bluuebunny/crossref_metadata_2025 huggingface dataset:
TOPOLOGY OF STEADY HEAT CONDUCTION IN A SOLID SLAB SUBJECT TO A NONUNIFORM BOUNDARY CONDITION: THE CARSLAW–JAEGER SOLUTION REVISITED
Authors: KASIMOVA R. G. , OBNOSOV YU. V.
Published: February 2013

Temperature distributions recorded by thermocouples in a solid body (slab) subject to surface heating are used in a mathematical model of two-dimensional heat conduction. The corresponding Dirichlet problem for a holomorphic function (complex potential), involving temperature and a heat stream function, is solved in a strip. The Zhukovskii function is reconstructed through singular integrals, involving an auxiliary complex variable. The complex potential is mapped onto an auxiliary half-plane. The flow net (orthogonal isotherms and heat lines) of heat conduction is compared with the known Carslaw–Jaeger solution and shows a puzzling topology of three regimes of energy fluxes for temperature boundary conditions common in passive thermal insulation. The simplest regime is realized if cooling of a shaded zone is mild and heat flows in a slightly distorted “resistor model” flow tube. The second regime emerges when cooling is stronger and two disconnected separatrices demarcate the back-flow of heat from a relatively hot segment of the slab surface to the atmosphere through relatively cold parts of this surface. The third topological regime is characterized by a single separatrix with a critical point inside the slab, where the thermal gradient is nil. In this regime the back-suction of heat into the atmosphere is most intensive. The closed-form solutions obtained can be used in assessment of efficiency of thermal protection of buildings.
‘Bonded by reverence toward the Buddha’: Asian decolonization, Japanese Americans, and the making of the Buddhist world, 1947–1965
Authors: Masatsugu Michael K.
Published: February 2013

This article examines Asian and Japanese American participation in a post-Second World War global movement for Buddhist revival. It looks at the role that Buddhism and the World Fellowship of Buddhists organization played in shaping transnational networks and the development of a global Buddhist perspective. It contextualizes the growth of a ‘Buddhist world’ within the history of decolonization and Japanese American struggles to reconstruct individual and community identities thoroughly disrupted by the war. The article considers Asian Buddhist approaches toward recognition as national and world citizens rather than colonial subjects and their influence on Japanese American Buddhists’ strategies for combating racial and religious discrimination in the United States. Finally, the article examines how Japanese Americans joined Asian efforts to formulate a distinctly Buddhist response to the Cold War. Buddhists hoped that Buddhism might serve as a ‘third power’ that would provide a critical check on a world increasingly polarized by Cold War politics and threatened by the prospects of nuclear war.
Getting tough on pain
Authors: Hunter Philip
Published: February 2013

More than a decade after the discovery of nociceptors, physicians still have very few options for treating chronic pain. Recent research on pain perception might finally be leading to new therapeutic strategies and drugs.
Programming biological models in Python using PySB
Authors: Lopez Carlos F , Muhlich Jeremy L , Bachman John A , Sorger Peter K
Published: February 2013

Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule‐based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule‐based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high‐level, action‐oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open‐source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.
Adenosine-binding motif mimicry and cellular effects of a thieno[2,3-d]pyrimidine-based chemical inhibitor of atypical protein kinase C isoenzymes
Authors: Kjær Svend , Linch Mark , Purkiss Andrew , Kostelecky Brenda , Knowles Phillip P. , Rosse Carine , Riou Philippe , Soudy Christelle , Kaye Sarah , Patel Bhavisha , Soriano Erika , Murray-Rust Judith , Barton Caroline , Dillon Christian , Roffey Jon , Parker Peter J. , McDonald Neil Q.
Published: February 2013

The aPKC [atypical PKC (protein kinase C)] isoforms ι and ζ play crucial roles in the formation and maintenance of cell polarity and represent attractive anti-oncogenic drug targets in Ras-dependent tumours. To date, few isoform-specific chemical biology tools are available to inhibit aPKC catalytic activity. In the present paper, we describe the identification and functional characterization of potent and selective thieno[2,3-d]pyrimidine-based chemical inhibitors of aPKCs. A crystal structure of human PKCι kinase domain bound to a representative compound, CRT0066854, reveals the basis for potent and selective chemical inhibition. Furthermore, CRT0066854 displaces a crucial Asn-Phe-Asp motif that is part of the adenosine-binding pocket and engages an acidic patch used by arginine-rich PKC substrates. We show that CRT0066854 inhibits the LLGL2 (lethal giant larvae 2) phosphorylation in cell lines and exhibits phenotypic effects in a range of cell-based assays. We conclude that this compound can be used as a chemical tool to modulate aPKC activity in vitro and in vivo and may guide the search for further aPKC-selective inhibitors.
Primary and secondary relaxation process in plastically crystalline cyanocyclohexane studied by 2H nuclear magnetic resonance. I
Authors: Micko B. , Lusceac S. A. , Zimmermann H. , Rössler E. A.
Published: February 2013

