bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of ionization energy change on valence band offset in organic p-n junction
Authors: Akaike Kouki , Kanai Kaname , Ouchi Yukio , Seki Kazuhiko
Published: September 2009

Valence band offsets at [6,6]-phenyl-C61-butyric acid methyl ester (PCBM)/metallophthalocyanine (MPc, M=Cu and Zn) interfaces have been investigated with ultraviolet photoelectron spectroscopy, which are organic p-n junctions in organic photovoltaics. The highest occupied molecular orbitals of MPcs rise toward the interface, while that of PCBM lowers. This behavior implies that the different energy band offsets from inorganic p-n junction are realized in organic p-n junction. The depletion layers were not observed at the interfaces. Such anomalous energy band offsets are attributed to the interfacial dipole and also ionization energy changes of MPcs and PCBM at the interface.
Transmission of doughnut light through a bull’s eye structure
Authors: Wang Lu-Lu , Ren Xi-Feng , Yang Rui , Guo Guang-Can , Guo Guo-Ping
Published: September 2009

We experimentally investigate the extraordinary optical transmission of doughnut light through a bull’s eye structure. Since the intensity is vanished in the center of the beam, almost all the energy reaches the circular corrugations (not on the hole), and excites surface plasmons, which propagate through the hole and reradiate photons. The transmitted energy is about 32 times of the energy input on the hole area. It is also interesting that the transmitted light has a similar spatial shape with the input light even though the diameter of the hole is much smaller than the wavelength of light.
Polymer hydrophilicity and hydrophobicity induced by femtosecond laser direct irradiation
Authors: Wang Z. K. , Zheng H. Y. , Lim C. P. , Lam Y. C.
Published: September 2009

Controlled modification of surface wettability of polymethyl methacrylate (PMMA) was achieved by irradiation of PMMA surface with femtosecond laser pulses at various laser fluences and focus distances. Fluences from 0.40 to 2.1 J/cm2 produced a hydrophobic surface and 2.1 to 52.7 J/cm2 (maximum investigated) produced a hydrophilic surface. Fluences less than 0.31 J/cm2 had no effect on the wettability of the raw PMMA. This change in wettability was caused dominantly by laser induced chemical structure modification and not by a change in surface roughness.
Lipid Core Peptide System for Gene, Drug, and Vaccine Delivery
Authors: Zhong Wei , Skwarczynski Mariusz , Toth Istvan
Published: September 2009

A vast number of biologically active compounds await efficient delivery to become therapeutic agents. Lipidation has been demonstrated to be a convenient and useful approach to improve the stability and transport across biological membranes of potential drug molecules. The lipid core peptide (LCP) system has emerged as a promising lipidation tool because of its versatile features. This review discusses the progress in the development of the LCP system to improve cell permeability of nucleotides, physicochemical properties of potential drugs, and vaccine immunogenicity. Emphasis was put on the application of the LCP system to deliver antigens for the prevention of group A streptococcus infection, novel techniques of conjugation of target molecules to the LCP, and new alterations of the LCP system itself.
A Molecular Chain of Four CoII Ions Stabilized by a Tris-Pyridyl/Bis-?-Diketonate Ligand
Authors: Barrios Leoní A. , Aguilà David , Roubeau Olivier , Murray Keith S. , Aromí Guillem
Published: September 2009

The synthesis and characterization of a tris-pyridyl/bis-β-diketone molecule (H2L) is reported. This compound acts as a hexadentate ligand towards CoII to facilitate the assembly of a tetranuclear molecular chain of closely spaced metals with formula [Co4L2(MeOH)8](NO3)4 (1), which exhibits a very flat [Co4L2]4+ platform, as determined by single-crystal X-ray diffraction crystallography. Complex 1 readily exchanges axial methanol ligands with water molecules. The bulk magnetization of the resulting hydrate, 1a, shows that the metals in the [Co4L2]4+ moiety exhibit spin-orbit coupling and antiferromagnetic exchange interactions.
Structures and Suzuki-Coupling of N-Heterocyclic Carbene Complexes of PdII with Coordinated Solvent and PPh3
Authors: Yen Swee Kuan , Koh Lip Lin , Huynh Han Vinh , Hor T. S. Andy
Published: September 2009

A series of mononuclear N,N-heterocyclic carbene (NNHC) complexes of PdII with mixed ligands of 1,3-dibenzylbenzimidazoly-2-ylidene and solvate (dimethyl sulfoxide, CH3CN, N,N-dimethylformamide, and pyridine) or PPh3 were prepared and characterized by X-ray single-crystal diffraction analysis. They are more active in the Suzuki–Miyaura coupling of selected aryl bromides than their N,S-heterocyclic carbene (NSHC) analogues.
Synthesis of Novel Diazabicycles and their Antiprotozoal Activities
Authors: Wolkinger Volker , Weis Robert , Belaj Ferdinand , Kaiser Marcel , Brun Reto , Saf Robert , Seebacher Werner
Published: September 2009

