bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined micro-beam Laue and white beam topography: mapping local lattice orientation and misorientation
Authors: Hofmann F. , Korsunsky A. M. , Abbey B. , Dolbnya I. , Xie M. , Song X. 
Published: November 2010

Micro-beam Laue diffraction is a well-established technique to determine lattice orientation and lattice structure. A polychromatic X-ray beam is used to illuminate a scattering volume within individual crystallites. The resulting diffraction pattern consists of a number of Laue spots. By refinement of the exact spot positions, lattice orientation and deviatoric elastic strain of the single crystalline scattering volume can be determined. Diffraction spot shape is linked to the orientation spread in the scattering volume arising due to the local dislocation structure. However, angular resolution of Laue diffraction spots is limited due to small sample-to-detector distance (~100 mm) and large Laue camera pixel size (~40 µm). In contrast, X-ray diffraction topography allows high-resolution imaging of an individual reflection from a crystal. On beamline B16 at the Diamond Light Source, we have combined micro-beam Laue diffraction with simultaneous collection of diffraction topographs, using a second high-resolution X-ray camera in the far field. In situ deformation of a single grain within a thin Ni foil has been studied using this setup. While detailed analysis is ongoing, some early results are presented here to allow an assessment of the technique's utility and future development possibilities.
Dynamic impact of Diamond Light Source foot bridge
Authors: Huang H. , Kay J. 
Published: November 2010

The main foot bridge provides access to linac, booster and storage ring facilities in the synchrotron of Diamond Light Source. The impact of the passage of pedestrian traffic and equipment across the bridge structure was noticeable to the site of beamlines below. One of them, I20, is the most sensitive beamline to such impact. The bridge obviously oscillated with even light traffic, and it was also assumed that this would couple to the storage ring structure where the bridge is mounted. The optics for beamline I20, for stability, stands directly on the slab within the I20 experimental area; this was however subject to excessive vibration transmitted by foot traffic from the overhead footbridge producing a vibration on the experimental floor of 86 nm whereas elsewhere in the experimental hall experiences only about 20 nm, demonstrating a four times increase in vibration caused by the pedestrian bridge. Vibration measurements on the ground underneath the bridge and finite element analyses clearly show that frequencies of 2 and 5 Hz were caused by the bridge and traffic on it. Several remedies were proposed. However, dampers will only damp out vibrations of around 5–6 Hz but not to damp out 2 Hz, which is caused directly by human foot steps. After investigation of cost and effectiveness and several vibration tests conducted, a compromise with extra propping at the mid-span of the bridge was eventually selected. Such reinforcement has been now implemented. The 5 Hz frequency has been successfully removed and a amplitude of 2 Hz also considerably reduced.
Envelope protein as molecular target for YFV (Yellow fever virus) drug discovery
Authors: Munikumar Manne , Pradhan Dibyabhaba , Priyadarshini I. Vani , Umamaheswari Amineni 
Published: November 2010

AbstractYellow fever (YF), a mosquito-borne viral haemorrhagic fever, is one of the most lethal viral diseases. Despite the availability of vaccines, yellow fever virus (YFV) strikes an estimated 2, 00,000 persons world-wide each year and causes 30,000 deaths approximately. There are no approved antiviral therapies for the treatment of YFV disease in humans. YFV 17D strain RNA genome is of 10,862 nucleotides, which encodes three structural proteins (C, PrM, and E) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). Identification of different protein functions facilitates a mechanistic understanding of YFV infection and opens novel means for drug development. Functional assignment of complete YFV proteome was done through support Vector machine (SVM). Significant functions of YFV Envelope (E) protein are Transmembrane, Aptamer-binding protein, Coat protein, Zinc-binding, Manganese-binding and Metal-binding etc. The E protein being non homologous to human and important in receptor binding, hemagglutination of erythrocytes at acidic pH, induction of the protective immune response, and involvement in an intraendosomal acid-catalyzed fusion step necessary for infection was selected as a potent molecular target against YFV drug discovery. 3D structure of target protein E protein is predicted using MODELLER9V6 and validated through PROCHECK analysis. The Binding site tool of Discovery Studio 2.0 was used to find sites all over protein. Heparin was identified as an important ligand against the molecular target and was docked to the functionally important binding site using LigandFit protocol. The YFV E protein -Heparin docking complex associated with strong hydrogen bonding with SER 483, GLN 443 and ALA 441 residues. The strong docking interaction may impede the infection causes due to association of YFV E protein and Core membrane. Further, the predicted model can be used as reference towards designing candidate drugs against YFV.
Comparative density functional theory study on the relative gas phase enthalpies and free energies of formation for the mono- through hepta-halogenated (X=F, Cl, Br) anthraquinones
Authors: Rayne Sierra , Forest Kaya 
Published: November 2010

