bluuebunny/crossref_metadata_2025 huggingface dataset:
Self‐organising multiuser matching in cellular networks: a score‐based mutually beneficial approach
Authors: Liu Dianxiong , Xu Yitao , Shen Liang , Xu Yuhua
Published: August 2016

In this study, the authors study the self‐organising user assignment problem for the multi‐user cooperation network. In the cellular network with user cooperation, idle users near the base station are seen as potential relay nodes, which can assist cell edge users to transmit data. Practically, the selfish nature of users is considered in the authors’ model. They design a score‐based system, where the strategies of relay assignment are affected by the historical behaviours of users. That means not only the transmission performance, but also the accumulative contributions of users are considered. The proposed score‐based system sufficiently encourages idle users to assist active users. Furthermore, the multi‐user assignment problem is formulated as a one‐to‐one matching game, in which idle users and active users rank one another individually based on their own preference. To address the issue, they propose a self‐organising mutually beneficial matching algorithm, which is proven to converge to a stable matching. Simulation results show that the proposed distributed algorithm yields well matching performance between source users and relay users, which is close to the optimal centralised results.
Zehn Jahre Entscheiderfabrik: Party in der Düsseldorfer Almhütte
Authors: Mau Jens
Published: August 2016

Die Macher der Entscheiderfabrik haben mit Weggefährten und Mitgliedern ein ereignisreiches Jahrzehnt gefeiert – mitten auf dem Düsseldorfer Messegelände in einer Almhütte mit Schießstand und anderen Attraktion.
Versorgung von Flüchtlingen: Die Schulung der Mitarbeiter ist extrem wichtig
Authors: Wenzel Kirsten
Published: August 2016

Die medizinische Versorgung von Asylbewerbern ist ein seit Monaten viel diskutiertes Thema. Stefanie Merse und Thorsten Kaatze, die Flüchtlingsbeauftragten der Uniklinik Essen, erklären, wie sie die Beschäftigten auf die neue Situation vorbereiten.
MDK-Kontrollen: Anti-Ärger-Software für Kliniken
Authors: Gaede Kirsten
Published: August 2016

Sie rauben Zeit, Nerven und oft auch erhoffte Erlöse: MDK-Anfragen. Die Software-Anbieter 3M, ID und MetaIT versprechen jetzt mit neuen Kodierhilfen weniger Stress und mehr Erlössicherheit.
Branche in Zahlen
Authors: Mewis Dirk
Published: August 2016

Dieser Artikel ist nur als PDF-Dokument verfügbar.
Zeitgemässe Beleuchtungskonzepte: Keine Lichtexperimente im Krankenhaus!
Authors: Thalmayr Maria
Published: August 2016

Innovative, das Tageslicht imitierende und dabei energiesparende Lichtlösungen sind durchaus vielversprechend, aber offenbar nicht immer schon reif für einen Einsatz im Krankenhaus. Technische Probleme sorgen derzeit mancherorts für Ernüchterung und zu der Erkenntnis: Intensivstationen und Patientenzimmer taugen nicht als Versuchslabor!
DGIV: Verbesserung der sektorenübergreifenden Versorgung und Bedarfsplanung
Authors: Spitzer Stefan
Published: August 2016

Zu diesem Thema wurde eine Kleine Anfrage aus der Bundestagsfraktion Die Linke an die Bundesregierung gestellt. Die Antwort stellt eine interessante Standortbestimmung dar.
Individualisierte Medizin: Ohne Big Data geht es nicht
Authors: Ekkernkamp Axel
Published: August 2016

Mein „Lieblingsthema“ Gesundheit 4.0 hat ordentlich Fahrt aufgenomme. Kongresse, große Beratungsunternehmen, Banken, Versicherungen und Landesregierungen haben Big Data im Gesundheitswesen auf die Agenda genommen. Eine besondere Rolle kommt dabei wie immer der Ärzteschaft zu: Eine aktuelle Umfrage der Deutschen Apotheker- und Ärztebank ergab, dass Praxen und Kliniken die Digitalisierung zwar begrüßen, aber auch fürchten. Zu hoch seien die Investitionen, zu groß die Risiken bezüglich Datenschutz und fehlender Renditen. Argumente, wie wir sie ähnlich auf dem Weg zur elektronischen Gesundheitskarte vernommen hatten. Zwei Fragen rücken dabei in den Mittelpunkt: Können mit der Digitalisierung völlig neue Krankheitsbilder diagnostiziert und behandelt werden, zumindest deutlich besser als früher? Und sollen die neuen Möglichkeiten arztunterstützend oder arztersetzend sein?
Preliminary design of a tangentially viewing imaging bolometer for NSTX-U
Authors: Peterson B. J. , Sano R. , Reinke M. L. , Canik J. M. , Delgado-Aparicio L. F. , Lore J. D. , Mukai K. , Gray T. K. , van Eden G. G. , Jaworski M. A.
Published: August 2016

