Inc. Complexity, 2010
Atomic Layer Deposition of NiO by the Ni(thd)2/H2O Precursor Combination
Authors: Lindahl Erik , Ottosson Mikael , Carlsson Jan‐Otto
Published: August 2009

Polycrystalline nickel oxide is deposited on SiO2 substrates by alternating pulses of bis(2,2,6,6‐tetramethylheptane‐3,5‐dionato)nickel(II) (Ni(thd)2) and H2O. The deposition process shows atomic layer deposition (ALD) characteristics with respect to the saturation behavior of the two precursors at deposition temperatures up to 275 °C. The growth of nickel oxide is shown to be highly dependent on surface hydroxide groups, and a large excess of H2O is required to achieve saturation. Throughout the deposition temperature range the amount of carbon in the film, originating from the metal precursor ligand, is in the range 1–2%. Above 275 °C ALD growth behavior is lost in favor of thermal decomposition of the metal precursor. The initial nucleation process is studied by atomic force microscopy (AFM) and reveals nucleation of well‐separated grains which coalesce to a continuous film after about 250 ALD cycles.
Flow cytometric detection of Pig‐A mutant red blood cells using an erythroid‐specific antibody: Application of the method for evaluating the in vivo genotoxicity of methylphenidate in adolescent rats
Authors: Dobrovolsky Vasily N. , Boctor Sherin Y. , Twaddle Nathan C. , Doerge Daniel R. , Bishop Michelle E. , Manjanatha Mugimane G. , Kimoto Takafumi , Miura Daishiro , Heflich Robert H. , Ferguson Sherry A.
Published: August 2009

A modified flow cytometry assay for Pig‐A mutant rat red blood cells (RBCs) was developed using an antibody that positively identifies rat RBCs (monoclonal antibody HIS49). The assay was used in conjunction with a flow cytometric micronucleus (MN) assay to evaluate gene mutation and clastogenicity/aneugenicity in adolescent male and female rats treated with methylphenidate hydrochloride (MPH). Sprague‐Dawley rats were treated orally with 3 mg/kg MPH (70/sex) or water (40/sex) 3 × /day on postnatal days (PNDs) 29–50. Eight additional rats (4/sex) were injected i.p. with N‐ethyl‐N‐nitrosourea (ENU) on PND 28. Blood was collected on PNDs 29, 50, and 90, and used for determining serum MPH levels and/or conducting genotoxicity assays. On the first and last days of MPH treatment (PNDs 29 and 50), serum MPH levels averaged 21 pg/μl, well within the clinical treatment range. Relative to our previously published method (Miura et al. [2008]; Environ Mol Mutagen 49: 614–629), the HIS49 Pig‐A mutation assay significantly reduced the background RBC mutant frequency; in the experiments with ENU‐treated rats, the modification increased the overall sensitivity of the assay 2–3 fold. Even with the increased assay sensitivity, the 21 consecutive days of MPH treatment produced no evidence of Pig‐A mutation induction (measured at PND 90); in addition, MPH treatment did not increase MN frequency (measured at PND 50). These results support the consensus view that the genotoxicity of MPH in pediatric patients reported earlier (El‐Zein et al. [2005]: Cancer Lett 230: 284–291) cannot be reproduced in animal models, suggesting that MPH at clinically relevant levels may be nongenotoxic in humans. Environ. Mol. Mutagen. 2010. Published 2009 by Wiley‐Liss, Inc.
On the development of a triple‐preserving Maxwell's equations solver in non‐staggered grids
Authors: Sheu Tony W. H. , Hung Y. W. , Tsai M. H. , Chiu P. H. , Li J. H.
Published: August 2009

We present in this paper a finite difference solver for Maxwell's equations in non‐staggered grids. The scheme formulated in time domain theoretically preserves the properties of zero‐divergence, symplecticity, and dispersion relation. The mathematically inherent Hamiltonian can be also retained all the time. Moreover, both spatial and temporal terms are approximated to yield the equal fourth‐order spatial and temporal accuracies. Through the computational exercises, modified equation analysis and Fourier analysis, it can be clearly demonstrated that the proposed triple‐preserving solver is computationally accurate and efficient for use to predict the Maxwell's solutions. Copyright © 2009 John Wiley & Sons, Ltd.
Numerical analysis of the effect of boundary layer thickness on vortex structures and heat transfer in the wake behind a hill
Authors: Yanaoka Hideki , Inamura Takao , Suenaga Yosuke , Abe Keisuke
Published: August 2009