We study the main (α-) and secondary (β-) relaxation in the plastically crystalline (PC) phase of cyanocyclohexane by various 2H nuclear magnetic resonance (NMR) methods (line-shape, spin-lattice relaxation, stimulated echo, and two-dimensional spectra) above and below the glass transition temperature Tg = 134 K. Our results regarding the α-process demonstrate that molecular motion is not governed by the symmetry of the lattice. Rather it is similar to the one reported for structural glass formers and can be modeled by a reorientation proceeding via a distribution of small and large angular jumps. A solid-echo line-shape analysis regarding the β-process below Tg yields again very similar results when compared to those of the structural glass formers ethanol and toluene. Hence we cannot confirm an intramolecular origin for the β-process in cyanocyclohexane. The fast β-process in the PC phase allows for the first time a detailed 2H NMR study of the process also at T > Tg: an additional minimum in the spin-lattice relaxation time reflecting the β-process is found. Furthermore the solid-echo spectra show a distinct deviation from the rigid limit Pake pattern, which allows a direct determination of the temperature dependent spatial restriction of the process. In Part II of this work, a quantitative analysis is carried out, where we demonstrate that within the model of a “wobbling in a cone” the mean cone angle increases above Tg and the corresponding relaxation strength is compared to dielectric results.
Fermi resonance in solid CO2 under pressure
Authors: Sode Olaseni , Keçeli Murat , Yagi Kiyoshi , Hirata So
Published: February 2013

The symmetric-stretching fundamental (ν1) and the bending first overtone (2ν2) of CO2, which are accidentally degenerate with the same symmetry, undergo a Fermi resonance and give rise to two Raman bands with a frequency difference of 107 cm−1 and an intensity ratio of 2.1. Both the frequency difference and intensity ratio can be varied by pressure applied to CO2 in condensed phases, which has been utilized as a spectroscopic geobarometer for minerals with CO2 inclusion. This study calculates the pressure dependence of the Fermi dyad frequency difference and intensity ratio by combining the embedded-fragment second-order Møller–Plesset perturbation calculations of harmonic frequencies of solid CO2 under pressure and the coupled-cluster singles and doubles with noniterative triples and vibrational configuration-interaction calculations of anharmonic frequencies of molecular CO2. It reproduces frequency difference quantitatively and intensity ratio qualitatively up to 10 GPa. The analysis of the results is shown to render strong support for one particular order of unperturbed frequencies, ν1 > 2ν2, in both the gas and solid phases, which has been a matter of controversy for decades.
Rigorously extensive orbital-invariant renormalized perturbative triples corrections from quasi-variational coupled cluster theory
Authors: Robinson James B. , Knowles Peter J.
Published: February 2013

We show that, by making use of the linked tensor objects inherent to the approach, Orbital-optimised Quasi-Variational Coupled Cluster Theory (OQVCCD) leads naturally to a computationally-trivial, rigorously extensive, and orbital-invariant renormalization of the standard (T) correction for the perturbative inclusion of the effects of connected triple excitations. The resulting prototype method, renormalized perturbative triple OQVCCD (R-OQVCCD(T)), is demonstrated to predict potential energy curves for single bond-breaking processes of significantly higher accuracy than OQVCCD with the standard perturbative triple-excitation correction (OQVCCD(T)) itself, and to be in good numerical correspondence with the existing renormalized (R-CCSD(T)) and completely renormalized (CR-CCSD(T)) coupled-cluster singles doubles triples methods, while continuing to provide descriptions of multiple bond-breaking processes of OQVCCD(T) quality.
Magnetohydrodynamic motion of a colloidal sphere with self-electrochemical surface reactions in a spherical cavity
Authors: Hsieh Tzu H. , Keh Huan J.
Published: February 2013

An analytical study is presented for the magnetic-field-induced motion of a colloidal sphere with spontaneous electrochemical reactions on its surface situated at the center of a spherical cavity filled with an electrolyte solution at the quasi-steady state. The zeta potential associated with the particle surface may have an arbitrary distribution, whereas the electric double layers adjoining the particle and cavity surfaces are taken to be thin relative to the particle size and the spacing between the solid surfaces. The electric current and magnetic flux density distributions are solved for the particle and fluid phases of arbitrary electric conductivities and magnetic permeabilities. Applying a generalized reciprocal theorem to the Stokes equations with a Lorentz force term resulting from these density distributions for the fluid motion, we obtain explicit formulas for the translational and angular velocities of the colloidal sphere valid for all values of the particle-to-cavity size ratio. The particle velocities decrease monotonically with an increase in this size ratio. For the limiting case of an infinitely large cavity, our result reduces to the relevant solution for an unconfined spherical particle. The boundary effect on the movement of the particle with interfacial self-electrochemical reactions induced by the magnetohydrodynamic force is equivalent to that in sedimentation and much stronger than that in general phoretic motions.
Comment on “The diatomic dication CuZn2+ in the gas phase” [J. Chem. Phys. 135, 034306 (2011)]
Authors: Fišer Jiří , Diez Reinaldo Pis , Franzreb Klaus , Alonso Julio A.
Published: February 2013

In this Comment, the density functional theory (DFT) calculations carried out by Diez et al. [J. Chem. Phys. 135, 034306 (2011)10.1063/1.3613624] are revised within the framework of the coupled-cluster single double triple method. These more sophisticated calculations allow us to show that the 2Σ+ electronic ground state of CuZn2+, characterized as the metastable ground state by DFT calculations, is a repulsive state instead. The 2Δ and 2Π metastable states of CuZn2+, on the other hand, should be responsible for the formation mechanism of the dication through the near-resonant electron transfer CuZn+ + Ar+ → CuZn2+ + Ar reaction.
Physisorption of functionalized gold nanoparticles on AlGaN/GaN high electron mobility transistors for sensing applications
Authors: Makowski M. S. , Kim S. , Gaillard M. , Janes D. , Manfra M. J. , Bryan I. , Sitar Z. , Arellano C. , Xie J. , Collazo R. , Ivanisevic A.
Published: February 2013

