bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping the stability clusters in bovine pancreatic ribonuclease A
Authors: Vilà Roger , Benito Antoni , Ribó Marc , Vilanova Maria
Published: April 2009

In the present work, we have thermodynamically characterized the thermally induced unfolding of 20 variants of bovine pancreatic ribonuclease A (RNase A) to experimentally describe the residues and the regions that are critical for the stability of the enzyme. The achieved results, complemented with previous studies by our group, allowed us to define the significance of the two hydrophobic nuclei present in the RNase A structure, as well as the contribution of the participating residues within each nucleus, to the global enzyme stability. We propose a structural model for the major and the minor hydrophobic nuclei of RNase A. The major nucleus is composite and located in the cavity delimited by α‐helices 1 and 3, and the β‐sheet that is formed by strands 2, 3, 5, and 6. It consists of a central tight packed part constituted by residues Phe8, Met13, Val54, Val57, Ile106, Val108, and Phe120. This central part is surrounded by a layer formed by residues Val63, Tyr73, Met79, Ile107, Val116, and Val118. The minor nucleus, although less complex, is also constituted by a tight packing that involves the side chains of residues Tyr25, Met29, Met30, Leu35, Phe46, and Tyr97, which fill the cavity that originates the β‐sheet formed by β‐strands 1, 4, and 5 together with α‐helix2. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1038–1047, 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
Descriptively quantitative relationship between mutated N‐acetylgalactosamine‐6‐sulfatase and mucopolysaccharidosis IVA
Authors: Yan Shaomin , Wu Guang
Published: April 2009

To study the quantitative relationship between the mutant N‐acetylgalactosamine‐6‐sulfatase and the occurrence of mucopolysaccharidosis IVA, the human N‐acetylgalactosamine‐6‐sulfatase with 117 mutations was quantified using the amino‐acid distribution probability, then the mutations and clinical outcomes were coupled using the cross‐impact analysis. The results show that a patient has 0.94 chance of being mucopolysaccharidosis IVA when a new mutation occurs in N‐acetylgalactosamine‐6‐sulfatase. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 399–404, 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
Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins
Authors: Merlino Antonello , Vitagliano Luigi , Howes Barry D. , Verde Cinzia , di Prisco Guido , Smulevich Giulietta , Sica Filomena , Vergara Alessandro
Published: April 2009

Recent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air‐exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis‐histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 Å resolution. The analysis of the electron density of the heme pocket shows, for both the α and the β iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1117–1125, 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
Conformations of heterochiral and homochiral proline‐pseudoproline segments in peptides: Context dependent cis–trans peptide bond isomerization
Authors: Kantharaju  , Raghothama Srinivasarao , Raghavender Upadhyayula Surya , Aravinda Subrayashastry , Shamala Narayanaswamy , Balaram Padmanabhan
Published: April 2009

The pseudoproline residue (ΨPro, L‐2,2‐dimethyl‐1,3‐thiazolidine‐4‐carboxylic acid) has been introduced into heterochiral diproline segments that have been previously shown to facilitate the formation of β‐hairpins, containing central two and three residue turns. NMR studies of the octapeptide Boc‐Leu‐Phe‐Val‐DPro‐ΨPro‐Leu‐Phe‐Val‐OMe (1), Boc‐Leu‐Val‐Val‐DPro‐ΨPro‐Leu‐Val‐Val‐OMe (2), and the nonapeptide sequence Boc‐Leu‐Phe‐Val‐DPro‐ΨPro‐DAla‐Leu‐Phe‐Val‐OMe (3) established well‐registered β‐hairpin structures in chloroform solution, with the almost exclusive population of the trans conformation for the peptide bond preceding the ΨPro residue. The β‐hairpin conformation of 1 is confirmed by single crystal X‐ray diffraction. Truncation of the strand length in Boc‐Val‐DPro‐ΨPro‐Leu‐OMe (4) results in an increase in the population of the cis conformer, with a cis/trans ratio of 3.65. Replacement of ΨPro in 4 by LPro in 5, results in almost exclusive population of the trans form, resulting in an incipient β‐hairpin conformation, stabilized by two intramolecular hydrogen bonds. Further truncation of the sequence gives an appreciable rise in the population of cis conformers in the tripeptide Piv‐DPro‐ΨPro‐Leu‐OMe (6). In the homochiral segment Piv‐Pro‐ΨPro‐Leu‐OMe (7) only the cis form is observed with the NMR evidence strongly supporting a type VIa β‐turn conformation, stabilized by a 4→1 hydrogen bond between the Piv (CO) and Leu (3) NH groups. The crystal structure of the analog peptide 7a (Piv‐Pro‐ΨH,CH3Pro‐Leu‐NHMe) confirms the cis peptide bond geometry for the Pro‐ΨH,CH3Pro peptide bond, resulting in a type VIa β‐turn conformation. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 405–416, 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
Rat mitochondrial manganese superoxide dismutase: Amino acid positions involved in covalent modifications, activity, and heat stability
Authors: Castellano Immacolata , Cecere Francesca , De Vendittis Alberto , Cotugno Roberta , Chambery Angela , Di Maro Antimo , Michniewicz Andzelika , Parlato Giuseppe , Masullo Mariorosario , Avvedimento Enrico Vittorio , De Vendittis Emmanuele , Ruocco Maria Rosaria
Published: April 2009