This study presents a three‐dimensional numerical analysis of the effect of boundary layer thickness on vortex structures and heat transfer behind a hill mounted in a laminar boundary layer. When the thickness of the velocity boundary layer is comparable to the hill height, a hairpin vortex is formed symmetrically to the center of the spanwise direction in the wake. A secondary vortex is formed between the legs, and horn‐shaped secondary vortices appear under the concave parts of the hairpin vortex. When the boundary layer thickness increases, the legs and horn‐shaped secondary vortices move toward the center of the spanwise direction, and thus heat transport and heat transfer increase there. At this time, high‐turbulence areas generated locally move toward the center of the spanwise direction with an increase in the boundary layer thickness. With a further increase in the boundary layer thickness, steady streamwise vortices are formed downstream of the hill, but the heat transfer decreases. © 2009 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20261
Processing of type I collagen gels using nonenzymatic glycation
Authors: Roy Rani , Boskey Adele , Bonassar Lawrence J.
Published: August 2009

This study focuses on the development of a novel method of nonenzymatic glycation of fibrillar collagen gels. In contrast to previous studies in which type I collagen gels were glycated in the solid state, this study presents a method for glycation in solution. The type I collagen in solution or gels was exposed to a range of ribose concentrations from 0 to 250 mM. The binding of ribose to collagen was documented using Fourier transform infrared (FTIR) spectroscopy. formation of advanced glycation end products (AGEs) was quantified by fluorescence measurement. The bulk compressive modulus and viscoelastic time constant of processed gels were determined in stress relaxation studies. Both methods of glycation enhanced ribose addition and AGE formation in a dose‐dependent manner, with glycation in the gel state being more efficient. Both methods enhanced mechanical properties similarly, with 250 mMribose treatment resulting in a 10‐fold increase in bulk modulus. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
The simplicity of males: Dwarf males of four species of Osedax (Siboglinidae; Annelida) investigated by confocal laser scanning microscopy
Authors: Worsaae Katrine , Rouse Greg W.
Published: August 2009

Dwarf males of the bone‐eating worms Osedax (Siboglinidae, Annelida) have been proposed to develop from larvae that settle on females rather than on bone. The apparent arrest in somatic development and resemblance of the males to trochophore larvae has been posited as an example of paedomorphosis. Here, we present the first investigation of the entire muscle and nervous system in dwarf males of Osedax frankpressi, O. roseus, O. rubiplumus, and O. “spiral” analyzed by multistaining and confocal laser scanning microscopy. Sperm shape and spermiogenesis, the sperm duct and internal and external ciliary patterns were likewise visualized. The males of all four species possess morphological traits typical of newly settled siboglinid larvae: a prostomium, a peristomium with a prototroch, one elongate segment and a second shorter segment. Each segment has a ring of eight long‐handled hooked chaetae. The longitudinal muscles are distributed as evenly spaced strands forming a grid with the thin outer circular muscles. Oblique protractor and retractor muscles are associated with each of the chaetal sacs. The nervous system comprises a cerebral ganglion, a prototroch nerve ring, paired dorsolateral longitudinal nerves, five ventral longitudinal nerves with paired, posterior ganglia and a terminal commissure, as well as a net of fine peripheral transverse plexuses surrounding the first segment. Internal ciliation occurs as paired ventrolateral bands along the first segment. The bands appear to lead the free mature sperm to a ciliated duct and seminal vesicle lying just behind the prototroch region. A duct then runs from the seminal vesicle into the dorsal part of the prostomium. The similarity of Osedax males to the larvae of Osedax and other siboglinid annelids as well as similarities shown here to the neuromuscular organization seen in other annelid larvae supports the hypothesis of paedomorphosis in males of Osedax. J. Morphol., 2010. © 2009 Wiley‐Liss, Inc.
Sulfur fertilization and light exposure during storage are critical determinants of the nutritional value of ready‐to‐eat friariello campano (Brassica rapa L. subsp. sylvestris)
Authors: Barbieri Giancarlo , Bottino Antonella , Orsini Francesco , De Pascale Stefania
Published: August 2009

BACKGROUND: The nutritional value of fresh vegetables can be affected at different steps within the field‐to‐market pipeline. Both pre‐ and post‐harvest factors should be considered in order to increase the produce quality and to preserve it until final consumption. In this study the effects of sulfur nutrition during plant growth and light exposure during storage on the nutritional value of ready‐to‐eat friariello campano (Brassica rapa L. subsp. sylvestris L. Janch. var. esculenta Hort.) were studied.

