bluuebunny/crossref_metadata_2025 huggingface dataset:
Trace element content and magnetic properties of commercial HOPG samples studied by ion beam microscopy and SQUID magnetometry
Authors: Spemann D. , Esquinazi P. , Setzer A. , Böhlmann W.
Published: October 2014

In this study, the impurity concentration and magnetic response of nine highly oriented pyrolytic graphite (HOPG) samples with different grades and from different providers were determined using ion beam microscopy and SQUID magnetometry. Apart from sideface contaminations in the as-received state, bulk contamination of the samples in most cases consists of disk-shaped micron-sized particles made of Ti and V with an additional Fe contamination around the grain perimeter. The saturation magnetization typically increases with Fe concentration, however, there is no simple correlation between Fe content and magnetic moment. The saturation magnetization of one, respectively six, out of nine samples clearly exceeds the maximum contribution from pure Fe or Fe3C. For most samples the temperature dependence of the remanence decreases linearly with T – a dependence found previously for defect-induced magnetism (DIM) in HOPG. We conclude that apart from magnetic impurities, additional contribution to the ferromagnetic magnetization exists in pristine HOPG in agreement with previous studies. A comparative study between the results of ion beam microscopy and the commonly used EDX analysis shows clearly that EDX is not a reliable method for quantitative trace elemental analysis in graphite, clarifying weaknesses and discrepancies in the element concentrations given in the recent literature.
The Big Picture: Effects of Surround on Immersion and Size Perception
Authors: Baranowski Andreas M , Hecht Heiko
Published: October 2014

Despite the fear of the entertainment industry that illegal downloads of films might ruin their business, going to the movies continues to be a popular leisure activity. One reason why people prefer to watch movies in cinemas may be the surround of the movie screen or its physically huge size. To disentangle the factors that might contribute to the size impression, we tested several measures of subjective size and immersion in different viewing environments. For this purpose we built a model cinema that provided visual angle information comparable with that of a real cinema. Subjects watched identical movie clips in a real cinema, a model cinema, and on a display monitor in isolation. Whereas the isolated display monitor was inferior, the addition of a contextual model improved the viewing immersion to the extent that it was comparable with the movie theater experience, provided the viewing angle remained the same. In a further study we built an identical but even smaller model cinema to unconfound visual angle and viewing distance. Both model cinemas produced similar results. There was a trend for the larger screen to be more immersive; however, viewing angle did not play a role in how the movie was evaluated.
Proximal-Distal, Not Medial-Lateral, Movement across an Edge Increases Discrimination of Edge Sharpness
Authors: Kent Christopher , Skinner Andy L , Weeds Carys , Benton Christopher P
Published: October 2014

Edges are fundamental properties of our environment and the objects we interact with. There is a lack of research on the haptic perception of edges, especially the sharpness of an edge. Skinner et al. [2013 PLoS ONE, 8(9): E73283] found that haptic discriminability of sharpness was clearly superior when using a relatively unrestrained, free exploration strategy compared with a static single touch strategy. In the free exploration condition two distinct movement patterns were frequently used by participants: a proximal-distal movement of the fingerpad across the test edge and a medial-lateral movement of the fingerpad along the test edge. Here, using the same stimuli and two-alternative forced-choice method of constant stimuli as Skinner et al. (2013), we demonstrate that a proximal-distal movement results in substantially lower sharpness discrimination thresholds than a medial-lateral movement. The underlying neurophysiology and implications for the design of haptic displays are considered.
Evaluating Aboriginal and Torres Strait Islander health promotion activities using audit and feedback
Authors: O'Donoghue Lynette , Percival Nikki , Laycock Alison , McCalman Janya , Tsey Komla , Armit Christine , Bailie Ross
Published: October 2014

Indigenous primary health care (PHC) services have been identified as exemplary models of comprehensive PHC; however, many practitioners in these services struggle to deliver effective health promotion. In particular, practitioners have limited capacity and resources to evaluate health promotion activities. Best practice health promotion is important to help address the lifestyle and wider factors that impact on the health of people and communities. In this paper, we report on the acceptability and feasibility of an innovative approach for evaluating the design of health promotion activities in four Indigenous PHC services in the Northern Territory. The approach draws on a popular continuous quality improvement technique known as audit and feedback (A&F), in which information related to best practice is gathered through the use of a standardised audit tool and fed back to practitioners. The A&F approach has been used successfully to improve clinical service delivery in Indigenous PHC; however, the technique has had limited use in health promotion. The present study found that facilitated participatory processes were important for the collection of locally relevant information and for contributing to improving PHC practitioners’ knowledge and understanding of best practice health promotion.
Epidemiology of Methicillin-Resistant Staphylococcus aureus Pneumonia in Community Hospitals
Authors: Lewis Sarah S. , Walker Vanessa J. , Lee Mi Suk , Chen Luke , Moehring Rebekah W. , Cox Christopher E. , Sexton Daniel J. , Anderson Deverick J.
Published: October 2014

Objective.

Describe the epidemiology of healthcare-related (ie, healthcare-associated and hospital-acquired) pneumonia due to methicillin-resistant Staphylococcus aureus (MRSA) among hospitalized patients in community hospitals.

Design.

