bluuebunny/crossref_metadata_2025 huggingface dataset:
CIGALE: a python Code Investigating GALaxy Emission
Authors: Boquien M. , Burgarella D. , Roehlly Y. , Buat V. , Ciesla L. , Corre D. , Inoue A. K. , Salas H.
Published: December 2018

Context. Measuring how the physical properties of galaxies change across cosmic times is essential to understand galaxy formation and evolution. With the advent of numerous ground-based and space-borne instruments launched over the past few decades we now have exquisite multi-wavelength observations of galaxies from the far-ultraviolet (FUV) to the radio domain. To tap into this mine of data and obtain new insight into the formation and evolution of galaxies, it is essential that we are able to extract information from their spectral energy distribution (SED).

Aims. We present a completely new implementation of Code Investigating GALaxy Emission (CIGALE). Written in python, its main aims are to easily and efficiently model the FUV to radio spectrum of galaxies and estimate their physical properties such as star formation rate, attenuation, dust luminosity, stellar mass, and many other physical quantities.

Methods. To compute the spectral models, CIGALE builds composite stellar populations from simple stellar populations combined with highly flexible star formation histories, calculates the emission from gas ionised by massive stars, and attenuates both the stars and the ionised gas with a highly flexible attenuation curve. Based on an energy balance principle, the absorbed energy is then re-emitted by the dust in the mid- and far-infrared domains while thermal and non-thermal components are also included, extending the spectrum far into the radio range. A large grid of models is then fitted to the data and the physical properties are estimated through the analysis of the likelihood distribution.

Results. CIGALE is a versatile and easy-to-use tool that makes full use of the architecture of multi-core computers, building grids of millions of models and analysing samples of thousands of galaxies, both at high speed. Beyond fitting the SEDs of galaxies and parameter estimations, it can also be used as a model-generation tool or serve as a library to build new applications.
Cyclotron lines in highly magnetized neutron stars
Authors: Staubert R. , Trümper J. , Kendziorra E. , Klochkov D. , Postnov K. , Kretschmar P. , Pottschmidt K. , Haberl F. , Rothschild R. E. , Santangelo A. , Wilms J. , Kreykenbohm I. , Fürst F.
Published: December 2018

Cyclotron lines, also called cyclotron resonant scattering features are spectral features, generally appearing in absorption, in the X-ray spectra of objects containing highly magnetized neutron stars, allowing the direct measurement of the magnetic field strength in these objects. Cyclotron features are thought to be due to resonant scattering of photons by electrons in the strong magnetic fields. The main content of this contribution focusses on electron cyclotron lines as found in accreting X-ray binary pulsars (XRBP) with magnetic fields on the order of several 1012Gauss. Also, possible proton cyclotron lines from single neutron stars with even stronger magnetic fields are briefly discussed. With regard to electron cyclotron lines, we present an updated list of XRBPs that show evidence of such absorption lines. The first such line was discovered in a 1976 balloon observation of the accreting binary pulsar Hercules X-1, it is considered to be the first direct measurement of the magnetic field of a neutron star. As of today (end 2018), we list 35 XRBPs showing evidence of one ore more electron cyclotron absorption line(s). A few have been measured only once and must be confirmed (several more objects are listed as candidates). In addition to the Tables of objects, we summarize the evidence of variability of the cyclotron line as a function of various parameters (especially pulse phase, luminosity and time), and add a discussion of the different observed phenomena and associated attempts of theoretical modeling. We also discuss our understanding of the underlying physics of accretion onto highly magnetized neutron stars. For proton cyclotron lines, we present tables with seven neutron stars and discuss their nature and the physics in these objects.
Normality and gap phenomena in optimal unbounded control
Authors: Motta Monica , Rampazzo Franco , Vinter Richard
Published: December 2018

Optimal unbounded control problems with affine control dependence may fail to have minimizers in the class of absolutely continuous state trajectories. For this reason, extended impulsive versions – which cannot be of measure-theoretic type – have been investigated, in which the domain is enlarged to include discontinuous state trajectories of bounded variation, and for which existence of minimizers is guaranteed. It is of interest to know whether the passage from the original optimal control problem to its extension introduces an infimum gap. This paper provides sufficient conditions for the absence of an infimum gap based on normality of extremals. In certain cases, the normality conditions reduce to simple verifiable criteria, which improve on earlier, directly-derived sufficient conditions for no infimum gap.
Die Implementierung der Telemedizin im urologischen Alltag
Authors: Struck Julian , Wenzel Mike , Heidenreich Axel , Merseburger Axel , Salem Johannes
Published: December 2018

