bluuebunny/crossref_metadata_2025 huggingface dataset:
X-ray absorption fine structure study of heavily P doped (111) and (001) diamond
Authors: Shikata Shinichi , Yamaguchi Koji , Fujiwara Akihiko , Tamenori Yusuke , Yahiro Jumpei , Kunisu Masahiro , Yamada Takatoshi
Published: February 2017

X-ray absorption fine structure (XANES) measurements were carried out for P doped (111) and (001) diamond films, and the results were compared with those from simulations. For the (111) spectrum, the main strong peak observed at 2147.0 eV and three broad peaks centered at 2150 eV, 2157 eV, and 2165 eV were observed. The assignment with the estimation by the simulation of the XANES peaks showed the interstitial sites additional to the substitutional site. The Extended X-ray Absorption Fine Structure (EXAFS) result of the P doped (111) diamond showed that the first and second neighboring peaks are observed at 1.21 A and 2.0 A, respectively. The assignment with the estimation by the simulation of the EXAFS peaks also showed the interstitial sites additional to the substitutional site. Overall, P in diamonds presumably has dopant sites in both the substitutional and interstitial sites.
Anion photoelectron spectroscopy of deprotonated ortho-, meta-, and para-methylphenol
Authors: Nelson Daniel J. , Gichuhi Wilson K. , Miller Elisa M. , Lehman Julia H. , Lineberger W. Carl
Published: February 2017

The anion photoelectron spectra of ortho-, meta-, and para-methylphenoxide, as well as methyl deprotonated meta-methylphenol, were measured. Using the Slow Electron Velocity Map Imaging technique, the Electron Affinities (EAs) of the o-, m-, and p-methylphenoxyl radicals were measured as follows: 2.1991±0.0014, 2.2177±0.0014, and 2.1199±0.0014 eV, respectively. The EA of m-methylenephenol was also obtained, 1.024±0.008 eV. In all four cases, the dominant vibrational progressions observed are due to several ring distortion vibrational normal modes that were activated upon photodetachment, leading to vibrational progressions spaced by ∼500 cm−1. Using the methylphenol O–H bond dissociation energies reported by King et al. and revised by Karsili et al., a thermodynamic cycle was constructed and the acidities of the methylphenol isomers were determined as follows: ΔacidH298K0=348.39±0.25, 348.82±0.25, 350.08±0.25, and 349.60±0.25 kcal/mol for cis-ortho-, trans-ortho-, m-, and p-methylphenol, respectively. The excitation energies for the ground doublet state to the lowest excited doublet state electronic transition in o-, m-, and p-methylphenoxyl were also measured as follows: 1.029±0.009, 0.962±0.002, and 1.029±0.009 eV, respectively. In the photoelectron spectra of the neutral excited states, C–O stretching modes were excited in addition to ring distortion modes. Electron autodetachment was observed in the cases of both m- and p-methylphenoxide, with the para isomer showing a lower photon energy onset for this phenomenon.
Dielectric relaxation and charged domain walls in (K,Na)NbO3-based ferroelectric ceramics
Authors: Esin A. A. , Alikin D. O. , Turygin A. P. , Abramov A. S. , Hreščak J. , Walker J. , Rojac T. , Bencan A. , Malic B. , Kholkin A. L. , Shur V. Ya.
Published: February 2017

The influence of domain walls on the macroscopic properties of ferroelectric materials is a well known phenomenon. Commonly, such “extrinsic” contributions to dielectric permittivity are discussed in terms of domain wall displacements under external electric field. In this work, we report on a possible contribution of charged domain walls to low frequency (10–106 Hz) dielectric permittivity in K1-xNaxNbO3 ferroelectric ceramics. It is shown that the effective dielectric response increases with increasing domain wall density. The effect has been attributed to the Maxwell-Wagner-Sillars relaxation. The obtained results may open up possibilities for domain wall engineering in various ferroelectric materials.
Relaxation processes and glass transition of confined polymer melts: A molecular dynamics simulation of 1,4-polybutadiene between graphite walls
Authors: Solar M. , Binder K. , Paul W.
Published: February 2017

Molecular dynamics simulations of a chemically realistic model for 1,4-polybutadiene in a thin film geometry confined by two graphite walls are presented. Previous work on melts in the bulk has shown that the model faithfully reproduces static and dynamic properties of the real material over a wide temperature range. The present work studies how these properties change due to nano-confinement. The focus is on orientational correlations observable in nuclear magnetic resonance experiments and on the local intermediate incoherent neutron scattering function, Fs(qz, z, t), for distances z from the graphite walls in the range of a few nanometers. Temperatures from about 2Tg down to about 1.15Tg, where Tg is the glass transition temperature in the bulk, are studied. It is shown that weakly attractive forces between the wall atoms and the monomers suffice to effectively bind a polymer coil that is near the wall. For a wide regime of temperatures, the Arrhenius-like adsorption/desorption kinetics of the monomers is the slowest process, while very close to Tg the Vogel-Fulcher-Tammann-like α-relaxation takes over. The α-process is modified only for z≤1.2 nm due to the density changes near the walls, less than expected from studies of coarse-grained (bead-spring-type) models. The weakness of the surface effects on the glass transition in this case is attributed to the interplay of density changes near the wall with the torsional potential. A brief discussion of pertinent experiments is given.
Area density of streptavidin can be evaluated by the number density of biotinylated microbubbles
Authors: Yokoi Yasuhiro , Yoshida Kenji , Otsuki Yuta , Watanabe Yoshiaki
Published: February 2017