Retrospective cohort study.

Setting.

Twenty-four community hospitals in the southeastern United States affiliated with the Duke Infection Control Outreach Network (median size, 211 beds; range, 103–658 beds).

Methods.

Adult patients with healthcare-related MRSA pneumonia admitted to study hospitals from January 1, 2008, to December 31, 2012, were identified using surveillance data. Seasonal and annual incidence rates (cases per 100,000 patient-days) were estimated using generalized estimating equation models. Characteristics of community-onset and hospital-onset cases were compared.

Results.

A total of 1,048 cases of healthcare-related pneumonia due to MRSA were observed during 5,863,941 patient-days. The annual incidence rate of healthcare-related MRSA pneumonia increased from 11.3 cases per 100,000 patient-days (95% confidence interval [CI], 6.8–18.7) in 2008 to 15.5 cases per 100,000 patient-days (95% CI, 8.4–28.5) in 2012 (P = .055). The incidence rate was highest in winter months and lowest in summer months (15.4 vs 11.1 cases per 100,000 patient-days; incidence rate ratio, 1.39 [95% CI, 1.06–1.82]; P = .016). A total of 814 cases (77.7%) were community-onset healthcare-associated pneumonia cases; only 49 cases (4.7%) were ventilator-associated cases. Of 811 patients whose disposition was known, 240 (29.6%) died during hospitalization or were discharged to hospice.

Conclusions.

From 2008 through 2012, the incidence of healthcare-related MRSA pneumonia among patients who were admitted to a large network of community hospitals increased, despite the decreasing incidence of invasive MRSA infections nationwide. Additional study is warranted to evaluate trends in this important and potentially modifiable public health problem.

Infect Control Hosp Epidemiol 2014;35(12):1452–1457
Evaluating Use of Neutral Electrolyzed Water for Cleaning Near-Patient Surfaces
Authors: Stewart M. , Bogusz A. , Hunter J. , Devanny I. , Yip B. , Reid D. , Robertson C. , Dancer S. J.
Published: October 2014

Objective.

This study aimed to monitor the microbiological effect of cleaning near-patient sites over a 48-hour period with a novel disinfectant, electrolyzed water.

Setting.

One ward dedicated to acute care of the elderly population in a district general hospital in Scotland.

Methods.

Lockers, left and right cotsides, and overbed tables in 30 bed spaces were screened for aerobic colony count (ACC), methicillin-susceptible Staphylococcus aureus (MSSA), and methicillin-resistant S. aureus (MRSA) before cleaning with electrolyzed water. Sites were rescreened at varying intervals from 1 to 48 hours after cleaning. Microbial growth was quantified as colony-forming units (CFUs) per square centimeter and presence or absence of MSSA and MRSA at each site. The study was repeated 3 times at monthly intervals.

Results.

There was an early and significant reduction in average ACC (360 sampled sites) from a before-cleaning level of 4.3 to 1.65 CFU/cm2 at 1 hour after disinfectant cleaning (P <.0001). Average counts then increased to 3.53 CFU/cm2 at 24 hours and 3.68 CFU/cm2 at 48 hours. Total MSSA/MRSA (34 isolates) decreased by 71% at 4 hours after cleaning but then increased to 155% (53 isolates) of precleaning levels at 24 hours.

Conclusions.

Cleaning with electrolyzed water reduced ACC and staphylococci on surfaces beside patients. ACC remained below precleaning levels at 48 hours, but MSSA/MRSA counts exceeded original levels at 24 hours after cleaning. Although disinfectant cleaning quickly reduces bioburden, additional investigation is required to clarify the reasons for rebound contamination of pathogens at near-patient sites.

Infect Control Hosp Epidemiol 2014;35(12):1505–1510
Scientific Explanation
Authors: Woodward James
Published: October 2014

Two important models of explanation in science are the deductive nomological model, which emphasizes subsumption of facts under laws, and the causal model, which takes explanations to be revealing of causes. These two models of explanation are outlined and given critical scrutiny. The chapter explores what the structure of an explanatory answer to a “why?” question might be in science and outlines the important idea that to explain is to place what occurs under a generalization, exceptionless or statistical, about what kinds of things occur. It notes a number of objections to that simple notion of explanation and explores some proposals to supplement this subsumption model of explanation, including the proposal to demand that explanations in science be unifying and the proposal that a basic notion of causation is essential to our concept of explanation.
Physics of Long-Range Interacting Systems
Authors: Campa A. , Dauxois T. , Fanelli D. , Ruffo S.
Published: October 2014