We describe the synthesis of new diaryl substituted diazabicyclo[3.2.1]octanes from diazepanes which were prepared by the reduction of diazepanones. The formation of the bicyclic system was optimized by microwave irradiation and the structures of the new compounds were established by single crystal structure analysis and NMR spectroscopy. All new compounds were tested for their potencies against Plasmodium falciparum K1 and Trypanosoma b. rhodesiense, the causative organisms of malaria tropica and the East African form of sleeping sickness.
An Octanuclear Iron(III) Cluster Complex Containing the Nitroso Bridging Ligand Carbamoylcyanonitrosomethanide
Authors: Chesman Anthony S. R. , Turner David R. , Moubaraki Boujemaa , Murray Keith S. , Deacon Glen B. , Batten Stuart R.
Published: September 2009

The synthesis, structure, and magnetism is reported for an antiferromagnetically coupled, disc-shaped cluster containing the anionic ligand carbamoylcyanonitrosomethanide (ccnm), [Fe8O6(MeO)6(ccnm)6], with an FeIII8O3 core.
Ferromagnetic [Mn3] Single-Molecule Magnets and Their Supramolecular Networks
Authors: Inglis Ross , Papaefstathiou Giannis S. , Wernsdorfer Wolfgang , Brechin Euan K.
Published: September 2009

The complexes [MnIII3O(Et-sao)3(O2CPh(Cl)2)(MeOH)3(H2O)] (1), [MnIII3O(Et-sao)3(ClO4)(MeOH)3] (2), [MnIII3O(Et-sao)3(O2Ph(CF3)2)(EtOH)(H2O)3] (3), and [MnIII3O(Ph-sao)3(O2C-anthra)(MeOH)4]·Ph-saoH2 (4·Ph-saoH2) display dominant ferromagnetic exchange interactions leading to molecules with S = 6 ground states. The molecules are single molecule magnets (SMM) displaying large effective energy barriers for magnetization reversal. In each case their crystal structures reveal multiple intermolecular H-bonding interactions. Single crystal hysteresis loop measurements demonstrate that these interactions are strong enough to cause a clear field bias, but too weak to transform the spin networks into classical antiferromagnets. These three-dimensional networks of exchange coupled SMMs demonstrate that quantum tunnelling magnetization can be controlled using exchange interactions, suggesting supramolecular chemistry can be exploited to modulate the quantum physics of molecular magnets.
Synthesis and Coordination Chemistry of Doubly-Tridentate Tripodal Pyridazine and Pyrimidine-Derived Ligands: Structural Interplay Between M2L and M2L2 (M = Ni and Pd) Complexes and Magnetic Properties of Iron(II) Complexes
Authors: Sumby Christopher J. , Leita Ben A. , Moubaraki Boujemaa , Murray Keith S. , Steel Peter J.
Published: September 2009

The coordination chemistry of three bridging doubly-tridentate ligands, including the known compound 3,6-bis(di-2-pyridylmethyl)pyridazine (1), which is structurally similar to 1,4-bis(di-2-pyridylmethyl)phthalazine (2), and two pyrimidine-linked compounds 4,6-bis(di-2-pyridylmethyl)pyrimidine (3), and 4,6-bis(di-2-pyridylamino)pyrimidine (4), was investigated with FeII, NiII, and PdII metal salts. Ligands 3 and 4 were synthesized in one-pot reactions from easily obtained starting materials; compound 3 was synthesized from di-2-pyridylmethane and 4,6-diiodopyrimidine in 48% yield, while ligand 4 was prepared by reacting di-2-pyridylamine with 4,6-dichloropyrimidine in 27% yield. During the synthesis of 4, an additional compound, 4-chloro-6-(di-2-pyridylamino)pyrimidine (5), with only one tridentate binding site was obtained in 30% yield. Reactions of 1, 3, and 4 with FeII or NiII salts gave two types of complexes, either discrete M2L or M2L2 assemblies. The PdII complexes obtained were also characterized as discrete M2L complexes. The compounds were characterized by a combination of NMR and IR spectroscopy, microanalysis and X-ray crystallography. Noticeable differences in the structures obtained for NiII coordination complexes with the carbon-linked (3) and nitrogen-linked (4) ligands were observed, whereby the nitrogen linker adopted a trigonal planar geometry and prevented tridentate facial coordination of the octahedral metal centres. The magnetic properties of dinuclear FeII complexes of 1 were examined to see if they showed spin-crossover effects, a feature recently observed by others in other dinuclear helicate complexes, but the complexes remained high-spin at all temperatures between 300 and 2 K.
A Tetranuclear Mixed-Valence Manganese Complex of a Diimine Ligand Derived from 1,4-Diformyl-2,3-dihydroxybenzene: Synthesis, Structure, and Magnetic Properties
Authors: Feltham Humphrey L. C. , Clérac Rodolphe , Brooker Sally
Published: September 2009