AlGaN/GaN high electron mobility transistors (HEMTs) were used to measure electrical characteristics of physisorbed gold nanoparticles (Au NPs) functionalized with alkanethiols with a terminal methyl, amine, or carboxyl functional group. Additional alkanethiol was physisorbed onto the NP treated devices to distinguish between the effects of the Au NPs and alkanethiols on HEMT operation. Scanning Kelvin probe microscopy and electrical measurements were used to characterize the treatment effects. The HEMTs were operated near threshold voltage due to the greatest sensitivity in this region. The Au NP/HEMT system electrically detected functional group differences on adsorbed NPs which is pertinent to biosensor applications.
Ultrafast laser-induced premelting and structural transformation of gold nanorod
Authors: Gan Yong , Jiang Shan
Published: February 2013

Femtosecond laser irradiation of a gold nanorod has been simulated by a method that couples two-temperature model into molecular dynamics. Numerical results show that the surface premelting occurs prior to the initiation of planar defect and propagates from the surface layer into the inside of nanorod. Pressure relaxation leads to high-frequency temperature oscillation and two-way transformation between fcc and disordered atoms produced by the dynamic stresses. Partial dislocation cores are initiated on the crystal surfaces due to high stresses, and then noticeable planar defects including stacking faults and twin boundaries on {111} close-packed planes are developed. Finally, only parallel twin boundaries are present in the nanorod, showing favorable agreement with the experimental observation.
Probing the electrical transport properties of intrinsic InN nanowires
Authors: Zhao S. , Salehzadeh O. , Alagha S. , Kavanagh K. L. , Watkins S. P. , Mi Z.
Published: February 2013

We have studied the electrical transport properties of intrinsic InN nanowires using an electrical nanoprobing technique in a scanning electron microscope environment. It is found that such intrinsic InN nanowires exhibit an ohmic conduction at low bias and a space charge limited conduction at high bias. It is further derived that such InN nanowires can exhibit a free carrier concentration as low as ∼1013 cm−3 and possess a very large electron mobility in the range of 8000–12 000 cm2/V s, approaching the theoretically predicted maximum electron mobility at room temperature. In addition, charge traps are found to distribute exponentially just below the conduction band edge, with a characteristic energy ∼65 meV.
Single and multi-particle passive microrheology of low-density fluids using sedimented microspheres
Authors: Domínguez García P. , Rubio M. A.
Published: February 2013

We present a technique of passive microrheology based on tracking micron-sized particles which are denser than the surrounding fluid and therefore they sediment into a quasi two-dimensional layer. Theoretical corrections for the diffusion coefficient of polystyrene, magnetic, and melamine resin microspheres, situated at different average heights above the bottom of the container cell, allow to unify the corresponding results for the zero-shear viscosity and the dynamic modulus on low-density fluids, such as low-concentration mixtures of glycerol and poly(ethylene oxide) in water and 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid. Limitations of the experimental and data analysis methodology are discussed by developing experimental-like simulations of Brownian fluids.
Atomistic simulation study of brittle failure in nanocrystalline graphene under uniaxial tension
Authors: Cao Ajing , Qu Jianmin
Published: February 2013

We show that, using molecular dynamic simulations, nanocrystalline (NC) graphene fails by brittle fracture along grain boundaries under uniaxial tension at room temperature. Initiated from either a grain-boundary triple junction or an array of vacancies on a preferential grain boundary, fracture occurs by unzipping atomic bonds along a preferential grain boundary. In sharp contrast to NC metals, no mobile dislocations are generated throughout the entire loading process, and the deformation remains fully elastic (albeit nonlinear) until the breaking of the first atomic bond due to high local stress near the initiation defect sites. Breaking of the first atomic bond triggers a cascade of bond breaking events along a preferential grain boundary that leads to the final brittle fracture failure. For the NC graphene monolayer sheet with an average grain size of ∼25 nm considered here, the predicted uniaxial tensile strength is 96.2 ± 4.2 GPa, which is one of the highest among all polycrystalline materials.
Iron-induced deep-level acceptor center in GaN/AlGaN high electron mobility transistors: Energy level and cross section
Authors: Silvestri Marco , Uren Michael J. , Kuball Martin
Published: February 2013

Dynamic transconductance dispersion measurements coupled with device physics simulations were used to study the deep level acceptor center in iron-doped AlGaN/GaN high electron mobility transistors (HEMT). From the extracted frequency dependent trap-conductance, an energy level 0.7 eV below the conduction band and a capture cross section of 10−13 cm2 were obtained. The approach presented in this work avoids the non-equilibrium electrical or optical techniques that have been used to date and extracts the device relevant trap characteristics in short channel AlGaN/GaN HEMTs. Quantitative prediction of the trap induced transconductance dispersion in HEMTs is demonstrated.
Microcrystalline diamond micromechanical resonators with quality factor limited by thermoelastic damping
Authors: Najar Hadi , Heidari Amir , Chan Mei-Lin , Yang Hseuh-An , Lin Liwei , Cahill David G. , Horsley David A.
Published: February 2013