The role of three amino acid residues (Q143, Y34, S82) of rat mitochondrial superoxide dismutase (ratSOD2) in the enzymatic activity, thermostability, and post‐translational modification of the enzyme was investigated through site‐directed mutagenesis studies. Six recombinant forms of the enzyme were produced, carrying the Q143 or H143 residue with or without the Y34F or S82A replacement. All proteins bound manganese as active cofactor and were organized as homotetramers. The greatest effect on the activity (sixfold reduction) was observed in ratSOD2 forms containing the H143 variant, whereas Y34F and S82A substitutions moderately reduced the enzymatic activity compared to the Q143 form. Heat inactivation studies showed the high thermo‐tolerance of ratSOD2 and allowed an evaluation of the related activation parameters of the heat inactivation process. Compared to Q143, the H143 variant was significantly less heat stable and displayed moderately lower enthalpic and entropic factors; the Y34F substitution caused a moderate reduction of heat stability, whereas the S82A replacement slightly improved the thermo‐tolerance of the Q143 variant; both substitutions significantly increased enthalpic and entropic factors of heat inactivation, the greatest effect being observed with S82A substitution. All recombinant forms of ratSOD2 were glutathionylated in Escherichia coli, a feature pointing to the high reactivity of ratSOD2 toward glutathione. Moreover, the S82 position of the enzyme was phosphorylated in an in vitro system containing human mitochondrial protein extracts as source of protein kinases. These data highlight the role played by some residues in ratSOD2 and suggest a fine regulation of the enzyme occurring in vivo. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1215–1226, 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
Single‐molecule pair studies of the interactions of the α‐GalNAc (Tn‐antigen) form of porcine submaxillary mucin with soybean agglutinin
Authors: Sletmoen Marit , Dam Tarun K. , Gerken Thomas A. , Stokke Bjørn T. , Brewer Curtis Fred
Published: April 2009

Mucins form a group of heavily O‐glycosylated biologically important glycoproteins that are involved in a variety of biological functions, including modulating immune response, inflammation, and adhesion. Mucins are also involved in cancer and metastasis and often express diagnostic cancer antigens. Recently, a modified porcine submaxillary mucin (Tn‐PSM) containing GalNAcα1‐O‐Ser/Thr residues was shown to bind to soybean agglutinin (SBA) with ∼106‐fold enhanced affinity relative to GalNAcα1‐O‐Ser, the pancarcinoma carbohydrate antigen. In this study, dynamic force spectroscopy is used to investigate molecular pairs of SBA and Tn‐PSM. A number of force jumps that demonstrate unbinding or rebinding events were observed up to a distance equal to 2.0 μm, consistent with the length of the mucin chain. The unbinding force increased from 103 to 402 pN with increasing force loading rate. The position of the activation barrier in the energy landscape of the interaction was 0.1 nm. The lifetime of the SBA–TnPSM complex in the absence of applied force was determined to be in the range 1.3–1.9 s. Kinetic parameters describing the rate of dissociation of other sugar lectin interactions are in the range 3.3 × 10−3–2.5 × 10−3 s. The long lifetime of the SBA‐TnPSM complex is compatible with a binding model in which lectin molecules “bind and jump” from α‐GalNAc residue to α‐GalNAc residue along the polypeptide chain of Tn‐PSM before dissociating. These findings have important implications for the molecular recognition properties of mucins. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 719–728, 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
Decreased secretion and unfolded protein response up‐regulation are correlated with intracellular retention for single‐chain antibody variants produced in yeast
Authors: Xu Ping , Robinson Anne Skaja
Published: April 2009

Heterologous protein expression can easily overwhelm a cell's capacity to properly fold protein, initiating the unfolded protein response (UPR), and resulting in a loss of protein expression. In the current model of the UPR, the chaperone BiP modulates the activation of the UPR due to its interactions with the signaling protein Ire1p and newly synthesized proteins. In this research, 4‐4‐20 scFv variants were generated by rational design to alter BiP binding to newly synthesized scFv proteins or via directed evolution aimed at improved secretion. Interestingly, the predicted BiP binding ability did not correlate significantly with the UPR. However, pulse‐chase analysis of scFv fate revealed that mutants with a decreased ER residence time were more highly secreted, indicating that improved protein folding was more likely the cause for improved secretion. In fact, decreased secretion correlated with increased binding by BiP, as determined by co‐immune precipitation studies. This suggests that the algorithm is not useful for in vivo prediction of variants, and that in vivo screens are more effective for finding variants with improved properties. Biotechnol. Bioeng. 2009; 104: 20–29 © 2009 Wiley Periodicals, Inc.
Targeted gene delivery to CD117‐expressing cells in vivo with lentiviral vectors co‐displaying stem cell factor and a fusogenic molecule
Authors: Froelich Steven , Ziegler Leslie , Stroup Katie , Wang Pin
Published: April 2009