This book deals with an important class of many-body systems: those where the interaction potential decays slowly for large inter-particle distance. In particular, systems where the decay is slower than the inverse inter-particle distance raised to the dimension of the embedding space. Gravitational and Coulomb interactions are the most prominent examples. However, it has become clear that long-range interactions are more common than previously thought. This has stimulated a growing interest in the study of long-range interacting systems, which has led to a much better understanding of the many peculiarities in their behaviour. The seed of all particular features of these systems, both at equilibrium and out-of-equilibrium, is the lack of additivity. It is now well understood that this does not prevent a statistical mechanics treatment. However, it does require a more in-depth study of the thermodynamic limit and of all related theoretical concepts. A satisfactory understanding of properties generally considered as oddities only a couple of decades ago has now been reached: ensemble inequivalence, negative specific heat, negative susceptibility, ergodicity breaking, out-of-equilibrium quasi-stationary-states, anomalous diffusion, etc. The first two parts describe the theoretical and computational instruments needed for addressing the study of both equilibrium and dynamical properties of systems subject to long-range forces. The third part of the book is devoted to discussing the applications of such techniques to the most relevant examples of long-range systems. The only prerequisite is a basic course in statistical mechanics.
A phenomenological density-scaling approach to lamellipodial actin dynamics
Authors: Lewalle Alexandre , Fritzsche Marco , Wilson Kerry , Thorogate Richard , Duke Tom , Charras Guillaume
Published: October 2014

The integration of protein function studied
in vitro
in a dynamic system like the cell lamellipodium remains a significant challenge. One reason is the apparent contradictory effect that perturbations of some proteins can have on the overall lamellipodium dynamics, depending on exact conditions. Theoretical modelling offers one approach for understanding the balance between the mechanisms that drive and regulate actin network growth and decay. Most models use a ‘bottom-up’ approach, involving explicitly assembling biochemical components to simulate observable behaviour. Their correctness therefore relies on both the accurate characterization of all the components and the completeness of the relevant processes involved. To avoid potential pitfalls due to this uncertainty, we used an alternative ‘top-down’ approach, in which measurable features of lamellipodium behaviour, here observed in two different cell types (HL60 and B16-F1), directly inform the development of a simple phenomenological model of lamellipodium dynamics. We show that the kinetics of F-actin association and dissociation scales with the local F-actin density, with no explicit location dependence. This justifies the use of a simplified kinetic model of lamellipodium dynamics that yields predictions testable by pharmacological or genetic intervention. A length-scale parameter (the lamellipodium width) emerges from this analysis as an experimentally accessible probe of network regulatory processes.
Separation of blood cells with differing deformability using deterministic lateral displacement
Authors: Holmes David , Whyte Graeme , Bailey Joe , Vergara-Irigaray Nuria , Ekpenyong Andrew , Guck Jochen , Duke Tom
Published: October 2014

Determining cell mechanical properties is increasingly recognized as a marker-free way to characterize and separate biological cells. This emerging realization has led to the development of a plethora of appropriate measurement techniques. Here, we use a fairly novel approach, deterministic lateral displacement (DLD), to separate blood cells based on their mechanical phenotype with high throughput. Human red blood cells were treated chemically to alter their membrane deformability and the effect of this alteration on the hydrodynamic behaviour of the cells in a DLD device was investigated. Cells of defined stiffness (glutaraldehyde cross-linked erythrocytes) were used to test the performance of the DLD device across a range of cell stiffness and applied shear rates. Optical stretching was used as an independent method for quantifying the variation in stiffness of the cells. Lateral displacement of cells flowing within the device, and their subsequent exit position from the device were shown to correlate with cell stiffness. Data showing how the isolation of leucocytes from whole blood varies with applied shear rate are also presented. The ability to sort leucocyte sub-populations (T-lymphocytes and neutrophils), based on a combination of cell size and deformability, demonstrates the potential for using DLD devices to perform continuous fractionation and/or enrichment of leucocyte sub-populations from whole blood.
A model of ionic transport and osmotic volume control in cochlear outer hair cells
Authors: West Timothy , Ashmore Jonathan
Published: October 2014

A computational model of the outer hair cell (OHC) of the mammalian cochlea is presented. It addresses the way in which movement of ions controls the cell shape and regulates pH. The model takes into account the possible chloride–bicarbonate exchange function of prestin, a protein highly expressed in the plasma membrane of OHCs. A model of intracellular pH transients following the imposition of a rapid acid load upon the cell has been adapted from the squid axon literature and further extended in order to investigate the effects of ion transport upon the osmotic flux of water into the cell. The model predicts the slow length changes of OHCs reported in the literature a feature which may control the contribution of OHCs to cochlear amplification.
Phase-locked spiking of inner ear hair cells and the driven noisy Adler equation
Authors: Shlomovitz Roie , Roongthumskul Yuttana , Ji Seung , Bozovic Dolores , Bruinsma Robijn
Published: October 2014

The inner ear constitutes a remarkably sensitive mechanical detector. This detection occurs in a noisy and highly viscous environment, as the sensory cells—the hair cells—are immersed in a fluid-filled compartment and operate at room or higher temperatures. We model the active motility of hair cell bundles of the vestibular system with the Adler equation, which describes the phase degree of freedom of bundle motion. We explore both analytically and numerically the response of the system to external signals, in the presence of white noise. The theoretical model predicts that hair bundles poised in the quiescent regime can exhibit sporadic spikes—sudden excursions in the position of the bundle. In this spiking regime, the system exhibits stochastic resonance, with the spiking rate peaking at an optimal level of noise. Upon the application of a very weak signal, the spikes occur at a preferential phase of the stimulus cycle. We compare the theoretical predictions of our model to experimental measurements obtained
in vitro
from individual hair cells. Finally, we show that an array of uncoupled hair cells could provide a sensitive detector that encodes the frequency of the applied signal.
Ensemble velocity of non-processive molecular motors with multiple chemical states
Authors: Vilfan Andrej
Published: October 2014

