bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards the use of protein A-tagged gold nanoparticles for signal amplification of electrochemical immunosensors in virus detection
Authors: Huy Tran Quang , Tuan Mai Anh , Thuy Nguyen Thanh , Chung Pham Van , Hong Hanh Nguyen Thi
Published: May 2012

In this paper we represent a study on the potential use of protein A-tagged gold nanoparticles applied for signal amplification of electrochemical immunosensors. Gold nanoparticles (GNPs) were synthesized by the chemical reduction of tetrachloroauric (III) acid trihydrate using sodium ascorbate, and then tagged with protein A (PrA) via ultracentrifugation. UV-Vis spectroscopy and transmission electron microscopy were used to verify the characteristics of formed GNPs/PrA complex. The analyzed results indicate that GNPs were found spherically, homogeneously, and with an average diameter of about 10 nm. Immunoelectron microscopy was then used to investigate the bioactivity of the GNPs/PrA complex in solution by the effective binding of GNPs to viral particles. Scanning electron and fluorescence microscopies were also used to investigate the distribution and the bioactivity of the GNPs/PrA complex on the surface of the interdigitated sensor. Consequently, this study provided some assumptions of the potential application of protein A-tagged gold nanoparticles for signal amplification of electrochemical immunosensors in virus detection from clinical samples.
Productivity Change under an Individual Transferable Quota Management System
Authors: Walden John B. , Kirkley James E. , Färe Rolf , Logan Philip
Published: May 2012

This study examines productivity change in the Mid‐Atlantic surfclam and ocean quahog fishery, which has been managed since 1990 using Individual Transferable Quotas (ITQ). Productivity change is estimated through a Malmquist index from 1981–2008, capturing change before and after implementation of the quota system. We then decompose the index to examine changes in technical efficiency, scale efficiency, and technical change. Our findings indicate that the ITQ system has not sustained gains in vessel productivity. These results are thought to be driven by spatial changes in biomass and the inability to access more productive fishing grounds.
Utilizing RNA-Seq data for de novo coexpression network inference
Authors: Iancu Ovidiu D. , Kawane Sunita , Bottomly Daniel , Searles Robert , Hitzemann Robert , McWeeney Shannon
Published: May 2012

Motivation: RNA-Seq experiments have shown great potential for transcriptome profiling. While sequencing increases the level of biological detail, integrative data analysis is also important. One avenue is the construction of coexpression networks. Because the capacity of RNA-Seq data for network construction has not been previously evaluated, we constructed a coexpression network using striatal samples, derived its network properties and compared it with microarray-based networks.

Results: The RNA-Seq coexpression network displayed scale-free, hierarchical network structure. We detected transcripts groups (modules) with correlated profiles; modules overlap distinct ontology categories. Neuroanatomical data from the Allen Brain Atlas reveal several modules with spatial colocalization. The network was compared with microarray-derived networks; correlations from RNA-Seq data were higher, likely because greater sensitivity and dynamic range. Higher correlations result in higher network connectivity, heterogeneity and centrality. For transcripts present across platforms, network structure appeared largely preserved. From this study, we present the first RNA-Seq data de novo network inference.

Contact:  iancuo@ohsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
FindGeo: a tool for determining metal coordination geometry
Authors: Andreini Claudia , Cavallaro Gabriele , Lorenzini Serena
Published: May 2012

Summary: Metals are essential for the structure and function of many proteins and nucleic acids. The geometrical arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. At present, however, this information can be retrieved only from the literature, which sometimes contains an improper or incorrect description of the geometry, and often lacks it altogether. Thus, we developed FindGeo to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-coordinating atoms in the input structure to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment.

Availability: FindGeo is freely available as a web service and as a stand-alone program at http://metalweb.cerm.unifi.it/tools/findgeo/.

Contact:  andreini@cerm.unifi.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ka-me: a Voronoi image analyzer
Authors: Khiripet Noppadon , Khantuwan Wongarnet , Jungck John R.
Published: May 2012

Summary: Ka-me is a Voronoi image analyzer that allows users to analyze any image with a convex polygonal tessellation or any spatial point distribution by fitting Voronoi polygons and their dual, Delaunay triangulations, to the pattern. The analytical tools include a variety of graph theoretic and geometric tools that summarize the distribution of the numbers of edges per face, areas, perimeters, angles of Delaunay triangle edges (anglograms), Gabriel graphs, nearest neighbor graphs, minimal spanning trees, Ulam trees, Pitteway tests, circumcircles and convexhulls, as well as spatial statistics (Clark–Evans Nearest Neighborhood and Variance to Mean Ratio) and export functions for standard relationships (Lewis's Law, Desch's Law and Aboav–Weaire Law).

Availability: Ka-me: a Voronoi image analyzer is available as an executable with documentation and sample applications from the BioQUEST Library (http://bioquest.org/downloads/kame_1.0.rar).

Contact:  noppadon.khiripet@nectec.or.th
graph2tab, a library to convert experimental workflow graphs into tabular formats
Authors: Brandizi Marco , Kurbatova Natalja , Sarkans Ugis , Rocca-Serra Philippe
Published: May 2012

Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve.

Results: We describe graph2tab, a library that implements methods to realise such a conversion in a size-optimised way. Our solution is generic and can be adapted to specific cases of data exporters or data converters that need to be implemented.

Availability and Implementation: The library source code and documentation are available at http://github.com/ISA-tools/graph2tab.

Contact:  brandizi@ebi.ac.uk.