The infrared imaging video bolometer (IRVB) measures plasma radiated power images using a thin metal foil. Two different designs with a tangential view of NSTX-U are made assuming a 640 × 480 (1280 × 1024) pixel, 30 (105) fps, 50 (20) mK, IR camera imaging the 9 cm × 9 cm × 2 μm Pt foil. The foil is divided into 40 × 40 (64 × 64) IRVB channels. This gives a spatial resolution of 3.4 (2.2) cm on the machine mid-plane. The noise equivalent power density of the IRVB is given as 113 (46) μW/cm2 for a time resolution of 33 (20) ms. Synthetic images derived from Scrape Off Layer Plasma Simulation data using the IRVB geometry show peak signal levels ranging from ∼0.8 to ∼80 (∼0.36 to ∼26) mW/cm2.
A bifurcation giving birth to order in an impulsively driven complex system
Authors: Seshadri Akshay , Sujith R. I.
Published: August 2016

Nonlinear oscillations lie at the heart of numerous complex systems. Impulsive forcing arises naturally in many scenarios, and we endeavour to study nonlinear oscillators subject to such forcing. We model these kicked oscillatory systems as a piecewise smooth dynamical system, whereby their dynamics can be investigated. We investigate the problem of pattern formation in a turbulent combustion system and apply this formalism with the aim of explaining the observed dynamics. We identify that the transition of this system from low amplitude chaotic oscillations to large amplitude periodic oscillations is the result of a discontinuity induced bifurcation. Further, we provide an explanation for the occurrence of intermittent oscillations in the system.
Correlation consistent basis sets for lanthanides: The atoms La–Lu
Authors: Lu Qing , Peterson Kirk A.
Published: August 2016

Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples, CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd2, GdF, and GdF3. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd2, 151.7 (−36.6) for GdF, and 447.1 (−295.2) for GdF3.
Design of the 2D electron cyclotron emission imaging instrument for the J-TEXT tokamak
Authors: Pan X. M. , Yang Z. J. , Ma X. D. , Zhu Y. L. , Luhmann N. C. , Domier C. W. , Ruan B. W. , Zhuang G.
Published: August 2016

A new 2D Electron Cyclotron Emission Imaging (ECEI) diagnostic is being developed for the J-TEXT tokamak. It will provide the 2D electron temperature information with high spatial, temporal, and temperature resolution. The new ECEI instrument is being designed to support fundamental physics investigations on J-TEXT including MHD, disruption prediction, and energy transport. The diagnostic contains two dual dipole antenna arrays corresponding to F band (90-140 GHz) and W band (75-110 GHz), respectively, and comprises a total of 256 channels. The system can observe the same magnetic surface at both the high field side and low field side simultaneously. An advanced optical system has been designed which permits the two arrays to focus on a wide continuous region or two radially separate regions with high imaging spatial resolution. It also incorporates excellent field curvature correction with field curvature adjustment lenses. An overview of the diagnostic and the technical progress including the new remote control technique are presented.
Characterization of an atomic hydrogen source for charge exchange experiments
Authors: Leutenegger M. A. , Beiersdorfer P. , Betancourt-Martinez G. L. , Brown G. V. , Hell N. , Kelley R. L. , Kilbourne C. A. , Magee E. W. , Porter F. S.
Published: August 2016

We characterized the dissociation fraction of a thermal dissociation atomic hydrogen source by injecting the mixed atomic and molecular output of the source into an electron beam ion trap containing highly charged ions and recording the x-ray spectrum generated by charge exchange using a high-resolution x-ray calorimeter spectrometer. We exploit the fact that the charge exchange state-selective capture cross sections are very different for atomic and molecular hydrogen incident on the same ions, enabling a clear spectroscopic diagnostic of the neutral species.
The response of a fast scintillator screen (YAP:Ce) to low energy ions (0-40 keV) and its use to detect fast-ion-loss in stellarator TJ-II
Authors: Martínez M. , Zurro B. , Baciero A. , Jiménez-Rey D. , Tribaldos V. , Malo M. , Crespo M. T. , Muñoz D.
Published: August 2016

A systematic study of scintillation materials was undertaken to improve the time resolution of the fast ion diagnostic currently installed at TJ-II stellarator. It was found that YAP:Ce (formula YAlO3:Ce, Yttrium Aluminum Perovskite doped with Cerium) ionoluminescence offers better sensitivity and time response compared to the standard detector material, SrGa2S4:Eu (TG-Green), currently used in TJ-II. A comparison between both materials was carried out by irradiating them with H+ ions of up to 40 keV using a dedicated laboratory setup. It is found that for the low energy ions of interest at TJ-II, YAP:Ce offers 20 times higher sensitivity than TG-Green and much faster decay time, 27 ns versus 540 ns. It is expected that the use of YAP:Ce in combination with a faster data acquisition and an ion counting software as part of the TJ-II ion luminescent probe will provide 20 times faster data on ion loss.
Stabilizing the hexagonal close packed structure of hard spheres with polymers: Phase diagram, structure, and dynamics
Authors: Edison John R. , Dasgupta Tonnishtha , Dijkstra Marjolein
Published: August 2016