Hintergrund Da eine Steigerung der Anzahl an zu versorgenden geriatrischen Patienten mit urologischen Krankheitsbildern in den kommenden Jahrzehnten zu erwarten ist und die Urologie zugleich mit anderen Fachbereichen um den medizinischen Nachwuchs konkurriert, werden alternative Modelle benötigt, um die medizinische Versorgung dieser Patienten sicherzustellen. Ein vielversprechender Ansatz stellt die Telemedizin dar. Hierbei werden sowohl räumliche als auch zeitliche Distanzen mittels Datenaustausch bzw. Telekommunikation überbrückt, um eine urologische Diagnostik und Therapie sicherzustellen.

Patienten/Material und Methoden Auswertung der relevanten, PubMed-gelisteten Artikel zu den Suchbegriffen „telemedicine“, „teleproctoring“, „telementoring“, „telerounding“ und „telecounseling“.

Ergebnisse Die vorliegenden Daten zeigen, dass telemedizinische Produkte durchweg eine hohe Patientenzufriedenheit bei einfacher Handhabung aufweisen. Telemedizin kann den Urologen durch eine höhere Therapieadhärenz und Monitoring der Patienten in ihrem gewohnten Umfeld entlasten und damit eine Optimierung der Therapie ermöglichen. Sie kann durch die verlässliche Übermittlung von Patientendaten und einer damit einhergehenden Erhöhung der Diagnosesicherheit die Patientenzufriedenheit und Bindung der Patienten an Klinik und Praxis erhöhen. Voraussetzung für ein Gelingen der Technik stellen eine adäquate Information von Patienten und teilnehmenden Ärzten sowie ein regelmäßiger Informationsaustausch über im Rahmen der Programme auftretende Probleme dar. Allerdings beschränken sich die bisherigen Anwendungen auf kleine Fall- und Beobachtungsstudien, eine Anwendung auf größere Patientenkohorten muss in Zukunft angestrebt werden, um die Anwendbarkeit telemedizinischer Produkte auf solide Daten stützten zu können.

Schlussfolgerung Die Telemedizin birgt großes Potenzial für die Versorgung urologischer Patienten. Ihr Einsatz in Kombination mit entsprechenden Serviceprogrammen stellt einen vielversprechenden Ansatz dar, um den durch demografischen Wandel und Ärztemangel ausgelösten Herausforderungen der urologischen Fachdisziplin zu begegnen und örtliche und zeitliche Begrenzungen zu überwinden.
Zukunft der Laparoskopie und Robotik in der Urologie
Authors: Rassweiler Jens , Goezen Ali , Klein Jan-Thorsten , Rassweiler-Seyfried Marie-Claire
Published: December 2018

Die Robotik hat die klassische Laparoskopie in den letzen Jahren etwas an den Rand gedrängt. Dennoch hat sich auch die Laparoskopie und Retroperitoneoskopie in den letzten Jahren technologisch weiterentwickelt mit 4K-Ultra-HD-Videotechnologie, 3D-HD-Videosystemen, miniaturisierten Instrumenten, modernen Schneid- und Koagulationsverfahren, Instrumenten mit 7 Freiheitsgraden und ergnomischen Plattformen Ethos Chair®. Aufgrund der auslaufendenden Patente von Intuitive Surgical wird ab 2019 eine Konkurrenzsituation mit neuen Herstellern von Operationsrobotern existieren. Diese müssen erst belegen, ob sie den hohen Qualitätsstandard der Da-Vinci-Serie (SI, X, XI) bieten können. Dies betrifft die Art der Konsole, Anordnung der Roboterarme, Technologie des 3D-Videosystems und Qualität und Freiheitsgrade der Endeffektoren. Robotersysteme für die Endourologie sind Avicenna Roboflex® für die flexible Ureteroskopie und AquaBeam®-System für die Roboter-assistierte Aquaablation der Prostata. Während Roboflex ähnlich dem Da-Vinci-System die Ergonomie des Eingriffes erleichtert, ersetzt die robotergestützte Aquaablation erstmals den Operateur.
Den Verschluss verhindern
Authors: Blocher David , Biberle Gerlinde , Poulakos Susanne
Published: December 2018