The development of a lentiviral system to deliver genes to specific cell types could improve the safety and the efficacy of gene delivery. Previously, we have developed an efficient method to target lentivectors to specific cells via an antibody–antigen interaction in vitro and in vivo. We report herein a targeted lentivector that harnesses the natural ligand–receptor recognition mechanism for targeted modification of c‐KIT receptor‐expressing cells. For targeting, we incorporate membrane‐bound human stem cell factor (hSCF), and for fusion, a Sindbis virus‐derived fusogenic molecule (FM) onto the lentiviral surface. These engineered vectors can recognize cells expressing surface CD117, resulting in efficient targeted transduction of cells in an SCF‐receptor dependent manner in vitro, and in vivo in xenografted mouse models. This study expands the ability of targeting lentivectors beyond antibody targets to include cell‐specific surface receptors. Development of a high titer lentivector to receptor‐specific cells is an attractive approach to restrict gene expression and could potentially ensure therapeutic effects in the desired cells while limiting side effects caused by gene expression in non‐target cells. Biotechnol. Bioeng. 2009; 104: 206–215 © 2009 Wiley Periodicals, Inc.
Metabolic and transcriptional response of recombinant Escherichia coli to elevated dissolved carbon dioxide concentrations
Authors: Baez Antonino , Flores Noemí , Bolívar Francisco , Ramírez Octavio T.
Published: April 2009

The effect of dissolved carbon dioxide (dCO2) concentration on the stoichiometric and kinetic constants and by‐product accumulation was determined for Escherichia coli cells producing recombinant green fluorescent protein (GFP). Constant dCO2, in the range of 20–300 mbar, was maintained during batch cultures by manipulating the inlet gas composition. As dCO2 increased, specific growth rate (µ) decreased, and acetate accumulation and the time for onset of GFP production increased. Maximum biomass yield on glucose and GFP concentration were affected for dCO2 above 70 and 150 mbar, respectively. Expression analysis of 16 representative genes showed that E. coli can respond at the transcriptional level upon exposure to increasing dCO2, and revealed possible mechanisms responsible for the detrimental effects of high dCO2. Genes studied included those involved in decarboxylation reactions (aceF, icdA, lpdA, sucA, sucB), genes from pathways of production and consumption of acetate (ackA, poxB, acs, aceA, fadR), genes from gluconeogenic and anaplerotic metabolism (pckA, ppc), genes from the acid resistance (AR) systems (adiA, gadA, gadC), and the heterologous gene (gfp). The transcription levels of tricarboxylic acid (TCA) cycle genes (icdA, sucA, sucB) and glyoxylate shunt (aceA) decreased as dCO2 increased, whereas fadR (that codes for a negative regulator of the glyoxylate operon) and poxB (that codes for PoxB which is involved in acetate production from pyruvate) were up‐regulated as dCO2 increased up to 150 mbar. Furthermore, transcription levels of genes from the AR systems increased as dCO2 increased up to 150 mbar, indicating that elevated dCO2 triggers an acid stress response in E. coli cells. Altogether, such results suggest that the increased acetate accumulation and reduction in µ, biomass yield and maximum GFP concentration under high dCO2 resulted from a lower carbon flux to TCA cycle, the concomitant accumulation of acetyl‐CoA or pyruvate, and the acidification of the cytoplasm. Biotechnol. Bioeng. 2009; 104: 102–110 © 2009 Wiley Periodicals, Inc.
Faecal calprotectin or lactoferrin can identify postoperative recurrence in Crohn's disease
Authors: Lamb C A , Mohiuddin M K , Gicquel J , Neely D , Bergin F G , Hanson J M , Mansfield J C
Published: April 2009

Background

Identifying Crohn's disease recurrence in symptomatic patients after ileocaecal resection is difficult. The aim of this study was to evaluate faecal concentrations of granulocyte degradation products in this setting.

Methods

A postoperative cohort of 13 patients was followed prospectively for 1 year with regular faecal calprotectin (FC) and lactoferrin (FL) measurements. A second postoperative cohort (median 24 months after resection) of 104 patients provided a single stool sample. Faecal measurements were compared with symptom diaries, the Harvey Bradshaw Index, endoscopic examination, C-reactive protein and platelet measurement.

Results

In the uncomplicated course, both markers normalized within 2 months. Both FC and FL correlated significantly with Harvey Bradshaw Index (P < 0·001). Twenty-eight patients with severely clinically active disease had high mean(s.e.) levels of FC (661·1(119·1) µg/g) and FL (116·6(32·2) µg/g); and 43 with clinically inactive disease had low levels of FC (70·2(27·1) µg/g) and FL (5·9(2·4) µg/g). In patients with mild to moderately clinically active disease, FC and FL identified individuals with and without recurrent inflammatory disease. Faecal markers were more accurate at predicting clinical disease activity than C-reactive protein, platelet count or endoscopic appearance.

Conclusion

FC and FL are non-invasive tests that can help to identify disease recurrence in symptomatic postoperative patients.
Quantitative determination of a novel enantiomeric tropane analog, (−)‐satropane, in biological fluids using liquid chromatography/tandem mass spectrometry
Authors: Fu Jun , Fang Chao , Cui Yong‐Yao , Yang Li‐Min , Zhu Liang , Feng Xue‐Mei , Zheng Pei‐Li , Lu Yang , Chen Hong‐Zhuan
Published: April 2009