We study the phase behaviour of a binary mixture of colloidal hard spheres and freely jointed chains of beads using Monte Carlo simulations. Recently Panagiotopoulos and co-workers predicted [Nat. Commun. 5, 4472 (2014)] that the hexagonal close packed (HCP) structure of hard spheres can be stabilized in such a mixture due to the interplay between polymer and the void structure in the crystal phase. Their predictions were based on estimates of the free-energy penalty for adding a single hard polymer chain in the HCP and the competing face centered cubic (FCC) phase. Here we calculate the phase diagram using free-energy calculations of the full binary mixture and find a broad fluid-solid coexistence region and a metastable gas-liquid coexistence region. For the colloid-monomer size ratio considered in this work, we find that the HCP phase is only stable in a small window at relatively high polymer reservoir packing fractions, where the coexisting HCP phase is nearly close packed. Additionally we investigate the structure and dynamic behaviour of these mixtures.
Characterization of atmospheric pressure H2O/O2 gliding arc plasma for the production of OH and O radicals
Authors: Roy N. C. , Hafez M. G. , Talukder M. R.
Published: August 2016

Atmospheric pressure H2O/O2 gliding arc plasma is generated by a 88 Hz, 6 kV AC power supply. The properties of the produced plasma are investigated by optical emission spectroscopy. The relative intensity, rotational, vibrational, excitation temperatures and electron density are studied as a function of applied voltage, electrode spacing, and oxygen flow rate. The rotational and vibrational temperatures are determined simulating the OH(A2Σ+(v″=0)→X2Π(v′=0)) bands with the aid of LIFBASE simulation software. The excitation temperature is obtained from the CuI transition taking non-thermal equilibrium condition into account employing intensity ratio method. The electron density is approximated from the  Hα Stark broadening using the Voigt profile fitting method. It is observed that the rotational and vibrational temperatures decrease with increasing electrode spacing and O2 flow rate, but increase with the applied voltage. The excitation temperature is found to increase with increasing applied voltage and O2 flow rate, but decrease with electrode spacing. The electron density increases with increasing applied voltage while it seems to be in a downward trend with increasing electrode spacing and O2 flow rate.
A multi-species 13-moment model for moderately collisional plasmas
Authors: Miller S. T. , Shumlak U.
Published: August 2016

Fluid-based models of collisional transport in multi-species plasmas have typically been applied to parameter regimes where a local thermal equilibrium is assumed. While this parameter regime is valid for low temperature and/or high density applications, it begins to fail as plasmas enter the collisionless regime and kinetic effects dominate the physics. A plasma model is presented that lays the foundation for extending the validity of the collisional fluid regime using an anisotropic 13-moment fluid model derived from the Pearson type-IV probability distribution. The model explicitly evolves the pressure tensor and heat flux vector along with the density and flow velocity to capture dynamics usually restricted to kinetic models. Each particle species is modeled individually and collectively coupled through electromagnetic and collisional interactions.
Faraday-effect polarimeter diagnostic for internal magnetic field fluctuation measurements in DIII-D
Authors: Chen J. , Ding W. X. , Brower D. L. , Finkenthal D. , Muscatello C. , Taussig D. , Boivin R.
Published: August 2016

Motivated by the need to measure fast equilibrium temporal dynamics, non-axisymmetric structures, and core magnetic fluctuations (coherent and broadband), a three-chord Faraday-effect polarimeter-interferometer system with fast time response and high phase resolution has recently been installed on the DIII-D tokamak. A novel detection scheme utilizing two probe beams and two detectors for each chord results in reduced phase noise and increased time response [δb ∼ 1G with up to 3 MHz bandwidth]. First measurement results were obtained during the recent DIII-D experimental campaign. Simultaneous Faraday and density measurements have been successfully demonstrated and high-frequency, up to 100 kHz, Faraday-effect perturbations have been observed. Preliminary comparisons with EFIT are used to validate diagnostic performance. Principle of the diagnostic and first experimental results is presented.
Public authority control strategy for opinion evolution in social networks
Authors: Chen Xi , Xiong Xi , Zhang Minghong , Li Wei
Published: August 2016

This paper addresses the need to deal with and control public opinion and rumors. Existing strategies to control public opinion include degree, random, and adaptive bridge control strategies. In this paper, we use the HK model to present a public opinion control strategy based on public authority (PA). This means utilizing the influence of expert or high authority individuals whose opinions we control to obtain the optimum effect in the shortest time possible and thus reach a consensus of public opinion. Public authority (PA) is only influenced by individuals' attributes (age, economic status, and education level) and not their degree distribution; hence, in this paper, we assume that PA complies with two types of public authority distribution (normal and power-law). According to the proposed control strategy, our experiment is based on random, degree, and public authority control strategies in three different social networks (small-world, scale-free, and random) and we compare and analyze the strategies in terms of convergence time (T), final number of controlled agents (C), and comprehensive efficiency (E). We find that different network topologies and the distribution of the PA in the network can influence the final controlling effect. While the effect of PA strategy differs in different network topology structures, all structures achieve comprehensive efficiency with any kind of public authority distribution in any network. Our findings are consistent with several current sociological phenomena and show that in the process of public opinion/rumor control, considerable attention should be paid to high authority individuals.
Diamagnetic “bubble” equilibria in linear traps
Authors: Beklemishev A. D.
Published: August 2016