Targeted microbubbles (TMBs) that specifically accumulate on target sites via biochemical bonds have been studied for using ultrasound diagnoses and therapies (e.g., ultrasound molecular imaging) in the research field. To understand the specific interactions between TMBs and their target molecules, a biosensor system with a quartz crystal microbalance (QCM) was constructed. In this system, TMBs become absorbed on their target molecule, which was fixed to the QCM surface via a self-assembled monolayer. Our previous studies showed that the system allowed the evaluation of the interaction between biotinylated MBs and the target molecule, streptavidin, by monitoring changes in the resonant frequency of QCM [Muramoto et al., Ultrasound Med. Biol., 40(5), 1027–1033 (2014)]. This paper investigates how the amount of streptavidin relates to the amount of absorbed biotinylated MBs. The amount of streptavidin on the QCM surface was evaluated by measuring the difference in its resonant frequency before and after the fixation of streptavidin. After which, the amount of absorbed MBs was also evaluated by measuring the frequency shift during the interaction between MBs and the target molecule. Our results showed a weak correlation between the amounts of bound MB and the density of streptavidin (correlation coefficient, r = 0.44), suggesting that the area density of target molecule can be evaluated by estimating the number density of TMBs.
Fingerprints of different interaction mechanisms on the collective modes in complex (dusty) plasmas
Authors: Khrapak Sergey A. , Klumov Boris A. , Thomas Hubertus M.
Published: February 2017

In this paper, we discuss the relations between the exact shape of interparticle interactions in complex (dusty) plasmas and the dispersion relation of the longitudinal collective mode. Several representative repulsive potentials, predicted previously theoretically, are chosen, and the corresponding dispersion relations are calculated using the quasi-crystalline approximation. Both weakly coupled and strongly coupled regimes are considered. It is shown that the long-wavelength portions of the dispersion curves can be sensitive to the long-range asymptote of the interaction potential. This can be used to discriminate between different interaction mechanisms operational in complex plasmas experimentally. Main requirements are briefly discussed.
Utilizing built infrastructure and otherwise non-utilizable space for solar PV power projects—A case study for an educational institution
Authors: Iftikhar Hamid , Waqas Adeel , Usman Ahmad , Mustafa Kamal , Afzal Muhammad Ali
Published: February 2017

Ground mounted solar PV systems utilize a large amount of land that could otherwise be used for different developmental activities, such as agricultural growth, fuel crops production, and industrial development. Utilizing the already built infrastructures such as building rooftops, parking sheds, and canal water systems for installation of solar PV projects has proven beneficial as it minimizes the procurement and opportunity cost of the land. Taking into consideration the best practices adopted globally, Pakistan must evolve its policy for a shift towards utilization of existing infrastructures rather than using prime lands for solar PV power projects. Building Integrated Photovoltaic (BIPV) systems have been effective for deployment and penetration of solar PV technology (SPVT) in different countries. In this paper, we present a case study, established on the basis of existing BIPV principles followed in developed countries. This case study proposes to utilize existing storm water drains, parking lots, and land across lake sites for solar PV system installation at an educational institution, National University of Sciences and Technology (NUST). A detailed analysis has been performed to evaluate the project's financial feasibility in terms of economic indexes such as Payback Period, Discounted Cash Flows, Net Present Value, and Internal Rate of Return. Results show that a 5 MW distributed solar PV system installed on an otherwise non-utilizable land at the university's premises shall provide a payback period of 7.09 years at an attractive internal rate of return of 13%.
Three-dimensional cathodoluminescence characterization of a semipolar GaInN based LED sample
Authors: Hocker Matthias , Maier Pascal , Tischer Ingo , Meisch Tobias , Caliebe Marian , Scholz Ferdinand , Mundszinger Manuel , Kaiser Ute , Thonke Klaus
Published: February 2017