A sensitive, accurate and precise liquid chromatography–tandem mass spectrometry method was developed for the determination of (−)‐satropane (3α‐paramethyl‐benzenesulfonyloxy‐6β‐acetoxy‐tropane) in rabbit aqueous humor. Since (−)‐satropane may be absorbed from the aqueous humour with resultant systemic side effects, the LC‐MS/MS method was also evaluated for its applicability in analyzing plasma samples containing this compound. (−)‐Satropane and phentolamine (the internal standard, represented as IS) were detected by multiple reaction monitoring using the transitions m/z 354–182 and 282–212, respectively. The calibration curve was linear over the ranges 2–500 and 5–1000 ng/mL, and the values of the lower limit of quantification were 2 and 5 ng/mL for the microdialysis dialysate and rat plasma samples, respectively. The intra‐day and inter‐day precision and accuracy were better than 8.6 and 6.00%, respectively, in both matrices investigated. The absolute recovery of the plasma samples was more than 76.30%. The average matrix effects of (−)‐satropane were 91.72 and 83.05% in the microdialysis dialysate and plasma samples, respectively. The validated method was successfully applied to analyze (−)‐satropane in microdialysis dialysate and rat plasma samples, and this assay has been used to quantify (‐)‐satropane in the pharmacokinetic and toxicokinetic studies in our laboratory. Copyright © 2009 John Wiley & Sons, Ltd.
A high‐performance liquid chromatographic analysis and preliminary pharmacokinetic characterization of 3′‐hydroxypterostilbene in rats
Authors: Takemoto Jody K. , Davies Neal M.
Published: April 2009

A high‐performance liquid chromatographic method was developed for the analysis of 3'‐hydroxypterostilbene. This method involves the use of a Luna® C18 column with ultraviolet detection at 325 nm. The mobile phase consisted of acetonitrile, water and formic acid (50:50:0.01, v/v/v) with a flow rate of 0.8 mL/min. The calibration curves were linear over the range 0.5–100.0 µg/mL. The mean extraction efficiency was between 97.40 and 111.16%. The precision of the assay was 0.196–14.39% (RSD%), and within 15% at the limit of quantitation (0.5 µg/mL). The bias of the assay was <16% and within 15% at the limit of quantitation. This assay was successfully applied to pre‐clinical pharmacokinetic samples from rat urine and serum. Copyright © 2009 John Wiley & Sons, Ltd.
Using process simulators in the study, design, and control of distillation columns for undergraduate chemical engineering courses
Authors: Castrellón T. , Botía D. C. , Gómez R. , Orozco G. , Gil I. D.
Published: April 2009

Nowadays high schools should teach students how to use the software that they will use at work. This article shows the importance to promote a closer relationship between the engineering computer programs offered by companies like Aspen Technology Inc., and the chemical engineering students. The methodology consists of creating a tutorial which illustrates, in an interesting way, subjects through engineering software packages. The main theme treated in this tutorial is distillation column simulation and design; it also includes a brief look into distillation column control by means of dynamic simulations. This article presents an interactive guide with three case studies, where the subjects of design and control for a binary simple system and the development of a simulation for a complex ternary system are studied. These guides were implemented in Separation Processes and Process Design courses and the guide evaluation results show an acceptance by the students. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 621–630, 2011
GilR, an Unusual Lactone‐Forming Enzyme Involved in Gilvocarcin Biosynthesis
Authors: Kharel Madan Kumar , Pahari Pallab , Lian Hui , Rohr Jürgen
Published: April 2009

Last at last: The terminal step of the gilvocarcin V (GV) biosynthetic pathway is an unusual lactone formation. Here we show that the enzyme, GilR, dehydrogenates the hemiacetal moiety of pregilvocarcin V to the lactone found in GV by using covalently bound FAD.

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Michael Additions versus Cycloaddition Condensations with Ethyl Nitroacetate and Electron‐Deficient Olefins
Authors: Trogu Elena , De Sarlo Francesco , Machetti Fabrizio
Published: April 2009

Ethyl nitroacetate (1) reacts with electron‐poor olefins in the presence of a base to give either the Michael adducts 3 or the isoxazoline cycloadducts 4, resulting from water elimination. The proportions of the two products depend on the reaction conditions and change in the course of the process. Kinetic profiles for the two reactions show that the cycloaddition‐condensations require long induction times that dramatically decrease upon addition of a copper salt to the catalytic system: the drops in the induction time cause increases in the proportion of cycloadducts 4, which are often the sole reaction products. This is the first report on the selective formation of products 3 and 4 from primary nitro compounds through modulation of the catalytic system.
Coherently Aligned Porphyrin‐Appended Polynorbornenes
Authors: Wang Hsian‐Wen , Liu Zhi‐Chang , Chen Chih‐Hsien , Lim Tsong‐Shin , Fann Wunshain , Chao Chih‐Gang , Yu Jian‐Yuan , Lee Shern‐Long , Chen Chun‐hsien , Huang Shou‐Ling , Luh Tien‐Yau
Published: April 2009

You can append on me! Porphyrin‐appended polynorbornenes derived from 5,6‐endo‐fused N‐arylpyrrolidenonorbornenes have been shown to have coherently aligned pendant groups that exhibit exciton coupling and fluorescence quenching in the absorption and emission profiles (see figure).

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Six different kinds of coherently aligned porphyrin‐appended polynorbornenes derived from 5,6‐endo‐fused N‐arylpyrrolidenonorbornenes have been synthesized. π–π interactions between the pendant groups are essential for dictating the photophysical properties of the polymers and the mechanism for the stereoselective formation of polymers. Splitting of the Soret band of polymers 2 a–c, which have alkyl‐substituted porphyrin pendant groups, suggests strong exciton coupling between chromophores. No splitting of the Soret band is observed for polymers 2 d–f, which have tetraaryl substituents on the porphyrin moiety. Significant fluorescence quenching is found in polymers 2 a–e, whereas only slightly reduced quantum yield is observed for 2 f. Time‐resolved fluorescence measurements also indicate a similar trend. The AFM image of 2 d on graphite shows aggregation to form a two‐dimensional, ordered pattern.
Self‐Assembly of Mn‐Doped ZnS Quantum Dots/Octa(3‐aminopropyl)octasilsequioxane Octahydrochloride Nanohybrids for Optosensing DNA
Authors: He Yu , Wang He‐Fang , Yan Xiu‐Ping
Published: April 2009

Simple plan! Nanohybrids have been built from capped Mn‐doped ZnS quantum dots and octa(3‐aminopropyl)octasilsequioxane octahydrochloride (OA‐POSS) by means of electrostatic self‐assembly for the development of a novel room‐temperature phosphorescence sensor for DNA sensing in biological fluids (see graphic).