An der Klinischen Abteilung für Pädiatrische Kardiologie der Universitätsklinik
für Kinder- und Jugendheilkunde des AKH Wien werden Kinder und Jugendliche aller
Altersgruppen betreut. Die Versorgung umfasst sowohl die Übernahme von
andernorts geborenen Kindern mit pränatal unbekannten Herzfehlern als auch die
postoperative Betreuung. Das Ziel des folgenden Beitrags ist es, die
spezifischen pflegerischen Herausforderungen bzw. Interventionen bei
Neugeborenen mit ductusabhängigen Herzfehlern aufzuzeigen.
Zwei pflegerische Tätigkeitsfelder
Authors: Lechner Iris
Published: December 2018

Iris Lechner ist Gesundheits- und Kinderkrankenpflegerin und hat bis Ende Februar
2018 im stationären Kinderhospiz St. Nikolaus in Bad Grönenbach gearbeitet.
Momentan lebt sie in der Schweiz und arbeitet dort als diplomierte
Pflegefachfrau an der Universitätsklinik für Kinderheilkunde auf der
pädiatrischen Hämatologie/Onkologie des Inselspitals Bern. Zudem ist sie seit
vier Jahren als Kinderkrankenpflegerin im jährlich stattfindenden Süddeutschen
Familienseminar tätig. In ihrem Beitrag stellt Iris Lechner aus eigener
Erfahrung zwei pflegerische Tätigkeitsfelder in der Kinder- und
Jugendhospizarbeit vor und gibt so einen wertvollen Blick in die skizzierten
Arbeitsbereiche.
Genetic profiling in der Diagnostik des hereditären Prostatakarzinoms – wo stehen wir?
Authors: Boehm Katharina , Thomas Christian , Tsaur Igor
Published: December 2018

Prostatakrebs weist im Vergleich zu anderen Tumorentitäten ein heterogenes genetisches Profil auf. Dementsprechend sind auch Mutationen, die das Prostatakarzinomrisiko erhöhen, vielfältig. Manche genetische Varianten fallen bei der Risikoerhöhung nur milde ins Gewicht. Andere Genmutationen (BRCA1 /2; HOXB13) erhöhen das Risiko jedoch teils erheblich. Insgesamt ist die Wahrscheinlichkeit für einen nicht familiär vorbelasteten Mann, ein Träger von Mutationen zu sein, welche mit einem erhöhten PCa-Risiko assoziiert sind, niedrig. Ist aber die familiäre Belastung durch in jungem Alter erkrankte Verwandte oder eine bereits bekannte Mutation in der Familie vorhanden, so steigt auch diese Wahrscheinlichkeit an. In diesen Fällen sollte die genetische Beratung und Testung in Betracht gezogen werden. Insbesondere soll hier an BRCA1 /2-Mutationen und HOXB13-Mutationen gedacht werden. Für die breite Bevölkerungsmasse kann genetic profiling bislang jedoch nicht die PSA-Wert-Bestimmung, mpMRT der Prostata und/oder die Prostatabiopsie im Rahmen der Vorsorge oder des diagnostischen Algorithmus ersetzen. Lediglich können Männer bei Vorliegen der mit PCa assoziierten Mutationen einem engmaschigeren und früheren Screening unterzogen werden und ggf. früher eine definitive Therapie erhalten.
Effect of Sodium Glucose Co-Transporter-2 Inhibition on the Aldosterone/Renin Ratio in Type 2 Diabetes Mellitus
Authors: Griffin Tomás , Islam Md , Blake Liam , Bell Marcia , Griffin Matthew , O’Shea Paula
Published: December 2018