A semipolar GaInN based light-emitting diode (LED) sample is investigated by three-dimensionally resolved cathodoluminescence (CL) mapping. Similar to conventional depth-resolved CL spectroscopy (DRCLS), the spatial resolution perpendicular to the sample surface is obtained by calibration of the CL data with Monte-Carlo-simulations (MCSs) of the primary electron beam scattering. In addition to conventional MCSs, we take into account semiconductor-specific processes like exciton diffusion and the influence of the band gap energy. With this method, the structure of the LED sample under investigation can be analyzed without additional sample preparation, like cleaving of cross sections. The measurement yields the thickness of the p-type GaN layer, the vertical position of the quantum wells, and a defect analysis of the underlying n-type GaN, including the determination of the free charge carrier density. The layer arrangement reconstructed from the DRCLS data is in good agreement with the nominal parameters defined by the growth conditions.
Structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy
Authors: Kanzyuba Vasily , Dong Sining , Liu Xinyu , Li Xiang , Rouvimov Sergei , Okuno Hanako , Mariette Henri , Zhang Xueqiang , Ptasinska Sylwia , Tracy Brian D. , Smith David J. , Dobrowolska Margaret , Furdyna Jacek K.
Published: February 2017

We describe the structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy on GaAs (111) substrates, as revealed by transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. When the Mn concentration is increased, the lattice of the ternary (Sn,Mn)Se films evolves quasi-coherently from a SnSe2 two-dimensional (2D) crystal structure into a more complex quasi-2D lattice rearrangement, ultimately transforming into the magnetically concentrated antiferromagnetic MnSe 3D rock-salt structure as Mn approaches 50 at. % of this material. These structural transformations are expected to underlie the evolution of magnetic properties of this ternary system reported earlier in the literature.
Effects of iron deficiency on anisotropy and ferromagnetic resonance linewidth in Bi-doped LiZn ferrite
Authors: Jiang Xiaona , Wang Wei , Yu Zhong , Sun Ke , Lan Zhongwen , Zhang Xinran , Harris Vincent G.
Published: February 2017

Bi-doped LiZn ferrites with different iron deficiencies were fabricated by a conventional ceramic method. Anisotropy constant (K1) was calculated and ferromagnetic resonance (FMR) linewidth (ΔH) was investigated. Crystalline anisotropy broadening linewidth (ΔHa) and porosity broadening linewidth (ΔHp) were derived by an approximate calculation based on dipolar narrowing theory, which play a significant role in contributions to FMR linewidth and occupy more than 90 % of ΔH. Physical and static magnetic properties of LiZn ferrite with iron deficiency are presented, which supports a decline in linewidths with increasing iron deficiency. Iron deficiency makes K1, ΔHa and ΔHp reduce. The results also show that ΔHp is the majority of contributions to ΔH in Bi-doped LiZn ferrite and densification is an effective method to decrease ΔH.
Enhancement of magnetic circular dichroism in bi-layered ZnO-Bi:YIG thin films
Authors: Mito Shinichiro , Shiotsu Yusaku , Sasano Junji , Takagi Hiroyuki , Inoue Mitsuteru
Published: February 2017

Bi-layered zinc oxide (ZnO) and bismuth substituted yttrium iron garnet (Bi:YIG) was fabricated and magneto-optically investigated. Enhancement of Faraday rotation and magnetic circular dichroism (MCD) was observed. The wavelength of MCD enhancement was in good agreement with exciton wavelength of ZnO. This enhancement was only observed in the bi-layer, and implies that the exciton generated in ZnO interacted with Bi:YIG. Because the exciton wavelength of ZnO can be controlled by electro-optic effect, this result has the potential for realizing voltage control of magneto-optic effect.
Spin pumping and the inverse spin hall effect in single crystalline Fe/Pt heterostructure
Authors: Huo Y. , Zeng F. L. , Zhou C. , Wu Y. Z.
Published: February 2017

Spin pumping effect in single crystalline Fe/Pt bilayer has been systematically studied by the measurements of the microwave absorption spectrum and the inverse spin hall voltage detection. The gilbert damping constant of Fe first increases with Pt thickness and then saturates at tPt>1.5 nm. The spin diffusion length can be determined as 1.5±0.4 nm, and the spin mixing conductance is (3.4±0.4)×1019 m-2. The inverse spin hall voltage is quantitatively separated from the spin rectification effect through the measurement of the magnetization angular dependence, and the estimated spin hall angle of Pt is 0.048±0.015, in consistent with the values determined in polycrystalline Pt films.
Facile synthesis and characterization of magnetochromatic Fe3O4 nanoparticles
Authors: Wang Wei , Zheng Lelin , Lu Fenghua , Hong Ruijiang , Chen Michael Z. Q. , Zhuang Lin
Published: February 2017

A facile synthetic method for magnetochromatic Fe3O4 nanoparticles (FNPs) with controllable size and optical properties has been fabricated by the combination of an improved solvothermal method and the usage of ultrasonic irradiation in the surface modification step. The improved solvothermal method enables the alteration of the size of nanoparticles (50nm to 180nm) in a competitively convenient way by adjusting the ratio of binary solvents, including diethylene glycol (DEG) and ethylene glycol (EG). In the surface modification step, the short-chain polyacrylic acid (PAA) is added as the surfactant with ultrasound-assisted method. In this research, due to magnetically-driven assembly FNPs forming photonic crystals, the reflection peaks show blue-shift as the magnetic field is increased from 181 to 2479G. In addition, on the basis of the calculation using Bragg’s Law, the thickness of the solvent layer is measured approximately 35nm, which accounts for the magnetochromatic properties as well as excellent dispersion.
Quantum interpolation for high-resolution sensing
Authors: Ajoy Ashok , Liu Yi-Xiang , Saha Kasturi , Marseglia Luca , Jaskula Jean-Christophe , Bissbort Ulf , Cappellaro Paola
Published: February 2017