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Solid‐State Structure of Free Base Guanidine Achieved at Last
Authors: Yamada Takahiro , Liu Xiaohui , Englert Ulli , Yamane Hisanori , Dronskowski Richard
Published: April 2009

“Crystal structure of the free base guanidine determined 148 years after the first synthesis”: A prototype structure unveiled—despite its provocative simplicity, the crystal structure of guanidine has not been previously described. 148 years after the first synthesis of guanidine, we now find two Y‐shaped symmetry‐independent molecules in the unit cell that are interconnected by a hydrogen‐bonding network, which results in a fascinating layered structure (see picture).

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Cover Picture: Minerals as Molecules—Use of Aqueous Oxide and Hydroxide Clusters to Understand Geochemical Reactions (Chem. Eur. J. 18/2009)
Authors: Casey William H. , Rustad James R. , Spiccia Leone
Published: April 2009

A model nanoparticle respresenting goethite (α‐FeOOH), an important soil mineral, is depicted in the center of the cover picture. The solvent‐accessible surface is represented by the translucent material, and the surface oxygen atoms are represented with spheres. The colors of the spheres give their average protonation states over the course of a molecular dynamics simulation, with red denoting FeOH2 groups and blue denoting FeOH groups. Iron or aluminum Baker–Figgis–Keggin isomers are shown in the corners. For more details on the chemistry of minerals see the Concept article by W. H. Casey, J. R. Rustad and L. Spiccia on page 4496 ff.

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Target‐Based Drug Discovery: the Emerging Success of Frontal Affinity Chromatography Coupled to Mass Spectrometry
Authors: Calleri Enrica , Temporini Caterina , Caccialanza Gabriele , Massolini Gabriella
Published: April 2009

Frontal affinity chromatography coupled to mass spectrometry (FAC–MS) has been reported as a potential method for screening compound mixtures against immobilized target proteins. The potentiality of this analytical approach is described and illustrated with a number of examples based on targets of pharmaceutical interest.

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Derivation of a Retinoid X Receptor Scaffold from Peroxisome Proliferator‐Activated Receptor γ Ligand 1‐Di(1H‐indol‐3‐yl)methyl‐4‐trifluoromethylbenzene
Authors: Dawson Marcia I. , Ye Mao , Cao Xihua , Farhana Lulu , Hu Qiong‐Ying , Zhao Yong , Xu Li Ping , Kiselyuk Alice , Correa Ricardo G. , Yang Li , Hou Tingjun , Reed John C. , Itkin‐Ansari Pamela , Levine Fred , Sanner Michel F. , Fontana Joseph A. , Zhang Xiao‐Kun
Published: April 2009

PPARγ agonist DIM‐Ph‐4‐CF3, a template for RXRα agonist (E)‐3‐[5‐di(1‐methyl‐1H‐indol‐3‐yl)methyl‐2‐thienyl] acrylic acid: DIM‐Ph‐CF3 is reported to inhibit cancer growth independent of PPARγ and to interact with NR4A1. As both receptors dimerize with RXR, and natural PPARγ ligands activate RXR, DIM‐Ph‐4‐CF3 was investigated as an RXR ligand. It displaces 9‐cis‐retinoic acid from RXRα but does not activate RXRα. Structure‐based direct design led to an RXRα agonist.

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1‐Di(1H‐indol‐3‐yl)methyl‐4‐trifluoromethylbenzene (DIM‐Ph‐4‐CF3) is reported to inhibit cancer cell growth and to act as a transcriptional agonist of peroxisome proliferator‐activated receptor γ (PPARγ) and nuclear receptor 4A subfamily member 1 (NR4A1). In addition, DIM‐Ph‐4‐CF3 exerts anticancer effects independent of these receptors because PPARγ antagonists do not block its inhibition of cell growth, and the small pocket in the NR4A1 crystal structure suggests no ligand can bind. Because PPARγ and NR4A1 heterodimerize with retinoid X receptor (RXR), and several PPARγ ligands transcriptionally activate RXR, DIM‐Ph‐4‐CF3 was investigated as an RXR ligand. DIM‐Ph‐4‐CF3 displaces 9‐cis‐retinoic acid from RXRα but does not transactivate RXRα. Structure‐based design using DIM‐Ph‐4‐CF3 as a template led to the RXRα transcriptional agonist (E)‐3‐[5‐di(1‐methyl‐1H‐indol‐3‐yl)methyl‐2‐thienyl]acrylic acid. Its docked pose in the RXRα ligand binding domain suggests that binding is stabilized by interactions of its carboxylate group with arginine 316, its indoles with cysteines 269 and 432, and its 1‐methyl groups with hydrophobic residues lining the binding pocket. As is expected of a selective activator of RXRα, but not of RARs and PPARγ, this RXRα agonist, unlike DIM‐Ph‐4‐CF3, does not appreciably decrease cancer cell growth or induce apoptosis at pharmacologically relevant concentrations.
Unlocking the Chemotherapeutic Potential of β‐Aminovinyl Ketones and Related Compounds
Authors: Gaber Hatem M. , Bagley Mark C.
Published: April 2009

The role of β‐aminovinyl ketonesas synthetic intermediates has been well categorised, but recent developments have shown an interesting array of applications and new chemotherapeutic potential, both in the preparation of biologically active heterocycles and as pharmacophores in their own right.