The plasma equilibrium in a linear trap at β ≈ 1 (or above the mirror-instability threshold) under the topology-conservation constraint evolves into a kind of diamagnetic “bubble.” This can take two forms: either the plasma body greatly expands in radius while containing the same magnetic flux, or, if the plasma radius is limited, the plasma distribution across flux-tubes changes, so that the same cross-section contains a greatly reduced flux. If the magnetic field of the trap is quasi-uniform around its minimum, the bubble can be made roughly cylindrical, with radius much larger than the radius of the corresponding vacuum flux-tube, and with non-paraxial ends. Then the effective mirror ratio of the diamagnetic trap becomes very large, but the cross-field transport increases. The confinement time can be found from solution of the system of equilibrium and transport equations and is shown to be τE≈τ∥τ⊥. If the cross-field confinement is not too degraded by turbulence, this estimate in principle allows construction of relatively compact fusion reactors with lengths in the range of a few tens of meters. In many ways, the described diamagnetic confinement and the corresponding reactor parameters are similar to those claimed by the field-reversed configurations.
Photoconductive detection of hydrogen in ZnO and rutile TiO2
Authors: Lavrov E. V. , Mchedlidze T. , Herklotz F.
Published: August 2016

Hydrogen donors in ZnO and rutile TiO2 are probed by means of photoconductivity and IR absorption. It is shown that the O–H bonds giving rise to the local vibrational modes (LVMs) of interstitial hydrogen at 3611 and 3290 cm−1 in the case of ZnO and TiO2, respectively, also occur in the photoconductivity spectra as Fano resonances. The effects of isotope substitution, concentration, sample thickness, influence of other donors present in both oxides are considered. Based on the shape and frequency of these resonances, it is concluded that the apparent ionization energy of interstitial hydrogen in rutile TiO2 is less than 300 meV. By a direct comparison, we also demonstrate that photoconductive detection of LVMs of defects in thin semiconductor films is superior to the standard IR absorption.
Comment on “Replica-exchange-with-tunneling for fast exploration of protein landscapes” [J. Chem. Phys. 143, 224102 (2015)]
Authors: Sakuraba Shun
Published: August 2016

In “Replica-exchange-with-tunneling for fast exploration of protein landscapes” [F. Yaşar et al., J. Chem. Phys. 143, 224102 (2015)], a novel sampling algorithm called “Replica Exchange with Tunneling” was proposed. However, due to its violation of the detailed balance, the algorithm fails to sample from the correct canonical ensemble.
A transport equation for reaction rate in turbulent flows
Authors: Sabelnikov V. A. , Lipatnikov A. N. , Chakraborty N. , Nishiki S. , Hasegawa T.
Published: August 2016

New transport equations for chemical reaction rate and its mean value in turbulent flows have been derived and analyzed. Local perturbations of the reaction zone by turbulent eddies are shown to play a pivotal role even for weakly turbulent flows. The mean-reaction-rate transport equation is shown to involve two unclosed dominant terms and a joint closure relation for the sum of these two terms is developed. Obtained analytical results and, in particular, the closure relation are supported by processing two widely recognized sets of data obtained from earlier direct numerical simulations of statistically planar 1D premixed flames associated with both weak large-scale and intense small-scale turbulence.
Intratumoral oxygen gradients mediate sarcoma cell invasion
Authors: Lewis Daniel M. , Park Kyung Min , Tang Vitor , Xu Yu , Pak Koreana , Eisinger-Mathason T. S. Karin , Simon M. Celeste , Gerecht Sharon
Published: August 2016

Significance

Previous works demonstrated the role of hypoxia in tumor development and metastasis. However, the understanding how oxygen (O
2
) gradients regulate early stages of tumor metastasis is lacking. Leveraging our O
2
-controlling hydrogel, we generated a 3D in vitro model that enables us to analyze cancer cell responses to O
2
gradients and small-molecule inhibitors. Using this approach, we present a previously unidentified concept in which O
2
acts as a 3D physicotactic agent during sarcoma tumor invasion, findings that are important for the understanding of the metastatic process. Through this concept, we also establish the 3D in vitro model as a platform for testing therapeutic targets and interventions for the treatment of sarcoma and potentially other cancers.
From mosque to mosque: past and present images of Islamic space in Greece
Authors: Kostopoulou Elektra
Published: August 2016

This essay is an attempt to chart recent developments in the field of Modern Greek Studies, focusing on shifting perceptions regarding Islam and Muslims. To do so, the essay positions the relevant literature in its historical context, touching upon both accomplishments and limitations. Its main proposition is that the Greek case is distinct yet connected to contemporary global contingencies and broader long-term regional dynamics. Athens remains the only European capital without a mosque. Moreover, despite recent academic endeavors, there exists today no coherent Greek field of Islamic Studies. That these absences have been brought recently under political and academic scrutiny constitutes, however, a noteworthy change. Most important, the traditional exclusion of Islam from the field of Modern Greek Studies does not suggest lack of relevance between the two but, quite to the contrary, reveals a set of loaded and complex socieconomic, geopolitical, and historical links that deserve to be studied in their own right.
Review of principles and methods of severe plastic deformation for producing ultrafine-grained tubes
Authors: Faraji G. , Kim H. S.
Published: August 2016