Supplementary Information: A supplementary document describes the theoretical and technical details about the library implementation.
Analysis of case–control association studies with known risk variants
Authors: Zaitlen Noah , Paşaniuc Bogdan , Patterson Nick , Pollack Samuela , Voight Benjamin , Groop Leif , Altshuler David , Henderson Brian E. , Kolonel Laurence N. , Marchand Loic Le , Waters Kevin , Haiman Christopher A. , Stranger Barbara E. , Dermitzakis Emmanouil T. , Kraft Peter , Price Alkes L.
Published: May 2012

Motivation: The question of how to best use information from known associated variants when conducting disease association studies has yet to be answered. Some studies compute a marginal P-value for each Several Nucleotide Polymorphisms independently, ignoring previously discovered variants. Other studies include known variants as covariates in logistic regression, but a weakness of this standard conditioning strategy is that it does not account for disease prevalence and non-random ascertainment, which can induce a correlation structure between candidate variants and known associated variants even if the variants lie on different chromosomes. Here, we propose a new conditioning approach, which is based in part on the classical technique of liability threshold modeling. Roughly, this method estimates model parameters for each known variant while accounting for the published disease prevalence from the epidemiological literature.

Results: We show via simulation and application to empirical datasets that our approach outperforms both the no conditioning strategy and the standard conditioning strategy, with a properly controlled false-positive rate. Furthermore, in multiple data sets involving diseases of low prevalence, standard conditioning produces a severe drop in test statistics whereas our approach generally performs as well or better than no conditioning. Our approach may substantially improve disease gene discovery for diseases with many known risk variants.

Availability: LTSOFT software is available online http://www.hsph.harvard.edu/faculty/alkes-price/software/

Contact:  nzaitlen@hsph.harvard.edu; aprice@hsph.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Reconstructing the population dynamics of sprat (Sprattus sprattus balticus) in the Baltic Sea in the 20th century
Authors: Eero Margit
Published: May 2012

Eero, M. 2012. Reconstructing the population dynamics of sprat (Sprattus sprattus balticus) in the Baltic Sea in the 20th century. – ICES Journal of Marine Science, 69: 1010–1018 . Long time-series of population dynamics are increasingly needed in order to understand human impacts on marine ecosystems and support their sustainable management. In this study, the estimates of sprat (Sprattus sprattus balticus) biomass in the Baltic Sea were extended back from the beginning of ICES stock assessments in 1974 to the early 1900s. The analyses identified peaks in sprat spawner biomass in the beginning of the 1930s, 1960s, and 1970s at ∼900 kt. Only a half of that biomass was estimated for the late 1930s, for the period from the late 1940s to the mid-1950s, and for the mid-1960s. For the 1900s, fisheries landings suggest a relatively high biomass, similar to the early 1930s. The exploitation rate of sprat was low until the development of pelagic fisheries in the 1960s. Spatially resolved analyses from the 1960s onwards demonstrate changes in the distribution of sprat biomass over time. The average body weight of sprat by age in the 1950s to 1970s was higher than at present, but lower than during the 1980s to 1990s. The results of this study facilitate new analyses of the effects of climate, predation, and anthropogenic drivers on sprat, and contribute to setting long-term management strategies for the Baltic Sea.
Brazilian sardine (Sardinella brasiliensis Steindachner, 1879) spawning and nursery habitats: spatial-scale partitioning and multiscale relationships with thermohaline descriptors
Authors: Moraes Luiz Eduardo de Souza , Gherardi Douglas Francisco Marcolino , Katsuragawa Mario , Paes Eduardo Tavares
Published: May 2012

de Souza Moraes, L. E., Marcolino Gherardi, D. F., Katsuragawa, M., and Tavares Paes, E. 2012. Brazilian sardine (Sardinella brasiliensis Steindachner, 1879) spawning and nursery habitats: spatial-scale partitioning and multiscale relationships with thermohaline descriptors. – ICES Journal of Marine Science, 69: 939–952. We provide a detailed account of the spatial structure of the Brazilian sardine (Sardinella brasiliensis) spawning and nursery habitats, using ichthyoplankton data from nine surveys (1976–1993) covering the Southeastern Brazilian Bight (SBB). The spatial variability of sardine eggs and larvae was partitioned into predefined spatial-scale classes (broad scale, 200–500 km; medium scale, 50–100 km; and local scale, <50 km). The relationship between density distributions at both developmental stages and environmental descriptors (temperature and salinity) was also explored within these spatial scales. Spatial distributions of sardine eggs were mostly structured on medium and local scales, while larvae were characterized by broad- and medium-scale distributions. Broad- and medium-scale surface temperatures were positively correlated with sardine densities, for both developmental stages. Correlations with salinity were predominantly negative and concentrated on a medium scale. Broad-scale structuring might be explained by mesoscale processes, such as pulsing upwelling events and Brazil Current meandering at the northern portion of the SBB, while medium-scale relationships may be associated with local estuarine outflows. The results indicate that processes favouring vertical stability might regulate the spatial extensions of suitable spawning and nursery habitats for the Brazilian sardine.
N-[2-(2-Hydroxyethoxy)phenethyl]phthalimide
Authors: Yang Er-Qun , Zhang Jun-Tao , Cao Xiao-Ping , Gu Jin-Zhong
Published: May 2012

The title compound, C18H17NO4, was obtained accidentally through acid-catalysed aromatization of a phthalimide-substituted 2-(1-hydroxyethyl)cyclohex-2-enone. It exhibits an intramolecular O—H...Oc (c = carbonyl) hydrogen bond and forms a three-dimensional network structure via π–π stacking interactions between adjacent benzene rings (phthalimide-to-phenylene and phthalimide-to-phthalimide), with centroid–centroid distances of 3.8262 (6) and 3.6245 (5) Å.
(Z)-1-[4-Fluoro-2-(pyrrolidin-1-yl)phenyl]-3-phenyl-2-(1H-1,2,4-triazol-1-yl)prop-2-en-1-one
Authors: Wen Qin-Mei , Yin Ben-Tao , Yan Cong-Yan , Zhou Cheng-He
Published: May 2012