We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain dependence of transition rates, reverse transition rates and nonlinearities in the elasticity can show interesting functional dependencies, which deviate significantly from the frequently assumed Michaelis–Menten form. We discuss how the order of events in the duty cycle can be inferred from the measured dependence. The model also predicts the possibility of velocity reversal at a certain ATP concentration if the duty cycle contains several conformational changes of opposite directionalities.
Stress distributions and cell flows in a growing cell aggregate
Authors: Delarue Morgan , Joanny Jean-François , Jülicher Frank , Prost Jacques
Published: October 2014

We discuss the short-time response of a multicellular spheroid to an external pressure jump. Our experiments show that 5 min after the pressure jump, the cell density increases in the centre of the spheroid but does not change appreciably close to the surface of the spheroid. This result can be explained if the cells are polarized which we show to be the case. Motivated by the experimental results, we develop a theory for polarized spheroids where the cell polarity is radial (except in a thin shell close to the spheroid surface). The theory takes into account the dependence of cell division and apoptosis rates on the local stress, the cell polarity and active stress generated by the cells and the dependence of active stress on the local pressure. We find a short-time increase of the cell density after a pressure jump that decays as a power law from the spheroid centre, which is in reasonable agreement with the experimental results. By comparing our theory to experiments, we can estimate the isotropic compression modulus of the tissue.
Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the ‘deep sea-1’ clade of marine methanotrophs
Authors: Tavormina Patricia L. , Hatzenpichler Roland , McGlynn Shawn , Chadwick Grayson , Dawson Katherine S. , Connon Stephanie A. , Orphan Victoria J.
Published: October 2014

We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1T, ‘whale fall 1’) that shares 98 % 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ≤94.6 % 16S rRNA gene sequence identity with species of the genus

Methylobacter

and ≤93.6 % 16S rRNA gene sequence identity with species of the genera

Methylomonas

and

Methylosarcina

. Strain WF1T represents the first cultivar from the ‘deep sea-1’ clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1T were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1T was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16 : 0, 16 : 1ω9c, 16 : 1ω9t, 16 : 1ω8c and 16 : 2ω9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1T, a capacity that had not been functionally demonstrated previously in members of

Methylobacter

. On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1T ( = LMG 28393T = ATCC BAA-2619T).
Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm
Authors: Farkas Milán , Táncsics András , Kriszt Balázs , Benedek Tibor , Tóth Erika M. , Kéki Zsuzsa , Veres Péter G. , Szoboszlay Sándor
Published: October 2014

A floc-forming, Gram-stain-negative, petroleum hydrocarbon-degrading bacterial strain, designated BucT, was isolated from a petroleum hydrocarbon-contaminated site in Hungary. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BucT formed a distinct phyletic lineage within the genus

Zoogloea

. Its closest relative was found to be

Zoogloea caeni

EMB43T (97.2 % 16S rRNA gene sequence similarity) followed by

Zoogloea oryzae

A-7T (95.9 %),

Zoogloea ramigera

ATCC 19544T (95.5 %) and

Zoogloea resiniphila

DhA-35T (95.4 %). The level of DNA–DNA relatedness between strain BucT and

Z. caeni

EMB43T was 31.6 %. Cells of strain BucT are facultatively aerobic, rod-shaped, and motile by means of a polar flagellum. The strain grew at temperatures of 5–35 °C (optimum 25–28 °C), and at pH 6.0–9.0 (optimum 6.5–7.5). The predominant fatty acids were C16 : 0, C10 : 0 3-OH, C12 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major respiratory quinone was ubiquinone-8 (Q-8) and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 63.2 mol%. On the basis of the chemotaxonomic, molecular and phenotypic data, isolate BucT is considered to represent a novel species of the genus

Zoogloea

, for which the name Zoogloea oleivorans sp. nov. is proposed. The type strain is BucT ( = DSM 28387T = NCAIM B 02570T).
Heterozygous gene truncation delineates the human haploinsufficient genome
Authors: Bartha István , Rausell Antonio , McLaren Paul J , Mohammadi Pejman , Tardaguila Manuel , Chaturvedi Nimisha , Fellay Jacques , Telenti Amalio
Published: October 2014

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene’s tolerance to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 protein coding autosomal genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutralde novomutation (p< 10−4). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases
SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants
Authors: Gehring Julian S. , Fischer Bernd , Lawrence Michael , Huber Wolfgang
Published: October 2014

Mutational signatures are patterns in the occurrence of somatic single nucleotide variants (SNVs) that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable, and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined methods and integrates with Bioconductor workflows. The R package SomaticSignatures is available as part of the Bioconductor project (R Core Team, 2014; Gentleman et al., 2004). Its documentation provides additional details on the methodology and demonstrates applications to biological datasets.
Crystal structure of 1,3-bis(1,3-dioxoisoindolin-1-yl)urea dihydrate: a urea-based anion receptor
Authors: Medrano Felipe , Lujano Sergio , Godoy-Alcántar Carolina , Tlahuext Hugo
Published: October 2014