Thin-film microcrystalline diamond micromechanical resonators with mechanical quality factor limited by thermoelastic dissipation in the diamond film are demonstrated. Surface micromachined double ended tuning fork resonators were fabricated from in-situ boron doped microcrystalline diamond films deposited using hot filament chemical vapor deposition. Time-domain thermoreflectance measurements show thermal conductivity of 110 W m−1 K−1 for heat transport through the thickness of the diamond film. Measurement of the quality factor of resonators spanning a frequency range 0.5–10 MHz shows a maximum Q = 81 646 and demonstrates good agreement with quality factor limited by thermoelastic dissipation using 100 W m−1 K−1 for the in-plane thermal conductivity of the diamond film.
Efficiency enhancement of organic photovoltaic devices using a Sm:Al compound electrode
Authors: Yang Bin-Bin , Zhang Dan-Dan , Lee Shuit-Tong , Li Yan-Qing , Tang Jian-Xin
Published: February 2013

An effective cathode consisting of samarium (Sm) doped aluminum (Al) layer and a pure Al layer is reported for application in organic photovoltaic cells (OPVs). Standard copper phthalocyanine (CuPc)/C60 OPVs using this bilayer cathode show dramatically increased short-circuit current density and power conversion efficiency, which are 64% increased by employing a appropriate ratio of 1:3 of Sm:Al layer as compared with that of control devices with pure Al cathode. The photoelectric properties reveal that the improved efficiency is mainly related to the balance of the enhanced electron collection ability and the optimized optical reflection of a Sm doped Al layer.
Analysis of DAZ gene expression in a partial AZFc deletion of the human Y chromosome
Authors: Kim Byunghyuk , Lee Wonkyung , Rhee Kunsoo , Kim Soo Woong , Paick Jae-Seung
Published: February 2013

The azoospermia factor c (AZFc) region of the Y chromosome consists of repetitive amplicons and is therefore highly susceptible to structural rearrangements, such as deletions and duplications. The b2/b3 deletion is a partial AZFc deletion that is conventionally determined by the selective absence of sY1191 in sequence-tagged site polymerase chain reaction (PCR) and is generally believed to retain two of the four deleted in azoospermia (DAZ) genes on the Y chromosome. In the present study we determined the copy number and expression of DAZ genes in sY1191-negative individuals. Using a DAZ dosage PCR assay and Southern blot analysis we evaluated the expression of four DAZ genes in five of six sY1191-negative individuals. Furthermore, cloning and immunoblot analyses revealed that three or more DAZ genes are expressed in sY1191-negative testes with germ cells. The results indicate that the selective absence of sY1191 not only means b2/b3 deletion with two DAZ genes, but also includes another AZFc configuration with four DAZ genes. These results exemplify the prevalence of variations in the AZFc region of the human Y chromosome.
PRICELESS CALCULATIONS
Authors: Pardo-Guerra Juan Pablo
Published: February 2013

In this article, I forward an analysis of the art market that seeks to emphasize the often unexamined yet central economizing practices that fuel the circulation of objects and thus contribute to the distinct patterns of consumption, ownership, and mobilization of the art world. In stressing these economizing practices, I attempt to make visible the underlying sociality and symbolic practices that provide aesthetic and cultural meaning to artistic objects and institutions. The analysis presented here derives from the so-called performativity program and that has been extended in recent years throughout economic sociology. Specifically, this article draws on the performativity program to highlight the mechanisms through which artistic objects are taken-into-account prior to their circulation in the market. As is argued, such forms of actuarial practice are not restricted to orienting action within networks of market exchange; rather, they are partly constitutive of the aesthetic and cultural values attached to art in contemporary capitalism.
Conserved and divergent features of kinetochores and spindle microtubule ends from five species
Authors: McIntosh J. Richard , O’Toole Eileen , Zhudenkov Kirill , Morphew Mary , Schwartz Cindi , Ataullakhanov Fazly I. , Grishchuk Ekaterina L.
Published: February 2013

Interfaces between spindle microtubules and kinetochores were examined in diverse species by electron tomography and image analysis. Overall structures were conserved in a mammal, an alga, a nematode, and two kinds of yeasts; all lacked dense outer plates, and most kinetochore microtubule ends flared into curved protofilaments that were connected to chromatin by slender fibrils. Analyses of curvature on >8,500 protofilaments showed that all classes of spindle microtubules displayed some flaring protofilaments, including those growing in the anaphase interzone. Curved protofilaments on anaphase kinetochore microtubules were no more flared than their metaphase counterparts, but they were longer. Flaring protofilaments in budding yeasts were linked by fibrils to densities that resembled nucleosomes; these are probably the yeast kinetochores. Analogous densities in fission yeast were larger and less well-defined, but both yeasts showed ring- or partial ring-shaped structures girding their kinetochore microtubules. Flaring protofilaments linked to chromatin are well placed to exert force on chromosomes, assuring stable attachment and reliable anaphase segregation.
Extracellular vesicles: Exosomes, microvesicles, and friends
Authors: Raposo Graça , Stoorvogel Willem
Published: February 2013

