bluuebunny/crossref_metadata_2025 huggingface dataset:
The Expression of RAC1 and Mineralocorticoid Pathway-Dependent Genes are Associated With Different Responses to Salt Intake
Authors: Tapia-Castillo Alejandra , Carvajal Cristian A. , Campino Carmen , Hill Caroline , Allende Fidel , Vecchiola Andrea , Carrasco Carmen , Bancalari Rodrigo , Valdivia Carolina , Lagos Carlos , Martinez-Aguayo Alejandro , Garcia Hernan , Aglony Marlene , Baudrand Rene F. , Kalergis Alexis M. , Michea Luis F. , Riedel Claudia A. , Fardella Carlos E.
Published: November 2014

BACKGROUND

Rac1 upregulation has been implicated in salt-sensitive hypertension as a modulator of mineralocorticoid receptor (MR) activity. Rac1 could affect the expression of oxidative stress markers, such as hemoxigenase-1 (HO-1) or nuclear factor-B (NF-κB), and the expression of neutrophil gelatinase-associated lipocalin (NGAL), a cytokine upregulated upon MR activation.

AIM

We evaluated RAC1 expression in relation of high salt intake and association with MR, NGAL, HO-1, and NF-κB expression, mineralo- and glucocorticoids levels, and inflammatory parameters.

SUBJECTS AND METHODS

We studied 147 adult subjects. A food survey identified the dietary sodium (Na) intake. RAC1 expression was considered high or low according to the value found in normotensive subjects with low salt intake. We determined the gene expression of RAC1, MR, NGAL, HO-1, NF-κB, and 18S, isolated from peripheral leukocytes. We measured aldosterone, cortisol, sodium, potassium excretion, metalloproteinase (MMP9 y MMP2), and C-reactive protein.

RESULTS

We identified 126 subjects with high Na-intake, 18 subjects had high, and 108 low-RAC1 expression. The subjects with high-RAC1 expression showed a significant increase in MR (P = 0.0002), NGAL (P < 0.0001) HO-1 (P = 0.0004), and NF-κB (P < 0.0001) gene expression. We demonstrated an association between RAC1 expression and MR (Rsp 0.64; P < 0.0001), NGAL (Rsp 0.48; P < 0.0001), HO-1 (Rsp 0.53; P < 0.0001), and NF-κB (Rsp0.52; P < 0.0001). We did not identify any association between RAC1 and clinical or biochemical variables.

CONCLUSIONS

RAC1 expression was associated with an increase in MR, NGAL, NF-κB, and HO-1 expression, suggesting that RAC1 could be a mediator of cardiovascular damage induced by sodium, and may also useful to identify subjects with different responses to salt intake.
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
Authors: Jones David T. , Singh Tanya , Kosciolek Tomasz , Tetchner Stuart
Published: November 2014

Motivation: Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues.

Results: Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts—around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV.

Availability and implementation: MetaPSICOV is available as a freely available web server at http://bioinf.cs.ucl.ac.uk/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV.

Contact:  d.t.jones@ucl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Western Balkans
Authors: Bugajski Janusz
Published: November 2014

The term Western Balkan is both geographic and political. It was initially employed by US and European policymakers to describe the part of the Balkan Peninsula that remained outside of both the North Atlantic Treaty Organization (NATO) and the European Union (EU) since the early 1990s. It included all seven states that were formed during the collapse of Yugoslavia (Bosnia-Herzegovina, Croatia, Kosovo, Macedonia, Montenegro, Serbia, and Slovenia) together with Albania, which was emerging from international isolation. During the 1990s, several of these emerging countries had experienced wars generated by nationalist politicians to establish “ethnically pure” territories and to restore or enlarge national statehood during the disintegration of the Socialist Federal Republic of Yugoslavia (SFRY). Following the EU’s Thessaloniki Summit in June 2003, commitments were made to include all the Western Balkan states in the European Union, and since that time Slovenia (in 2004) and Croatia (in 2013) have become EU members. NATO also underscored its commitments to integrating the region, and Slovenia (in 2004), Croatia (in 2009), Albania (in 2009), and Montenegro (in 2017) all entered the alliance. The remaining states have experienced persistent problems in qualifying for EU and NATO entry. In many cases, reforms remain incomplete and some states confront prolonged disputes over governmental powers, administrative borders, and even their sovereign status. Incomplete, conflicted, or contested states present serious challenges for the region’s institutional absorption into both NATO and the EU.
Clinical Linguistics
Authors: Cummings Louise
Published: November 2014