The whole molecule of the title compound, C17H10N4O5·2H2O, is generated by twofold rotation symmetry and it crystallized as a dihydrate. The planes of the phthalimide moieties and the urea unit are almost normal to one another, with a dihedral angle of 78.62 (9)°. In the crystal, molecules are linked by N—H...O and O—H...O hydrogen bonds, forming a three-dimensional framework structure. The crystal packing also features C—H...O hydrogen bonds and slipped parallel π–π interactions [centroid–centroid distance = 3.6746 (15) Å] involving the benzene rings of neighbouring phthalimide moieties.
Crystal structure of 1-tosyl-1,2,3,4-tetrahydroquinoline
Authors: Jeyaseelan S. , Asha K.V. , Venkateshappa G. , Raghavendrakumar P. , Palakshamurthy B.S.
Published: October 2014

In the title compound, C16H17NO2S, the heterocyclic ring adopts a half-chair conformation and the bond-angle sum at the N atom is 350.2°. The dihedral angle between the planes of the aromatic rings is 47.74 (10)°. In the crystal, molecules are linked by C—H...O hydrogen bonds to generate [010] chains.
Crystal structure of dimethyl 3,3′-[(3-nitrophenyl)methylene]bis(1H-indole-2-carboxylate) ethanol monosolvate
Authors: Sun Hong-Shun , Li Yu-Long , Jiang Hong , Xu Ning , Xu Hong
Published: October 2014

In the title compound, C27H21N3O6·C2H5OH, the indole ring systems are approximately perpendicular to each other, with a dihedral angle of 89.3 (5)°; the plane of the benzene ring is oriented with respect to the indole ring systems at 49.9 (5) and 73.4 (3)°. In the crystal, molecules are linked by N—H...O and O—H...O hydrogen bonds and weak C—H...π interactions into a three-dimensional supramolecular architecture. A void of 33.0 (7) Å3is observed in the crystal structure. The solvent ethanol molecule acts as a donor, forming an O—H...O hydrogen bond, reinforcing the framework structure.
Crystal structure of bis(dimethylammonium) hexaaquanickel(II) bis(sulfate) dihydrate
Authors: Held Peter
Published: October 2014

In the title salt, (C2H8N)2[Ni(H2O)6)](SO4)2·2H2O, the NiIIcation is located on a centre of inversion and exhibits a slightly distorted octahedral arrangement of water molecules. The Ni—O bond lengths in the complex [Ni(H2O)6]2+cation show a distribution as in the related Tutton salt (NH4)2[Ni(H2O)6](SO4)2, but are longer in average [2.056 (13)versus2.037 (12) Å]. The noncoordinating water molecules and dimethylammonium cations connect the sulfate and [Ni(H2O)6]2+octahedraviaO—H...O and N—H...O hydrogen bonds from weak up to medium strength into a three-dimensional framework whereby the complex metal cations and sulfate anions are arranged in sheets parallel (001).
Crystal structure of difenoconazole
Authors: Cho Seonghwa , Kang Gihaeng , Lee Sangjin , Kim Tae Ho
Published: October 2014

In the title compound difenoconazole [systematic name: 1-({2-[2-chloro-4-(4-chlorophenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl}methyl)-1H-1,2,4-triazole], C19H17Cl2N3O3, the dihedral angle between the planes of the 4-chlorophenyl and 2-chlorophenyl rings is 79.34 (9)°, while the dihedral angle between the planes of the triazole ring and the dioxolanyl group is 59.45 (19)°. In the crystal, pairs of C—H...N hydrogen bonds link adjacent molecules, forming dimers withR22(6) loops. In addition, the dimers are linked by C—H...O hydrogen bonds, resulting in a three-dimensional architecture. Disorder was modeled for one C atom of the dioxolanyl group over two sets of sites with an occupancy ratio of 0.566 (17):0.434 (17).
Crystal structure of (E)-N-[(E)-3-(4-methoxyphenyl)allylidene]naphthalen-1-amine
Authors: Lee Jae Kyun , Cha Joo Hwan , Cho Yong Seo , Min Sun-Joon , Lee Joon Kyun
Published: October 2014

In the title compound, C20H17NO, the dihedral angle between the mean planes of the 4-methoxyphenyl ring and the naphthalene ring is 69.50 (7)°. The methoxy group is almost coplanar with the benzene ring to which it is connected [Cb—Cb—Om—Cm torsion angle of −7.9 (2)°; b = benzene and m = methoxy] and the imine group displays a C—C—N=C torsion angle is −57.2 (2)°. The imine (C=N) group has anEconformation. In the crystal, weak π–π interactions between the benzene rings [centroid–centroid distance = 3.7781 (10) Å] are observed.
Crystal structure of isobutylammonium hydrogen oxalate hemihydrate
Authors: Dziuk Błażej , Zarychta Bartosz , Ejsmont Krzysztof
Published: October 2014