RESULTS: Fresh weight loss was higher in light‐storage treatment. During storage, light exposure reduced leaf nitrate content, although no effect could be attributed to sulfur nutrition. Sulfur increased both lipophilic and hydrophilic antioxidant activity. The hydrophilic antioxidant activity linearly decreased during storage, whereas the lipophilic activity increased over time. However, no differences could be attributed to light exposure during storage for this parameter. Results on colorimetric indexes and their relation with the chlorophyll content are also reported.

CONCLUSIONS: Ready‐to‐eat friariello quality may be improved with an enhanced antioxidant activity and reduced nitrate content by combining, respectively, increased sulfur availability during plant growth and exposure to light during storage. On the other hand, light exposure caused a more rapid decline in produce fresh weight during storage. Copyright © 2009 Society of Chemical Industry
Galapagos: Darwin, evolution, and ENT
Authors: Bluestone Charles D.
Published: August 2009

This year is especially important in the history of the theory of evolution; 2009 is the bicentennial anniversary of the birth of Charles Darwin and the sesquicentennial anniversary of his publication, The Origin of Species. Darwin visited the Galapagos Islands as a young man, which greatly influenced his thinking. My son Jim and I had the good fortune to visit these islands in January 2009 and see firsthand what led Darwin to arrive at his monumental insights into the origins of life on this planet. I have described my observations and related some of this experience to the ear, nose, and throat, albeit with whimsy in several instances. Nonetheless, some of the adaptations in the animals on these unique islands may have bearing on my hypotheses related to the incidence and pathogenesis of otitis media in humans. It is hoped the reader will share my enthusiasm for the experience we had on these fantastic islands and tour them in the future. Laryngoscope, 2009
A novel pH‐sensitive and freeze‐thawed carboxymethyl chitosan/poly(vinyl alcohol) blended hydrogel for protein delivery
Authors: Li Yan , Du Yumin , Tang Yufeng , Wang Xiaoying
Published: August 2009

BACKGROUND: Blended hydrogels are widely applied in medical fields. They can provide many advantages, such as biocompatibility and biodegradability. Many materials and methods are used to obtain blended hydrogels. In this work, carboxymethyl chitosan (CMCS) and poly(vinyl alcohol) (PVA) blended hydrogels were prepared using the freezing and thawing technique. The properties of the hydrogels prepared, i.e. gel fraction, swelling and pH‐responsive behaviors, were investigated.

RESULTS: The gel fraction increased with increasing time of freezing and thawing as determined through gravimetric analysis. It was also found that the equilibrium degree of swelling improved obviously due to the addition of CMCS compared to pure PVA hydrogel. The blended hydrogel with composition CMCS/PVA 80/20 (by weight) possessed the highest swelling ratio. The results of the influence of pH values on the swelling behavior showed that minimum swelling ratios of the hydrogels occurred near the isoelectric point of CMCS. Protein release studies were performed under various pH conditions: the release was much slower under acid than under basic conditions. The release showed a burst in the first 15 h and then steadily increased.

CONCLUSION: The addition of CMCS can improve the physical properties of pure PVA hydrogels and provide pH sensitivity. It is concluded that PVA hydrogels containing CMCS could be potentially applied as oral delivery systems for protein drugs. Copyright © 2009 Society of Chemical Industry
Carboxy group derivatization for enhanced electron‐transfer dissociation mass spectrometric analysis of phosphopeptides
Authors: Zhang Lijuan , Xu Yawei , Lu Haojie , Yang Pengyuan
Published: August 2009