Clinical linguistics is the application of linguistic concepts, theories, and methods to the study of language disorders. These disorders can result from impairment of, or breakdown in, one or more of the following language components: prosody, phonology, morphology, syntax, semantics, pragmatics, and discourse. Some language disorders have their onset in the developmental period (developmental language disorders), while others occur for the first time in late childhood and adulthood (acquired language disorders). Language disorders can compromise the reception or understanding of language and/or its expression or production, with impairments possible across a range of modalities (spoken, written, and signed language). This branch of linguistics is inextricably linked to speech-language pathology (also known as speech and language therapy in the United Kingdom), the clinical discipline responsible for the assessment, diagnosis, and treatment of clients with a range of communication disorders (and not just language disorders). However, clinical linguistics is nonetheless a distinct linguistic discipline that is not in any way subsumed by speech-language pathology. In addition to having a detailed knowledge of linguistic disciplines, the speech-language pathologist must understand a range of medical conditions and their likely impact on language skills in children and adults.
Leon Festinger
Authors: Hatfield Elaine , Carpenter Megan , Thornton Paul , Rapson Richard
Published: November 2014

Leon Festinger was born in Brooklyn, New York, on 8 May 1919 to Russian-Jewish immigrants, Alex Festinger and Sara Solomon Festinger. Leon’s father, an embroidery manufacturer, had left Russia an atheist and a radical, and he remained faithful to these convictions throughout his life. In his youth, Leon attended Boys’ High School, in Brooklyn. A number of authors have penned comprehensive biographies of his early life. Among the best are those written by his colleagues Jack W. Brehm and George A. Milite (see Brehm 1998, Milite 2001, both cited under Legacy).
Observations of umbral dots and their physical models
Authors: Watanabe Hiroko
Published: November 2014

The Hinode satellite opens a new era in sunspot research, because of its high spatial resolution and temporal stability. Fine-scale structures in sunspots, called umbral dots (UDs), have become one of the hottest topics in terms of close observations of magnetoconvection. In this paper, a brief review of the observed properties of UDs is given based on recent literature. UDs born in the periphery of the umbra exhibit inward migration, and their speeds are positively correlated with the magnetic field inclination. Longer-lasting UDs tend to be larger and brighter, while the lifetimes of UDs show no relation to their background magnetic field strength. UDs tend to disappear, or stop their proper motion by colliding with a locally strong field region. The spatial distribution of UDs is not uniform over an umbra, but is rather located at the boundaries of cellular patterns. From our two-dimensional correlation analysis, we measured the characteristic width of the cell boundaries (≈ 0${^{\prime\prime}_{.}}$5) and the size of the cells (≈ 6″). We then performed a simplified analysis to obtain statistics of how the UD distribution is random or clustered using Hinode blue continuum images. We have found a hint that the UDs become less dense and more clustered for later-phase sunspots. These results may be related to the evolutional change of the subsurface structure of a sunspot. Based on these observational results, we discuss their physical models by means of numerical simulations of magnetoconvection.
The rheology of three-phase suspensions at low bubble capillary number
Authors: Truby J. M. , Mueller S. P. , Llewellin E. W. , Mader H. M.
Published: November 2014

We develop a model for the rheology of a three-phase suspension of bubbles and particles in a Newtonian liquid undergoing steady flow. We adopt an ‘effective-medium’ approach in which the bubbly liquid is treated as a continuous medium which suspends the particles. The resulting three-phase model combines separate two-phase models for bubble suspension rheology and particle suspension rheology, which are taken from the literature. The model is validated against new experimental data for three-phase suspensions of bubbles and spherical particles, collected in the low bubble capillary number regime. Good agreement is found across the experimental range of particle volume fraction (

0
≤

ϕ

p

≲
0.5

) and bubble volume fraction (

0
≤

ϕ

b

≲
0.3

). Consistent with model predictions, experimental results demonstrate that adding bubbles to a dilute particle suspension at low capillarity increases its viscosity, while adding bubbles to a concentrated particle suspension decreases its viscosity. The model accounts for particle anisometry and is easily extended to account for variable capillarity, but has not been experimentally validated for these cases.
Changes in the quality and secondary metabolites of kohlrabi during storage
Authors: Park Me Hea , Seo Jeong Min , Kim Sun Ju , Kim Won Bae , Lee Jung Soo , Choi Ji Weon
Published: November 2014

To determine the optimal shelf life for maintaining the high quality of kohlrabi, the changes in the physiological and secondary metabolites of kohlrabi stems during storage were investigated. The results showed that the kohlrabi maintained its marketable quality for two weeks at room temperature and for two months in cold storage (4°C). Interestingly, the total phenol and flavonoid contents sharply declined along with the quality deterioration after two-week storage at room temperature. Moreover, insignificant changes in these compounds were observed for two months during the cold storage. The secondary metabolites of the kohlrabi were also influenced by its storage condition. The total phenol and total flavonoid contents of the kohlrabi significantly increased with the storage periods at low temperature, and significantly decreased with the storage periods at room temperature. In terms of the packaging, no significant difference in the total phenol content of the kohlrabi was found between the packaged and non-packaged types of storage. However, the flavonoid content of the packaged kohlrabi was higher than that of the non-packaged kohlrabi at the end of their storage. The content of glucosinolates, an anti-cancer ingredient was maintained during the storage, so the vegetables remained good sources of these compounds when stored in cold storage even for a long period. This study showed a close correlation between the secondary metabolites and the change in the quality of kohlrabi during storage. The results also suggested that secondary metabolites such as phenolics can be considered quality indicators of the shelf life of kohlrabi.
Quality characteristics of low salted garlic Doenjang during fermentation
Authors: Cho Kye-Man , Kang Jae-Ran , Kim Gyeong-Min , Kang Min-Jung , Hwang Chung-Eun , Jeong Young-Shim , Kim Jeong-Hwan , Lee Chang-Kwon , Shin Jung-Hye
Published: November 2014