An acyclic hexadentate diimine ligand, H4L1, was prepared in situ in methanol by the condensation of 1,4-diformyl-2,3-dihydroxybenzene (1) with 2-aminoethanol, and complexed directly with two equivalents of MnII(OAc)2·4H2O or MnIII(OAc)3·2H2O, or with one equivalent of each. All three of these one-pot reactions gave the mixed-valent tetrametallic complex [MnII2MnIII2(L1)2(OAc)2(solvents)4], [2(solvents)4]. An X-ray crystal structure determination on [2(MeOH)4]·2MeOH revealed a centre of inversion in the middle of the complex. The four metal ions are in an almost planar array, sandwiched by two offset ligands which provide all of the equatorial donors, with the axial sites occupied by acetate ions and methanol molecules. The two manganese(II) ions are seven coordinate and centrally located, whereas the two manganese(III) ions are Jahn–Teller elongated octahedra and are located in the outer sites. Magnetic analysis of an air-dried sample, [2(MeOH)2(H2O)2]·3H2O, showed that weak antiferromagnetic interactions between the manganese ions dominate, resulting in a low ground spin state.
Mixed-Valent Polynuclear Cobalt Complexes Incorporating Tetradentate Phenoxyamine Ligands
Authors: Ang Joo Chuan , Mulyana Yanyan , Ritchie Chris , Clérac Rodolphe , Boskovic Colette
Published: September 2009

The new potentially tetradentate ligand precursor 2-[(bis(2-hydroxyethyl)amino)methyl]-4,6-bis-tert-butylphenol (H3L) has been synthesized and characterized. The reaction of H3L with cobalt(ii) acetate has afforded the novel mixed-valent tetra- and pentanuclear cobalt complexes [CoII2CoIII2(OAc)2(L)2(HL)] (1) and [CoIICoIII4(OAc)2(L)4] (2). Single-crystal X-ray diffraction studies of these complexes indicate different coordination geometries for the divalent cobalt centres in each complex, with distorted trigonal bipyramidal and distorted tetrahedral coordination evident in 1 and 2, respectively. The variable temperature magnetic susceptibility data for complex 1 reveal behaviour dominated by antiferromagnetic coupling between the two cobalt(ii) centres. Their approximate trigonal bipyramidal coordination geometries give rise to a 4A′2 ground term, allowing a spin-only treatment assuming local spin quantum numbers of Si = 3/2. Fitting the data to the Heisenberg exchange Hamiltonian (Ĥex = –2JS·1S2) results in J = –6.9(1) cm–1 and g = 2.30(5).
Colorimetric Sensor Array for Qualitative Water Analysis
Authors: Chan Shu Ann , Lee Jun-Seok , Chang Young-Tae
Published: September 2009

A chemosensor array comprising 45 off-the-shelf colorimetric dyes, dubbed the Singapore Tongue (SGT), that is capable of discriminating different brands of bottled water and waters of different geographical attribute is described. Twelve kinds of bottled waters were tested by the SGT, and changes of absorbance spectra were analyzed by unsupervised classification methods to validate the SGT system for water analysis. All 12 bottled waters were discriminated at 1 × concentration, and SGT could distinguish the identity of samples of the waters diluted up to 100 times, except distilled waters. Following the study of 63 tap waters in different mass rapid transit stations in Singapore, two distinct clusters were observed from a principal component analysis plot, which correspond to the origin of the tap water. The successful discrimination and identification of in this study demonstrates the practical application of the SGT as a simple tool for water analysis.
Highly Twisted C=C Double Bonds in 4-Methyleneisoxazolones
Authors: Kvaskoff David , Bernhardt Paul V. , Koch Rainer , Wentrup Curt
Published: September 2009

As determined by X-ray crystallography, isoxazol-5(4H)-one derivatives 12–19 feature dihedral angles around the exocyclic C4=C6 double bonds of 26–90°. In the most highly twisted bis-tert-butylamino derivatives 18 and 19, the C4–C6 bonds are essentially single bonds. Density functional theory calculations at the B3LYP/6-31G(d) level with inclusion of a simulated solvent field, which helps stabilize zwitterionic structures, are in good agreement with the experimental crystallographic data. A good correlation between bond lengths and calculated π/π* orbital occupation quotients is observed. A good correlation between the twisting angle and the charge separation, measured by the calculated negative charge on the isoxazolone moiety, is also observed. Low barriers to rotation about the twisted exocyclic double bonds C4=C6 in compounds 13, 20, and 21 (ΔG
‡ = 15–16 kcal mol–1 (63–67 kJ mol–1)) were determined by dynamic 1H NMR coalescence measurements. The rotational barrier for 17 was estimated to be less than 10 kcal mol–1. The rotational barriers for compounds 10 and 18 were calculated to be ~8 kcal mol–1.
Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel
Authors: Zhang Ce , Shao Pei Ge , van Kan Jeroen A. , van der Maarel Johan R. C.
Published: September 2009

The effect of dextran nanoparticles on the conformation and compaction of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. It was observed that the DNA molecules elongate and eventually condense into a compact form with increasing volume fraction of the crowding agent. Under crowded conditions, the channel diameter is effectively reduced, which is interpreted in terms of depletion in DNA segment density in the interfacial region next to the channel wall. Confinement in a nanochannel also facilitates compaction with a neutral crowding agent at low ionic strength. The threshold volume fraction for condensation is proportional to the size of the nanoparticle, due to depletion induced attraction between DNA segments. We found that the effect of crowding is not only related to the colligative properties of the agent and that confinement is also important. It is the interplay between anisotropic confinement and osmotic pressure which gives the elongated conformation and the possibility for condensation at low ionic strength.
No place like home?
Authors: Just Sine Nørholm
Published: September 2009