Severe plastic deformation (SPD) is known to be the best method for producing bulk ultrafine-grained and nanostructured materials with excellent properties. Different SPD methods were developed that are suitable for sheet and bulk solid materials. During the past decade, efforts have been made to create effective SPD processes suitable for producing cylindrical tubes. In this paper, we review SPD processes intended to produce ultrafine-grained and nanostructured tubes, and their effects on material properties. The paper will focus on introduction of the tube SPD processes, and then comparison of them based on their advantages and disadvantages from the viewpoints of processing and properties.
Rapid Detection of Cyprinid Herpesvirus 3 in Latently Infected Koi by Recombinase Polymerase Amplification
Authors: Prescott Meagan A. , Reed Aimee N. , Jin Ling , Pastey Manoj K.
Published: August 2016

Since the emergence of cyprinid herpesvirus 3 (CyHV-3), outbreaks have been devastating to Common Carp Cyprinus carpio and koi (a variant of Common Carp), leading to high economic losses. Current diagnostics for detecting CyHV-3 are limited in sensitivity and are further complicated by latency. Here we describe the detection of CyHV-3 by recombinase polymerase amplification (RPA). The RPA assay can detect as low as 10 copies of the CyHV-3 genome by an isothermal reaction and yields results in approximately 20 min. Using the RPA assay, the CyHV-3 genome can be detected in the total DNA of white blood cells isolated from koi latently infected with CyHV-3, while less than 10% of the latently infected koi can be detected by a real-time PCR assay in the total DNA of white blood cells. In addition, RPA products can be detected in a lateral flow device that is cheap and fast and can be used outside of the diagnostic lab. The RPA assay and lateral flow device provide for the rapid, sensitive, and specific amplification of CyHV-3 that with future modifications for field use and validation could lead to enhanced surveillance and early diagnosis of CyHV-3 in the laboratory and field.

Received September 14, 2015; accepted April 9, 2016 Published online August 2, 2016
Uniform bounds in F-finite rings and lower semi-continuity of the F-signature
Authors: Polstra Thomas
Published: August 2016

This paper establishes uniform bounds in characteristic

p
p

rings which are either F-finite or essentially of finite type over an excellent local ring. These uniform bounds are then used to show that the Hilbert-Kunz length functions and the normalized Frobenius splitting numbers defined on the spectrum of a ring converge uniformly to their limits, namely the Hilbert-Kunz multiplicity function and the F-signature function. From this we establish that the F-signature function is lower semi-continuous. Lower semi-continuity of the F-signature of a pair is also established. We also give a new proof of the upper semi-continuity of Hilbert-Kunz multiplicity, which was originally proven by Ilya Smirnov.
Preperiodic portraits for unicritical polynomials over a rational function field
Authors: Doyle John
Published: August 2016

Let

K
K

be an algebraically closed field of characteristic zero, and let

K

:=
K
(
t
)

\mathcal {K} := K(t)

be the rational function field over

K
K

. For each

d
≥
2

d \ge 2

, we consider the unicritical polynomial

f
d

(
z
)
:=

z
d

+
t
∈

K

[
z
]

f_d(z) := z^d + t \in \mathcal {K}[z]

, and we ask the following question: If we fix

α
∈

K

\alpha \in \mathcal {K}

and integers

M
≥
0

M \ge 0

,

N
≥
1

N \ge 1

, and

d
≥
2

d \ge 2

, does there exist a place

p

∈

S
p
e
c

K
[
t
]

\mathfrak {p} \in \mathrm {Spec} K[t]

such that, modulo

p

\mathfrak {p}

, the point

α
\alpha

enters into an

N
N

-cycle after precisely

M
M

steps under iteration by

f
d

f_d

? We answer this question completely, concluding that the answer is generally affirmative and explicitly giving all counterexamples. This extends previous work by the author in the case that

α
\alpha

is a constant point.
Extended de Finetti theorems for boolean independence and monotone independence
Authors: Liu Weihua
Published: August 2016

We construct several new spaces of quantum sequences and their quantum families of maps in the sense of Sołtan. The noncommutative distributional symmetries associated with these quantum maps are noncommutative versions of spreadability and partial exchangeability. Then, we study simple relations between these symmetries. We will focus on studying two kinds of noncommutative distributional symmetries: monotone spreadability and boolean spreadability. We provide an example of a spreadable sequence of random variables for which the usual unilateral shift is an unbounded map. As a result, it is natural to study bilateral sequences of random objects, which are indexed by integers, rather than unilateral sequences. At the end of the paper, we will show Ryll-Nardzewski type theorems for monotone independence and boolean independence: Roughly speaking, an infinite bilateral sequence of random variables is monotonically (boolean) spreadable if and only if the variables are identically distributed and monotone (boolean) with respect to the conditional expectation onto its tail algebra. For an infinite sequence of noncommutative random variables, boolean spreadability is equivalent to boolean exchangeability.
ReactPRED: a tool to predict and analyze biochemical reactions
Authors: Sivakumar Tadi Venkata , Giri Varun , Park Jin Hwan , Kim Tae Yong , Bhaduri Anirban
Published: August 2016

Motivation: Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same.