A novel strategy based on carboxy group derivatization is presented for specific characterization of phosphopeptides. By tagging the carboxy group with 1‐(2‐pyrimidyl) piperazine (PP), the ion charge states of phosphopeptides can be largely enhanced, showing great advantages for sequencing phosphorylated peptides with electron‐transfer dissociation MS. Besides, after PP‐derivatization, most non‐specific bindings can be avoided by eliminating the interaction between the carboxy group and TiO2, greatly improving the specificity of TiO2‐based phosphopeptide enrichment strategy. Moreover, being tagged with a hydrophobic group, the retention time of phosphopeptides in RPLC can be prolonged, overcoming the difficulty of separating phosphopeptides in RPLC‐based approach. Together with several other advantages, such as ease of handling, rapid reaction time, broad applicability and good reproducibility, this PP‐derivatization method is promising for high‐throughput phosphoproteome research.
Mobility shift detection of phosphorylation on large proteins using a Phos‐tag SDS‐PAGE gel strengthened with agarose
Authors: Kinoshita Eiji , Kinoshita‐Kikuta Emiko , Ujihara Hiromi , Koike Tohru
Published: August 2009

We describe a novel technique of phosphate‐affinity SDS‐PAGE using Phos‐tag to analyze large phosphoproteins with molecular masses of more than 200 kDa. The protein phosphoisotypes were clearly separated as up‐shifted migration bands in a 3% w/v polyacrylamide gel containing 20 μM Phos‐tag and 0.5% w/v agarose. In subsequent immunoblotting, the procedure permitted the determination of the phosphoisotypes of high‐molecular‐mass proteins, such as mTOR (289 kDa), ATM kinase (350 kDa), and 53BP1 (213 kDa).
Autoantibody to glial fibrillary acidic protein in the sera of cattle with bovine spongiform encephalopathy
Authors: Nomura Sachiko , Miyasho Taku , Maeda Naoyuki , Doh‐ura Katsumi , Yokota Hiroshi
Published: August 2009

It is desirable to make the diagnosis in live cattle with bovine spongiform encephalopathy (BSE), and thus surrogate markers for the disease have been eagerly sought. Serum proteins from BSE cattle were analyzed by 2‐D Western blotting and TOF‐MS. Autoantibodies against proteins in cytoskeletal fractions prepared from normal bovine brains were found in the sera of BSE cattle. The protein recognized was identified to be glial fibrillary acidic protein (GFAP), which is expressed mainly in astrocytes in the brain. The antigen protein, GFAP, was also found in the sera of BSE cattle. The percentages of both positive sera in the autoantibody and GFAP were 44.0% for the BSE cattle, 0% for the healthy cattle, and 5.0% for the clinically suspected BSE‐negative cattle. A significant relationship between the presence of GFAP and the expression of its autoantibody in the serum was recognized in the BSE cattle. These findings suggest a leakage of GFAP into the peripheral blood during neurodegeneration associated with BSE, accompanied by the autoantibody production, and might be useful in understanding the pathogenesis and in developing a serological diagnosis of BSE in live cattle.
Cliques in mitotic spindle network bring kinetochore‐associated complexes to form dependence pathway
Authors: Chen Tzu‐Chi , Lee Sheng‐An , Chan Chen‐Hsiung , Juang Yue‐Li , Hong Yi‐Ren , Huang Yei‐Hsuan , Lai Jin‐Mei , Kao Cheng‐Yan , Huang Chi‐Ying F.
Published: August 2009

The mitotic spindle is an essential molecular machine for chromosome segregation during mitosis. Achieving a better understanding of its organization at the topological level remains a daunting task. To determine the functional connections among 137 mitotic spindle proteins, a protein–protein interaction network among queries was constructed. Many hub proteins, which connect more than one query and serve as highly plausible candidates for expanding the mitotic spindle proteome, are ranked by conventional degree centrality and a new subnetwork specificity score. Evaluation of the ranking results by literature reviews and empirical verification of SEPT6, a novel top‐ranked hub, suggests that the subnetwork specificity score could enrich for putative spindle‐related proteins. Topological analysis of this expanded network shows the presence of 30 3‐cliques and six 4‐cliques (fully connected subgraphs) that, respectively, reside in eight kinetochore‐associated complexes, of which seven are evolution conserved. Notably, these complexes strikingly form dependence pathways for the assembly of the kinetochore complex. These analyses indicate the feasibility of using network topology, i.e. cliques, to uncover novel pathways to accelerate our understanding of potential biological processes.
Helically chiral poly(quinoxalin‐2,3‐diyl)s: Toward the synthesis of stereoregular polymeric organocatalysts
Authors: Reggelin Michael , Scholz Johannes , Hamburger Manuel
Published: August 2009