Media representations of the EU provide significant clues as to how citizens make sense of the EU/Europe, wherefore analyses of such representations are central to European studies as such. This paper aims to explain how the media represented the EU at the onset of the European constitutional process. To that end the paper employs a modified version of frame analysis which includes a corpus linguistic identification of dominant topical frames and a close discursive-rhetorical reading of the formal framing of the topics. The analysis shows that the news coverage offers the readers no sense of belonging to the EU. On the one hand, citizens are represented as being disengaged from the European integration process. On the other hand, the EU is not represented as a stable entity. Instead, the EU is defined as the very process which citizens are said to shun.
At the intersection between power and knowledge
Authors: Milani Tommaso M.
Published: September 2009

The aim of this article is to analyse a policy document in which the Swedish Liberal Party attempts to substantiate the proposal to introduce a Swedish language test for naturalisation by referring to academic production. Taking this specific text as a case in point, the article draws upon Critical Discourse Analysis and Foucault’s notion of governmentality to show how the rationalisation and legitimation of a particular political proposal is inextricably related to processes of knowledge production. Governmentality will also allow us to understand that language requirements for citizenship are a tangible manifestation of an advanced liberal political rationality in late modernity.
What’s in a pear film narrative?
Authors: Blackwell Sarah E.
Published: September 2009

This study examines twenty pear film narratives (Chafe 1980), produced by native speakers of Castilian Spanish, following the ‘frames/schema’ model used by Tannen and Wallat (1993) in their study of a medical examination/interview. By analyzing the narratives in terms of interactive frames (originally defined by Bateson 1954) and knowledge schemas, we can see how frames and schemas interact and how participants’ expectations influence framings. Using a discourse-analytical approach, I show how various linguistic elements in the discourse convey (implicitly or explicitly) the speakers’ framings (i.e. the activities they are participating in when speaking) and their expectations about the study itself, films, elements in the pear film and their perceived roles when speaking. Segments of the discourse can convey simultaneous (merged) framings or sequential framings. The analysis shows that in order to fully account for the discourse produced during the Spanish narrators’ retelling of the pear film, we must take into consideration the participants’ underlying knowledge schemas resulting from their cultural experiences living in a rural town in Spain, the influence of and assumptions about the situation in which they find themselves and about the activity they are participating in, and the fact that the narrative discourse is co-constructed as an interactive conversational activity with interlocutors who are family members or friends of the narrators.
Glucose Promotes Stress Resistance in the Fungal PathogenCandida albicans
Authors: Rodaki Alexandra , Bohovych Iryna M. , Enjalbert Brice , Young Tim , Odds Frank C. , Gow Neil A.R. , Brown Alistair J.P.
Published: September 2009

Metabolic adaptation, and in particular the modulation of carbon assimilatory pathways during disease progression, is thought to contribute to the pathogenicity of Candida albicans. Therefore, we have examined the global impact of glucose upon the C. albicans transcriptome, testing the sensitivity of this pathogen to wide-ranging glucose levels (0.01, 0.1, and 1.0%). We show that, like Saccharomyces cerevisiae, C. albicans is exquisitely sensitive to glucose, regulating central metabolic genes even in response to 0.01% glucose. This indicates that glucose concentrations in the bloodstream (approximate range 0.05–0.1%) have a significant impact upon C. albicans gene regulation. However, in contrast to S. cerevisiae where glucose down-regulates stress responses, some stress genes were induced by glucose in C. albicans. This was reflected in elevated resistance to oxidative and cationic stresses and resistance to an azole antifungal agent. Cap1 and Hog1 probably mediate glucose-enhanced resistance to oxidative stress, but neither is essential for this effect. However, Hog1 is phosphorylated in response to glucose and is essential for glucose-enhanced resistance to cationic stress. The data suggest that, upon entering the bloodstream, C. albicans cells respond to glucose increasing their resistance to the oxidative and cationic stresses central to the armory of immunoprotective phagocytic cells.
Expression and Activity of Phosphodiesterase Isoforms during Epithelial Mesenchymal Transition: The Role of Phosphodiesterase 4
Authors: Kolosionek Ewa , Savai Rajkumar , Ghofrani Hossein Ardeschir , Weissmann Norbert , Guenther Andreas , Grimminger Friedrich , Seeger Werner , Banat Gamal Andre , Schermuly Ralph Theo , Pullamsetti Soni Savai
Published: September 2009