Results: ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application.

Availability and implementation: ReactPRED is available at: https://sourceforge.net/projects/reactpred/.

Contact:  anirban.b@samsung.com or ty76.kim@samsung.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
HiPub: translating PubMed and PMC texts to networks for knowledge discovery
Authors: Lee Kyubum , Shin Wonho , Kim Byounggun , Lee Sunwon , Choi Yonghwa , Kim Sunkyu , Jeon Minji , Tan Aik Choon , Kang Jaewoo
Published: August 2016

Summary: We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery. Using a combination of two different named-entity recognition resources, HiPub can recognize genes, proteins, diseases, drugs, mutations and cell lines in texts, and achieve high precision and recall. HiPub extracts biomedical entity-relationships from texts to construct context-specific networks, and integrates existing network data from external databases for knowledge discovery. It allows users to add additional entities from related articles, as well as user-defined entities for discovering new and unexpected entity-relationships. HiPub provides functional enrichment analysis on the biomedical entity network, and link-outs to external resources to assist users in learning new entities and relations.

Availability and Implementation: HiPub and detailed user guide are available at http://hipub.korea.ac.kr.

Contact:  kangj@korea.ac.kr, aikchoon.tan@ucdenver.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Did high-energy astrophysical sources contribute to Martian atmospheric loss?
Authors: Atri Dimitra
Published: August 2016

Mars is believed to have had a substantial atmosphere in the past. Atmospheric loss led to depressurization and cooling, and is thought to be the primary driving force responsible for the loss of liquid water from its surface. Recently, Mars Atmosphere and Volatile Evolution observations have provided new insight into the physics of atmospheric loss induced by Interplanetary Coronal Mass Ejections and solar wind interacting with the Martian atmosphere. In addition to solar radiation, it is likely that its atmosphere has been exposed to radiation bursts from high-energy astrophysical sources which become highly probable on time-scales of ∼Gy and beyond. These sources are capable of significantly enhancing the rates of photoionization and charged particle-induced ionization in the upper atmosphere. We use Monte Carlo simulations to model the interaction of charged particles and photons from astrophysical sources in the upper Martian atmosphere and discuss its implications on atmospheric loss. Our calculations suggest that the passage of the Solar system though dense interstellar clouds is the most significant contributor to atmospheric loss among the sources considered here.
Outpatient Antibiotic Prescribing Practices for Uncomplicated Urinary Tract Infection in Women in the United States, 2002–2011
Authors: Kobayashi Miwako , Shapiro Daniel J. , Hersh Adam L. , Sanchez Guillermo V. , Hicks Lauri A.
Published: August 2016

Background.  Urinary tract infection (UTI) is one of the most common diagnoses leading to an antibiotic prescription for women seeking ambulatory care. Understanding current national outpatient antibiotic prescribing practices will help ongoing stewardship efforts to optimize antibiotic use; however, information on recent national outpatient antibiotic prescribing trends for UTI is limited.

Methods.  We analyzed the National Ambulatory Medical Care and National Hospital Ambulatory Medical Care Survey datasets from 2002 to 2011. Outpatient visits of women aged ≥18 years with a diagnosis of uncomplicated UTI were included for analysis. We conducted weighted descriptive analyses, examined time trends in antibiotic prescribing, and used multivariable logistic regression to identify patient and provider factors associated with fluoroquinolone prescribing.

Results.  A total of 7111 visits were identified. Eighty percent of visits resulted in an antibiotic prescription; fluoroquinolones were the most frequently prescribed antibiotics throughout the study period (49% overall). Older patients (adjusted odds ratio [AOR] for adults aged ≥70 years = 2.5; 95% confidence interval [CI], 1.6–3.8) and patients treated by internists (AOR = 2.0; 95% CI, 1.1–3.3) were more likely than younger patients and those treated by family practitioners to receive fluoroquinolones. Outpatient visits in the West US Census region were less likely to be associated with fluoroquinolone prescribing (AOR = 0.6; 95% CI, .4–1.0) compared with visits in the Northeast.

Conclusions.  Fluoroquinolones were the most frequently selected antibiotic treatment for uncomplicated UTI in women during the study period. Outpatient antibiotic stewardship initiatives should include efforts to reduce overuse of fluoroquinolones for uncomplicated UTI.
Identification, Distribution, and Pathogenicity of Diatrypaceae and Botryosphaeriaceae Associated with Citrus Branch Canker in the Southern California Desert
Authors: Mayorquin Joey S. , Wang Danny H. , Twizeyimana Mathias , Eskalen Akif
Published: August 2016