We investigated the changes in the quality characteristics of Doenjang with low salt contents (6, 8, 10, and 12%) and 10% garlic. The Doenjang was analyzed at an interval of a week during its fermentation for six weeks, at room temperature. Its L color gradually decreased, but its a and b colors did not change significantly. Its salinity increased by about 1% after six weeks. In contrast, immediately after its preparation, its pH was gradually decreased and its acidity was increased for the fermentation. The reducing sugar was significantly increased from 1.34~1.88 g/100 g immediately after its preparation to 7.25~9.13 g/100 g after six weeks, which was higher as the salt concentration decreased. The amino-type nitrogen doubled from 100~130 mg% at 0 week to 210~290 mg% at six weeks, which were lower with the higher salt concentrations. The growth curve of the Bacillus fermentation strains of Doenjang increased to two weeks but gradually decreased since, and the growth of the Bacillus was favorable for up to two weeks in the Doenjang with 10% and 12% salt added. Otherwise, the yeast was reduced rapidly during the early fermentation of the Doenjang, and slightly changed after three weeks of fermentation. The results of this study showed that the reducing sugar and amino-type nitrogen contents of the low-salt garlic Doenjang were higher with the lower salt dose, and the physicochemical quality of the 6%-salt Doenjang was not significantly affected. Thus, we suggest that low-salt Doenjang can be manufactured with the addition of 6% salt and 10% garlic.
The quality and sensory characteristics of tofu with various levels of black garlic extract
Authors: Sim Hye-Jin , Hwang Cho-Rong , Kang Min-Jung , Kim Gyeong-Min , Shin Jung-Hye
Published: November 2014

The quality and sensory characteristics of tofu were investigated with various levels of black garlic extract (BE) added to it in 0, 1, 3, 5 and 7%-weight soymilk, before it was coagulated with MgCl2 (MC, BEM-A, BEM-B, BEM-C and BEM-D) and concentrated to 8 °Brix deep ground sea-like water (SC, BES-A, BES-B, BES-C and BES-D). The overall acceptability of the tofu samples was higher (SC > BES-A > BEM-A) than that of the other samples. The addition of BE was influenced by the color, flavor and taste of the tofu, and the more BE was added, the tougher the tofu became. The tofu yield with various amounts of black garlic extract did not significantly differ among the samples. The pH range was 5.61~6.15 and decreased as more BE was added, whereas the turbidity increased. Also, the L value of the tofu decreased as more BE was added. The a value showed a tendency opposite that of the L value. The b value did not significantly differ among the samples. The texture profile analysis of the tofus showed that the hardness, chewiness, and gumminess significantly increased as more BE was added. In conclusion, it was found that the addition of 1% BE will improve the quality and sensory characteristics of tofu.
Anti-thrombosis and anti-oxidative activity of the root of Arctium lappa L.
Authors: Kim Mi-Sun , Lee Ye-Seul , Sohn Ho-Yong
Published: November 2014

To investigate anti-thrombosis and anti-oxidation activities of the root of Arctium lappa L (RALL), which has been used as foodstuff and oriental medicine in Korea, the ethanol extract and its subsequent organic solvent fractions of the RALL were prepared. The yield of ethanol extraction was 10.94%, and the content of total polyphenol and total sugar of ethanol extract were 5.01 and 694.53 mg/g, respectively. The fraction yields of n-hexane, ethylacetate (EA), butanol and water residue were 1.62, 0.42, 5.98 and 85.38%, respectively. In anticoagulation activity assay, the ethanol extract of RALL did not show significant changes in thrombin time (TT), prothrombin time (PT) and activated partial thromboplastin time (aPTT), whereas the EA fractions showed 13 folds extended TT, PT, and aPTT respectively. Interestingly, the water residue showed strong activation effect against blood clotting factors with shortened aPTT, which might provide the evidence of coagulation agent of RALL in folk remedy. In anti-platelet aggregation assay, the activity of the ethanol extract and its fractions were comparable to that of aspirin. Especially the EA fraction showed 2-folds higher inhibitory activity than aspirin. In anti-oxidation activity assay, the EA fraction also showed strong in DPPH, ABTS and nitrite scavenging activity, and reducing power activity. The extract and fractions of RALL have ignorable hemolytic activity against human RBC up to 0.5 mg/mL concentration. Our results suggest that the EA fraction of RALL have potentials as safe and novel anti-thrombosis agent.
Effects of vitamin C on the formation of aflatoxin B1-DNA adduct in rat livers treated with radiation and aflatoxin B1
Authors: Kim Soyoung , Kim Hansoo , Kang Jin-Soon
Published: November 2014