The synthesis of seven new aromatic diisocyanide monomers is described and a rationale for their stability is given, as well as their behavior in the palladium‐mediated aromatizing polymerization yielding helically chiral poly(quinoxalin‐2,3‐diyl)s (PQs). Acceleration of the otherwise slow polymerization by microwave heating was observed. The polymers are designed to display potential organocatalytically active functionalities (e.g., phenols, pyridines) nearby stereolabile biaryl axes, which are asymmetrically governed by the configurationally stable helical backbone. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 4830–4839, 2009
Comparison of structure‐based and threading‐based approaches to protein functional annotation
Authors: Brylinski Michal , Skolnick Jeffrey
Published: August 2009

To exploit the vast amount of sequence information provided by the Genomic revolution, the biological function of these sequences must be identified. As a practical matter, this is often accomplished by functional inference. Purely sequence‐based approaches, particularly in the “twilight zone” of low sequence similarity levels, are complicated by many factors. For proteins, structure‐based techniques aim to overcome these problems; however, most require high‐quality crystal structures and suffer from complex and equivocal relations between protein fold and function. In this study, in extensive benchmarking, we consider a number of aspects of structure‐based functional annotation: binding pocket detection, molecular function assignment and ligand‐based virtual screening. We demonstrate that protein threading driven by a strong sequence profile component greatly improves the quality of purely structure‐based functional annotation in the “twilight zone.” By detecting evolutionarily related proteins, it considerably reduces the high false positive rate of function inference derived on the basis of global structure similarity alone. Combined evolution/structure‐based function assignment emerges as a powerful technique that can make a significant contribution to comprehensive proteome annotation. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Template‐based and free modeling by RAPTOR++ in CASP8
Authors: Xu Jinbo , Peng Jian , Zhao Feng
Published: August 2009

We developed and tested RAPTOR++ in CASP8 for protein structure prediction. RAPTOR++ contains four modules: threading, model quality assessment, multiple protein alignment, and template‐free modeling. RAPTOR++ first threads a target protein to all the templates using three methods and then predicts the quality of the 3D model implied by each alignment using a model quality assessment method. Based upon the predicted quality, RAPTOR++ employs different strategies as follows. If multiple alignments have good quality, RAPTOR++ builds a multiple protein alignment between the target and top templates and then generates a 3D model using MODELLER. If all the alignments have very low quality, RAPTOR++ uses template‐free modeling. Otherwise, RAPTOR++ submits a threading‐generated 3D model with the best quality. RAPTOR++ was not ready for the first 1/3 targets and was under development during the whole CASP8 season. The template‐based and template‐free modeling modules in RAPTOR++ are not closely integrated. We are using our template‐free modeling technique to refine template‐based models. Proteins 2009. © 2009 Wiley‐Liss, Inc.
ACE inhibitors: their propertiesand current role in hypertension
Authors: Ooi Sze‐Yuan , Ball Stephen
Published: August 2009

ACE inhibitors remain the first‐line choice of treatment of hypertension in patients under 55 years, and second line in other patient groups. Our Drug Review considers their properties and the latest evidence for their use in hypertension, followed by further sources of information and an analysis of prescription data. Copyright © 2009 Wiley Interface Ltd.
Robust observer–controller compensator design using the loop shaping design procedure and the algebraic method
Authors: Lee An‐Chen , Pan Yi‐Ren , Huang Yuan‐Yong
Published: August 2009