In the title molecule, C21H19FN4O, the triazole ring forms dihedral angles of 67.0 (1) and 59.6 (1)° with the phenyl and fluoro-substituted benzene rings, respectively. The dihedral angle between the phenyl ring and the fluoro-substituted benzene ring is 79.1 (1)°. The pyrrolidine ring is in a half-chair conformation. In the crystal, weak C—H...O and C—H...N hydrogen bonds connect molecules into layers parallel to (001).
1,1′-Bicyclohexyl-1,1′-diyl 1,1′-biphenyl-2,2′-dicarboxylate
Authors: Fun Hoong-Kun , Quah Ching Kheng , Wu Dongdong , Zhang Yan
Published: May 2012

The title compound, C26H28O4, lies about a crystallographic twofold rotation axis. The cyclohexane rings adopt a chair conformation. The two benzene rings form a dihedral angle of 40.82 (3)°. No significant intra- or intermolecular interactions are observed in the crystal structure.
1,1′-Bicyclopropyl-1,1′-diyl 1,1′-biphenyl-2,2′-dicarboxylate
Authors: Fun Hoong-Kun , Quah Ching Kheng , Xu Kai
Published: May 2012

In the title compound, C20H16O4, the two benzene rings form a dihedral angle of 45.70 (4)°. In the crystal, molecules are linked via C—H...O interactions into layers lying parallel to the bc plane.
14,15-Didehydrohellebrigenin
Authors: Yu Tong , Tian Hai-Yan , Yuan Xiao-Feng , Hu Shu-Zhi , Jiang Ren-Wang
Published: May 2012

The title compound, C24H30O5, is the didehydro product of the steroid hellebrigenin (systematic name: 3β,5,14-trihydroxy-19-oxo-5β-bufa-20,22-dienolide). It consists of three cyclohexane rings (A, B and C), a five-membered ring (D) and a six-membered lactone ring (E). The stereochemistry of the ring junctions are A/B cis, B/C trans and C/D cis. Cyclohexane rings A, B and C have normal chair conformations. The five-membered ring D with the C=C bond adopts an envelope conformation. Lactone ring E is essentially planar with a mean derivation of 0.006 (4) Å and is β-oriented at the C atom of ring D to which it is attached. There is an O—H...O hydrogen bond in the molecule involving the hydroxy groups. In the crystal, O—H...O hydrogen bonds link the molecules into chains propagating along [010]. The chains are linked by C—H...O contacts into a three-dimensional network.
4-Cyanopyridinium chloride
Authors: Zheng Wen-Ni
Published: May 2012

In the crystal structure of the title salt, C6H5N2
+·Cl−, the pyridinium cation links to the Cl− anion via an N—H...Cl hydrogen bond. Weak C—H...Cl interactions also occur.
cyclo-Tetrakis{μ-N′-[(8-oxidoquinolin-7-yl)methylidene]isonicotinohydrazidato}tetrazinc tetrahydrate
Authors: Wu Xiang-Wen , Li Qing-Long , Ma Jian-Ping , Dong Yu-Bin
Published: May 2012

In the title compound, [Zn4(C16H10N4O2)4]·4H2O, the N′-[(8-oxidoquinolin-7-yl)methylidene]isonicotinohydrazidate (L
2−) ligand binds to the metal ions, forming stable five- and six-membered chelate rings, leaving the pyridyl groups free. The compound is a tetranuclear ZnII complex centered about a fourfold roto-inversion axis, with the ligand coordinating in the doubly deprotonated form. The ZnII atom has a distorted square-pyramidal geometry being coordinated by one N and two O-atom donors from the doubly deprotonated L
2− ligand, and by one N atom and one O-atom donor from a symmetry-related L
2− ligand. In the crystal, four symmetry-related lattice water molecules, centred about a fourfold roto-inversion axis, form a cyclic tetramer through O—H...O hydrogen bonds. These tetramers connect to the complex molecules through O—H...N hydrogen bonds, forming a chain propagating along [100]. Neighbouring molecules are linked by π–π interactions [centroid–centroid distance = 3.660 (2) Å] involving the quinolidine rings.
Methyl (E)-2-({2-[(E)-(hydroxyimino)methyl]phenoxy}methyl)-3-(4-methylphenyl)acrylate
Authors: Ganesh G. , Srinivasan J. , Govindan E. , Bakthadoss M. , SubbiahPandi A.
Published: May 2012

In the title compound, C19H19NO4, the dihedral angle between the mean planes through the benzene rings is 82.18 (7)°. The C=N double bond is trans-configured. The molecules are linked into centrosymmetric dimers via pairs of O—H...N hydrogen bonds with the motif R
2
2(6). The crystal packing also features C—H...O interactions. The methyl group attached to one of the aromatic rings is disordered over two almost equally occupied positions [occpancy ratio = 0.51 (4):0.49 (4)].
2,5-Bis[(3-chlorobenzyl)sulfanyl]-1,3,4-thiadiazole
Authors: Sun Na-Bo , Jin Jian-Zhong , Ke Wei
Published: May 2012

The complete molecule of the title compound, C16H12Cl2N2S3, is generated by crystallographic twofold symmetry, with the S atom of the thiadiazole ring lying on the rotation axis. The dihedral angle between the mean planes of the 1,3,4-thiadiazole and benzene rings is 87.19 (7)°. In the crystal, molecules are linked by C—H...N interactions and short S...S contacts [3.3389 (9) Å] occur.
(E)-4-Methyl-N′-(3-nitrobenzylidene)benzohydrazide
Authors: Hu Hua-Nan , Liu Shi-Yong
Published: May 2012