The objective of this study was to examine the effects of vitamin C on the formation of aflatoxin B1 (AFB1)-DNA adduct and AFB1-induing cellular oxidative damage in rat livers treated with radiation and AFB1. Six-week-old male Sprague-Dawley rats were randomly divided into five groups: the control group, the AFB1-treated group, the group treated with AFB1 and vitamin C, the group treated with X-ray and AFB1, and the group treated with X-ray and AFB1 with vitamin C. On the first day of the experiment, only one dose of X-rays was exposed to the entire liver at 1,500 cGy. Next, vitamin C was injected at 10 mg/kg body weight via intraperitoneal injection, followed an hour later by the administration of 0.4 mg/kg of AFB1 via intraperitoneal injection. These treatments were administered every three days for 15 days. On the 16th day, the animals were sacrificed. The AFB1 contents of the rat sera were determined via indirect competitive ELISA. In the quantitative analysis of AFB1 in the rat sera via ELISA, 5.17±0.34 ng/mL of AFB1 was detected in the AFB1-treated groups, but the amount decreased more significantly to 3.23±0.76 ng/mL in the groups treated with AFB1 and vitamin C (p<0.01) than in the AFB1-treated groups. The effect of vitamin C on AFB1-DNA adduct formation was determined via ELISA. The values of AFB1-DNA adduct formation were 9.38±0.41 ng/ml in the AFB1-treated groups, but the amount decreased more significantly to 5.28±0.32 ng/mL in the groups treated with AFB1 and vitamin C (p<0.01) than in the AFB1-treated groups. Immunohistochemistry revealed that the accumulation of the AFB₁was not observed in the normal liver tissue (G1). The AFB1-positive materials were observed in the central vein and the portal vein of the liver tissue from the AFB1 (G2) treatment or the X-ray and AFB1 (G4) co-treatment, but the AFB1-positive materials were observed weakly in the group treated with vitamin C (G3 and G5). These results indicate that vitamin C had ameliorating effects on the AFB1 accumulation of liver tissue.
High-synconformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures ofShewanella oneidensisMR-1 uridine phosphorylase in the free form and in complex with uridine
Authors: Safonova Tatyana N. , Mikhailov Sergey N. , Veiko Vladimir P. , Mordkovich Nadezhda N. , Manuvera Valentin A. , Alekseev Cyril S. , Kovalchuk Mikhail V. , Popov Vladimir O. , Polyakov Konstantin M.
Published: November 2014

Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Expression of UP fromShewanella oneidensisMR-1 (SoUP) was performed inEscherichia coli. The high-resolution X-ray structure of SoUP was solved in the free form and in complex with uridine. A crystal of SoUP in the free form was grown under microgravity and diffracted to ultrahigh resolution. Both forms of SoUP contained sulfate instead of phosphate in the active site owing to the presence of ammonium sulfate in the crystallization solution. The latter can be considered as a good mimic of phosphate. In the complex, uridine adopts a high-synconformation with a nearly planar ribose ring and is present only in one subunit of the hexamer. A comparison of the structures of SoUP in the free form and in complex with the natural substrate uridine showed that the subunits of the hexamer are not identical, with the active sites having either an open or a closed conformation. In the monomers with the closed conformation, the active sites in which uridine is absent contain a glycerol molecule mimicking the ribose moiety of uridine.
Improved crystal orientation and physical properties from single-shot XFEL stills
Authors: Sauter Nicholas K. , Hattne Johan , Brewster Aaron S. , Echols Nathaniel , Zwart Petrus H. , Adams Paul D.
Published: November 2014

X-ray diffraction patterns from still crystals are inherently difficult to process because the crystal orientation is not uniquely determined by measuring the Bragg spot positions. Only one of the three rotational degrees of freedom is directly coupled to spot positions; the other two rotations move Bragg spots in and out of the reflecting condition but do not change the direction of the diffracted rays. This hinders the ability to recover accurate structure factors from experiments that are dependent on single-shot exposures, such as femtosecond diffract-and-destroy protocols at X-ray free-electron lasers (XFELs). Here, additional methods are introduced to optimally model the diffraction. The best orientation is obtained by requiring, for the brightest observed spots, that each reciprocal-lattice point be placed into the exact reflecting condition implied by Bragg's law with a minimal rotation. This approach reduces the experimental uncertainties in noisy XFEL data, improving the crystallographicRfactors and sharpening anomalous differences that are near the level of the noise.
ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell
Authors: Kowiel Marcin , Jaskolski Mariusz , Dauter Zbigniew
Published: November 2014