Significance

Nanoscale magnetic resonance imaging enabled by quantum sensors is a promising path toward the outstanding goal of determining the structure of single biomolecules at room temperature. We develop a technique, which we name “quantum interpolation,” to improve the frequency resolution of these quantum sensors far beyond limitations set by the experimental controlling apparatus. The method relies on quantum interference to achieve high-fidelity interpolation of the quantum dynamics between hardware-allowed time samplings, thus allowing high-resolution sensing. We demonstrate over two orders of magnitude resolution gains, and discuss applications of our work to high-resolution nanoscale magnetic resonance imaging.
Intrinsically disordered proteins drive enamel formation via an evolutionarily conserved self-assembly motif
Authors: Wald Tomas , Spoutil Frantisek , Osickova Adriana , Prochazkova Michaela , Benada Oldrich , Kasparek Petr , Bumba Ladislav , Klein Ophir D. , Sedlacek Radislav , Sebo Peter , Prochazka Jan , Osicka Radim
Published: February 2017

Significance

Formation of the hardest mineralized tissue in vertebrates, tooth enamel, relies on a unique set of enamel matrix proteins (EMPs). These EMPs assemble into a 3D extracellular organic matrix that directs the deposition of calcium and phosphate ions into hydroxyapatite crystallites. However, the molecular basis of EMP assembly into the organic matrix remains poorly understood. This study shows that self-assembly of the key EMPs, ameloblastin and amelogenin, involves a short linear amino acid motif that is evolutionarily conserved from the first tetrapods to man. Functionality of this motif in ameloblastin is shown to be essential for organization of the enamel organic matrix and for proper organization of hydroxyapatite crystallites into the compact bundles that determine the structure and mechanical resistance of enamel.
Insights into immune system development and function from mouse T-cell repertoires
Authors: Sethna Zachary , Elhanati Yuval , Dudgeon Crissy R. , Callan Curtis G. , Levine Arnold J. , Mora Thierry , Walczak Aleksandra M.
Published: February 2017

Significance

The immune system defends against pathogens in part via a diverse population of T cells that display different surface receptor proteins [T-cell receptors (TCRs)] designed to recognize MHC-presented foreign peptides. Receptor diversity is produced by an initial random gene recombination process, followed by selection for proteins that fold correctly and bind weakly to self-peptides. Using data from mice of different ages, from embryo to young adult, we quantify the changes with time in the way receptors are generated and selected for function. We find a strong increase in repertoire diversity, occurring shortly after birth, due to a sharp increase in the number of random nucleotide insertions in the primitive TCR gene recombination process. Differences between thymic and blood TCR sequence distributions allow us to infer subtle details of this “turning on” of the mouse immune system.
Replication of
Vibrio cholerae
classical CTX phage
Authors: Kim Eun Jin , Yu Hyun Jin , Lee Je Hee , Kim Jae-Ouk , Han Seung Hyun , Yun Cheol-Heui , Chun Jongsik , Nair G. Balakrish , Kim Dong Wook
Published: February 2017

Significance

Vibrio cholerae
O1, the causative agent of the disease cholera, has two biotypes: namely classical and El Tor. The disease is the principal manifestation of a potent toxin known as cholera toxin, produced by the bacteria. Generation of a toxin producing
V. cholerae
strain arises by infection of a toxin gene-carrying phage (CTX phage) that becomes integrated into its genome. Experimental evidence has shown the replication and transmission of the type-specific phage in the El Tor strains, but this has not been experimentally demonstrated in the classical strains and the exact mechanism was not known. This study provides laboratory evidence that illustrates the genesis of toxigenic classical biotype strains.
Who Has the Biggest Bulls? Royal Power and the Persepolis Apadāna
Authors: Morgan Janett
Published: February 2017

Relationships between power and architecture are a feature of all great civilizations and the Achaemenid world was no exception to this. The architecture of Achaemenid buildings and their relief sculpture was designed to reflect and reinforce the power and status of the Great King. At the heart of this visual program lay the audience hall (apadāna) at Persepolis. In seeking to explain and understand the messages written into this building, we tend to approach the structure as a completed work and view it from the last point in its lifecycle. As a result, we focus on its tribute procession relief and allow ideas of empire to dominate our gaze. This limits our ability to understand how and why the building’s intended audience and message of power might have diverged at different stages in its construction. This article re-examines the art and architecture of the audience hall at Persepolis and redirects the viewer’s gaze to the images of bulls rather than the tribute procession. In focusing on the role of bulls in the scheme of decoration, the article presents a more nuanced reading of the building in its historical, social and architectural context. It shows how Darius I used the Persepolis apadāna to display his authority to rule and to assert the primacy of his status amongst his fellow elites.
Surface characterisation of electroplated tinplate with different coating mass
Authors: Wu F. J. , Liu X. J. , Xiao X.
Published: February 2017