This paper investigates robust observer‐controller compensator design using Vidyasagar's structure (VS). VS has a unit matrix parameter H similar to the Q parameter for the Youla–Kucera parameterization. VS can be designed based on the left coprimeness of the central controller in the H∞‐loop shaping design procedure (H∞‐LSDP) and therefore can preserve the intrinsic properties of the H∞‐LSDP. This paper introduces algebraic methods to simplify the design of H in the VS controller by solving specific algebraic equations. In particular, the algebraic design of H can achieve two things. First, a dynamic H adjusts the tracking performance and yields the integral action. Second, a dynamic H rejects the input and output sinusoidal disturbances with known frequencies. These attributes are indications of the flexibility of the proposed method since the output‐feedback controller design of the H∞‐LSDP cannot easily deal with such conditions. This paper discusses the achieved loop and the closed‐loop behavior of the system with VS, and also gives two numerical examples. The first example shows that the proposed method results in a better design in many aspects than the resulting from H∞‐LSDP. The second example shows the application of the proposed method to rejecting input and output step disturbances, and input and output multiple sinusoidal disturbances, for which the H∞‐LSDP can hardly be used. Copyright © 2009 John Wiley & Sons, Ltd.
Anatomy‐Specific Pancreatic Stump Management to Reduce the Risk of Pancreatic Fistula After Pancreatic Head Resection
Authors: Tajima Yoshitsugu , Kuroki Tamotsu , Tsuneoka Noritsugu , Adachi Tomohiko , Kosaka Taiichiro , Okamoto Tatsuya , Takatsuki Mitsuhisa , Eguchi Susumu , Kanematsu Takashi
Published: August 2009

Background

The anatomical status of the pancreatic remnant after a pancreatic head resection varies greatly among patients. The aim of the present study was to improve management of the pancreatic remnant for reducing pancreatic fistula after pancreatic head resection.

Methods

Ninety‐five consecutive patients who underwent an end‐to‐side, duct‐to‐mucosa pancreaticojejunostomy after pancreatic head resection were included in the study. To approximate the pancreatic stump to the jejunum, the transfixing and interrupted suture techniques were used in 51 and 44 patients, respectively. We modified the interrupted suture technique according to the anatomical status of the pancreatic remnant, i.e., the shape of the pancreatic stump and the location of the pancreatic duct.

Results

There was no operative mortality in this study. Overall, 14 patients (15%) developed a clinically relevant pancreatic fistula. Certain anatomical features, including a small pancreatic duct, a soft, nonfibrotic pancreatic gland, and a pancreatic duct adjacent to the posterior cut edge, were significantly associated with pancreatic fistula. The fistula rate in the interrupted suture group was 7%, lower than that (22%) in the transfixing suture group (P = 0.036), and it was not influenced by pancreatic anatomy. Multivariate analysis identified a nonfibrotic pancreas (versus fibrotic pancreas; odds ratio [OR] 12.58, 95% CI 1.2–23.9; P = 0.001), a soft pancreas (versus hard pancreas; OR 4.67, CI 1.2–51.1; P = 0.006), and the transfixing suture technique (versus interrupted suture technique; OR 9.91, CI 1.7–57.5; P = 0.003) as significant predictors of clinically relevant pancreatic fistula.

Conclusions

Pancreatic anastomosis modified according to the pancreatic anatomy is effective in reducing the risk of pancreatic fistula formation with end‐to‐side, duct‐to‐mucosa pancreaticojejunostomy after pancreatic head resection.
Rabbits (Oryctolagus cuniculus) select small seeds when feeding on the fruits of Corema album
Authors: Larrinaga Asier R.
Published: August 2009

Herbivores are hypothesized to consume fruits and seeds while foraging on the vegetative parts of plants. A small seed size is an important condition for this foliage‐as‐fruit hypothesis to be proved, but has received little attention at the intra‐specific level. We measured Corema album seeds ingested by rabbits and those collected from plants and found that rabbits are actively selecting for small seeds. The mechanisms of this selection remain unclear, although my results discard (1) the phenology of consumption, (2) effects of gut passage, and (3) intra‐plant heterogeneity of seed sizes as possible mechanisms.
Determination of hip reduction in spica cast treatment for DDH: A comparison of radiography and ultrasound
Authors: Eberhardt Oliver , Zieger Michael , Langendoerfer Michael , Wirth Thomas , Fernandez Francisco F.
Published: August 2009

Purpose

In this retrospective study we compared the efficacy of ultrasound and radiography for determining the position of the femoral head after closed or open reduction in DDH.

Materials and methods

The ultrasound was performed using the van Douveren technique by a transinguinal approach through a perineal window of the spica cast. Sixty-eight a.p. radiographs of the pelvis were correlated to 68 ultrasound images.