Epithelial–mesenchymal transition (EMT) has emerged as a critical event in the pathogenesis of organ fibrosis and cancer and is typically induced by the multifunctional cytokine transforming growth factor (TGF)-β1. The present study was undertaken to evaluate the potential role of phosphodiesterases (PDEs) in TGF-β1-induced EMT in the human alveolar epithelial type II cell line A549. Stimulation of A549 with TGF-β1 induced EMT by morphological alterations and by expression changes of the epithelial phenotype markers E-cadherin, cytokeratin-18, zona occludens-1, and the mesenchymal phenotype markers, collagen I, fibronectin, and α-smooth muscle actin. Interestingly, TGF-β1 stimulation caused twofold increase in total cAMP-PDE activity, contributed mostly by PDE4. Furthermore, mRNA and protein expression demonstrated up-regulation of PDE4A and PDE4D isoforms in TGF-β1-stimulated cells. Most importantly, treatment of TGF-β1 stimulated epithelial cells with the PDE4-selective inhibitor rolipram or PDE4 small interfering RNA potently inhibited EMT changes in a Smad-independent manner by decreasing reactive oxygen species, p38, and extracellular signal-regulated kinase phosphorylation. In contrast, the ectopic overexpression of PDE4A and/or PDE4D resulted in a significant loss of epithelial marker E-cadherin but did not result in changes of mesenchymal markers. In addition, Rho kinase signaling activated by TGF-β1 during EMT demonstrated to be a positive regulator of PDE4. Collectively, the findings presented herein suggest that TGF-β1 mediated up-regulation of PDE4 promotes EMT in alveolar epithelial cells. Thus, targeting PDE4 isoforms may be a novel approach to attenuate EMT-associated lung diseases such as pulmonary fibrosis and lung cancer.
Sox9 Family Members Negatively Regulate Maturation and Calcification of Chondrocytes through Up-Regulation of Parathyroid Hormone–related Protein
Authors: Amano Katsuhiko , Hata Kenji , Sugita Atsushi , Takigawa Yoko , Ono Koichiro , Wakabayashi Makoto , Kogo Mikihiko , Nishimura Riko , Yoneda Toshiyuki
Published: September 2009

Sox9 is a transcription factor that plays an essential role in chondrogenesis and has been proposed to inhibit the late stages of endochondral ossification. However, the molecular mechanisms underlying the regulation of chondrocyte maturation and calcification by Sox9 remain unknown. In this study, we attempted to clarify roles of Sox9 in the late stages of chondrocyte differentiation. We found that overexpression of Sox9 alone or Sox9 together with Sox5 and Sox6 (Sox5/6/9) inhibited the maturation and calcification of murine primary chondrocytes and up-regulated parathyroid hormone–related protein (PTHrP) expression in primary chondrocytes and the mesenchymal cell line C3H10T1/2. Sox5/6/9 stimulated the early stages of chondrocyte proliferation and development. In contrast, Sox5/6/9 inhibited maturation and calcification of chondrocytes in organ culture. The inhibitory effects of Sox5/6/9 were rescued by treating with anti-PTHrP antibody. Moreover, Sox5/6/9 bound to the promoter region of the PTHrP gene and up-regulated PTHrP gene promoter activity. Interestingly, we also found that the Sox9 family members functionally collaborated with Ihh/Gli2 signaling to regulate PTHrP expression and chondrocyte differentiation. Our results provide novel evidence that Sox9 family members mediate endochondral ossification by up-regulating PTHrP expression in association with Ihh/Gli2 signaling.
A dictionary to identify small molecules and drugs in free text
Authors: Hettne Kristina M. , Stierum Rob H. , Schuemie Martijn J. , Hendriksen Peter J. M. , Schijvenaars Bob J. A. , Mulligen Erik M. van , Kleinjans Jos , Kors Jan A.
Published: September 2009

Motivation: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers.

Results: We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB and ChemIDplus. Rule-based term filtering, manual check of highly frequent terms and disambiguation rules were applied. We tested the combined dictionary and the dictionaries derived from the individual resources on an annotated corpus, and conclude the following: (i) each of the different processing steps increase precision with a minor loss of recall; (ii) the overall performance of the combined dictionary is acceptable (precision 0.67, recall 0.40 (0.80 for trivial names); (iii) the combined dictionary performed better than the dictionary in the chemical recognizer OSCAR3; (iv) the performance of a dictionary based on ChemIDplus alone is comparable to the performance of the combined dictionary.

Availability: The combined dictionary is freely available as an XML file in Simple Knowledge Organization System format on the web site http://www.biosemantics.org/chemlist.

Contact:  k.hettne@erasmusmc.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
3D-SURFER: software for high-throughput protein surface comparison and analysis
Authors: La David , Esquivel-Rodríguez Juan , Venkatraman Vishwesh , Li Bin , Sael Lee , Ueng Stephen , Ahrendt Steven , Kihara Daisuke
Published: September 2009

Summary: We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites as well as protrusions and flat regions can also be identified and visualized.

Availability: 3D-SURFER is a web application that can be freely accessed from: http://dragon.bio.purdue.edu/3d-surfer

Contact:  dkihara@purdue.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
Authors: Shen Ronglai , Olshen Adam B. , Ladanyi Marc
Published: September 2009

Motivation: The molecular complexity of a tumor manifests itself at the genomic, epigenomic, transcriptomic and proteomic levels. Genomic profiling at these multiple levels should allow an integrated characterization of tumor etiology. However, there is a shortage of effective statistical and bioinformatic tools for truly integrative data analysis. The standard approach to integrative clustering is separate clustering followed by manual integration. A more statistically powerful approach would incorporate all data types simultaneously and generate a single integrated cluster assignment.