In this paper, electrodeposited tinplates with different coating mass have been characterised by SEM, XRD, XPS, and EDS. The results indicate that a much lower coating mass may lead to an ununiformly distributed tin coating layer. To obtain a qualified tin coating with lower tin mass, the roughness of the base steel surface should be strictly controlled to gain a flat surface with lower roughness and defects. Cr2O3 and Cr(OH)3 were found as the main composition of passivation film with Cr2O3 locating at the outermost film surface, and the amount of Sn element increases and Cr element decreases as a function of depth from the surface of tin coating. In addition, the amount of Fe impurity in the plating bath should be strictly controlled as its presence in tin coating is harmful to coating corrosion resistance.
Red Snapper Distribution on Natural Habitats and Artificial Structures in the Northern Gulf of Mexico
Authors: Karnauskas Mandy , Walter John F. , Campbell Matthew D. , Pollack Adam G. , Drymon J. Marcus , Powers Sean
Published: February 2017

In 2011, an intensive, multiple-gear, fishery-independent survey was carried out in the northern Gulf of Mexico (GOM) to collect comprehensive age and length information on Red Snapper Lutjanus campechanus. Based on this synoptic survey, we produced a spatial map of Red Snapper relative abundance that integrates both gear selectivity effects and ontogenetically varying habitat usage. Our methodology generated a spatial map of Red Snapper at a 10-km2 grid resolution that is consistent with existing knowledge of the species: Red Snapper occurred in relatively high abundances at depths of 50–90 m along the coasts of Texas and Louisiana and in smaller, patchy “hot spots” at a variety of depths along the Alabama coast and the west Florida shelf. Red Snapper biomass and fecundity estimates were higher for the northwestern GOM than for the northeastern GOM, as the latter area contained mostly smaller, younger individuals. The existence of similar surveys on petroleum platforms and artificial reefs also enabled us to calculate their relative contribution to Red Snapper distribution compared with that of natural habitats. We estimated that for the youngest age-classes, catch rates were approximately 20 times higher on artificial structures than on natural reefs. Despite the high catch rates observed on artificial structures, they represent only a small fraction of the total area in the northern GOM; thus, we estimated that they held less than 14% of Red Snapper abundance. Because artificial structures—particularly petroleum platforms—attract mostly the youngest individuals, their contribution was even lower in terms of total population biomass (7.8%) or spawning potential (6.4%). Our estimates of Red Snapper relative abundance, biomass, and spawning potential can be used to design spatial management strategies or as inputs to spatial modeling techniques.
Realisms and Indexicalities of Photographic Propositions
Authors: Ball Christopher
Published: February 2017

In the eras of both film-based and digital photography, and to differing degrees and with differing consequences in documentary and art photography, the role of indexicality in establishing the veracity of the image has been paramount in photo theory. There is a need, however, for expanding the ways we think about indexicality in photography. In addition to the familiar concepts of the trace, citation, reference, social diacritics, interactional cues, and artists’ intentions, the indexicality of photography may be better understood through appeal to less direct, or more densely mediated, modalities of indexicality. These include qualia (hypostatically abstracted -nesses), dicentization (the upshifting of icons into indexes of contiguity), and propositionality (the assertion of messages subject to truth claims).
The Open Throat: Deceptive Sounds, Facts of Firstness, and the Interactional Emergence of Voice
Authors: Harkness Nicholas
Published: February 2017

This article develops a Peircean conceptualization of qualia as “facts of firstness” by examining the pedagogical pragmatics of a voice lesson in which an intersubjective orientation to vocal sound via listening becomes a subjective orientation to voice production via bodily feeling. I focus specifically on various attempts by a teacher and a student collaboratively to repair and cultivate the student’s voice by generating and isolating qualia across proprioceptive and introspective dimensions. By tracing the sensuous semiotic modes through which qualia become crucial pragmatic signals in the process of “opening” the student’s throat, I demonstrate how these facts of firstness function as cultural emergents that are produced by and accessible through communicative, interactional, intersubjective conduct.
Signatura rerum: Semiotics of the Subnuclear
Authors: Roy Arpita
Published: February 2017