Results

Thirty-two radiographs were not useful for precisely determining the femoral head position, whereas the criteria described by van Douveren et al. could be identified in all ultrasound images. All ultrasound images in the study were useful and gave reliable information about the position of the femoral head.

Conclusion

Consequently, standard radiographic documentation is no longer used as a standard in our clinic. MRI and CT are reserved for special cases. We recommend transinguinal ultrasound as a standard diagnostic method to determine the position of the femoral head in hip spica casts safely and reliably.
Cholesterol reverts Triton X‐100 preferential solubilization of sphingomyelin over phosphatidylcholine: A 31P‐NMR study
Authors: Ahyayauch Hasna , Collado M. Isabel , Goñi Félix M. , Lichtenberg Dov
Published: August 2009

The distribution of phosphatidylcholine (PC) and sphingomyelin (SM) between the solubilized (micellar) and non‐solubilized (lamellar) fractions arising from bilayers composed of PC and SM, with or without cholesterol (Chol) has been measured under conditions of partial, incomplete solubilization by Triton X‐100. Quantitation is achieved by 31P‐NMR determination of the composition of mixed micelles in the range of bilayer‐micelle coexistence. We find that the solubilized fraction of bilayers consisting of binary mixtures of PC and SM is rich in SM, as expected from previous data on solubilization of pure PC and pure SM liposomes. In contrast, after partial solubilization of ternary mixtures of PC, SM and Chol, the solubilized fraction becomes SM‐poor, as observed in the partial solubilization of biomembranes.
Social(ist) engineering. Taming the devils of the Polish Bieszczady
Authors: Lehmann Rosa
Published: August 2009

This article explores the background of social engineering in the Bieszczady in the 1950s and 1960s, when a revolutionary political leadership ventured to impose a new socialist order in an area ravaged by war and ethnic cleansing. The article addresses two questions: first, what were the conditions that resulted in the failure of socialist engineering in the Bieszczady, and second, what were the consequences of this failure for relationships at the local level? One thesis put forward is that the relative weakness of the Polish state vis-à-vis the local setting left plenty of room for local residents to develop a dynamic social order of their own.
On inertial effects in the Moffatt–Pukhnachov coating-flow problem
Authors: KELMANSON MARK A.
Published: August 2009

The effects are investigated of including inertial terms, in both small- and large-surface-tension limits, in a remodelling of the influential and fundamental problem first formulated by Moffatt and Pukhnachov in 1977: that of viscous thin-film free-surface Stokes flow exterior to a circular cylinder rotating about its horizontal axis in a vertical gravitational field.

An analysis of the non-dimensionalizations of previous related literature is made and the precise manner in which different rescalings lead to the asymptotic promotion or demotion of pure-inertial flux terms over gravitational-inertial terms is highlighted. An asymptotic mass-conserving evolution equation for a perturbed-film thickness is derived and solved using two-timescale asymptotics with a strained fast timescale. By using an algebraic manipulator to automate the asymptotics to high orders in the small expansion parameter of the ratio of the film thickness to the cylinder radius, consistent a posteriori truncations are obtained.

Via two-timescale and numerical solutions of the evolution equation, new light is shed on diverse effects of inertia in both small- and large-surface-tension limits, in each of which a critical Reynolds number is discovered above which the thin-film evolution equation has no steady-state solution due to the strength of the destabilizing inertial centrifugal force. Extensions of the theory to the treatment of thicker films are discussed.
A two-phase flow description of the initiation of underwater granular avalanches
Authors: PAILHA MICKAËL , POULIQUEN OLIVIER
Published: August 2009