Despite the existence of numerous useful conventions in structural crystallography, for example for the choice of the asymmetric part of the unit cell or of reciprocal space, surprisingly no standards are in use for the placement of the molecular model in the unit cell, often leading to inconsistencies or confusion. A conceptual solution for this problem has been proposed for macromolecular crystal structures based on the idea of the anti-Cheshire unit cell. Here, a program and server (calledACHESYM; http://achesym.ibch.poznan.pl) are presented for the practical implementation of this concept. In addition, the first task ofACHESYMis to find an optimal (compact) macromolecular assembly if more than one polymer chain exists.ACHESYMprocesses PDB (atomic parameters andTLSmatrices) and mmCIF (diffraction data) input files to produce a new coordinate set and to reindex the reflections and modify their phases, if necessary.
Crystal structure ofN-(tert-butoxycarbonyl)phenylalanyldehydroalanine isopropyl ester (Boc–Phe–ΔAla–OiPr)
Authors: Lenartowicz Paweł , Makowski Maciej , Zarychta Bartosz , Ejsmont Krzysztof
Published: November 2014

In the title compound, the dehydrodipeptide (Boc–Phe–ΔAla–OiPr, C20H28N2O5), the molecule has atransconformation of theN-methylamide group. The geometry of the dehydroalanine moiety is to some extent different from those usually found in simple peptides, indicating conjugation between the H2C=C group and the peptide bond. The bond angles around dehydroalanine have unusually high values due to the steric hindrance, the same interaction influencing the slight distortion from planarity of the dehydroalanine. The molecule is stabilized by intramolecular interactions between the isopropyl group and the N atoms of the peptide main chain. In the crystal, an N—H...O hydrogen bond links the molecules into ribbons, giving a herringbone head-to-head packing arrangement extending along the [100] direction. In the stacks, the molecules are linked by weak C—H...O hydrogen-bonding associations.
Crystal structure of bromido-fac-tricarbonyl[5-phenyl-3-(pyridin-2-yl)-1H-1,2,4-triazole-κ2N,N′]rhenium(I)
Authors: Piletska Kseniia , Domasevitch Konstantin V. , Shtemenko Alexander V.
Published: November 2014

In the title compound, [ReBr(C13H10N4)(CO)3], the ReIatom has a distorted octahedral coordination environment. Two N atoms of the 5-phenyl-3-(pyridin-2-yl)-1H-1,2,4-triazole ligand and two of the three carbonyl groups occupy the equatorial plane of the complex, with the third carbonyl ligand and the bromide ligand in the axial positions. The three carbonyl ligands are arranged in afacconfiguration around the ReIatom. Mutual N—H...Br hydrogen bonds arrange molecules into centrosymmetric dimers. Additional stabilization within the crystal structure is provided by C—H...O and C—H...Br hydrogen bonds, as well as by slipped π–π stacking interactions [centroid-to-centroid distance = 3.785 (5) Å], defining a three-dimensional network.
Crystal structure ofN-(tert-butoxycarbonyl)glycyl-(Z)-β-bromodehydroalanine methyl ester [Boc–Gly–(β-Br)(Z)ΔAla–OMe]
Authors: Lenartowicz Paweł , Makowski Maciej , Zarychta Bartosz , Ejsmont Krzysztof
Published: November 2014

The title compound, C11H17BrN2O5, is a dehydroamino acid with a C=C bond between the α- and β-C atoms. The amino acid residues are linkedtransto each other and there are no strong intramolecular hydrogen bonds. The torsion angles indicate a non-helical conformation of the molecule. The dipeptide folding is influenced by an intermolecular N—H...O hydrogen bond and also minimizes steric repulsion. In the crystal, molecules are linked by strong N—H...O hydrogen bonds, generating (001) sheets. The sheets are linked by weak C—H...O and C—H...Br bonds and short Br...Br [3.4149 (3) Å] interactions.
Crystal structure of 2-hydroxyimino-2-(pyridin-2-yl)-N′-[1-(pyridin-2-yl)ethylidene]acetohydrazide
Authors: Plutenko Maxym O. , Lampeka Rostislav D. , Haukka Matti , Nordlander Ebbe
Published: November 2014

The molecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å), with the planes of the two pyridine rings inclined to one another by 5.51 (7)°. The oxime group issynto the amide group, probably due to the formation of an intramolecular N—H...N hydrogen bond that forms anS(6) ring motif. In the crystal, molecules are linked by pairs of bifurcated O—H...(O,N) hydrogen bonds, forming inversion dimers. The latter are linkedviaC—H...O and C—H...N hydrogen bonds, forming sheets lying parallel to (502). The sheets are linkedviaπ–π stacking interactions [inter-centroid distance = 3.7588 (9) Å], involving the pyridine rings of inversion-related molecules, forming a three-dimensional structure.
Structural invariance upon antiferromagnetic ordering in geometrically frustrated swedenborgite, CaBaCo2Fe2O7
Authors: Reim J. D. , Rosén E. , Schweika W. , Meven M. , Leo N. R. , Meier D. , Fiebig M. , Schmidt M. , Kuo C.-Y. , Pi T.-W. , Hu Z. , Valldor M.
Published: November 2014