On July 4, 2012, experimental physicists on the Large Hadron Collider near Geneva, in Switzerland, announced the historic discovery of the Higgs boson. After analyzing trillions of proton-to-proton collisions, two teams of physicists concluded that signatures of diphotons in the final state were evidence of the long-sought-after Higgs particle. The answerability of a particle search to polysemic signals raises a deeply provocative question: In what ways does a sign facilitate the discovery of a thing? Drawing on fieldwork at the Large Hadron Collider complex, this article attempts to probe the semiosis of signatures as a palimpsest of inherent possibilities spanning the width of the universe, which is neither a contingent ordering of the Saussurean kind nor a brick-by-brick Peircean construct. What it eloquently foregrounds is the capacity of a class of signs to reflect the presence of objects, even those that are materially nonexistent, which resolves many a metaphysical perplexity involving language, thought, and reality. In the process, this article makes a case for the role of meaningful, qualitative evaluations, which lie at the root of experimental searches, and explains how these qualitative evaluations are a more trustworthy source of discoveries in particle physics than metrics or magnitudes.
Qualia as Value and Knowledge: Histories of European Porcelain
Authors: Gal Susan
Published: February 2017

Porcelain is, today, a familiar material of dishes, figurines, vases, and tiles. As commodities, they are enregistered social indexicals, so that the aphorism fits: you are what you drink, eat, or in this case eat on—or know how to admire as collector or connoisseur. This does not yet tell us, however, what qualities are picked out as shared by object and user, on what axis of social distinction. I argue that this everyday material, exactly because of the varied qualities it has been presumed to embody, has been swept up in changing regimes of knowledge, in economic strategies, and in making political and ethical discourses persuasive. In European history over the last few centuries, it has been embedded in diverse axes of differentiation, enlisted and changed not only as sign but also as material in strikingly different ontological projects.
Qualia and Ontology: Language, Semiotics, and Materiality; an Introduction
Authors: Chumley Lily
Published: February 2017

Qualia—sensory experiences of abstract qualities such as heat, texture, color, sound, stink, hardness, and so on—focus attention on prototypically “material” entities. But how is the ontological category of materiality constituted by conventional qualities, or qualisigns? For instance, how does the sound made by knuckles knocking on a table come to be an exemplary experience of, and a conventional sign for, “materiality”? What ontologies might undermine the seeming naturalness of this category, and to what effect? This issue contributes to the growing literature on semiotic approaches to materiality by arguing that attention to qualia, as sensorial and somatic experiences mediated by cultural qualisigns of value (Munn 1986), offers a useful analytic approach to the dialectics of matter (substrate, affordance) and nonmatter (idea, concept, category). The articles in this issue describe how modes of being and becoming are represented in and organized by discourses on qualia and demonstrate the crucial role of qualia and qualisigns in “ontological politics” (Mol 1999).
Supplementary comparison EURAMET.L-S23 (#1269) high precision roundness measurement by error separation techniques
Authors: Prieto Emilio , Muñoz Rafael , Arce Aelio A , Bergmans Rob , Kotte Gerard , Holmberg Maria , Svendsmark Maria , Toftegaard Jens Bo , Astrua Milena , Pisani Marco , Saraiva Fernanda , Eusebio Liliana , Nouira Hichem , Salgado José
Published: February 2017

At its meeting in October 2012, the EURAMET Technical Committee for Length, EURAMET TC-L, decided that a key comparison on high precision roundness measurement by multi-step method shall be carried out with CEM acting as the pilot laboratory. The roundness standards to be calibrated were chosen to be a glass hemisphere with a diameter of about 50 mm and a sphere with a diameter of about 30 mm.

A goal of the key comparisons for topics in dimensional metrology is to demonstrate the equivalence of routine calibration services offered by NMIs to clients, as listed in appendix C of the Mutual Recognition Agreement (MRA). To this end, participants in this comparison agreed to use the same apparatus and methods as routinely applied to client artefacts. The comparison was registered in March 2013 as Project EURAMET 1269 and at KCDB as supplementary comparison EURAMET.L-S23.2013.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Renal Sympathetic Denervation: A Viable Option for Treating Resistant Hypertension
Authors: Schlaich Markus P
Published: February 2017

Accumulating evidence from mainly uncontrolled clinical studies with various types of ablation catheters have shown that renal denervation (RDN) can be applied safely and is effective in lowering blood pressure (BP) in patients with treatment-resistant hypertension. Sustained BP lowering has been documented up to 3 years. Furthermore, RDN has been associated with regression of target organ damage, such as left ventricular hypertrophy, arterial stiffness, and others. Several studies indicate potential benefit in other common clinical conditions associated with increased sympathetic tone including chronic kidney disease and heart failure. However, the recently published Symplicity HTN-3 study, the largest and most rigorously designed sham-controlled clinical trial, while confirming the safety of the procedure, failed to demonstrate a BP lowering effect beyond that of a sham procedure in patients with resistant hypertension. Efforts to unravel the reasons for the discrepant results from Symplicity HTN-3 have focused on a range of potential confounders including anatomical and procedural aspects. Indeed, data from post-hoc analyses indicate that sufficient RDN may not have been achieved in the majority of patients in Symplicity HTN-3. Furthermore, recent evidence from human postmortem and functional animal studies revealed new insights into the anatomical distribution of renal nerves and their accessibility by intravascular approaches. Initial results from recent clinical trials integrating these important findings indeed seem to confirm that RDN remains a viable option for the treatment of hypertension. Thorough further investigations will be key to determine the true potential of RDN in clinical conditions characterized by increased sympathetic drive.
Healthy Lifestyle and Blood Pressure Variability in Young Adults
Authors: Maseli Anna , Aeschbacher Stefanie , Schoen Tobias , Fischer Andreas , Jung Manuel , Risch Martin , Risch Lorenz , Conen David
Published: February 2017

BACKGROUND

The aim of this study was to assess the relationships between healthy lifestyle metrics and blood pressure variability (BPV) in young and healthy adults.