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Medicinal chemists are accustomed to using the products of Knoevenagel‐type condensations as auxiliaries for the synthesis of N‐containing heteroaromatic compounds. One such example of these chemical building blocks are β‐aminovinyl ketones—valuable synthetic intermediates that have been used in the preparation of pyridines, pyrimidines, pyrazoles, and many other heterocyclic motifs. This review highlights their recent use in the synthesis of biologically active targets as part of drug discovery programmes and in natural product synthesis. However, it is becoming increasingly evident that the enaminone motif may serve as a therapeutic pharmacophore in its own right. This review highlights the range of biological responses that β‐aminovinyl ketones elicit, including as antitumour, antibacterial, and anticonvulsant agents. Thus, with a broad spectrum of biological properties and as versatile chemical intermediates, it is clear that β‐aminovinyl ketones offer great potential in the search for new chemotherapeutic agents.
Applications of parallel processing technologies in heuristic search planning: methodologies and experiments
Authors: Phan Tu Huy , Pontelli Enrico , Son Tran Cao , To Son Thanh
Published: April 2009

The goal of this paper is to investigate the application of parallel programming techniques to boost the performance of heuristic search‐based planning systems in various aspects. It shows that an appropriate parallelization of a sequential planning system often brings gain in performance and/or scalability. We start by describing general schemes for parallelizing the construction of a plan. We then discuss the applications of these techniques to two domain‐independent heuristic search‐based planners—a competitive conformant planner (CPA) and a state‐of‐the‐art classical planner (FF). We present experimental results—on both shared memory and distributed memory platforms—which show that the performance improvements and scalability are obtained in both cases. Finally, we discuss the issues that should be taken into consideration when designing a parallel planning system and relate our work to the existing literature. Copyright © 2009 John Wiley & Sons, Ltd.
Dynamic file system semantics to enable metadata optimizations in PVFS
Authors: Kuhn Michael , Kunkel Julian Martin , Ludwig Thomas
Published: April 2009

Modern file systems maintain extensive metadata about stored files. While metadata typically is useful, there are situations when the additional overhead of such a design becomes a problem in terms of performance. This is especially true for parallel and cluster file systems, where every metadata operation is even more expensive due to their architecture. In this paper several changes made to the parallel cluster file system Parallel Virtual File System (PVFS) are presented. The changes target at the optimization of workloads with large numbers of small files. To improve the metadata performance, PVFS was modified such that unnecessary metadata is not managed anymore. Several tests with a large quantity of files were performed to measure the benefits of these changes. The tests have shown that common file system operations can be sped up by a factor of two even with relatively few changes. Copyright © 2009 John Wiley & Sons, Ltd.
A numerical model for the oscillation frequency, the amplitude and the phase‐noise of MOS‐current‐mode‐logic ring oscillators
Authors: Nocente Michele , Fontanelli Donald , Palestri Pierpaolo , Nonis Roberto , Esseni David , Selmi Luca
Published: April 2009

This paper presents a new model for the frequency of oscillation, the oscillation amplitude and the phase‐noise of ring oscillators consisting of MOS‐current‐mode‐logic delay cells. The numerical model has been validated through circuit simulations of oscillators designed with a typical 130 nm CMOS technology. A design flow based on the proposed model and on circuit simulations is presented and applied to cells with active loads. The choice of the cell parameters that minimize phase‐noise and power consumption is addressed. Copyright © 2009 John Wiley & Sons, Ltd.
The voltage mirror–current mirror pair as a universal element
Authors: Soliman Ahmed M. , Saad Ramy A.
Published: April 2009

The voltage mirror–current mirror (VM–CM) pair is shown to be a universal active element. It provides two alternative realizations for the nullor. The VM–CM pair is also capable of realizing the op amp and all the four types of the current conveyors namely CCII−, CCII+, ICCII− and ICCII+ as special cases. Copyright © 2009 John Wiley & Sons, Ltd.
Induction of DNA damage response by the supravital probes of nucleic acids
Authors: Zhao Hong , Traganos Frank , Dobrucki Jurek , Wlodkowic Donald , Darzynkiewicz Zbigniew
Published: April 2009