Centimetre-sized single crystals of high-quality CaBaCo2Fe2O7were synthesized by the optical floating zone technique. The metal-to-metal stoichiometry and oxygen content were confirmed by spectroscopy and thermal reduction experiments. The hexagonal symmetryP63mc(No. 186) well describes the powder X-ray and neutron diffraction as well as single-crystal neutron diffraction at all measured temperatures. This symmetry is also consistent with optical second harmonic generation data obtained between 10 and 295 K. However, a satisfactory structure description from single-crystal neutron diffraction data needs an oxygen split position. Specific heat, magnetic susceptibility and powder neutron diffraction data indicate a magnetic phase transition atTN= 159 K to an antiferromagnetic ground state, but with a persisting hexagonal symmetry and intrinsic geometric frustration.
Experimental uncertainties of three-dimensional pair distribution function investigations exemplified on the diffuse scattering from a tris-tert-butyl-1,3,5-benzene tricarboxamide single crystal
Authors: Simonov Arkadiy , Weber Thomas , Steurer Walter
Published: November 2014

Diffuse scattering from a substitutionally disordered tris-tert-butyl-1,3,5-benzene tricarboxamide single crystal is analyzed with the three-dimensional difference pair distribution function (3D-ΔPDF) method. The real structure of the crystal is shown to consist of infinite polar molecular stacks along thecaxis, which are laterally packed in a hexagonal fashion. The orientation of the stacks is disordered, but neighboring stacks strongly prefer antiparallel arrangements. Quantitative orientational pair correlation coefficients are determined for all lateral pairs separated by less than 100 Å. A careful analysis of the factors influencing the accuracy of the 3D-ΔPDF refinement is presented. It is shown that the effect of statistical errors is small compared to systematic errors coming from diffraction geometry distortions, reciprocal space resolution or incompletely corrected background. Various strategies for identifying and decreasing systematic errors are discussed. The impact of the systematic errors on the uncertainty of the results is not just specific for 3D-ΔPDF investigations but also relevant for other quantitative diffuse scattering modeling techniques.
A Bayesian approach to removal of incoherent scattering from neutron total-scattering data
Authors: Gagin Anton , Levin Igor
Published: November 2014

A Bayesian statistics approach for subtraction of incoherent scattering from neutron total-scattering data has been developed and implemented in a public domain software package. In this approach, the estimated background signal associated with incoherent scattering maximizes the posterior probability, which combines the likelihood of this signal in reciprocal and real spaces with the prior that favors smooth lines. The probability distributions are constructed according to the principle of maximum entropy. The method enables robust subtraction of incoherent-scattering backgrounds while providing estimated uncertainties for recovered signals. The developed procedure was first tested using simulated data and then demonstrated using three representative experimental data sets, collected on bulk materials and nanoparticles, featuring distinct ratios of coherent to incoherent scattering.
Quantification of the information in small-angle scattering data
Authors: Pedersen Martin Cramer , Hansen Steen Laugesen , Markussen Bo , Arleth Lise , Mortensen Kell
Published: November 2014

Small-angle X-ray and neutron scattering have become increasingly popular owing to improvements in instrumentation and developments in data analysis, sample handling and sample preparation. For some time, it has been suggested that a more systematic approach to the quantification of the information content in small-angle scattering data would allow for a more optimal experiment planning and a more reliable data analysis. In the present article, it is shown how ray-tracing techniques in combination with a statistically rigorous data analysis provide an appropriate platform for such a systematic quantification of the information content in scattering data. As examples of applications, it is shown how the exposure time at different instrumental settings or contrast situations can be optimally prioritized in an experiment. Also, the gain in information by combining small-angle X-ray and neutron scattering is assessed. While solution small-angle scattering data of proteins and protein–lipid complexes are used as examples in the present case study, the approach is generalizable to a wide range of other samples and experimental techniques. The source code for the algorithms and ray-tracing components developed for this study has been made available on-line.
Cloning, purification, crystallization and 1.57 Å resolution X-ray data analysis of AmsI, the tyrosine phosphatase controlling amylovoran biosynthesis in the plant pathogenErwinia amylovora
Authors: Benini Stefano , Caputi Lorenzo , Cianci Michele
Published: November 2014

The Gram-negative bacteriumErwinia amylovorais a destructive pathogen of plants belonging to the Rosaceae family. Amongst its pathogenicity factors,E. amylovoraproduces the exopolysaccharide amylovoran, which contributes to the occlusion of plant vessels, causing wilting of shoots and eventually resulting in plant death. Amylovoran biosynthesis requires the presence of 12 genes (fromamsA toamsL) clustered in theamsregion of theE. amylovoragenome. They mostly encode glycosyl transferases (AmsG, AmsB, AmsD, AmsE, AmsJ and AmsK), proteins involved in amylovoran translocation and assembly (AmsH, AmsL and AmsC), and also a tyrosine kinase (AmsA) and a tyrosine phosphatase (AmsI), which are both involved in the regulation of amylovoran biosynthesis. The low-molecular-weight protein tyrosine phosphatase AmsI was overexpressed as a His6-tagged protein inEscherichia coli, purified and crystallized. X-ray diffraction data were collected to a maximum resolution of 1.57 Å in space groupP3121.
Crystallization and preliminary X-ray diffraction analysis of Trap1 complexed with Hsp90 inhibitors
Authors: Jeong Hanbin , Kang Byoung Heon , Lee Changwook
Published: November 2014