Methods: We developed a joint latent variable model for integrative clustering. We call the resulting methodology iCluster. iCluster incorporates flexible modeling of the associations between different data types and the variance–covariance structure within data types in a single framework, while simultaneously reducing the dimensionality of the datasets. Likelihood-based inference is obtained through the Expectation–Maximization algorithm.

Results: We demonstrate the iCluster algorithm using two examples of joint analysis of copy number and gene expression data, one from breast cancer and one from lung cancer. In both cases, we identified subtypes characterized by concordant DNA copy number changes and gene expression as well as unique profiles specific to one or the other in a completely automated fashion. In addition, the algorithm discovers potentially novel subtypes by combining weak yet consistent alteration patterns across data types.

Availability: R code to implement iCluster can be downloaded at http://www.mskcc.org/mskcc/html/85130.cfm

Contact:  shenr@mskcc.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genome analysis with inter-nucleotide distances
Authors: Afreixo Vera , Bastos Carlos A. C. , Pinho Armando J. , Garcia Sara P. , Ferreira Paulo J. S. G.
Published: September 2009

Motivation: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis. Several mapping schemes have been used in the past, but they seem unrelated to any intrinsic characteristic of DNA. The objective of this work was to find a mapping scheme directly related to DNA characteristics and that would be useful in discriminating between different species. Mathematical models to explore DNA correlation structures may contribute to a better knowledge of the DNA and to find a concise DNA description.

Results: We developed a methodology to process DNA sequences based on inter-nucleotide distances. Our main contribution is a method to obtain genomic signatures for complete genomes, based on the inter-nucleotide distances, that are able to discriminate between different species. Using these signatures and hierarchical clustering, it is possible to build phylogenetic trees. Phylogenetic trees lead to genome differentiation and allow the inference of phylogenetic relations. The phylogenetic trees generated in this work display related species close to each other, suggesting that the inter-nucleotide distances are able to capture essential information about the genomes. To create the genomic signature, we construct a vector which describes the inter-nucleotide distance distribution of a complete genome and compare it with the reference distance distribution, which is the distribution of a sequence where the nucleotides are placed randomly and independently. It is the residual or relative error between the data and the reference distribution that is used to compare the DNA sequences of different organisms.

Contact:  vera@ua.pt
Effect of Storage Temperature for Paddy on Consumer Perception of Cooked Rice
Authors: Jang Eun‐Hee , Lim Seung‐Taik , Kim Sang‐Sook
Published: September 2009

Effect of storage temperature (ST) (5, 15, and 25°C) for paddy on the consumer perception of cooked rice (CR) was investigated with six major rice cultivars in Korea (Ilmibyeo, Chucheongbyeo, Ilpumbyeo, Hwayeongbyeo, Nampyeongbyeo, and Odaebyeo) after 12 months of storage. Germination rate (GR) of the paddy, grading characteristics (percentages of head rice, broken kernels, damaged kernels, colored kernels and chalky kernels) of milled rice (MR) kernels, texture profile analysis (hardness, springiness, cohesiveness, adhesiveness, and chewiness) and color (L*, a*, and b*) of CR were measured. Also, consumer testing on CR was done with 108 consumers. Consumers evaluated acceptability for odor, appearance, taste, texture, and overall purchase intent, and willingness to pay (WTP) of CR. After 12 months of storage, physicochemical characteristics of MR and CR were significantly different depending on ST. The significant difference among three ST of paddy was noted for GR, color b* value, fat acidity of MR, and overall consumer acceptability of CR. The GR was constant during 12 months of storage at 5°C, whereas a significant decrease of GR was noted for all six cultivars within 12 months of storage at 25°C. The average WTP for rice stored at 5°C for 12 months was $U.S. 45.68/20 kg, whereas WTP for rice stored at 15°C and 25°C were $U.S. 44.19/20 kg and $U.S. 41.87/20 kg, respectively, implying the importance of ST on grain quality and product value by consumers. Overall consumer acceptability had high correlation coefficient with WTP (r = 0.985). Overall consumer acceptability had highest correlation with GR of paddy (r = 0.861), followed by b* value of CR (r = –0.826), fat acidity (r = –0.768), cohesiveness (r = 0.733), and hardness (r = –0.650) of CR by TA, implying GR of paddy and b* value of CR could be used as indicators for eating quality of rice.
Sensory Evaluation of Barley Chocolate Chip Cookies by Consumers with Different Demographic Background and Eating Patterns
Authors: Omary María Botero , Rosentrater Kurt A. , Lewis Douglas S. , Arndt Elizabeth , Frost Diana J. , Winstone Lauren M.
Published: September 2009