In the title compound, C15H13N3O3, the dihedral angle between the benzene rings is 1.01 (3)° and that between the nitro group and its attached ring is 5.99 (15)°. In the crystal, molecules are linked by N—H...O hydrogen bonds generating C(4) chains along [010].
1,1′′-Bis(prop-2-en-1-yl)-1,1′′,2,2′′-tetrahydrodispiro[indole-3,7′-[6,9]diazatricyclo[7.3.0.02,6]dodecane-8′,3′′-indole]-2,2′′-dione
Authors: Al Mamari Khalil , Ennajih Hamid , Bouhfid Rachid , Essassi El Mokhtar , Ng Seik Weng
Published: May 2012

The molecule of the title compound, C30H32N4O2, lies on a twofold rotation axis that passes through the mid-points of the C—C bonds of the piperazine ring, which adopts a chair conformation. The pyrrolidine ring that is fused to the piperazine ring adopts an envelope conformation (in which the N atom represents the flap). The indoline fused-ring system is nearly planar (r.m.s. deviation = 0.044 Å); the two symmetry-related indoline fused-rings systems are aligned at 71.44 (3)°.
Bis{benzyl 2-[4-(4-methoxyphenyl)butan-2-ylidene]hydrazinecarbodithioato-κ2
N
2,S}nickel(II)
Authors: Tan Ming-Yueh , Ravoof Thahira Begum S. A. , Tahir Mohamed Ibrahim Mohamed , Crouse Karen A. , Tiekink Edward R. T.
Published: May 2012

The complete molecule of the title complex, [Ni(C19H21N2OS2)2], is generated by the application of twofold symmetry. The NiII atom is N,S-chelated by two hydrazinecarbodithioate ligands, which provide an N2S2 donor set that defines a distorted square-planar geometry, the S atoms being approximately cis. The conformation of the chelate ring is an envelope with the NiII atom being the flap atom. The dihedral angle between the least-squares planes through the chelate rings = 30.10 (6)°. Supramolecular chains propagated by glide symmetry along the c axis and mediated by C—H...N contacts feature in the crystal packing.
(μ-Naphthalene-1,5-disulfonato-κ2
O
1:O
5)bis[triaqua(glycinato-κ2
N,O)copper(II)]
Authors: Gao Shan , Ng Seik Weng
Published: May 2012

In the title compound, [Cu2(C2H4NO2)2(C10H6O6S2)(H2O)6], the naphthalenedisulfonate group lies on a center of inversion and bridges two glycinate-chelated CuII atoms. The CuII atom exists in a CuNO4 square-pyramidal geometry that is distorted towards an octahedron owing to a long Cu—Osulfonate bond [2.636 (2) Å]. In the crystal, extensive N—H...O and O—H...O hydrogen bonds link adjacent molecules into a three-dimensional network
3,3′-[1,2-Phenylenebis(methylene)]bis(1-ethyl-1H-benzimidazol-1-ium) bis(hexaflourophosphate)
Authors: Haque Rosenani A. , Iqbal Muhammad Adnan , Rosli Mohd Mustaqim , Fun Hoong-Kun
Published: May 2012

In the title compound, C26H28N4
2+·2PF6
−, the complete cation is generated by a crystallographic twofold axis. The benzimidazole ring is almost planar (r.m.s. deviation = 0.0207 Å) and makes dihedral angles of 50.12 (2)° with its symmetry-related component and 65.81 (2)° with the central benzene ring. In the crystal, molecules are linked into a three-dimensional network by C—H...F interactions. A π–π interaction with a centroid–centroid distance of 3.530 (1) Å is observed. Four F atoms of the hexafluorophosphate anion are disordered over two sets of sites in a 0.889 (6):0.111 (6) ratio.
4-Acetamidoanilinium nitrate monohydrate
Authors: Riahi Sana , Mrad Mohamed Lahbib , Ferretti Valeria , Lefebvre Frederic , Ben Nasr Cherif
Published: May 2012

In the title hydrated salt, C8H11N2O+·NO3
−·H2O, the N—C bond distances [1.349 (2) and 1.413 (2) Å] along with the sum of the angles (359.88°) around the acetamide N atom clearly indicate that the heteroatom has an sp
2 character. The ammonium group is involved in a total of three N—H...O hydrogen bonds, two of these are with a water molecule, which forms two O—H...O hydrogen bonds. All these hydrogen bonds link the ionic units and the water molecule into infinite planar layers parallel to (100). The remaining two N—H...O interactions in which the ammoniun group is involved link these layers into an infinite three-dimensional network.
Redetermined structure of oxaline: absolute configuration using Cu Kα radiation
Authors: Qu Peng , Wu Zhi-Yong , Zhu Wei-Ming
Published: May 2012

In the title compound, C24H25N5O4, the stereogenic C atom bonded to three N atoms and one C atom has an S configuration and its directly bonded neighbour has an R configuration. An intramolecular N—H...O hydrogen bond supports the near coplanarity of the two C3N2-five-membered rings [dihedral angle = 5.64 (10)°]. In the crystal, molecules are linked by N—H...N hydrogen bonds, forming a C(8) chain propagating in [001]. The chains are connected by C—H...O interactions, generating a three-dimensional network. The previous study [Nagel et al. (1974). Chem. Commun. pp. 1021–1022] did not establish the absolute structure and no atomic coordinates were published or deposited.
Propanaminium p-toluenesulfonate
Authors: Jin Yu
Published: May 2012

In the crystal structure of the title salt, C3H10N+·C7H7O3S−, N—H...O hydrogen bonds involving the ammonium groups of the cations and the sulfonate O atoms result in the formation of a three-dimensional network.
4-[2-(4-Hydroxyphenyl)ethyl]-3-propyl-1H-1,2,4-triazol-5(4H)-one
Authors: Öztürk Yildirim Sema , Butcher Ray J. , Ünlüer Dilek , Köysal Yavuz
Published: May 2012