In the title hydrated molecular salt, C4H12N+·C2HO4−·0.5H2O, the O atom of the water molecule lies on a crystallographic twofold axis. The dihedral angle between the CO2and CO2H planes of the anion is 18.47 (8)°. In the crystal, the anions are connected to each other by strong near-linear O—H...O hydrogen bonds. The water molecules are located between the chains of anions and isobutylamine cations; their O atoms participate as donors and acceptors, respectively, in O—H...O and N—H...O hydrogen bonds, which form channels (dimensions = 4.615 and 3.387 Å) arranged parallel to [010].
Crystal structure of 3-[(E)-2-(4-phenyl-1,3-thiazol-2-yl)hydrazin-1-ylidene]indolin-2-one
Authors: Halasangi Bhimashankar M. , Badami Prema S. , Patil Sangamesh A. , Anil Kumar G. N.
Published: October 2014

In the title molecule, C17H12N4OS, the thiazole ring forms a dihedral angle of 10.8 (2)° with the phenyl ring and an angle of 3.1 (3)° with the indole ring system [which has a maximum deviation of 0.035 (2) Å]. The dihedral angle between the planes of the phenyl ring and the indole ring system is 11.5 (1)°. An intramolecular N—H...O hydrogen bond is observed. In the crystal, pairs of N—H...O hydrogen bonds form inversion dimers with anR22(8) graph-set motif.
Crystal structure of 2,5-dimethylanilinium hydrogen maleate
Authors: Mathlouthi Maha , Janzen Daron E. , Rzaigui Mohamed , Smirani Sta Wajda
Published: October 2014

The crystal structure of the title salt, C8H12N+·C4H3O4−, consists of a 2,5-dimethylanilinium cation and an hydrogen maleate anion. In the anion, a strong intramolecular O—H...O hydrogen bond is observed, leading to anS(7) graph-set motif. In the crystal, the cations and anions pack in alternating layers parallel to (001). The ammonium group undergoes intermolecular N—H...O hydrogen-bonding interactions with the O atoms of three different hydrogen maleate anions. This results in the formation of ribbons extending parallel to [010] with hydrogen-bonding motifs of the typesR44(12) andR44(18).
Crystal structure ofN-[(E)-(1,3-benzodioxol-5-yl)methylidene]-4-chloroaniline
Authors: García-Merinos J. Pablo , López Yliana , González-Campos J. Betzabe , Aviña-Verduzco Judit A. , Río Rosa E. del , Santillan Rosa
Published: October 2014

In the title compound, C14H10ClNO2, obtained by the condensation of 4-chloroaniline and piperonal, the five-membered ring is almost planar (r.m.s. deviation = 0.023 Å) and the dihedral angle between the aromatic rings is 43.22 (14)°. In the crystal, a short O...Cl contact of 3.173 (2) Å is observed. The molecules are arranged into corrugated (010) layers.
Crystal structure ofN,N-diethylbenzene-1,4-diaminium dinitrate
Authors: Bouaoud Yasmina , Smith Graham , Merazig Hocine , Setifi Zouaoui
Published: October 2014

In the structure of the title molecular salt, C10H18N22+·2NO3−, the dinitrate salt of 4-(N,N-diethylamino)aniline, the two ethyl groups lie almost perpendicular to the plane of the benzene ring [the ring-to-ethyl C—C—N—C torsion angles are −59.5 (2) and 67.5 (3)°]. The aminium groups of the cation form inter-species N—H...O hydrogen bonds with the nitro O-atom acceptors of both anions, giving rise to chain substructures lying alongc. The chains are linkedviafurther N—H...O hydrogen bonds, forming two-dimensional networks lying parallel to (010). These sheets are linked by C—H...O hydrogen bonds, forming a three-dimensional structure.
Crystal structure of 3-amino-5,5-dimethyl-2-[(E)-2-nitroethenyl]cyclohex-2-en-1-one
Authors: Vigante Brigita , Stepanovs Dmitrijs , Pelss Andrejs , Mishnev Anatoly
Published: October 2014

The asymmetric unit of the title compound, C10H14N2O3, contains two independent molecules with similar conformations. In the both molecules, the cyclohexene rings adopt the same envelope conformation with the flap C atoms lying 0.658 (3) and 0.668 (3) Å from the mean planes formed by the remaining atoms. In the crystal, adjacent molecules are connectedviaN—H...O hydrogen bonds and weak C—H...O interactions, forming supramolecular layers parallel to (-101).
Crystal structure of ethyl 5-(3-fluorophenyl)-2-[(4-fluorophenyl)methylidene]-7-methyl-3-oxo-2H,3H,5H-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxylate
Authors: Krishnamurthy M. S. , Nagarajaiah H. , Begum Noor Shahina
Published: October 2014

In the title molecule, C23H18F2N2O3S, the pyrimidine ring is in a half-chair conformation and the 3-fluorophenyl group is in the axial position. The thiazole ring (r.m.s. deviation = 0.0252 Å) forms dihedral angles of 84.8 (7) and 9.6 (7)° with the 3-fluoro-substituted and 4-fluoro-substituted benzene rings, respectively. In the crystal, weak C—H...F and C—H...O hydrogen bonds connect molecules, forming zigzag chains along thebaxis. In addition π–π stacking interactions with a centroid–centroid distance of 3.7633 (9) Å connect these chains into laddersviainversion-related 4-fluorophenyl groups.
Comparison of crystal structures of 4-(benzo[b]thiophen-2-yl)-5-(3,4,5-trimethoxyphenyl)-2H-1,2,3-triazole and 4-(benzo[b]thiophen-2-yl)-2-methyl-5-(3,4,5-trimethoxyphenyl)-2H-1,2,3-triazole
Authors: Penthala Narsimha Reddy , Madadi Nikhil Reddy , Bommagani Shobanbabu , Parkin Sean , Crooks Peter A.
Published: October 2014