The aim of this study was to assess the potential DNA damage response (DDR) to four supravitally used biomarkers Hoechst 33342 (Ho 42), DRAQ5, DyeCycle Violet (DCV), and SYTO 17. A549 cells were exposed to these biomarkers at concentrations generally applied to live cells and their effect on histone H2AX (Ser 139), p53 (Ser15), ATM (Ser1981), and Chk2 (Thr68) phosphorylation was assessed using phospho‐specific Abs. Short‐term treatment with Ho 42 led to modest degree of ATM activation with no evidence of H2AX, Chk2, or p53 phosphorylation. However, pronounced ATM, Chk2, and p53 phosphorylation and perturbed G2 progression were seen after 18 h. While short‐term treatment with DRAQ5 induced ATM activation with no effect on H2AX, Chk2, and p53, dramatic changes marked by a high degree of H2AX, ATM, Chk2, and p53 phosphorylation, all occurring predominantly in S phase cells, and a block in cell cycle progression, were seen after 18 h exposure. These changes suggest that the DRAQ5‐induced DNA lesions may become converted into double‐strand DNA breaks during replication. Exposure to DCV also led to an increase in the level of activated ATM and Chk2 as well as of phosphorylated p53 and accumulation of cells in G2M and S phase. Exposure to SYTO 17 had no significant effect on any of the measured parameters. The data indicate that supravital use of Ho 42, DRAQ5, and DCV induces various degrees of DDR, including activation of ATM, Chk2 and p53, which may have significant consequences on regulatory cell cycle pathways and apoptosis. © 2009 International Society for Advancement of Cytometry.
Nachweis der Feuerwiderstandsdauer von Ziegeldecken durch Kombination von Versuch und Simulation
Authors: Jäger Wolfram , Ortlepp Sebastian
Published: April 2009

Der Nachweis der Feuerwiderstandsdauer von Ziegeldecken erfolgte bisher i. d. R. über Brandversuche, die sehr aufwendig und teuer sind. Der Beitrag zeigt, wie durch Kombination von Versuch, Simulation und ingenieurmäßiger Betrachtung eine bedeutende Aufwandsreduzierung erreicht werden kann.

Im Rahmen der Typenstatik von zwei Ziegeldecken Typ 22 (17+5) und Typ 25 (20+5) konnte ohne Estrich und Putz die Feuerwiderstandsdauer F60‐A erreicht werden. Mit einem zusätzlichen unterseitigen Putz (1cm Gipsputz) und mit einem schwimmenden Estrich (≥ 2,5 cm) wurde die Klasse F90‐A erreicht. Um die Feuerwiderstandsklasse F90‐A für Typ 22 und Typ 25 auch ohne Putz und Estrich zu erreichen, wurde für den Deckentyp mit Aufbeton Typ22 (17+5) eine Brandprüfung durchgeführt. Ausgehend von den Ergebnissen dieses Versuches fand eine weitergehende Auswertung und Verallgemeinerung auf andere Deckentypen statt, die nachfolgend vorgestellt wird.
Deutschland braucht neue Wohnungen – Kampagne für den Wohnungsbau
Authors: Rast Ronald
Published: April 2009

Die Anfang 2009 gestartete Kampagne “Impulse für den Wohnungsbau” setzt sich für eine Verbesserung der bestehenden politischen Rahmenbedingungen im Wohnungsbau ein. Hintergrund ist der bestehende Mangel an bezahlbaren und geeigneten Wohnungen. Obwohl jährlich 400000 Wohnungen benötigt werden, wurden in 2008 weniger als 200000 fertiggestellt. Die Deutsche Gesellschaft für Mauerwerksbau und der Bundesverband Deutscher Baustoff‐Fachhandel engagieren sich gemeinsam mit weiteren Verbänden und Unternehmen aus dem Wohnungsbau und der Immobilienwirtschaft für das Grundbedürfnis Wohnen. Gemeinsames Ziel ist, die Handlungsfelder der Zukunft auf die politische Agenda zu setzen: Die Menschen in Deutschland brauchen bezahlbare, barrierefreie und energieeffiziente Wohnungen.
Accuracy of a low priced liquid‐based method for cervical cytology in 632 women referred for colposcopy after a positive Pap smear
Authors: van Hemel B. M. , Buikema H. J. , Groen H. , Suurmeijer A. J. H.
Published: April 2009

The aim of this quality controlling study was to determine the accuracy of liquid‐based cytology (LBC) with the Turbitec® cytocentrifuge technique. Cervical smears of 632 women, who were referred to our CIN outpatient department, after at least two smears with ASCUS or higher were evaluated and compared with the histological outcome. In 592 cases the smears revealed abnormalities of squamous epithelium, and in 40 cases the abnormalities of glandular epithelium. In the group of squamous epithelium abnormalities, the sensitivity for LSIL was 39.7% and the specificity was 89.2%; for the LSIL+ group, these values were 89.4% and 91.4%, respectively. For HSIL the sensitivity was 68.3% and the specificity 92.8%, for the HSIL+ group 82.3% and 92.3%, respectively. The ASCUS rate was low (2.4%). The Turbitec cytocentrifuge method was proved to be a very good LBC method for cervical smears. Because of a comparable accuracy together with a lower price, this LBC method outweighs commercial alternatives. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Hodgkin's lymphoma: Diagnostic difficulties in fine‐needle aspiration cytology
Authors: Das Dilip K. , Francis Issam M. , Sharma Prem N. , Sathar Sitara A. , John Bency , George Sara S. , Mallik Mrinmay K. , Sheikh Zaffar A. , Haji Bahiyah E. , Pathan Shahed K. , Madda John P. , Mirza Kahvic , Ahmed Mahamoud S. , Junaid Thamradeen A.
Published: April 2009