Health organizations have recommended an increase in consumption of whole grains, total dietary fiber, and soluble fiber to help reduce the potential risk factor for the development of type‐2 diabetes, obesity, and cardiovascular disease, among others. The purpose of this project was to determine the sensory characteristics of chocolate chip (CC) cookies containing a high‐soluble fiber whole barley flour (HSFWB). Cookies with 0, 30, 50, and 70% HSFWB were evaluated for appearance, color, flavor, texture, and overall acceptability using a 9‐point hedonic scale. Forty‐nine students, faculty, and staff tested the cookies on three different days. Demographic and behavioral data on age, gender, ethnicity, frequency of eating CC cookies, daily effort to consume fiber (FD), consumption of reduced‐fat (RF) cookies, and texture preference (TP) of CC cookies were collected. The 50% HSFWB cookie could be potentially marketed among older consumers (22+), males, Hispanics, individuals who consume CC cookies at least once a week, those making a FD in their diet, persons who consume RF cookies, as well as those who have no TP for CC cookies. A response surface relating flavor and texture to overall acceptability produced almost equivalent results to the multivariate PLS results in terms of predicting overall acceptability, which facilitates analysis and interpretation.
Qualitative Zymographic Studies of Major Proteinases from Malted Sorghum (Sorghum bicolor L.) and Effects of Cultivar
Authors: Mokhawa Gaone , Ralefala Malebogo P. , Bulawayo Bernard B. , Ezeogu Lewis I.
Published: September 2009

Proteolysis during cereal germination is vital both to seedling growth and the success of commercial malting and brewing. In this study, proteinases in proteolytic extracts from seeds and germinated grains of 11 Botswana sorghum cultivars were analyzed and partially characterized by one‐dimensional electrophoresis on SDS‐PAGE gels containing incorporated gelatin. Proteinase polymorphism was detected in both germinated and ungerminated sorghum grains. Fifteen distinct proteinase bands, with Mr values of 27,000–100,000 were detected in sorghum malt extract, while ungerminated sorghum displayed a maximum of four bands (Mr ≈ 78,000–100,000). Band numbers and identity varied markedly according to cultivar. More proteinase bands were detected at pH 4.6, than at pH 6.2 and 7.0, suggesting pH optima considerably below neutrality. Cysteine‐proteinases constituted a higher proportion (9 of 15) of the detected sorghum malt proteinases and were most detectable at pH 4.6. Multiple representatives were also detected for both serine‐ and metallo‐proteinases, although these were more active at pH 6.2 and 7.0. 1‐10 Phenanthroline inhibited malt metallo‐proteinase more strongly than EDTA, suggesting that these enzymes were most probably zinc‐dependent. Aspartyl‐proteinases were not detected, probably because of the substrate employed. Results indicate that the sorghum proteinase system is complex.
A Modified Extensigraph Method for Evaluating Dough Properties of Hard Wheat Breeding Lines
Authors: Chen R. Y. , Seabourn B. W. , Xie F. , Herald T. J.
Published: September 2009

A modified extensigraph method reduced sample quantity to 100 g from 300 g and testing time by half with easy dough preparation compared to the AACC standard extensigraph method, which challenges wheat breeding programs where the sample size is small and evaluations of large numbers of samples are demanded. Correlation coefficients (r) for 93 pairs of each of six extensigraph dough characteristics of 31 different tested wheat samples were r = 0.95 for resistance‐to‐extension, r = 0.80 for extensibility, r = 0.93 for ratio of resistance‐to‐extension to extensibility, r = 0.92 for ratio of maximum resistance‐to‐extension to extensibility, and r = 0.81 for area under the curve (energy). Correlation coefficients for the measurements of extensigraph dough characteristics at each of three rest‐time tests between the modified and standard methods were significant. Some dough mixing characteristics and bake tests correlated better with dough extension characteristics when determined by the modified method. Repeatability of the modified method test was good. The modified extensigraph method can be a useful alternative to the standard method for the milling and baking industries, crop quality surveys, and wheat quality research.
Optical imaging-guided cancer therapy with fluorescent nanoparticles
Authors: Jiang Shan , Gnanasammandhan Muthu Kumara , Zhang Yong
Published: September 2009

The diagnosis and treatment of cancer have been greatly improved with the recent developments in nanotechnology. One of the promising nanoscale tools for cancer diagnosis is fluorescent nanoparticles (NPs), such as organic dye-doped NPs, quantum dots and upconversion NPs that enable highly sensitive optical imaging of cancer at cellular and animal level. Furthermore, the emerging development of novel multi-functional NPs, which can be conjugated with several functional molecules simultaneously including targeting moieties, therapeutic agents and imaging probes, provides new potentials for clinical therapies and diagnostics and undoubtedly will play a critical role in cancer therapy. In this article, we review the types and characteristics of fluorescent NPs,
in vitro
and
in vivo
imaging of cancer using fluorescent NPs and multi-functional NPs for imaging-guided cancer therapy.
Assessing the root of bilaterian animals with scalable phylogenomic methods
Authors: Hejnol Andreas , Obst Matthias , Stamatakis Alexandros , Ott Michael , Rouse Greg W. , Edgecombe Gregory D. , Martinez Pedro , Baguñà Jaume , Bailly Xavier , Jondelius Ulf , Wiens Matthias , Müller Werner E. G. , Seaver Elaine , Wheeler Ward C. , Martindale Mark Q. , Giribet Gonzalo , Dunn Casey W.
Published: September 2009