Cells release into the extracellular environment diverse types of membrane vesicles of endosomal and plasma membrane origin called exosomes and microvesicles, respectively. These extracellular vesicles (EVs) represent an important mode of intercellular communication by serving as vehicles for transfer between cells of membrane and cytosolic proteins, lipids, and RNA. Deficiencies in our knowledge of the molecular mechanisms for EV formation and lack of methods to interfere with the packaging of cargo or with vesicle release, however, still hamper identification of their physiological relevance in vivo. In this review, we focus on the characterization of EVs and on currently proposed mechanisms for their formation, targeting, and function.
Endothelial cell–specific lymphotoxin-β receptor signaling is critical for lymph node and high endothelial venule formation
Authors: Onder Lucas , Danuser Renzo , Scandella Elke , Firner Sonja , Chai Qian , Hehlgans Thomas , Stein Jens V. , Ludewig Burkhard
Published: February 2013

The development of lymph nodes (LNs) and formation of LN stromal cell microenvironments is dependent on lymphotoxin-β receptor (LTβR) signaling. In particular, the LTβR-dependent crosstalk between mesenchymal lymphoid tissue organizer and hematopoietic lymphoid tissue inducer cells has been regarded as critical for these processes. Here, we assessed whether endothelial cell (EC)–restricted LTβR signaling impacts on LN development and the vascular LN microenvironment. Using EC-specific ablation of LTβR in mice, we found that conditionally LTβR-deficient animals failed to develop a significant proportion of their peripheral LNs. However, remnant LNs showed impaired formation of high endothelial venules (HEVs). Venules had lost their cuboidal shape, showed reduced segment length and branching points, and reduced adhesion molecule and constitutive chemokine expression. Due to the altered EC–lymphocyte interaction, homing of lymphocytes to peripheral LNs was significantly impaired. Thus, this study identifies ECs as an important LTβR-dependent lymphoid tissue organizer cell population and indicates that continuous triggering of the LTβR on LN ECs is critical for lymphocyte homeostasis.
Reliability and Validity of a Standardized Measure of Influenza Vaccination Coverage among Healthcare Personnel
Authors: Libby Tanya E. , Lindley Megan C. , Lorick Suchita A. , MacCannell Taranisia , Lee Soo-Jeong , Smith Carmela , Geevarughese Anita , Makvandi Monear , Nace David A. , Ahmed Faruque
Published: February 2013

Objective.

To evaluate the reliability and validity of a standardized measure of healthcare personnel (HCP) influenza vaccination.

Setting.

Acute care hospitals, long-term care facilities, ambulatory surgery centers, physician practices, and dialysis centers from 3 US jurisdictions.

Participants.

Staff from 96 healthcare facilities randomly sampled from 234 facilities that completed pilot testing to assess the feasibility of the measure.

Methods.

Reliability was assessed by comparing agreement between facility staff and project staff on the classification of HCP numerator (vaccinated at facility, vaccinated elsewhere, contraindicated, declined) and denominator (employees, credentialed nonemployees, other nonemployees) categories. To assess validity, facility staff completed a series of case studies to evaluate how closely classification of HCP groups aligned with the measure's specifications. In a modified Delphi process, experts rated face validity of the proposed measure elements on a Likert-type scale.

Results.

Percent agreement was high for HCP vaccinated at the facility (99%) and elsewhere (95%) and was lower for HCP who declined vaccination (64%) or were medically contraindicated (64%). While agreement was high (more than 90%) for all denominator categories, many facilities' staff excluded nonemployees for whom numerator and denominator status was difficult to determine. Validity was lowest for credentialed and other nonemployees.

Conclusions.

The standardized measure of HCP influenza vaccination yields reproducible results for employees vaccinated at the facility and elsewhere. Adhering to true medical contraindications and tracking decimations should improve reliability. Difficulties in establishing denominators and determining vaccination status for credentialed and other nonemployees challenged the measure's validity and prompted revision to include a more limited group of nonemployees.
PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data
Authors: Leday Gwenaël G.R. , van de Wiel Mark A.
Published: February 2013

Summary: DNA copy number and mRNA expression are commonly used data types in cancer studies. Available software for integrative analysis arbitrarily fixes the parametric form of the association between the two molecular levels and hence offers no opportunities for modelling it. We present a new tool for flexible modelling of this association. PLRS uses a wide class of interpretable models including popular ones and incorporates prior biological knowledge. It is capable to identify the gene-specific type of relationship between gene copy number and mRNA expression. Moreover, it tests the strength of the association and provides confidence intervals. We illustrate PLRS using glioblastoma data from The Cancer Genome Atlas.

Availability and implementation: PLRS is implemented as an R package and available from Bioconductor (as of version 2.12; http://bioconductor.org). Additional code for parallel computations is available as Supplementary Material.

Contact:  g.g.r.leday@vu.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Nozzle: a report generation toolkit for data analysis pipelines
Authors: Gehlenborg Nils , Noble Michael S. , Getz Gad , Chin Lynda , Park Peter J.
Published: February 2013

Summary: We have developed Nozzle, an R package that provides an Application Programming Interface to generate HTML reports with dynamic user interface elements. Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big datasets. The package can be applied to any project where user-friendly reports need to be created.

Availability: The R package is available on CRAN at http://cran.r-project.org/package=Nozzle.R1. Examples and additional materials are available at http://gdac.broadinstitute.org/nozzle. The source code is also available at http://www.github.com/parklab/Nozzle.