METHODS

A population-based sample of 1,999 individuals aged 25–41 years was investigated. A lifestyle-score from 0 (most unhealthy) to 7 (most healthy) was calculated by giving one point for each of the following components: never smoking cigarettes, adhering to a healthy diet, performing moderate or intense physical activity, having a body mass index <25 kg/m2, a total cholesterol <200 mg/dl, a glycated hemoglobin <5.7%, or a conventional BP <120/80 mm Hg. Standardized ambulatory 24-hour BP measurements were obtained in all individuals. BPV was defined as the SD of all individual ambulatory BP recordings. We constructed multivariable linear regression models to assess the relationships between the lifestyle-score and BPV. None of the results were adjusted for multiple testing.

RESULTS

Median age was 37 years and 46.8% were men. With increasing lifestyle-score, systolic and diastolic BPV is decreasing linearly (P for trend <0.0001), even after multivariable adjustment. Per 1-point increase in lifestyle-score, the β-coefficient (95% confidence interval) for systolic and diastolic 24-hour BPV was −0.03 (−0.03; −0.02) and −0.04 (−0.05; −0.03), respectively, both P for trend <0.0001. These relationships were attenuated but remained statistically significant after additional adjustment for mean individual BP.

CONCLUSION

In this study of young and healthy adults, adopting a healthy lifestyle was associated with a lower BPV. These associations were independent of mean BP levels.
AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs
Authors: Jiang Biaobin , Kloster Kyle , Gleich David F , Gribskov Michael
Published: February 2017

Motivation: Diffusion-based network models are widely used for protein function prediction using protein network data and have been shown to outperform neighborhood-based and module-based methods. Recent studies have shown that integrating the hierarchical structure of the Gene Ontology (GO) data dramatically improves prediction accuracy. However, previous methods usually either used the GO hierarchy to refine the prediction results of multiple classifiers, or flattened the hierarchy into a function–function similarity kernel. No study has taken the GO hierarchy into account together with the protein network as a two-layer network model.

Results: We first construct a Bi-relational graph (Birg) model comprised of both protein–protein association and function–function hierarchical networks. We then propose two diffusion-based methods, BirgRank and AptRank, both of which use PageRank to diffuse information on this two-layer graph model. BirgRank is a direct application of traditional PageRank with fixed decay parameters. In contrast, AptRank utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. We evaluate the ability of both methods to predict protein function on yeast, fly and human protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design four different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly discovered function prediction to comprehensively evaluate predictability of all six methods. We find that both BirgRank and AptRank outperform the previous methods, especially in missing function prediction when using only 10% of the data for training.

Availability and Implementation: The MATLAB code is available at https://github.rcac.purdue.edu/mgribsko/aptrank.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Succinct colored de Bruijn graphs
Authors: Muggli Martin D , Bowe Alexander , Noyes Noelle R , Morley Paul S , Belk Keith E , Raymond Robert , Gagie Travis , Puglisi Simon J , Boucher Christina
Published: February 2017

Motivation

In 2012, Iqbal et al. introduced the colored de Bruijn graph, a variant of the classic de Bruijn graph, which is aimed at ‘detecting and genotyping simple and complex genetic variants in an individual or population’. Because they are intended to be applied to massive population level data, it is essential that the graphs be represented efficiently. Unfortunately, current succinct de Bruijn graph representations are not directly applicable to the colored de Bruijn graph, which requires additional information to be succinctly encoded as well as support for non-standard traversal operations.

Results

Our data structure dramatically reduces the amount of memory required to store and use the colored de Bruijn graph, with some penalty to runtime, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible.

Availability and Implementation

https://github.com/cosmo-team/cosmo/tree/VARI

Supplementary information

Supplementary data are available at Bioinformatics online.
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection
Authors: Moal Iain H , Barradas-Bautista Didier , Jiménez-García Brian , Torchala Mieczyslaw , van der Velde Arjan , Vreven Thom , Weng Zhiping , Bates Paul A , Fernández-Recio Juan
Published: February 2017

Motivation

In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction.

Results

Atomic modeling of protein–protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100.

Availability and Implementation

IRaPPA has been implemented in the SwarmDock server (http://bmm.crick.ac.uk/∼SwarmDock/), pyDock server (http://life.bsc.es/pid/pydockrescoring/) and ZDOCK server (http://zdock.umassmed.edu/), with code available on request.