A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic
Xenoturbella
within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.
Evolution of weaponry in female bovids
Authors: Stankowich Theodore , Caro Tim
Published: September 2009

Weaponry is ubiquitous in male ungulates and is driven by intrasexual selection, but the mystery surrounding its sporadic presence in females remains unsolved. Female horns are often smaller and shaped differently to male horns, suggesting a different function; indeed, hypotheses explaining the presence of female horns include competition for food, male mollification and defence against predators. Here we use comparative phylogenetic analyses to show that females are significantly more likely to bear horns in bovids that are conspicuous due to large body size and living in open habitats than inconspicuous species living in closed habitats or that are small. An inability to rely on crypsis or take refuge in deep vegetation has apparently driven the evolution of horns for defence against predators in female bovids, a finding supported by many field observations. Typically, exceptions are small species where females are territorial (e.g. duikers) and use horns in intrasexual contests. Furthermore, we suggest that conspicuousness and territoriality hypotheses may explain other instances of female cranial weaponry (i.e. antlers and ossicones) in other horned ruminants. Our phylogenetic reconstruction indicates that the primary function of horns in females is linked to antipredator defence in most clades, but occasionally to intrasexual competition in others.
Social learning about egg-laying substrates in fruitflies
Authors: Sarin Sachin , Dukas Reuven
Published: September 2009

Social learning, defined as learning from other individuals, has had dramatic effects on some species, including humans, in whom it has generated a rich culture. As a first step in examining the evolution of and mechanisms underlying social learning in insects, we tested for social learning in fruitflies (
Drosophila melanogaster
). Focal females (observers) that experienced novel food together with mated females (models), who had laid eggs on that food, subsequently exhibited a stronger preference for laying eggs on that food over another novel food compared with focal females that experienced the food alone. We observed no social learning, however, when observers experienced food with potentially more ambiguous social information provided by the presence of either virgin models or aggregation pheromone. This first documentation of social learning about egg-laying substrates in fruitflies builds on recent data indicating intricate use of social information by fruitflies and opens up exciting avenues for research on the evolution and neurogenetics of social learning using biology's major model system.
The bounce of the body in hopping, running and trotting: different machines with the same motor
Authors: Cavagna G. A. , Legramandi M. A.
Published: September 2009

The bouncing mechanism of human running is characterized by a shorter duration of the brake after ‘landing’ compared with a longer duration of the push before ‘takeoff’. This landing–takeoff asymmetry has been thought to be a consequence of the force–velocity relation of the muscle, resulting in a greater force exerted during stretching after landing and a lower force developed during shortening before takeoff. However, the asymmetric lever system of the human foot during stance may also be the cause. Here, we measure the landing–takeoff asymmetry in bouncing steps of running, hopping and trotting animals using diverse lever systems. We find that the duration of the push exceeds that of the brake in all the animals, indicating that the different lever systems comply with the basic property of muscle to resist stretching with a force greater than that developed during shortening. In addition, results show both the landing–takeoff asymmetry and the mass-specific vertical stiffness to be greater in small animals than in large animals. We suggest that the landing–takeoff asymmetry is an index of a lack of elasticity, which increases with increasing the role of muscle relative to that of tendon within muscle–tendon units.
Stable Transcription Activities Dependent on an Orientation of Tam3 Transposon Insertions intoAntirrhinumand Yeast Promoters Occur Only within Chromatin
Authors: Uchiyama Takako , Fujino Kaien , Ogawa Takashi , Wakatsuki Akihito , Kishima Yuji , Mikami Tetsuo , Sano Yoshio
Published: September 2009

Transposon insertions occasionally occur in the promoter regions of plant genes, many of which are still capable of being transcribed. However, it remains unclear how transcription of such promoters is able to occur. Insertion of the Tam3 transposon into various genes of Antirrhinum majus can confer leaky phenotypes without its excision. These genes, named Tam3-permissible alleles, often contain Tam3 in their promoter regions. Two alleles at different anthocyanin biosynthesis loci, nivearecurrens∷Tam3 (nivrec) and pallidarecurrens∷Tam3 (palrec), both contain Tam3 at a similar position immediately upstream of the promoter TATA-box; however, these insertions had different phenotypic consequences. Under conditions where the inserted Tam3 is immobilized, the nivrec line produces pale red petals, whereas the palrec line produces no pigment. These pigmentation patterns are correlated with the level of transcripts from the nivrec or palrec alleles, and these transcriptional activities are independent of DNA methylation in their promoter regions. In nivrec, Tam3 is inserted in an orientation that results in the 3′ end of Tam3 adjacent to the 5′ region of the gene coding sequence. In contrast, the palrec allele contains a Tam3 insertion in the opposite orientation. Four of five different nonrelated genes that are also Tam3-permissible alleles and contain Tam3 within the promoter region share the same Tam3 orientation as nivrec. The different transcriptional activities dependent on Tam3 orientation in the Antirrhinum promoters were consistent with expression of luciferase reporter constructs introduced into yeast chromosomes but not with transient expression of these constructs in Antirrhinum cells. These results suggest that for Tam3 to sustain stable transcriptional activity in various promoters it must be embedded in chromatin.