Contact:  peter_park@hms.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Total marine fishery catch for the Azores (1950–2010)
Authors: Pham Christopher K. , Canha Angela , Diogo Hugo , Pereira João G. , Prieto Rui , Morato Telmo
Published: February 2013

Pham, C. K., Canha, A., Diogo, H., Pereira, J. G., Prieto, R., and Morato, T. 2013. Total marine fishery catch for the Azores (1950–2010). – ICES Journal of Marine Science, 70: 564–577. Official fishery statistics often fail to report what has been truly extracted from the marine environment. Therefore, in this study, we estimated illegal, unreported, and unregulated (IUU) catch in the context of a small-scale fishery (the Azores) and provide an improved compilation of official catches, including whaling. Reconstructed removals during 1950–2010 total 1.10 million t (95% CI, 1.06–1.16 million t), a factor of 1.17 higher than the amount reported in Azorean official statistics. Unreported catches were attributed to foreign fishing activities (27%), recreational fishing (25%), discards from the demersal fishing fleet (21%), baitfish for the pole-and-line tuna fishery (11%), discards from pelagic longlining (7%), local pelagic fleet landing outside the Azores (3%), coastal invertebrate harvesting (6%), and big-game fishing (0.1%). The overall low level of unreported catches compared to other locations might reflect the small-scale nature of the fisheries, the geographic isolation of the islands, and the small size of its community.
Faltering lemming cycles reduce productivity and population size of a migratory Arctic goose species
Authors: Nolet Bart A. , Bauer Silke , Feige Nicole , Kokorev Yakov I. , Popov Igor Yu. , Ebbinge Barwolt S.
Published: February 2013

The huge changes in population sizes of Arctic‐nesting geese offer a great opportunity to study population limitation in migratory animals. In geese, population limitation seems to have shifted from wintering to summering grounds. There, in the Arctic, climate is rapidly changing, and this may impact reproductive performance, and perhaps population size of geese, both directly (e.g. by changes in snow melt) or indirectly (e.g. by changes in trophic interactions).

Dark‐bellied brent geese (Branta bernicla berniclaL.) increased 20‐fold since the 1950s. Its reproduction fluctuates strongly in concert with the 3‐year lemming cycle. An earlier analysis, covering the growth period until 1988, did not find evidence for density dependence, but thereafter the population levelled off and even decreased. The question is whether this is caused by changes in lemming cycles, population density or other factors like carry‐over effects.

Breeding success was derived from proportions of juveniles. We used an information‐theoretical approach to investigate which environmental factors best explained the variation in breeding success over nearly 50 years (1960–2008). We subsequently combinedGLMpredictions of breeding success with published survival estimates to project the population trajectory since 1991 (year of maximum population size). In this way, we separated the effects of lemming abundance and population density on population development.

Breeding success was mainly dependent on lemming abundance, the onset of spring at the breeding grounds, and the population size of brent goose. No evidence was found for carry‐over effects (i.e. effects of conditions at main spring staging site). Negative density dependence was operating at a population size above c. 200 000 individuals, but the levelling off of the population could be explained by faltering lemming cycles alone.

Lemmings have long been known to affect population productivity of Arctic‐nesting migratory birds and, more recently, possibly population dynamics of resident bird species, but this is the first evidence for effects of lemming abundance on population size of a migratory bird species. Why lemming cycles are faltering in the last two decades is unclear, but this may be associated with changes in winter climate at Taimyr Peninsula (Siberia).
A highly conserved mycobacterial cholesterol catabolic pathway
Authors: García‐Fernández Esther , Frank Daniel J. , Galán Beatriz , Kells Petrea M. , Podust Larissa M. , García José L. , Ortiz de Montellano Paul R.
Published: February 2013

Degradation of the cholesterol side‐chain in Mycobacterium tuberculosis is initiated by two cytochromes P450, CYP125A1 and CYP142A1, that sequentially oxidize C26 to the alcohol, aldehyde and acid metabolites. Here we report characterization of the homologous enzymes CYP125A3 and CYP142A2 from Mycobacterium smegmatis mc2 155. Heterologously expressed, purified CYP125A3 and CYP142A2 bound cholesterol, 4‐cholesten‐3‐one, and antifungal azole drugs. CYP125A3 or CYP142A2 reconstituted with spinach ferredoxin and ferredoxin reductase efficiently hydroxylated 4‐cholesten‐3‐one to the C‐26 alcohol and subsequently to the acid. The X‐ray structures of both substrate‐free CYP125A3 and CYP142A2 and of cholest‐4‐en‐3‐one‐bound CYP142A2 reveal significant differences in the substrate binding sites compared with the homologous M. tuberculosis proteins. Deletion only of cyp125A3 causes a reduction of both the alcohol and acid metabolites and a strong induction of cyp142 at the mRNA and protein levels, indicating that CYP142A2 serves as a functionally redundant back up enzyme for CYP125A3. In contrast to M. tuberculosis, the M. smegmatis Δcyp125Δcyp142 double mutant retains its ability to grow on cholesterol albeit with a diminished capacity, indicating an additional level of redundancy within its genome.
Identifying and managing nonsuicidal self‐injurious behavior in the primary care setting
Authors: Kameg Kirstyn M. , Spencer Woods Audra , Szpak Janene Luther , McCormick Marcy
Published: February 2013

Purpose

To provide an overview of nonsuicidal self‐injurious behavior (NSSIB) for nurse practitioners (NPs) who see patients with this complex phenomenon in primary care settings.