Several members of the families Botryosphaeriaceae and Diatrypaceae are known as canker and dieback pathogens of a number of woody hosts. Because desert citrus production in California can occur in proximity to table grape production, it was suspected that fungi associated with grapevine cankers might also be associated with citrus branch canker and dieback decline. To determine the fungi associated with branch canker and dieback disease of citrus in the southern California desert regions, surveys were conducted from 2011 to 2013 in the major citrus-growing regions of Riverside, Imperial, and San Diego Counties. Cankered tissues were collected from branches showing symptoms typical of branch canker and dieback. Various fungal species were recovered from necrotic tissues and species were identified morphologically and by phylogenetic comparison of partial sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2), β-tubulin gene, and elongation factor 1-α genes with those of other species in GenBank. Four fungi, including Neoscytalidium hyalinum, Eutypella citricola, E. microtheca, and an unnamed Eutypella sp., were associated with branch canker. N. hyalinum was the most frequently recovered fungus from symptomatic tissues (31%) followed by E. citricola (10%), E. microtheca (4%), and the Eutypella sp. (2%). In pathogenicity tests, all fungi caused lesions when inoculated on ‘Lisbon’ lemon (citrus) branches. Lesions caused by the Eutypella sp. were significantly longer than those of the other Eutypella spp.; however, they did not differ significantly from those produced by N. hyalinum. The most-parsimonious unrooted trees based on the combined data of ITS and partial β-tubulin gene region sequences showed three distinct clades of Eutypella spp. (E. citricola, E. microtheca, and an unidentified Eutypella sp.). Similarly, ITS and partial translation elongation factor 1-α gene region sequences differentiated two species of Neoscytalidium, N. hyalinum and N. novaehollandiae. Identifying the diversity, distribution, and occurrence of these fungal pathogens is useful for the management of citrus branch canker and dieback disease in the desert citrus-growing regions of California.
Population Diversity and Sensitivity to Azoxystrobin of Alternaria brassicicola in New York State
Authors: Kreis Rachel A. , Dillard Helene R. , Smart Christine D.
Published: August 2016

Alternaria brassicicola is the causal agent of Alternaria leaf spot, a common disease of brassica crops in New York State. New York isolates of A. brassicicola were collected from a variety of brassica crops and locations to evaluate the population diversity and screen for fungicide sensitivity. Isolates were genotyped for 10 microsatellite loci and assayed for sensitivity to azoxystrobin, a quinone outside inhibitor fungicide. The New York State population of A. brassicicola was found to have high levels of genotypic diversity and the population was found to be in linkage disequilibrium. Based on in vitro assays, the effective concentrations of azoxystrobin reducing spore germination by 50% ranged from 0.22 to 14.12 μg/ml. In order to confirm the sensitivity of 47 isolates to azoxystrobin, the cytb gene was characterized and sequenced to determine whether any of the mutations known to confer resistance to azoxystrobin were present. The mutations F129L, G137R, and G143A were not detected in the isolates studied.
Effect of Leaf Mold Mulch, Biochar, and Earthworms on Mycorrhizal Colonization and Yield of Asparagus Affected by Fusarium Crown and Root Rot
Authors: Elmer W. H.
Published: August 2016

Asparagus can suffer from a crown and root rot caused by Fusarium oxysporum f. sp. asparagi and F. proliferatum. The disease is exacerbated when allelopathic toxins from old, rotting asparagus crowns are present in the soil. To minimize the damage from the replant problem, three strategies were examined: (i) biochar, (ii) application of earthworms (Lumbricus terrestris), and (iii) leaf mold to serve as a compost mulch and food source for earthworms. In a greenhouse, asparagus transplants were grown in soil amended with pathogen-infested asparagus residues or in nonamended soil, then both types of soil were augmented with biochar, earthworms, the combination of biochar and earthworms, or no treatment. Biochar increased arbuscular mycorrhizae (AM) colonization by 170% and reduced the incidence of root lesions by 57%; however, plant weight was not affected by any of the soil treatments and there were no significant interactions among the main effects. In the absence of infested asparagus residues, biochar reduced plant growth by 32%. Field plots that had severe crown and root rot, along with two other fields that had never been planted to asparagus, were planted with asparagus crowns and treated with leaf mold mulch, earthworms plus leaf mold mulch, biochar, or biochar plus earthworms plus leaf mold mulch. Untreated plots served as the control treatment. One year later, asparagus roots sampled from plots in the two new fields had a threefold increase in AM colonization when treated with biochar compared with control plots. Biochar did not increase yield over the duration of the 2012 to 2014 harvests when compared with that of the control plots. No soil treatment affected root colonization by AM in the field where Fusarium crown and root rot was severe. Compared with the untreated control plots, the leaf mold mulch treatment applied alone increased the marketable yields in each year of harvest. Combining leaf mold with earthworms provided no added benefit. Soil amendment with leaf mulch alone may hold promise for improving asparagus production in newly planted asparagus fields.
Donald Metcalf AC. 26 February 1929 — 15 December 2014
Authors: Nicola Nicos A.
Published: August 2016

Donald Metcalf was one of Australia's most distinguished medical researchers and is acknowledged internationally as the father of the modern field of haemopoietic growth factors. He defined the hierarchy of haemopoietic progenitor cells, purified and cloned the major molecular regulators of their growth and maturation, determined their mechanisms of action and participated in their development for clinical use in cancer patients. He received numerous awards and distinctions during his career, but was most pleased by the fact that his life's work improved human health.
Mutations in the catalytic domain of human β-cardiac myosin that cause early onset hypertrophic cardiomyopathy significantly increase the fundamental parameters that determine ensemble force and velocity
Authors: Adhikari Arjun S. , Kooiker Kristina B. , Liu Chao , Sarkar Saswata S. , Bernstein Daniel , Spudich James A. , Ruppel Kathleen M.
Published: August 2016