The title compound, C19H17N3O3S (I), was prepared by a [3 + 2]cycloaddition azide condensation reaction using sodium azide and L-proline as a Lewis base catalyst.N-Methylation of compound (I) using CH3I gave compound (II), C20H19N3O3S. The benzothiophene ring systems in (I) and (II) are almost planar, with r.m.s deviations from the mean plane = 0.0205 (14) in (I) and 0.016 (2) Å in (II). In (I) and (II), the triazole rings make dihedral angles of 32.68 (5) and 10.43 (8)°, respectively, with the mean planes of the benzothiophene ring systems. The trimethoxy phenyl rings make dihedral angles with the benzothiophene rings of 38.48 (4) in (I) and 60.43 (5)° in (II). In the crystal of (I), the molecules are linked into chains by N—H...O hydrogen bonds withR21(5) ring motifs. After theN-methylation of structure (I), no hydrogen-bonding interactions were observed for structure (II). The crystal structure of (II) has a minor component of disorder that corresponds to a 180° flip of the benzothiophene ring system [occupancy ratio 0.9363 (14):0.0637 (14)].
Crystal structures of 3,6-diallyltetracyclo[6.3.0.04,11.05,9]undeca-2,7-dione and 1,7-diallylpentacyclo[5.4.0.02,6. 03,10.05,9]undecane-8,11-dione: allylated caged compounds
Authors: Kotha Sambasivarao , Seema Vital , Deodhar Deepak , Shaikh Mobin
Published: October 2014

The title compounds, C17H20O2(1) and C17H18O2(2), are allylated caged compounds. In (1), the carbon atoms bearing the allyl groups are far apart [2.9417 (17) Å], hence the expected ring-closing metathesis (RCM) protocol failed to give a ring-closing product. When these carbon atoms are connected by a C—C bond as in (2), the distance between them is much smaller [1.611 (3) Å] and consequently the RCM process was successful. The caged carbon skeleton of (1) can be described as a fusion of four five-membered rings and one six-membered ring. All four five-membered rings exhibit envelope conformations. The structure of compound (2) consists of four five-membered rings, of which two are cyclopentanone rings bonded at the 2, 4 and 5 positions and linked at the 3-carbons by a methylene bridge. It also consists of one four-membered and two six-membered rings. All four five-membered rings adopt envelope conformations. In the crystal of (1), molecules are linkedviaC—H...O hydrogen bonds, forming sheets lying parallel to (010). In the crystal of (2), molecules are linkedviaC—H...O hydrogen bonds forming chains along [100].
Crystal structure of (3-carboxypropyl)triphenylphosphonium hexafluoridophosphate
Authors: Hillesheim Patrick C. , Scipione Kent A. , Stokes Sean L.
Published: October 2014

In the title molecular salt, C22H22O2P+·PF6−, the side chain of the cation adopts ananti–gaucheconformation [P—C—C—C and C—C—C—C torsion angles = −179.11 (10) and −77.18 (16)°, respectively]. In the crystal, the cations are linked into carboxylic acid inversion dimers by pairs of O—H...O hydrogen bonds. Weak C—H...F and C—H...(F,F) hydrogen bonds connect the components into a three-dimensional network, but there are no aromatic π–π stacking interactions.
Crystallization and preliminary X-ray diffraction studies of anL-amino-acid oxidase fromLachesis mutavenom
Authors: Ullah Anwar , Masood Rehana , Spencer Patrick Jack , Murakami Mário Tyago , Arni Raghuvir Krishnaswamy
Published: October 2014

Snake-venom proteins form multi-component defence systems by the recruitment and rapid evolution of nonvenomous proteins and hence serve as model systems to understand the structural modifications that result in toxicity. L-Amino-acid oxidases (LAAOs) are encountered in a number of snake venoms and have been implicated in the inhibition of platelet aggregation, cytotoxicity, haemolysis, apoptosis and haemorrhage. An L-amino-acid oxidase fromLachesis mutavenom has been purified and crystallized. The crystals belonged to space groupP21, with unit-cell parametersa= 66.05,b= 79.41,c= 100.52 Å, β = 96.55°. The asymmetric unit contained two molecules and the structure has been determined and partially refined at 3.0 Å resolution.
Crystallization and preliminary X-ray diffraction data of β-galactosidase fromAspergillus niger
Authors: Rico-Díaz Agustín , Vizoso Vázquez Ángel , Cerdán M. Esperanza , Becerra Manuel , Sanz-Aparicio Julia
Published: October 2014