Data sources

Selected research and clinical reviews.

Conclusions

NSSIB is characterized as a low‐lethality, repetitive act that can alter or cause damage to the body tissue. Among researchers and those who work directly with young people, there is a general consensus that NSSIB is increasing in prevalence. Unfortunately, NPs often view self‐injuring patients negatively, likely because of a lack of knowledge as to how to help this special patient population.

Implications for practice

Appropriate treatment can be initiated in the primary care setting; however, NPs must be aware of how and when to refer to specialty mental health services. Those with psychiatric comorbidities such as mood lability, anxiety, chronic emptiness or depersonalization, dysphoria, loneliness, anhedonia, or borderline personality disorder require management by mental health specialists. Patients experiencing NSSIB in response to command auditory hallucinations need immediate medical attention.
Intravenous Ethanol Increases Extracellular Dopamine in the Medial Prefrontal Cortex of the Long–Evans Rat
Authors: Schier Christina J. , Dilly Geoffrey A. , Gonzales Rueben A.
Published: February 2013

Background

Ethanol (EtOH) affects prefrontal cortex functional roles such as decision making, working memory, and behavioral control. Yet, the pharmacological effect of EtOH on dopamine, a neuromodulator in the medial prefrontal cortex (mPFC), is unclear. Past studies exploring this topic produced conflicting outcomes; however, a handful of factors (temporal resolution, method of drug administration, estrous cycle) possibly contributed to these discrepancies. We sought to mitigate these factors in order to elucidate EtOH's pharmacological effects on mPFC dopamine in Long–Evans rats.

Methods

We administered experimental solutions via an intravenous (iv), handling‐free route, monitored dopamine in the mPFC via microdialysis (10‐minute samples), and used male rats to avoid estrous cycle/EtOH interactions. First, we rapidly (approximately 2.7 ml/min) or slowly (approximately 0.6 ml/min) administered 1.0 g/kg EtOH and saline infusions, showing that the experimental methods did not contribute to dopamine changes. Then, a cumulative dosing protocol was used to administer 0.25, 0.75, 1.50, and 2.25 g/kg iv EtOH doses to evaluate dose–response. Finally, we monitored dialysate EtOH levels during an oral EtOH self‐administration session to compare the dialysate EtOH levels achieved during the pharmacological experiments to those seen during self‐administration.

Results

IV administration of a rapid or slow 1.0 g/kg EtOH infusion resulted in similar significant 55 ± 9 and 63 ± 15% peak dialysate dopamine increases, respectively. The 0.25, 0.75, 1.50, and 2.25 g/kg EtOH doses produced a nonsignificant 17 ± 5% and significant 36 ± 15, 68 ± 19, and 86 ± 20% peak dialysate dopamine increases, respectively. Self‐administration dialysate EtOH concentrations fell within the range of concentrations noted during the EtOH dose–response curve.

Conclusions

These experiments show that, using experimental methods that minimize possibly confounding factors, acute iv EtOH increases extracellular dopamine in the mPFC in a dose‐dependent manner, thereby clarifying EtOH's pharmacological effects on the mesocortical dopamine system.
Nicotinic Acetylcholine Receptors are Sensors for Ethanol in Lung Fibroblasts
Authors: Ritzenthaler Jeffrey D. , Roser‐Page Susanne , Guidot David M. , Roman Jesse
Published: February 2013

Background

Chronic ethanol (EtOH) abuse in humans is known to independently increase the incidence of and mortality due to acute lung injury in at‐risk individuals. However, the mechanisms by which EtOH affects lung cells remain incompletely elucidated. In earlier work, we reported that EtOH increased the expression in lung fibroblasts of fibronectin, a matrix glycoprotein implicated in lung injury and repair. This effect was blocked by α‐bungarotoxin, a neurotoxin that binds certain nicotinic acetylcholine receptors (nAChRs) thereby implicating nAChRs in this process. Here, we examine the identity of these receptors.

Methods

Mouse lung fibroblasts were stimulated with EtOH (60 mM) or acetylcholine (100 to 500 μM) and evaluated for the expression of fibronectin and nAChRs. Inhibitors to nAChRs or the antioxidant N‐acetyl cysteine (NAC) were used to assess changes in fibronectin expression. Animals exposed to EtOH for up to 6 weeks were used to evaluate the expression of nAChRs in vivo.

Results

First, in EtOH‐treated fibroblasts, we observed increased expression of α4 and α9 nAChR subunits. Second, we found that acetylcholine, a natural ligand for nAChRs, mimicked the effects of EtOH. Dihydro‐β‐erythroidin hydrobromide, a competitive inhibitor of α4 nAChR, blocked the increase in fibronectin expression and cell proliferation. Furthermore, EtOH‐induced fibronectin expression was inhibited in cells silenced for α4 nAChR. However, EtOH‐treated cells showed increased α‐bungarotoxin binding suggesting that α4 nAChR mediates the effects of EtOH via a ligand‐independent pathway. Knowing there are several important cysteine residues near the ligand‐binding site of α4 nAChRs, we tested the antioxidant NAC and found that it too blocked the induction of fibronectin expression by EtOH. Also, fibroblasts exposed to oxidant stress showed increased fibronectin expression that was blocked with α‐bungarotoxin. Finally, we showed increased expression of α4 nAChRs in the lung tissue of mice and rats exposed to EtOH suggesting a role for these receptors in vivo.