It is commonly believed that cytodiagnosis of Hodgkin's lymphoma (HL) is much easier than that of non‐Hodgkin lymphoma (NHL). However, recognition of certain NHL subtypes with Reed‐Sternberg (R‐S)‐like cells and results of immunohistochemical studies point to the contrary. To study the limitations of cytology in diagnosis of HL, fine‐needle aspiration (FNA) smears of 130 lymphoma or suspected lymphoma cases were reviewed. Initial and reviewed cytodiagnoses were compared with histopathology in 89 cases. Immunocytochemical and immunohistochemical studies were performed in 56 and 59 cases, respectively. Among histologically diagnosed HL cases, definitive cytodiagnosis of HL (initial as well as reviewed) was significantly less frequent than cytodiagnosis of NHL among histologically diagnosed NHL cases (P = 0.0328 and = 0.0001, respectively). On the other hand, cytologically diagnosed HL/NHL cases were significantly more frequent in the former group (P = 0.0001 and = 0.0018, respectively). ALCL and TCRBCL were the two NHL subtypes which created confusion with HL in FNA smears. Twenty‐one cytohistological concordant HL cases and equal number of discordant cases were compared. When compared with discordant group, the patients in concordant group were significantly younger (P = 0.045). Hodgkin/Hodgkin‐like cells and typical R‐S cells were significantly more frequent in FNA smears of the concordant group (P = 0.0478 and = 0.0431, respectively). Immunocytochemical and immunohistochemical studies showed good correlation with histological diagnosis of HL. It is suggested that proper interpretation of cytologic features, together with use of immunocytochemical parameters can help in reducing the margin of error in cytodiagnois of HL. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Epithelioid cell cluster in cerebrospinal fluid: An unusual finding in tubercular meningitis
Authors: Arif S. H. , Rahman Khaliqur , Khalid Mohammad , Hassan Mohd. Jaseem , Qaseem S. M. Danish , Huda Md. Fakhrul
Published: April 2009

Tubercular meningitis is one of the serious manifestations of tuberculosis. It remains a significant contributor to the morbidity and mortality in children. Meningeal involvement in tuberculosis is detected by physical, chemical and cytological examination of cerebrospinal fluid (CSF). The cytological picture of CSF in tubercular meningitis is quite similar to that of viral meningitis showing a mixed population of lymphoid series cells. The presence of epithelioid cell cluster is very rare finding. We present here such a case of 2½ yr old boy who presented with fever off and on for 2 months and altered sensorium along with vomiting for 2–3 days. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Adrenal extranodal NK/T‐cell lymphoma diagnosed by fine‐needle aspiration and cerebrospinal fluid cytology and immunophenotyping: A case report
Authors: Dunning Karla K. , Wudhikarn Kitsada , Safo Anthony‐Osei , Holman Carol J. , McKenna Robert W. , Pambuccian Stefan E.
Published: April 2009

The cytologic findings of an extranodal NK/T‐cell lymphoma (NKTCL) presenting as a large adrenal mass with leptomeningeal involvement diagnosed by CT‐guided fine‐needle aspiration and cerebrospinal fluid (CSF) cytology are described. The 65‐year‐old Caucasian patient presented with progressive headache and multiple cranial nerve neuropathies. Magnetic resonance imaging showed leptomeningeal enhancement surrounding the conus medullaris and cauda equine, and a subsequent PET/CT demonstrated a large right adrenal gland mass. Fine‐needle aspiration of the adrenal mass showed occasional large pleomorphic cells with prominent nucleoli, moderate amounts of cytoplasm, and rare large cells with sparse cytoplasmic granules admixed with numerous small lymphocytes. Initial flow cytometry from this sample showed no clonal B‐cell population. Immunoperoxidase stains performed on the cell block/core specimen showed that the large atypical cells were positive for CD2, CD30, CD43 and CD56, TIA‐1, granzyme, and perforin, but for none of the other T‐cell markers used (CD3, CD4, CD5, CD8, CD45RO), which stained the abundant background lymphocytes. A CSF specimen showed similar neoplastic cells and flow cytometry showed an NK‐cell population with aberrant immunophenotype. The cytologic findings of the neoplastic cells and the extensive panel of immunoperoxidase stains allowed the diagnosis of NKTCL, which was confirmed by the subsequent flow‐cytometric immunophenotyping performed on the CSF. This is, to the best of our knowledge, the first case of NKTCL diagnosed by FNA of the adrenal gland and by CSF cytology. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Comparison between a traditional single still image and a multiframe video image along the z‐axis of the same microscopic field of interest in cytology: Which does contribute to telecytology?
Authors: Yamashiro Katsushige , Taira Kiyomi , Matsubayashi Satoshi , Azuma Manabu , Okuyama Dai , Nakajima Manami , Takeda Hiroko , Suzuki Hiroaki , Kawamura Naoki , Wakao Fumihiko , Yagi Yukako
Published: April 2009

The limitation of cytologic still images is one of the reasons why telecytology has not met with widespread acceptance by the cytology community. Cytologic still image only displays a single depth of field, and this is a particularly acute problem in cytology where the specimen is often much thicker than a single microscopic depth of focus. In this article, we examine the validity of a “z‐axis” video of a microscopic field of interest.

After observing videos of fields of interest from 10 cases, five cytotechnologists reached suitable cytologic findings and diagnosed the fields correctly in great majority of cases. Five other cytotechnologists, who looked only at a single representative still image, could not always make a correct diagnosis. The difference between two observer groups was statistically significant by Wilcoxon's matched pairs signed‐rank test.

The results indicate that “z‐axis” video of microscopic field of interest provides a similar experience to “focusing through” observation of the specimen under a microscope and may improve an accuracy of primary telecytodiagnosis. And we expect that video image telecytology will strongly influence cytology, especially in education and training. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.