Supplementary information

Supplementary data are available at Bioinformatics online.
Statistical database analysis of the role of loop dynamics for protein–protein complex formation and allostery
Authors: Gu Yina , Li Da-Wei , Brüschweiler Rafael
Published: February 2017

Motivation

Protein loops show rich conformational dynamics properties on a wide range of timescales as they play an essential role for many cellular functions during protein–protein interactions and recognition processes. However, little is known about the detail behavior of loops upon protein binding including allostery.

Results

We report the loop motions and their dominant timescales for a library of 230 proteins that form protein–protein complexes using the ToeLoop predictor of loop dynamics. We applied the analysis to proteins in both their complex and free state and relate specific loop properties to their role in protein recognition. We observe a strong tendency of loops that move on relatively slow timescales of tens of ns to sub-μs to be directly involved in binding and recognition processes. Complex formation leads to a significant reduction in loop flexibility at the binding interface, but in a number of cases it can also trigger increased flexibility in distal loops in response to allosteric conformational changes. The importance of loop dynamics and allostery is highlighted by a case study of an antibody-antigen complex. Furthermore, we explored the relationship between loop dynamics and experimental binding affinities and found that a prevalence of high loop rigidity at the binding interface is an indicator of increased binding strength.

Availability and Implementation

http://spin.ccic.ohio-state.edu/index.php/toeloopppi

Supplementary information

Supplementary data are available at Bioinformatics online.
Genome-wide genetic heterogeneity discovery with categorical covariates
Authors: Llinares-López Felipe , Papaxanthos Laetitia , Bodenham Dean , Roqueiro Damian ,   COPDGene Investigators, Borgwardt Karsten
Published: February 2017

Motivation

Genetic heterogeneity is the phenomenon that distinct genetic variants may give rise to the same phenotype. The recently introduced algorithm Fast Automatic Interval Search (FAIS) enables the genome-wide search of candidate regions for genetic heterogeneity in the form of any contiguous sequence of variants, and achieves high computational efficiency and statistical power. Although FAIS can test all possible genomic regions for association with a phenotype, a key limitation is its inability to correct for confounders such as gender or population structure, which may lead to numerous false-positive associations.

Results

We propose FastCMH, a method that overcomes this problem by properly accounting for categorical confounders, while still retaining statistical power and computational efficiency. Experiments comparing FastCMH with FAIS and multiple kinds of burden tests on simulated data, as well as on human and Arabidopsis samples, demonstrate that FastCMH can drastically reduce genomic inflation and discover associations that are missed by standard burden tests.

Availability and Implementation

An R package fastcmh is available on CRAN and the source code can be found at: https://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/fastcmh.html

Supplementary information

Supplementary data are available at Bioinformatics online.
Threshold-seq: a tool for determining the threshold in short RNA-seq datasets
Authors: Magee Rogan , Loher Phillipe , Londin Eric , Rigoutsos Isidore
Published: February 2017

We present ‘Threshold-seq,’ a new approach for determining thresholds in deep-sequencing datasets of short RNA transcripts. Threshold-seq addresses the critical question of how many reads need to support a short RNA molecule in a given dataset before it can be considered different from ‘background.’ The proposed scheme is easy to implement and incorporate into existing pipelines.

Availability and Implementation

Source code of Threshold-seq is freely available as an R package at: http://cm.jefferson.edu/threshold-seq/

Supplementary information

Supplementary data are available at Bioinformatics online.
PMAnalyzer: a new web interface for bacterial growth curve analysis
Authors: Cuevas Daniel A , Edwards Robert A
Published: February 2017

Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high-throughput, spectrophotometers capable of processing tens of 96-well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user-friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample-replicate growth curves and several statistical analyses.

Availability and Implementation

PMAnalyzer v2.0 can be found at https://edwards.sdsu.edu/pmanalyzer/. Source code for the pipeline can be found on GitHub at https://github.com/dacuevas/PMAnalyzer. Source code for the online implementation can be found on GitHub at https://github.com/dacuevas/PMAnalyzerWeb.

Supplementary information

Supplementary data are available at Bioinformatics online.
MotifMap-RNA: a genome-wide map of RBP binding sites
Authors: Liu Yu , Sun Sha , Bredy Timothy , Wood Marcelo , Spitale Robert C , Baldi Pierre
Published: February 2017

Motivation

RNA plays a critical role in gene expression and its regulation. RNA binding proteins (RBPs), in turn, are important regulators of RNA. Thanks to the availability of large scale data for RBP binding motifs and in vivo binding sites results in the form of eCLIP experiments, it is now possible to computationally predict RBP binding sites across the whole genome.

Results

We describe MotifMap-RNA, an extension of MotifMap which predicts binding sites for RBP motifs across human and mouse genomes and allows large scale querying of predicted binding sites.

Availability and Implementation

The data and corresponding web server are available from: http://motifmap-rna.ics.uci.edu/ as part of the MotifMap web portal.

Supplementary information

Supplementary data are available at Bioinformatics online.