AbstractGas phase standard state (298.15 K, 1 atmosphere) relative enthalpies and free energies of formation were calculated for all mono- through hepta-halogenated (X=F, Cl, Br) anthraquinone congeners using the B3LYP, BHandHLYP, M062X, PBE0, and B97D density functionals with the 6-311++G(d,p) basis set. All levels of theory yielded similar results with strong intra- and inter-method correlations for both the relative enthalpy and free energy values and the corresponding thermodynamic stability rank. Within each homolog group, the most thermodynamically stable isomers are those which maximize substitution at the lateral positions (2, 3, 7, and 8) versus the less stabilizing peri positions (1, 4, 6, and 9), while also minimizing destabilizing adjacent substitution patterns (1/2, 2/3, 3/4, 6/7, 7/8, and 8/9). These trends are consistent regardless of halogen substituent or theoretical method employed, and are analogous to those predicted for other classes of halogenated ortho-diaryl systems with single connecting atoms.
Structures, enthalpies of formation, and ionization energies for the parent and binary mixed carbon, silicon, nitrogen, and phosphorus cubane derivatives: A G4MP2 theoretical study
Authors: Rayne Sierra , Forest Kaya 
Published: November 2010

AbstractGas phase standard state (298.15 K, 1 atm) structures, enthalpies of formation, and ionization energies (IEs) were calculated at the G4MP2 composite method level of theory for the parent and binary mixed carbon, silicon, nitrogen, and phosphorus cubane derivatives. Increasing nitrogen content increases the enthalpies of formation for the carbon-nitrogen, nitrogen-phosphorus, and silicon-nitrogen binary cubanes, with the opposite enthalpies of formation trend for increasing phosphorus content within the carbon-phosphorus, nitrogen-phosphorus, and silicon-phosphorus derivatives. Varying carbon/silicon content in the carbon-silicon cubanes results in no general trends for enthalpies of formation. Isomerization enthalpies within the homolog groups having more than one isomer vary widely with atomic composition and substitution patterns. Increasing nitrogen content of the carbon-nitrogen and nitrogen-phosphorus derivatives increases the IE, increasing silicon content in the carbon-silicon cubanes and phosphorus content of the carbon-phosphorus cubanes decreases the IE, while no IE clear trends are evident based on relative atomic content for the silicon-nitrogen and silicon-phosphorus compounds. The binary mixed carbon, silicon, nitrogen, and phosphorus cubane derivatives are predicted to display potentially tunable thermodynamic stability and redox behavior depending on the atom identities and relative positions.
Geometries of the perchlorinated and perbrominated C~3~ through C~6~ n-alkanes: A comparative density functional theory study
Authors: Rayne Sierra , Forest Kaya 
Published: November 2010

AbstractGas phase standard state (298.15 K, 1 atm) geometries of the perchlorinated and perbrominated C~3~ through C~6~ n-alkanes were calculated using the B3LYP, B97D, M062X, and PBE0 density functionals with the 6-311++G(d,p) basis set. For both halogen classes and at all levels of theory, the C~3~ compounds adopt a trans conformation analogous to that of perfluoropropane. Similar to their perfluorinated counterparts, the perchlorinated and perbrominated C~4~ through C~6~ n-alkanes are predicted to have helical geometries. In contrast to perfluoroalkyl chains, the central CCCC dihedral angles of the perchlorinated and perbrominated derivatives are expected to decline with increasing chain length.
Principles for the post-GWAS functional characterisation of risk loci
Authors: Monteiro Alvaro , Coetzee Gerhard , Freedman Matthew , De Biasi Mariella , Casey Graham , Duggan Dave , Risch Angela , Plass Christoph , Liu Pengyuan , James Michael , Vikis Haris , Tichelaar Jay , You Ming , Gayther Simon , Mills Ian 
Published: November 2010