Hypertrophic cardiomyopathy (HCM) is a heritable cardiovascular disorder that affects 1 in 500 people. In infants it can be particularly severe and it is the leading cause of sudden cardiac death in pediatric populations. A high percentage of HCM is attributed to mutations in β-cardiac myosin, the motor protein that powers ventricular contraction. This study reports how two mutations that cause early-onset HCM, D239N and H251N, affect the mechanical output of human β-cardiac myosin at the molecular level. We observe extremely large increases (25% – 95%) in the actin gliding velocity, single molecule intrinsic force, and ATPase activity of the two mutant myosin motors compared to wild type myosin. In contrast to previous studies of HCM-causing mutations in human β-cardiac myosin, these mutations were striking in that they caused changes in biomechanical parameters that were both greater in magnitude and more uniformly consistent with a hyper-contractile phenotype. In addition, S1-S2 binding studies revealed a significant decrease in affinity of the H251N motor for S2, suggesting that this mutation may further increase hyper-contractility by releasing active motors from a sequestered state. This report shows, for the first time, a clear and significant gain in function for all tested molecular biomechanical parameters due to HCM mutations in human β-cardiac myosin.
Advances in the recovery of haplotypes from the metagenome
Authors: Nicholls Samuel M. , Aubrey Wayne , de Grave Kurt , Schietgat Leander , Creevey Christopher J. , Clare Amanda
Published: August 2016

High-throughput DNA sequencing has enabled us to look beyond consensus reference sequences to the variation observed in sequences within organisms; their haplotypes. Recovery, or assembly of haplotypes has proved computationally difficult and there exist many probabilistic heuristics that attempt to recover the original haplotypes for a single organism of known ploidy. However, existing approaches make simplifications or assumptions that are easily violated when investigating sequence variation within a metagenome.

We propose the metahaplome as the set of haplotypes for any particular genomic region of interest within a metagenomic data set and present Hansel and Gretel, a data structure and algorithm that together provide a proof of concept framework for the recovery of true haplotypes from a metagenomic data set. The algorithm performs incremental haplotype recovery, using smoothed Naive Bayes — a simple, efficient and effective method.

Hansel and Gretel pose several advantages over existing solutions: the framework is capable of recovering haplotypes from metagenomes, does not require a priori knowledge about the input data, makes no assumptions regarding the distribution of alleles at variant sites, is robust to error, and uses all available evidence from aligned reads, without altering or discarding observed variation. We evaluate our approach using synthetic metahaplomes constructed from sets of real genes and show that up to 99% of SNPs on a haplotype can be correctly recovered from short reads that originate from a metagenomic data set.
RECRUITMENT OF GROUPER BROODSTOCK ON THE BASIS OF SINGLE LOCUS DNA MARKERS
Authors: Rodrigues Kenneth F. , Tani Ahmad Z. , Baharum Syarul N.
Published: August 2016

Scientific breeding programs are founded on the screening and recruitment of genetically diverse broodstock, with the ultimate aim of developing heterogeneous breeding populations that host a collection of desirable traits. Single locus DNA markers can be applied to facilitate the process of selection as they are species specific, reliable, reproducible and easy to use. This study set forth to develop a library of single locus DNA markers for two commercially cultured species of groupers,Epinephelus fuscoguttatusandE. corallicola. DNA was isolated from one representative specimen of each species and utilized to construct shotgun genomic libraries. DNA sequences derived from the library were selected for the development of 42 and 41 single locus DNA markers forE. fuscoguttatusandE. corallicolarespectively. The markers were then tested against randomly selected specimens obtained from the wild. Genotyping results revealed that the species specific primers demonstrated the ability to distinguish between individuals from the same species into distinct operational taxonomic units (OTUs) on the basis of their differential DNA profiles, thus establishing a basis for selection based on genetic heterogeneity. The findings of this study present a strong case for the application of single locus DNA markers as molecular tools for the selection of broodstock on the basis of genotyping.
Spherical: an iterative workflow for assembling metagenomic datasets
Authors: Hitch Thomas , Creevey Christopher J
Published: August 2016

The consensus emerging from microbiome studies is that they are far more complex than previously thought, requiring deep sequencing. As deep sequenced datasets provide greater coverage than previous datasets, recovering a higher proportion of reads to the assembly is still a challenge. To tackle this issue, we set of to identify if multiple iterations of assembly would allow for otherwise lost contigs to be formed and studied and if so, how successful is such an avenue at improving the current methodology.

A simulated metagenomic dataset was initially used to identify if multiple iterations of assembly produce useable contigs or mis-assembled artefacts were produced. Once we had confirmed that the secondary iterations were producing both accurate contigs without a reduction in contig quality we applied this methodology in the form ofSphericalto 3 metagenomic studies.

The additional contigs produced by Spherical increased the number of reads aligning to an identified gene by 11–109% compared to the initial iterations assembly. As the size of the dataset increased, as did the amount of data multiple iterations were able to add.

Availability

Spherical is implemented in Python 2.7 and available for use under a MIT licence agreement at:https://github.com/thh32/Spherical