β-Galactosidase fromAspergillus niger(An-β-Gal), belonging to the family 35 glycoside hydrolases, hydrolyzes the β-galactosidase linkages in lactose and other galactosides. It is extensively used in industry owing to its high hydrolytic activity and safety. The enzyme has been expressed in yeasts and purified by immobilized metal-ion affinity chromatography for crystallization experiments. The recombinant An-β-Gal, deglycosylated to avoid heterogeneity of the sample, has a molecular mass of 109 kDa. Rod-shaped crystals grew using PEG 3350 as the main precipitant agent. A diffraction data set was collected to 1.8 Å resolution.
Purification, crystallization and preliminary X-ray diffraction analysis of pyridoxal kinase fromPlasmodium falciparum(PfPdxK)
Authors: Kronenberger Thales , Lunev Sergey , Wrenger Carsten , Groves Matthew R.
Published: October 2014

Pyridoxal kinases (PdxK) catalyze the phosphorylation of vitamin B6precursors. Thus, these enzymes are an essential part of many metabolic processes in all organisms. The protozoan parasitePlasmodium falciparum(the main causative agent of Malaria tropica) possesses a uniquede novoB6-biosynthesis pathway in addition to a interconversion pathway based on the activity of plasmodial PdxK (PfPdxK). The role of PdxK in B6salvage has prompted previous authors to suggest PdxK as a promising target for structure-based antimalarial drug design. Here, the expression, purification, crystallization and preliminary X-ray diffraction analysis ofPfPdxK are reported.PfPdxK crystals have been grown in space groupP21, with unit-cell parametersa= 52.7,b= 62.0,c= 93.7 Å, β = 95°. A data set has been collected to 2 Å resolution and an initial molecular-replacement solution is described.
Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin
Authors: Jagadeesan G. , Malathy P. , Gunasekaran K. , Harikrishna Etti S. , Aravindhan S.
Published: October 2014

Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal systemP3121, with unit-cell parametersa=b= 55.64,c= 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.
Structure of type II dehydroquinase fromPseudomonas aeruginosa
Authors: Reiling Scott , Kelleher Alan , Matsumoto Monica M. , Robinson Gonteria , Asojo Oluwatoyin A.
Published: October 2014

Pseudomonas aeruginosacauses opportunistic infections and is resistant to most antibiotics. Ongoing efforts to generate much-needed new antibiotics include targeting enzymes that are vital forP. aeruginosabut are absent in mammals. One such enzyme, type II dehydroquinase (DHQase), catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate, a necessary step in the shikimate pathway. This step is vital for the proper synthesis of phenylalanine, tryptophan, tyrosine and other aromatic metabolites. The recombinant expression, purification and crystal structure of catalytically active DHQase fromP. aeruginosa(PaDHQase) are presented. Cubic crystals belonging to space groupF23, with unit-cell parametersa=b=c= 125.39 Å, were obtained by vapor diffusion in sitting drops and the structure was refined to anRfactor of 16% at 1.74 Å resolution. PaDHQase is a prototypical type II DHQase with the classical flavodoxin-like α/β topology.
Purification, crystallization and preliminary crystallographic investigation of FrnE, a disulfide oxidoreductase fromDeinococcus radiodurans
Authors: Panicker Lata , Misra Hari Sharan , Bihani Subhash Chandra
Published: October 2014

In prokaryotes, Dsb proteins catalyze the formation of native disulfide bonds through an oxidative folding pathway and are part of the cell machinery that protects proteins from oxidative stress.Deinococcus radioduransis an extremophile which shows unparalleled resistance to ionizing radiation and oxidative stress. It has a strong mechanism to protect its proteome from oxidative damage. The genome ofDeinococcusshows the presence of FrnE, a Dsb protein homologue that potentially provides the bacterium with oxidative stress tolerance. Here, crystallization and preliminary X-ray crystallographic analysis of FrnE fromD. radioduransare reported. Diffraction-quality single crystals were obtained using the hanging-drop vapour-diffusion method with reservoir solution consisting of 100 mMsodium acetate pH 5.0, 10% PEG 8000, 15–20% glycerol. Diffraction data were collected on an Agilent SuperNova system using a microfocus sealed-tube X-ray source. The crystal diffracted to 1.8 Å resolution at 100 K. The space group of the crystal was found to beP21221, with unit-cell parametersa= 47.91,b= 62.94,c= 86.75 Å, α = β = γ = 90°. Based on Matthews coefficient analysis, one monomer per asymmetric unit is present in the crystal, with a solvent content of approximately 45%.
New crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 in two conformations
Authors: Thach Trung Thanh , Lee Sangho
Published: October 2014

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.
Overproduction, crystallization and preliminary X-ray crystallographic analysis ofEscherichia colitRNAN6-threonylcarbamoyladenosine dehydratase
Authors: Kim Sunmin , Kim Keon Young , Park Jeong Kuk , Lee Byung Il , Kim Yun-Gon , Park SangYoun
Published: October 2014

Escherichia colitRNAN6-threonylcarbamoyladenosine dehydratase (TcdA), previously called CsdL or YgdL, was overproduced and purified fromE. coliand crystallized using polyethylene glycol 3350 as a crystallizing agent. X-ray diffraction data were collected to 2.70 Å resolution under cryoconditions using synchrotron X-rays. The crystals belonged to space groupP21, with unit-cell parametersa= 65.4,b= 96.8,c= 83.3 Å, β = 111.7°. According to the Matthews coefficient, the asymmetric unit may contain up to four subunits of the monomeric protein, with a crystal volume per protein mass (VM) of 2.12 Å3 Da−1and 42.1% solvent content.