AbstractSeveral challenges lie ahead in assigning functionality to susceptibility SNPs. For example, most effect sizes are small relative to effects seen in monogenic diseases, with per allele odds ratios usually ranging from 1.15 to 1.3. It is unclear whether current molecular biology methods have enough resolution to differentiate such small effects. Our objective here is therefore to provide a set of recommendations to optimize the allocation of effort and resources in order maximize the chances of elucidating the functional contribution of specific loci to the disease phenotype. It has been estimated that 88% of currently identified disease-associated SNP are intronic or intergenic. Thus, in this paper we will focus our attention on the analysis of non-coding variants and outline a hierarchical approach for post-GWAS functional studies.
Inferring the location and scale of mixing between habitat areas of lesser sandeel through information from the fishery
Authors: Jensen Henrik , Rindorf Anna , Wright Peter J. , Mosegaard Henrik 
Published: November 2010

Abstract
Jensen, H., Rindorf, A., Wright, P. J., and Mosegaard, H. 2011. Inferring the location and scale of mixing between habitat areas of lesser sandeel through information from the fishery. – ICES Journal of Marine Science, 68: 43–51. Sandeels are small pelagic fish that play an important role in the diet of a range of natural predators. Because of their limited capture by traditional survey gear, little is known about their large-scale distribution or the degree of mixing between habitat areas. Detailed information collected directly from the fishery was used to map fishing grounds, which were then assumed to reflect the foraging habitat of the species. Length distributions from individual hauls were used to assess differences in the distributions as a function of distance between samples. Sandeel foraging habitat covered some 5% of the total area of the North Sea. Mixing between neighbouring fishing grounds was too low to eliminate differences in length distributions at distances between grounds down to 5 km. Within fishing grounds, mixing was sufficient to eliminate differences in length distributions at scales <28 km but insufficient at greater distances. The lack of mixing between grounds may result in large differences in sandeel abundance among adjacent fishing grounds. Further, notable abundance at one end of an extensive fishing ground is not necessarily indicative of similar abundance at its other end.
Discrete Change in Volatile Anesthetic Sensitivity in Mice with Inactivated Tandem Pore Potassium Ion Channel TRESK
Authors: Chae Yun Jeong , Zhang Jianan , Au Paul , Sabbadini Marta , Xie Guo-Xi , Yost C. Spencer 
Published: November 2010

Background
We investigated the role of tandem pore potassium ion channel (K2P) TRESK in neurobehavioral function and volatile anesthetic sensitivity in genetically modified mice.

Methods
Exon III of the mouse TRESK gene locus was deleted by homologous recombination using a targeting vector. The genotype of bred mice (wild type, knockout, or heterozygote) was determined using polymerase chain reaction. Morphologic and behavioral evaluations of TRESK knockout mice were compared with wild-type littermates. Sensitivity of bred mice to isoflurane, halothane, sevoflurane, and desflurane were studied by determining the minimum alveolar concentration preventing movement to tail clamping in 50% of each genotype.

Results
With the exception of decreased number of inactive periods and increased thermal pain sensitivity (20% decrease in latency with hot plate test), TRESK knockout mice had healthy development and behavior. TRESK knockout mice showed a statistically significant 8% increase in isoflurane minimum alveolar concentration compared with wild-type littermates. Sensitivity to other volatile anesthetics was not significantly different. Spontaneous mortality of TRESK knockout mice after initial anesthesia testing was nearly threefold higher than that of wild-type littermates.