The asymmetric unit of the title compound, C13H17N3O2, contains eight crystallographically independent molecules. The planes of the benzene and triazole rings in the eight molecules make dihedral angles of 5.53 (13), 9.33 (13), 19.28 (11), 17.36 (8), 12.84 (12), 8.03 (8), 19.97 (11), and 7.98 (8)°. The eight molecules in the asymmetric unit are linked by intermolecular O—H...O and N—H...O hydrogen bonds, forming a three-dimensional network.
8-Hydroxy-2-methylquinolinium tetrachlorido(quinolin-8-olato-κ2
N,O)stannate(IV)
Authors: Najafi Ezzatollah , Amini Mostafa M. , Ng Seik Weng
Published: May 2012

The reaction of 8-hydroxyquinoline, 2-methylquinolin-8-ol and stannic chloride yields the protonated 8-hydroxy-2-methylquinolinium species. In the title salt, (C10H10NO)[Sn(C9H6NO)Cl4], the SnIV cation is N,O-chelated by the quinolin-8-olate anion and is further coordinated by four Cl− anions in a distorted cis-SnNOCl4 octahedral geometry. In the crystal, the cation is linked to the anion by an O—H...O hydrogen bond.
2-Cyano-1-methylpyridinium nitrate
Authors: Koplitz Lynn V. , Mague Joel T. , Kammer Michael N. , McCormick Cameron A. , Renfro Heather E. , Vumbaco David J.
Published: May 2012

In the title compound, C7H7N2
+·NO3
−, all atoms except the methyl H atoms lie on a crystallographic mirror plane. The interlayer distance, including that between aligned N atoms from alternating cations and anions in adjacent layers, is exceptionally short at 3.055 (1) Å. Two-dimensional C—H...O hydrogen-bonded networks link cations to anions, while C—H...N interactions link cations within each layer. Anion–π interactions with the cations assist in binding the layers together.
2-[(Propan-2-yloxy)carbonyl]quinolin-1-ium tetrachlorido(quinoline-2-carboxylato-κ2
N,O)stannate(IV)
Authors: Najafi Ezzatollah , Amini Mostafa M. , Ng Seik Weng
Published: May 2012

In the title salt, (C13H14NO2)[Sn(C10H6NO2)Cl4], the SnIV cation is N,O-chelated by the quinolincarboxylate unit and further coordinated by four Cl− anions in a distorted octahedral geometry. In the crystal, the 2-[(propan-2-yloxy)carbonyl]quinolin-1-ium cation is linked to the Sn complex anion by an N—H...O hydrogen bond.
Tris(1H-benzimidazole-κN
3)(pyridine-2,6-dicarboxylato-κ3
O
2,N,O
6)nickel(II)
Authors: Li Yue-Hua , Li Feng-Feng , Liu Xin-Hua , Zhao Ling-Yan
Published: May 2012

In the title complex, [Ni(C7H3NO4)(C7H6N2)3], the NiII ion is coordinated by two carboxylate O atoms and the N atom from a pyridine-2,6-dicarboxylate ligand and by three N atoms from three benzimidazole ligands to form a slightly distorted octahedral geometry. In the crystal, molecules are linked by N—H...O hydrogen bonds to form a three-dimensional network.
4-Amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide–4-nitrobenzoic acid (1/1)
Authors: Smith Graham , Wermuth Urs D.
Published: May 2012

In the asymmetric unit of the title co-crystal, C7H5NO4·C12H14N4O2S, there are two independent but conformationally similar heterodimers, which are formed through intermolecular N—H...Ocarboxy and carboxyl–pyrimidine O—H...N hydrogen-bond pairs, giving a cyclic motif [graph set R
2
2(8)]. The dihedral angles between the rings in the sulfonamide molecules are 78.77 (8) and 82.33 (9)° while the dihedral angles between the ring and the CO2H group in the acids are 2.19 (9) and 7.02 (10)°. A two-dimensional structure parallel to the ab plane is generated from the heterodimer units through hydrogen-bonding associations between NH2 and sulfone groups. Between neighbouring two-dimensional arrays there are two types of aromatic π–π stacking interactions involving either one of the pyrimidine rings and a 4-nitrobenzoic acid molecule [minimum ring centroid separation = 3.5886 (9) Å] or two acid molecules [minimum ring centroid separation = 3.7236 (10) Å].
10-Hydroxybenzo[h]quinolin-1-ium tetrachlorido(pyridine-2-carboxylato-κ2
N,O)stannate(IV) methanol monosolvate
Authors: Najafi Ezzatollah , Amini Mostafa M. , Ng Seik Weng
Published: May 2012

The reaction of 4-(dimethylamino)pyridine, picolinic acid and stannic chloride yields the title monosolvated salt, (C13H10NO)[SnCl4(C6H4NO2)]·CH3OH. The SnIV atom is N,O-chelated by the picolinate ion in a cis-SnNOCl4 octahedral geometry. The cation is linked to the methanol solvent molecule by an O—H...O hydrogen bond; the solvent molecule itself is a hydrogen-bond donor to the uncoordinating carboxylate O atom of the anion. The cations and anions are linked by weak N—H...Cl interactions, forming a chain running along the b axis.
(E)-N′-Hydroxy-1,3-diphenyl-4,5-dihydro-1H-pyrazole-5-carboximidamide
Authors: Chandra  , Srikantamurthy N. , Umesha K. B. , Jeyaseelan S. , Mahendra M.
Published: May 2012

In the molecule of the title compound, C16H16N4O, the pyrazole ring makes dihedral angles of 8.52 (13) and 9.26 (12)° with the phenyl rings. The dihedral angle between the benzene rings is 1.86 (13)°. In the crystal, molecules are linked into centrosymmetric dimers via pairs of O—H...N hydrogen bonds. Weak N—H...N interactions connect the dimers into a chain along the [100] direction. The pyrazole ring adopts a highly flattened envelope conformation.
[Bis(pyridin-2-ylmethyl)amine-κ3
N,N′,N′′]tricarbonylrhenium(I) bromide hemihydrate
Authors: Schutte Marietjie , Muller Theunis J. , Visser Hendrik G. , Roodt Andreas
Published: May 2012