Conclusions

Altogether, our observations suggest that α4 nAChRs serve as sensors for EtOH‐induced oxidant stress in lung fibroblasts, thereby revealing a new mechanism by which EtOH may affect lung cells and tissue remodeling and pointing to nAChRs as potential targets for intervention.
Identification of galactose‐α‐1,3‐galactose in the gastrointestinal tract of the tick Ixodes ricinus; possible relationship with red meat allergy
Authors: Hamsten C. , Starkhammar M. , Tran T. A. T. , Johansson M. , Bengtsson U. , Ahlén G. , Sällberg M. , Grönlund H. , van Hage M.
Published: February 2013

Patients with IgE antibodies against the carbohydrate epitope galactose‐α‐1,3‐galactose (α‐Gal) have reported severe allergic reactions after consumption of red meat. Investigations have revealed associations between IgE to α‐Gal and tick bites. We provide the first direct evidence that α‐Gal is present within ticks thus potentially explaining the relationship between tick exposure and sensitization to α‐Gal, with development of red meat allergy as a secondary phenomena. Serum from Swedish patients with delayed severe reactions to red meat was included in the study. A dose‐dependent inhibition of IgE responses to α‐Gal by the tick Ixodes ricinus is demonstrated. Furthermore, using cryostat‐cut sections of I. ricinus, we show that both a monoclonal and a polyclonal antibody against α‐Gal stains the gastrointestinal tract of the tick. The same pattern is seen when staining with patient sera IgE positive to α‐Gal. These results confirm that the α‐Gal epitope is present in I. ricinus and imply host exposure to α‐Gal during a tick bite. This provides further evidence that tick bites are associated with IgE responses to α‐Gal and red meat allergy.
Augmenting pancreatic anastomosis during whipple operation with fibrin glue: a beneficial technical modification?
Authors: Conaglen Paul J. , Collier Neil A.
Published: February 2013

Introduction

Various techniques have been described to try and reduce the rate of anastomotic leak following pancreaticoduodenectomy, which remains a challenge for pancreatic surgeons worldwide. We outline a technique to reinforce the pancreatic anastomosis with a double layer of fibrin glue between suture lines.

Methods

Our technique for pancreatic anastomosis is described in detail. A review of consecutive pancreaticoduodenectomies by a single surgeon (NAC) since introduction of fibrin glue anastomosis reinforcement was compared with a historical control cohort performed by the same surgeon.

Results

Thirty‐two consecutive pancreaticoduodenectomies were undertaken between March 2008 and March 2012 by a single surgeon, 30 patients had fibrin glue augmentation of the pancreatico‐gastrostomy anastomosis. Median length of stay was 12 days. There were no pancreatic leaks or mortality since adopting fibrin glue for the pancreatic anastomosis; however; this single surgeon series is not large enough to provide statistical evidence of a difference since glue was adopted.

Discussion

Our results since the incorporation of this step in pancreaticoduodenectomy are encouraging. Selective use of glue is worthy of consideration in difficult cases, although confirmation of a reduction in pancreatic leak rate is not yet established, and we advocate a multi‐institution randomized controlled trial to explore this.
Paediatric normative data for urine NGAL/creatinine ratio
Authors: Rybi–Szumińska Agnieszka , Wasilewska Anna , Litwin Miecyslaw , Kułaga Zbigniew , Szumiński Michal
Published: February 2013

Aim

The objective of this study was to establish age‐dependent urine NGAL (neutrophil gelatinase‐associated lipocalin)/creatinine ratio values in healthy children and adolescents.

Methods

The study was performed using a random sample of 172 healthy children and adolescents (M–88, F–84), aged median 9.75 (0.2–17.9) years. Urine NGAL concentration was measured using a commercially available ELISA kit (R&D Systems, USA).

Results

Median concentrations of urine NGAL/creatinine in particular age groups were analysed using anova. The differences between the youngest group of children under the age of 6 years and the rest of examined population were statistically significant. There were no differences in urine NGAL/creatinine between other age groups. Statistically significant negative correlation between urine NGAL/creatinine and age of subjects was found (r = −0.29, p < 0.05).

Conclusion

In the study, normative values of urine NGAL/creatinine for subjects aged 0.2–17.9 years have been established. These data may help clinicians and researchers to improve the interpretation of urine NGAL/creatinine ratio in children and adolescents. However, further studies using numerous data should be conducted to add reference values for urine NGAL partitioned by age and gender.
Arthur, James et al ed (2012) Research methods and methodologies in educationSage (London & Thousand Oaks CA) isbn 978‐0‐85702‐039‐0 456 pp £26.99 (paper and e‐versions; boards £75) http://www.sagepub.co.uk/arthur
Authors: El‐Farargy Nancy
Published: February 2013

Aimed at postgraduates within education and educational research methods courses, this book integrates the theoretical and practical aspects of educational research. It journeys through designing, planning and conducting research to analytical techniques, impact and dissemination. Whether you are a new educational researcher or more established, you might find your own copy of this book useful for in‐depth study or for reference: borrow a copy to help you decide.

Nancy El‐Farargy