Conclusions
TRESK alone is not critical for baseline central nervous system function but may contribute to the action of volatile anesthetics. The inhomogeneous change in anesthetic sensitivity corroborates findings in other K2P knockout mice and supports the theory that the mechanism of volatile anesthetic action involves multiple targets. Although it was not shown in this study, a compensatory effect by other K2P channels may also contribute to these observations.
Slowing of the Hippocampal θ Rhythm Correlates with Anesthetic-induced Amnesia
Authors: Perouansky Misha , Rau Vinuta , Ford Tim , Oh S. Irene , Perkins Mark , Eger Edmond I , Pearce Robert A. 
Published: November 2010

Background
Temporary, antegrade amnesia is one of the core desirable endpoints of general anesthesia. Multiple lines of evidence support a role for the hippocampal θ rhythm, a synchronized rhythmic oscillation of field potentials at 4-12 Hz, in memory formation. Previous studies have revealed a disruption of the θ rhythm at surgical levels of anesthesia. We hypothesized that θ-rhythm modulation would also occur at subhypnotic but amnestic concentrations. Therefore, we examined the effect of three inhaled agents on properties of the θ rhythm considered critical for the formation of hippocampus-dependent memories.

Methods
We studied the effects of halothane and nitrous oxide, two agents known to modulate different molecular targets (GABAergic [γ-aminobutyric acid] vs. non-GABAergic, respectively) and isoflurane (GABAergic and non-GABAergic targets) on fear-conditioned learning and θ oscillations in freely behaving rats.

Results
All three anesthetics slowed θ peak frequency in proportion to their inhibition of fear conditioning (by 1, 0.7, and 0.5 Hz for 0.32% isoflurane, 60% N2O, and 0.24% halothane, respectively). Anesthetics inconsistently affected other characteristics of θ oscillations.

Conclusions
At subhypnotic amnestic concentrations, θ-oscillation frequency was the parameter most consistently affected by these three anesthetics. These results are consistent with the hypothesis that modulation of the θ rhythm contributes to anesthetic-induced amnesia.
Bose–Einstein condensation and superfluidity of trapped polaritons in graphene and quantum wells embedded in a microcavity
Authors: Berman Oleg L. , Kezerashvili Roman Ya. , Lozovik Yurii E. , Snoke David W. 
Published: November 2010

The theory for spontaneous coherence of short-lived quasiparticles in two-dimensional excitonic systems is reviewed, in particular, quantum wells (QWs) and graphene layers (GLs) embedded in microcavities. Experiments with polaritons in an optical microcavity have already shown evidence of Bose–Einstein condensation (BEC) in the lowest quantum state in a harmonic trap. The theory of BEC and superfluidity of the microcavity excitonic polaritons in a harmonic potential trap is presented. Along the way, we determine a general method for defining the superfluid fraction in a two-dimensional trap, within the angular momentum representation. We discuss BEC of magnetoexcitonic polaritons (magnetopolaritons) in a QW and GL embedded in an optical microcavity in high magnetic field. It is shown that Rabi splitting in graphene is tunable by the external magnetic field
B
, while in a QW the Rabi splitting does not depend on the magnetic field in the strong
B
limit.
Disruption of Cultured Cells by Nitrogen Cavitation: Figure 1.
Authors: Simpson Richard J. 
Published: November 2010

INTRODUCTIONCell disruption by nitrogen decompression from a pressurized vessel is a rapid and effective way to homogenize cells and tissues, to release intact organelles, and to prepare cell membranes. Cells are placed in a pressure vessel and large quantities of oxygen-free nitrogen are dissolved in the cells under high pressure (~5500 kilopascals [kPa], equivalent to 800 pounds per square inch [psi]). When the pressure is released suddenly, the nitrogen bubbles out of solution, rupturing the cell membrane and releasing the cell contents. Nitrogen cavitation is well suited for mammalian and plant cells and fragile bacteria, but is less effective with yeast, fungi, spores, or other cell types with tough cell walls. The chemical and physical stresses imposed by nitrogen cavitation on enzymes and subcellular compartments are minimized compared with ultrasonic and mechanical homogenizing methods. Unlike lysis methods relying on shear stresses and friction, there is no heat damage to proteins and organelles during nitrogen cavitation. Indeed, the method is accompanied by an adiabatic expansion that cools the sample instead. Also, labile cell components are protected from oxidation by the inert nitrogen gas. Furthermore, nitrogen does not alter the pH of the suspending medium. The process is fast and uniform because the same disruptive forces are applied within each cell and throughout the sample, ensuring reproducible cell-free homogenates. Finally, variable sample sizes (e.g., from ~1 mL to 1 L or more) can be accommodated with most commercial systems.
DNA Extraction from Freeze-Dried Plant Tissue with CTAB in a 96-Well Format
Authors: Hsia An-Ping , Chen Hsin D. , Ohtsu Kazuhiro , Schnable Patrick S. 
Published: November 2010