The title compound, fac-[Re(C12H12N3)(CO)3]Br·0.5H2O, crystallizes with a cationic rhenium(I) unit, a bromide ion and half a water molecule, situated on a twofold rotation axis, in the asymmetric unit. The ReI atom is facially surrounded by three carbonyl ligands and a tridentate bis(pyridin-2-ylmethyl)amine ligand in a distorted octahedral environment. N—H...Br, O—H...Br, C—H...O and C—H...Br hydrogen bonds are present in the crystal structure and π–π stacking is also observed [centroid–centroid distances = 3.669 (1) Å and 4.054 (1) Å], giving rise to a three-dimentional network. The molecules pack in a head-to-head fashion along the ac plane.
1-(4-Fluorophenyl)-2-(phenylsulfonyl)ethanone
Authors: Abdel-Aziz Hatem A. , Ghabbour Hazem A. , Chantrapromma Suchada , Fun Hoong-Kun
Published: May 2012

In the title compound, C14H11FO3S, the unit comprising the ethanone and 4-fluorophenyl groups is essentially planar, with an r.m.s. deviation of 0.0084 (2) Å for the ten non-H atoms, and it makes a dihedral angle of 37.31 (10)° with the phenyl ring. In the crystal, molecules are linked by pairs of weak C—H...O hydrogen bonds into inversion dimers with R
2
2(16) graph-set motifs. The dimers are stacked along the b axis through further C—H...O hydrogen bonds.
4-(Dimethylamino)pyridinium tetrachlorido(pyridine-2-carboxylato-κ2
N,O)stannate(IV)
Authors: Najafi Ezzatollah , Amini Mostafa M. , Ng Seik Weng
Published: May 2012

The reaction of 4-(dimethylamino)pyridine, picolinic acid and stannic chloride yields the title salt, (C7H11N2)[SnCl4(C6H4NO2)], in which the SnIV atom is N,O-chelated by the picolinate ion in a cis-SnNOCl4 octahedral geometry. The cation is linked to the anion by an N—H...O hydrogen bond.
Diet overlap among flatfish species in the southern North Sea
Authors: Schückel S. , Sell A. F. , Kröncke I. , Reiss H.
Published: May 2012

The diets of two non‐commercial flatfish species (solenette Buglossidium luteum and scaldfish Arnoglossus laterna) and two commercial flatfish species (dab Limanda limanda and plaice Pleuronectes platessa) were compared in a study area in the German Bight (southern North Sea) to investigate prey‐resource partitioning between these species. The diets of A. laterna and B. luteum mainly comprised crustaceans (harpacticoids, amphipods, cumaceans and decapods), whereas the diet of L. limanda and P. platessa consisted mainly of polychaetes. The Schoener index, calculated for different fish size classes between these flatfish species, showed a biologically significant diet overlap between small‐sized L. limanda and P. platessa and B. luteum and A. laterna, using similar prey resources of smaller prey (e.g. amphipods, harpacticoids and juvenile bivalves). In contrast, with increasing body size, a change in the diet of L. limanda and P. platessa towards larger prey occurred (e.g. polychaetes and decapods), resulting in low diet overlap values with B. luteum and A. laterna. Due to these size‐related differences in resource use, it is assumed that there is reduced interspecific competition for prey between larger L. limanda and P. platessa and both non‐commercial flatfishes, probably facilitating resource partitioning within the same area. In contrast, smaller L. limanda and P. platessa may compete directly for the same prey resources with B. luteum and A. laterna. Furthermore, prey availability of most important prey items of the studied flatfishes was relatively low in the study area. Therefore, increasing abundances of B. luteum and A. laterna in the southern North Sea since the late 1980s, owing to fishing effects and climate change, might affect the population dynamics of L. limanda and P. platessa.
GB‐to‐TNT: facilitating creation of matrices from GenBank and diagnosis of results in TNT
Authors: Goloboff Pablo A. , Catalano Santiago A.
Published: May 2012

This paper presents a pipeline, implemented in an open‐source program called GB→TNT (GenBank‐to‐TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences included in a GenBank file. The user defines the genomic region to be retrieved and several filters (genome, length of the sequence, taxonomic group, etc.); each genomic region represents a different data block in the final TNT matrix. GB→TNT first generates Fasta files from the input GenBank files, then creates an alignment for each of those (by calling an alignment program), and finally merges all the aligned files into a single TNT matrix. The new version of TNT can make use of the taxonomic information contained in the terminal names, allowing easy diagnosis of results, evaluation of fit between the trees and the taxonomy, and automatic labelling or colouring of tree branches with the taxonomic groups they represent.

© The Willi Hennig Society 2012.
Medicinal Δ9‐tetrahydrocannabinol (dronabinol) impairs on‐the‐road driving performance of occasional and heavy cannabis users but is not detected in Standard Field Sobriety Tests
Authors: Bosker Wendy M. , Kuypers Kim P. C. , Theunissen Eef L. , Surinx Anke , Blankespoor Roos J. , Skopp Gisela , Jeffery Wayne K. , Walls H. Chip , van Leeuwen Cees J. , Ramaekers Johannes G.
Published: May 2012

Aims

The acute and chronic effects of dronabinol [medicinal Δ9‐tetrahydrocannabinol (THC)] on actual driving performance and the Standard Field Sobriety Test (SFST) were assessed. It was hypothesized that occasional users would be impaired on these tests and that heavy users would show less impairment due to tolerance.

Design, setting and participants

Double‐blind, placebo‐controlled, randomized, three‐way cross‐over study. Twelve occasional and 12 heavy cannabis users (14 males/10 females) received single doses of placebo, 10 and 20 mg dronabinol.