A theoretical model based on a depth-averaged version of two-phase flow equations is developed to describe the initiation of underwater granular avalanches. The rheology of the granular phase is based on a shear-rate-dependent critical state theory, which combines a critical state theory proposed by Roux & Radjai (1998), and a rheological model recently proposed for immersed granular flows. Using those phenomenological constitutive equations, the model is able to describe both the dilatancy effects experienced by the granular skeleton during the initial deformations and the rheology of wet granular media when the flow is fully developed. Numerical solutions of the two-phase flow model are computed in the case of a uniform layer of granular material fully immersed in a liquid and suddenly inclined from horizontal. The predictions are quantitatively compared with experiments by Pailha, Nicolas & Pouliquen (2008), who have studied the role of the initial volume fraction on the dynamics of underwater granular avalanches. Once the rheology is calibrated using steady-state regimes, the model correctly predicts the complex transient dynamics observed in the experiments and the crucial role of the initial volume fraction. Quantitative predictions are obtained for the triggering time of the avalanche, for the acceleration of the layer and for the pore pressure.
The dynamics and rheology of a dilute suspension of hydrodynamically Janus spheres in a linear flow
Authors: RAMACHANDRAN ARUN , KHAIR ADITYA S.
Published: August 2009

The creeping motion of a hydrodynamically ‘Janus’ spherical particle, whose surface is partitioned into two distinct regions, is investigated. On one region, fluid adjacent to the particle obeys the no-slip condition, whereas on the other, fluid slips past the particle. The fore-aft asymmetry of this ‘slip–stick’ sphere (Swan & Khair, J. Fluid Mech., vol. 606, 2008, p. 115) leads to a number of interesting results when it is placed in different flows, which is illustrated by computing the particle motion to first order in the ratio of slip length to particle radius. For example, in a pure straining field the sphere attains an equilibrium orientation either along the compressional or extensional axis of the flow, depending on the ratio of slip-to-stick surface areas. In a simple shear flow, on the other hand, the slip–stick sphere undergoes a periodic rotational motion, or Jeffrey orbit. Moreover, depending on its initial orientation, the particle can either follow a periodic {translational} orbit or undergo a net displacement along the flow direction. Lastly, to first order in the volume fraction of slip–stick spheres, the suspension rheology is non-Newtonian, with non-zero first and second normal stress differences.
Flow separation from a stationary meniscus
Authors: SÉBILLEAU J. , LIMAT L. , EGGERS J.
Published: August 2009

We consider the steady flow near a free surface at intermediate to high Reynolds numbers, both experimentally and theoretically. In our experiment, an axisymmetric capillary meniscus is suspended from a cylindrical tube, held slightly above a horizontal water surface. A flow of dyed water is released through the tube into the reservoir, and flow lines are thus recorded. At low Reynolds numbers, flow lines follow the free surface, and injected water spreads horizontally inside the container. Increasing the Reynolds number, the injected fluid penetrates to a certain distance into the bath, but ultimately follows the free surface. Above a critical Reynolds number of approximately 60, the flow separates from the free surface in the meniscus region and a jet projects vertically into the bath. We find no indication that the flow reattaches at higher Reynolds numbers, nor are our findings sensitive to surface contamination. We show theoretically and confirm experimentally that the separating streamline forms a right angle with the free surface.
Structure of benthic macroinvertebrates and dynamics in the northern lagoon of Tunis
Authors: Tlig-Zouari S. , Mami T. , Maamouri F.
Published: August 2009

Sampling data on abiotic parameters and benthic communities in the northern lagoon of Tunis were obtained seasonally from November 1999 to November 2000. Abiotic parameters studied revealed evident improvement of water quality compared with previous. Indeed, management has re-established a tidal marine influence (Gulf of Tunis), induced a remarkable change in physico-chemical parameters and as a consequence, a regulation of the lagoon environmental quality. A total of 90 species of benthic macroinvertebrates, belonging to seven different taxa were collected in the northern lagoon of Tunis. A comparison of ecological indices indicate significant variations in the spatial and seasonal distribution and structure of the benthic community and reflect changes that might be related to open marine water and climatic influences as well as effects of discharge of the neighbouring city. Generally, the lagoon macrobenthic community appeared to be better structured, richer and more diverse than the one described before sanitation works began. However, significant disturbance of the benthic communities is detected in the south-eastern lagoon zone (C) and is dominated by disturbance indicator species. In contrast, the Station A2 which is sufficiently influenced by marine currents, is dominated by species of marine affinity and indicates an undisturbed zone. Multivariate analysis indicates heterogeneity in the benthic community structure between stations and suggests that the most significant variations of abundance occur in the groups: Anthozoa, Placophora, Cephalopoda, Ascidia and Echinodermata. The results of correspondence analysis also testify to a gradational distribution of benthic species in relation to hydrological and edaphic (organic matter) factors.