INTRODUCTIONThis protocol is a modified version of DNA isolation using cetyltrimethylammonium bromide (CTAB) and 96-well plates. It is high-throughput, which facilitates the analysis of large mapping populations. The DNA yield is adequate for at least 100-500 polymerase chain reaction (PCR) procedures.
Transfection of Mammalian Cells with Fluorescent Protein Fusions
Authors: Spector David L. , Goldman Robert D. 
Published: November 2010

INTRODUCTIONFluorescent protein fusions (FPFs) have been used to address a wide range of questions in individual cells as well as in specific tissues of particular organisms. However, investigators must take extreme care when using FPFs to ensure that the resultant fusion protein is expressed at or close to the endogenous level of the parent protein, and also that it is full length, localizes correctly, and behaves normally once incorporated in the cell. Although transient transfection methods can be used to introduce DNA coding for FPFs, in many cases it is beneficial and/or essential to develop stable cell lines expressing the fusion protein of interest. In addition to providing more native levels of expression, the individual clones can be generated from single cells, the integration site of the plasmid can be mapped, and the copy number can be determined. Moreover, because every cell in the population is expressing the fusion protein, cell cycle analyses and biochemical fractionation are significantly easier to accomplish. This article presents a protocol for generating, selecting, and screening stable cell lines expressing FPFs.
Locomotor Activity Level Monitoring Using the Drosophila Activity Monitoring (DAM) System: Figure 1.
Authors: Pfeiffenberger Cory , Lear Bridget C. , Keegan Kevin P. , Allada Ravi 
Published: November 2010

INTRODUCTIONAdult behavioral assays have been used with great success in Drosophila melanogaster to identify circadian rhythm genes. In particular, the locomotor activity assay can identify altered behavior patterns over the course of several days in small populations, or even individual flies. Commercially available, highly efficient automated systems allow for continuous data collection from large numbers of individuals, and analytical tools make it possible to quickly analyze multiple aspects of circadian behavior from each experiment. These features make the locomotor activity assay useful for high-throughput analyses, leading to the rapid discovery and functional characterization of many Drosophila circadian rhythm genes. The locomotor assay described here can simultaneously assess both circadian and sleep behavior, and several methods can be used to analyze the data generated from such assays. This protocol details the use of the Drosophila Activity Monitoring (DAM) System from TriKinetics. Briefly, the system records activity from individual flies maintained in sealed tubes placed in activity monitors. An infrared beam directed through the midpoint of each tube measures an “activity event” each time a fly crosses the beam. Events detected over the course of each consecutive sampling interval are summed and recorded over the course of the experiment for each fly. The general approaches described here can be applied to a wide range of behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity.
Processing Circadian Data Collected from the Drosophila Activity Monitoring (DAM) System: Figure 1.
Authors: Pfeiffenberger Cory , Lear Bridget C. , Keegan Kevin P. , Allada Ravi 
Published: November 2010

INTRODUCTIONAdult behavioral assays have been used with great success in Drosophila melanogaster to identify circadian rhythm genes. In particular, the locomotor activity assay can identify altered behavior patterns over the course of several days in small populations, or even individual flies. Generally, circadian behavior is assayed during a period of 12 h light:12 h dark cycling (LD entrainment) followed by conditions of constant darkness (DD). LD activity profiles provide a qualitative image of daily activity bouts, and the data can be used to quantitatively assess the phase and/or amplitude of particular bouts. Additional activity assessments made from entrained flies that have been shifted to constant darkness can provide insight into the state of internal clocks and the ability of these clocks to drive rhythmic outputs. Typical LD DD runs assess both free-running rhythmicity and period length with χ2 periodogram (P’gram) analysis. This protocol describes the use of ClockLab (a MATLAB-based program) and the Counting Macro (an Excel-based program) to analyze circadian locomotor activity data collected using the Drosophila Activity Monitoring (DAM) System from TriKinetics. Specific procedures are described to analyze free-running rhythmicity and period length for individual flies, and assess group activity plots during both entrainment and constant conditions.