Hsp90 is a molecular chaperone responsible for the assembly and regulation of many cellular client proteins. In particular, Trap1, a mitochondrial Hsp90 homologue, plays a pivotal role in maintaining mitochondrial integrity, protecting against apoptosis in cancer cells. The N (N-terminal)-M (middle) domain of human Trap1 was crystallized in complex with Hsp90 inhibitors (PU-H71 and BIIB-021) by the hanging-drop vapour-diffusion method at pH 6.5 and 293 K using 15% PEG 8K as a precipitant. Diffraction data were collected from crystals of the Trap1–PU-H71 (2.7 Å) and Trap1–BIIB-021 (3.1 Å) complexes to high resolution at a synchrotron-radiation source. Preliminary X-ray diffraction analysis revealed that both crystals belonged to space groupP41212 orP43212, with unit-cell parametersa=b= 69.2,c= 252.5 Å, and contained one molecule per asymmetric unit according to Matthews coefficient calculations.
A simple technique to reduce evaporation of crystallization droplets by using plate lids with apertures for adding liquids
Authors: Zipper Lauren E. , Aristide Xavier , Bishop Dylan P. , Joshi Ishita , Kharzeev Julia , Patel Krishna B. , Santiago Brianna M. , Joshi Karan , Dorsinvil Kahille , Sweet Robert M. , Soares Alexei S.
Published: November 2014

A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fitting the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under different conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63–82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. The results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations.
Prevalence and genomic characterization of porcine parvoviruses detected in Chiangmai area of Thailand in 2011
Authors: Saekhow Prayuth , Ikeda Hidetoshi
Published: November 2014

Porcine parvovirus (PPV) causes reproductive failure in sows and has spread worldwide. Several new types of porcine parvoviruses have recently been identified in pig herds. The prevalence of five porcine parvoviruses in the Chiangmai area of Thailand was studied. The prevalence in 80 pigs was 53% for PPV (PPV‐Kr or ‐NADL2 being the new abbreviations), 83% for PPV2 (CnP‐PARV4), 73% for PPV3 (P‐PARV4), 44% for PPV4 (PPV4), and 18% for PBo‐likeV (PBoV7). Over 60% of the pigs carried more than three of the five porcine parvoviruses and occurrence together of the two pairs of viral genes, PPV1/PPV3 and PPV2/PBo‐likeV were observed. Phylogenetic analyses for PPV2 and PPV3 indicated the existence of only two major clades of PPV2 and one major clade of PPV3.
Interview‐based sighting histories can inform regional conservation prioritization for highly threatened cryptic species
Authors: Turvey Samuel T. , Trung Cao Tien , Quyet Vo Dai , Nhu Hoang Van , Thoai Do Van , Tuan Vo Cong Anh , Hoa Dang Thi , Kacha Kouvang , Sysomphone Thongsay , Wallate Sousakhone , Hai Chau Thi Thanh , Thanh Nguyen Van , Wilkinson Nicholas M.
Published: November 2014

The use of robust ecological data to make evidence‐based management decisions is frequently prevented by limited data quantity or quality, and local ecological knowledge (LEK) is increasingly seen as an important source of information for conservation. However, there has been little assessment of LEK's usefulness for informing prioritization and management of landscapes for threatened species, or assessing comparative species status across landscapes.

A large‐scale interview survey in the Annamite Mountains (Vietnam and Lao PDR) compiled the first systematic LEK data set for saola Pseudoryx nghetinhensis, one of the world's rarest mammals, and eight other ungulates. Saola conservation is hindered by uncertainty over continued presence across much of its proposed distribution. We analysed comparative LEK‐based last‐sighting data across three landscapes to determine whether regional sighting histories support previous suggestions of landscape importance for saola conservation (Hue‐Quang Nam: top‐priority Vietnamese landscape; Pu Mat: lower priority Vietnamese landscape; Viengthong: high‐priority Lao landscape) and whether they constitute an effective spatial prioritization tool for cryptic species management.

Wild pig and red muntjac may be the only Annamite ungulates with stable populations; the regional status of all other species appears to be worse. Saola have declined more severely and/or are significantly rarer than most other ungulates and have been seen by relatively few respondents. Saola were also frequently considered locally rarest or declining, and never as species that had not declined.

In contrast to other species, there are no regional differences in saola sighting histories, with continued persistence in all landscapes challenging suggestions that regional status differs greatly. Remnant populations persist in Vietnam despite heavy hunting, but even remote landscapes in Lao may be under intense pressure.