Measurements

Standard deviation of lateral position (SDLP; i.e. weaving) is the primary measure of road‐tracking control. Time to speed adaptation (TSA) is the primary reaction‐time measure in the car‐following test. Percentage of impaired individuals on the SFST and subjective high on a visual analogue scale were secondary measures.

Findings

Superiority tests showed that SDLP (P = 0.008) and TSA (P = 0.011) increased after dronabinol in occasional users. Equivalence tests demonstrated that dronabinol‐induced increments in SDLP were bigger than impairment associated with BAC of 0.5 mg/ml in occasional and heavy users, although the magnitude of driving impairment was generally less in heavy users. The SFST did not discriminate between conditions. Levels of subjective high were comparable in occasional and heavy users.

Conclusions

Dronabinol (medicinal tetrahydrocannabinol) impairs driving performance in occasional and heavy users in a dose‐dependent way, but to a lesser degree in heavy users due possibly to tolerance. The Standard Field Sobriety Test is not sensitive to clinically relevant driving impairment caused by oral tetrahydrocannabinol.
Characteristics of Epstein–Barr virus hepatitis among patients with jaundice or acute hepatitis
Authors: Vine L. J. , Shepherd K. , Hunter J. G. , Madden R. , Thornton C. , Ellis V. , Bendall R. P. , Dalton H. R.
Published: May 2012

Background

Abnormal liver blood tests are common in Epstein–Barr virus (EBV) infection, but symptomatic hepatitis is rare. The demographics, clinical features and outcome of EBV hepatitis are incompletely understood, particularly in the elderly people.

Aim

To identify the demographics, presenting features and natural history of EBV hepatitis.

Methods

Retrospective review of 1995 consecutive patients attending the jaundice hotline clinic over a 13‐year period. Data collected included demographic information, presenting features, clinical and laboratory parameters, radiology imaging and clinical outcome.

Results

Seventeen of 1995 (0.85%) had EBV hepatitis. The median age was 40 years (range 18–68 years). Ten of 17 (59%) patients were aged >30 years, and seven of 17 (41%) patients were aged ≥60 years. Fifteen of 17 (88%) patients presented with clinical/biochemical evidence of jaundice. Seventeen of 17 (100%) patients had a serum lymphocytosis at presentation. 2/17 (12%) patients with EBV hepatitis presented with the classical features of infectious mononucleosis (fever, sore throat and lymphadenopathy). Splenomegaly was present in 15/17 (88%) of patients. Symptoms lasted for a median 8 weeks (range 1–12 weeks). Three of 17 (18%) patients required a brief hospital admission.

Conclusions

In patients presenting with jaundice/hepatitis, EBV hepatitis is an uncommon diagnosis and causes a self‐limiting hepatitis. The diagnosis is suggested by the presence of a lymphocytosis and/or splenomegaly. The majority of patients do not have infectious mononucleosis. Compared with infectious mononucleosis, EBV hepatitis affects an older age group, with nearly half of patients being aged more than 60 years. The diagnosis should be considered in all patients with unexplained hepatitis irrespective of their age.
Two conversational practices for encouraging adults with intellectual disabilities to reflect on their activities
Authors: Antaki C.
Published: May 2012

Background  Staff can encourage adults with intellectual disabilities to reflect on their experiences in a number of ways. Not all are equally successful interactionally.

Methods  Conversation Analysis is used to examine c. 30 h of recordings made at two service‐provider agencies.

Results  I identify two practices for soliciting reflection: both start with open‐ended ‘test’ questions, but they differ on how these are followed up. A more interrogatory practice is to follow up with alternatives and yes/no questions. A more facilitative practice is to give hints and elaborate the replies.

Conclusions  I discuss the differences between the two practices in terms of the institutional agendas that guide the staff's interactional routines. With regard to the more successful one, I note the sensitivity of using ‘hints’ when asking about clients' own experiences.
Persistent hepatitis C virus (HCV) infection impairs HCV‐specific cytotoxic T cell reactivity through Mcl‐1/Bim imbalance due to CD127 down‐regulation
Authors: Larrubia J. R. , Lokhande M. U. , García‐Garzón S. , Miquel J. , González‐Praetorius A. , Parra‐Cid T. , Sanz‐de‐Villalobos E.
Published: May 2012

Summary.  In persistent hepatitis C virus (HCV) infection, HCV‐specific cytotoxic T lymphocyte (CTL) reactivity is impaired and this affects HCV control. Interleukin‐7 receptor (CD127) expression on these cells could regulate CTL reactivity through Mcl‐1/Bim balance modulation. Bim is a pro‐apoptotic molecule blocked by the action of Mcl‐1. Mcl‐1/Bim expression and T cell reactivity on HCV‐specific CTLs were compared according to CD127 phenotype. Peripheral blood lymphocytes (PBL) from HLA‐A2+ HCV+ patients were obtained. HCV‐specific CTLs were visualized by staining PBL with anti‐CD8 and HLA‐A2/peptide pentameric complexes (pentamer). Mcl‐1/Bim/CD127 phenotype of HCV‐specific CTLs was tested by staining detectable CD8+/pentamer+ cells with anti‐Mcl‐1/Bim/CD127 antibodies. HCV‐specific CTL proliferation ability after specific in vitro challenge was tested in the presence and absence of pancaspase inhibitor z‐VAD‐fmk. All stained cells were analysed by flow cytometry. CD127low‐expressing HCV‐specific CTLs associated with high HCV viraemia, while CD127high correlated with undetectable viral loads (P < 0.001). Directly ex vivo, pentamer+ cell frequency was similar according to CD127 expression level. Nevertheless, CD127low pentamer+ cell proliferation after specific in vitro challenge was impaired (P < 0.05), although this was corrected by z‐VAD‐fmk treatment (P < 0.05). Mcl‐1 expression was low directly ex vivo (P < 0.01), and Bim was up‐regulated after antigen encounter (P < 0.05) of CD127low pentamer+ cells. The ex vivo difference between Mcl‐1 and Bim expression on pentamer+ cells correlated positively with CD127 expression level (P < 0.001) and with pentamer+ cell reactivity (P < 0.05). In summary, a low ex vivo Mcl‐1 expression and Bim up‐regulation after antigen encounter are involved in CD127low HCV‐specific CTL hyporeactivity during chronic infection, but it can be overcome by apoptosis blockade.
Neither philopatric nor panmictic: microsatellite and mtDNA evidence suggests lack of natal homing but limits to dispersal in Pacific lamprey
Authors: SPICE ERIN K. , GOODMAN DAMON H. , REID STEWART B. , DOCKER MARGARET F.
Published: May 2012

Most species with lengthy migrations display some degree of natal homing; some (e.g. migratory birds and anadromous salmonids) show spectacular feats of homing. However, studies of the sea lamprey (Petromyzon marinus) indicate that this anadromous species locates spawning habitat based on pheromonal cues from larvae rather than through philopatry. Previous genetic studies in the anadromous Pacific lamprey (Entosphenus tridentatus) have both supported and rejected the hypothesis of natal homing. To resolve this, we used nine microsatellite loci to examine the population structure in 965 Pacific lamprey from 20 locations from central British Columbia to southern California and supplemented this analysis with mitochondrial DNA restriction fragment length polymorphism analysis on a subset of 530 lamprey. Microsatellite analysis revealed (i) relatively low but often statistically significant genetic differentiation among locations (97% pairwise FST values were <0.04 but 73.7% were significant); and (ii) weak but significant isolation by distance (r2 = 0.0565, P = 0.0450) but no geographic clustering of samples. The few moderate FST values involved comparisons with sites that were geographically distant or far upstream. The mtDNA analysis—although providing less resolution among sites (only 4.7%FST values were significant)—was broadly consistent with the microsatellite results: (i) the southernmost site and some sites tributary to the Salish Sea were genetically distinct; and (ii) southern sites showed higher haplotype and private haplotype richness. These results are inconsistent with philopatry, suggesting that anadromous lampreys are unusual among species with long migrations, but suggest that limited dispersal at sea precludes panmixia in this species.
Evolution of TPS20‐related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites
Authors: Gonzales‐Vigil Eliana , Hufnagel David E. , Kim Jeongwoon , Last Robert L. , Barry Cornelius S.
Published: May 2012

A systematic screen of volatile terpene production in the glandular trichomes of 79 accessions of Solanum habrochaites was conducted and revealed the presence of 21 mono‐ and sesquiterpenes that exhibit a range of qualitative and quantitative variation. Hierarchical clustering identified distinct terpene phenotypic modules with shared patterns of terpene accumulation across accessions. Several terpene modules could be assigned to previously identified terpene synthase (TPS) activities that included members of the TPS‐e/f subfamily that utilize the unusual cis‐prenyl diphosphate substrates neryl diphosphate and 2z,6z‐farnesyl diphosphate. DNA sequencing and in vitro enzyme activity analysis of TPS‐e/f members from S. habrochaites identified three previously unassigned enzyme activities that utilize these cisoid substrates. These produce either the monoterpenes α‐pinene and limonene, or the sesquiterpene 7‐epizingiberene, with the in vitro analyses that recapitulated the trichome chemistry found in planta. Comparison of the distribution of S. habrochaites accessions with terpene content revealed a strong preference for the presence of particular TPS20 alleles at distinct geographic locations. This study reveals that the unusually high intra‐specific variation of volatile terpene synthesis in glandular trichomes of S. habrochaites is due at least in part to evolution at the TPS20 locus.
In vitro up‐regulation of HLA‐G using dexamethasone and hydrocortisone in first‐trimester trophoblast cells of women experiencing recurrent miscarriage
Authors: Akhter A. , Faridi R. M. , Das V. , Pandey A. , Naik S. , Agrawal S.
Published: May 2012

The trophoblast cells at the maternal–fetal interface express an unusual combination of human leukocyte antigen (HLA)‐C, HLA‐E and HLA‐G. Altered expression of HLA‐G on the extravillous cytotrophoblast has been implicated in the etiology of recurrent miscarriages (RMs). We have assessed HLA‐G expression in extravillous cytotrophoblast in cell cultures prepared from RM patients and compared with those of first‐trimester voluntarily terminated normal pregnancies (control). Glucocorticoids, dexamethasone and hydrocortisone were examined for their role in modulation of the HLA‐G expression. HLA‐G promoter and 3′UTR variants were investigated for their effect on the transcription of HLA‐G. Cultured cytotrophoblast cells from the first‐trimester RM patients were treated with dexamethasone and hydrocortisone (dose concentration 0–1000 ng/ml). HLA‐G gene transcription was determined by semiquantitative and quantitative real‐time polymerase chain reaction (RT‐PCR), while protein expression was determined by a specific enzyme‐linked immunosorbent assay (ELISA), flow cytometry and western blot analyses. HLA‐G polymorphisms were detected by PCR and/or sequence‐based typing. Low level of HLA‐G was observed in untreated trophoblast cells obtained from RM patients as compared with controls. Upon treatment with glucocorticoids, the expression of HLA‐G in these cells was up‐regulated in a dose‐dependent manner (P < 0.05), with no change in cellular proliferation and viability. There was no significant association between HLA‐G polymorphism in RM patients and controls. HLA‐G is minimally expressed in cultured trophoblast cells of RM patients. It can be up‐regulated upon exposure with both dexamethasone and hydrocortisone. Glucocorticoids have the potential to modulate HLA‐G expression in vitro, and can be further examined for their therapeutic applicability in RM.