Synthesis and applications. Our local ecological knowledge data suggest that intact saola populations probably no longer exist, but individuals persist in all three landscapes, making management activities to reduce hunting pressure on ungulates in each landscape a conservation priority. Analysis of last‐sighting histories can constitute an important conservation tool when robust data are otherwise unavailable, and collection of last‐sighting records should be incorporated more widely into field studies and management of other highly threatened, cryptic species.
Photographic Analyses Using Skin Detail of the Hand: A Methodology and Evaluation,
Authors: Malone Christina A.
Published: November 2014

Skin features have been employed by law enforcement agencies for suspect and victim identification. Comparisons of hand have arisen in casework where images have been submitted where a face was not present but a hand was visible. This research utilizes a collection of 128 hands from employees of the U.S. Army Criminal Investigation Laboratory to examine the frequency and distribution of skin detail on the dorsal surface of the hand. To assess the location of features, the hand was segmented into 14 regions using readily discernible anatomical landmarks. Overall, 2618 pigmented lesions and 92 scars or injuries were documented. When comparing the regions with one another, Regions 1–10 had fewer pigmented lesions than Regions 11–14. There was no pattern to the distribution of scars throughout the regions. The findings presented a foundation for one possible method that may differentiate hands based on the frequency and distribution of such features.
Exposures to Conducted Electrical Weapons (IncludingTASER®Devices): How Many and for How Long are Acceptable?
Authors: Jauchem James R.
Published: November 2014

TASER®conducted electrical weapons (CEWs) are an important law‐enforcement tool. The purposes of this study are a) to review recent literature regarding potential pathophysiological responses to applications ofCEWs, and other related issues and b) to evaluate whether enough data exist to determine the acceptability of longer‐duration (or repeated) exposures. This is a narrative review, using a multidisciplinary approach of analyzing reports from physiological, legal‐medical, and police‐strategy literature sources. In general, short‐duration exposures toCEWs result in limited effects. Longer‐duration or repeated exposures may be utilized with caution, although there are currently not enough data to determine the acceptability of all types of exposures. Data examined in the literature have inherent limitations. Appropriateness of specific types ofCEWusage may be determined by individual police agencies, applying risk/benefit analyses unique to each organization. While more research is recommended, initial concepts of potential future long‐duration or repeatedCEWapplications are presented.
A legal geography of property, tenure, exclusion, and rights in Cambodia: exposing an incongruous property narrative for non‐Western settings
Authors: Gillespie Josephine
Published: November 2014

The scholarship of legal geography provides an alternative way of conceptualising human–environmental relationships. While laws determine access to and regulate use of land through practices of bounding and excluding, geographical studies provide insights into the way that both physical and social processes create places. The meeting of these perspectives is invaluable. Legal geography perspectives are coming of age in an era when transdisciplinary perspectives on human/nonhuman–landscape interactions are of core concern to wider land use policy considerations. This paper draws on legal geography scholarship about property framed around three key concepts (1) tenure security, (2) exclusion, and (3) rights to reveal the social complexity surrounding these issues. This complexity is magnified in non‐Western settings, and in this paper, the legal geography perspective of analysis is extended to a developing country context. Using Cambodia as the primary setting, this paper challenges the unquestioning exportation of a dominant ‘Western’ property model into non‐Western contexts.
Microstructure Features of Proventriculus and Ultrastructure of the Gastric Gland Cells in Chinese Taihe Black‐bone Silky Fowl (Gallus gallus domesticus Brisson)
Authors: Zhang H. , Ge T. , Peng S. , Zhong S. , Zhou Z.
Published: November 2014

To investigate microstructure of proventriculus and ultrastructure of the gastric gland cells from Chinese Taihe black‐bone silky fowl (BSF), the proventriculus of 4‐week‐old BSF was sampled. Conventional histological and transmission electron microscope (TEM) methods were used in this study. The wall of the Taihe BSF proventriculus was consisted of four layers, the mucous, submucosa, muscularis externa and the serosa as others birds. The muscularis externa of the birds' proventriculus contained three layers. Much of the melanin was present in loose connective tissue of lamina propria, submucosa, and muscularis externa unlike others. In addition, the ultrastructure of the gastric gland cells was observed by TEM. There was only one kind of gland cell, for example oxynticopeptic cell in proventriculus of Taihe BSF. The oxynticopeptic cells contained numerous mitochondria, cisternae of rough endoplasmic reticulum (CRER), intracellular canaliculi (IC) that secrete hydrochloric acid and small amounts of pepsinogen granules. The rough endoplasmic reticulum (RER) was irregular cisternae with ribosomes and surrounded tightly the mitochondria along their configuration. The electron‐dense pepsinogen granules were round with various sizes. The neighbouring oxynticopeptic cells were closed up with tight junction and gap junction. The inter‐space between the neighbouring oxynticopeptic cells was stenosis or was filled with electron‐dense extracellular substance. In conclusion, the gastric gland cells of Chinese Taihe BSF proventriculus were only oxynticopeptic cells that secrete hydrochloric acid and pepsinogen, but no parietal cells and chief cells of mammal. The gastric gland cells of proventriculus were underdeveloped compared with those of mammals.