The aldosterone to renin ratio (ARR) is recommended for case detection of primary aldosteronism (PA). Several factors including medications can undermine its diagnostic accuracy. The objective was to explore the effect of Sodium Glucose Co-Transporter-2 Inhibition on the ARR in patients with type 2 diabetes mellitus (T2DM) who were prescribed a Sodium Glucose Co-Transporter-2 Inhibitor (SGLT-2i) as part of routine clinical care. The primary outcomes were intra-individual changes in aldosterone, renin and ARR. Participants were recruited at routine diabetes outpatient visits as part of a prospective longitudinal study. Eligible participants were prescribed standard doses of empagliflozin and sampled at baseline (pre-SGLT-2i) and at their next routine outpatient visit (post-SGLT-2i). After a mean of 198 (±87) days on SGLT-2i treatment (n=20), there was a significant reduction in HbA1c, BMI, eGFR and serum triglycerides and a significant increase in serum creatinine and sodium. Compared with baseline, there was a significant increase in median direct renin concentration (mIU/l) [40.3 (6.2–249.5) vs. 70.2 (7.0, 551.0) (p=0.005)] and no significant change in median plasma aldosterone concentration (pmol/l) [296 (101, 685) vs. 273 (101, 794) (p=0.541)] with a significant reduction in median ARR (pmol/mIU) [6.9 (0.6–70.7) vs. 5.3 (0.2–39.3) (p=0.007)]. The proportion of participants with a screen positive ARR decreased from 20% (pre-SGLT-2i) to 5% (post-SGLT-2i) (p=0.248). Although performed in a relatively small cohort of medically complex patients, the study indicates that SGLT-2i therapy has the potential to cause false-negative screening for PA in the setting of T2DM. Future confirmatory studies should include patients with confirmed PA.
Pharmacokinetics of Prenylflavonoids following Oral Ingestion of Standardized Epimedium Extract in Humans
Authors: Teo Yi , Cheong Wei , Cazenave-Gassiot Amaury , Ji Shanshan , Logan Susan , Lee Zhi , Li Jun , Seng Kok , Lee Lawrence , Yong Eu
Published: December 2018

Leaves of the Epimedium plant are traditionally consumed for bone health and other indications. The aim of this study was to establish the safety and pharmacokinetics of the metabolites of prenylflavonoids (icariin, icariside I, icariside II, icaritin, and desmethylicaritin) following single doses of a defined Epimedium prenylflavonoid extract in humans. A single oral dose of 370, 740, or 1110 mg of a standardized Epimedium prenylflavonoid extract was administered to 30 healthy male subjects in a randomized, placebo-controlled trial. Serum samples were collected over a 48-h period and analyzed by liquid chromatography-tandem mass spectrometry and non-compartmental pharmacokinetic modelling. Epimedium prenylflavonoid extracts were well tolerated and no adverse effects were observed. The principle metabolites detected in the serum were icariside II and desmethylicaritin. Icariside II had a T
max of between 4.1 – 4.3 h, reaching a maximum AUC0→∞ of 23.0 (17.5, 29.9) h×ng/mL (median [IQR: interquartile range]) with the highest dose of the Epimedium prenylflavonoid. On the other hand, desmethylicaritin had a delayed T
max of 24.1 – 24.4 h and reached a maximum AUC0→∞ of 126.1 (62.4, 202.9) h×ng/mL. The median maximum plasma concentration and AUC0→∞ of desmethyliciaritin showed an increase with higher doses of the Epimedium prenylflavonoid (p < 0.05). Icariin, icariside I, and icaritin levels were below detection limits. Levels of Epimedium prenylflavonoid metabolites observed in this study were consistent with levels demonstrated to have anti-osteoporotic effects in cellular and animal studies. Coupled with the favorable safety profile of the extract observed, further studies are required to explore the utility of Epimedium prenylflavonoid extracts to prevent osteoporosis in postmenopausal women.
Gold-Catalyzed Cyclization/Intermolecular Methylene Transfer ­Sequence of O-Propargylic Oximes Derived from Glyoxylates
Authors: Gima Shinya , Shiga Keigo , Terada Masahiro , Nakamura Itaru
Published: December 2018

We successfully extended our gold-catalyzed skeletal rearrangement reaction of O-propargylic oximes through C=N bond cleavage to include substrates having an ester group on the oxime moiety, affording the corresponding 2-isoxazolines having an alkoxycarbonylmethylene group at the 4-position in good to high yields. Our mechanistic studies indicated that the transfer of the alkoxycarbonylmethylene group proceeded in an intermolecular manner, confirming that the reaction proceeds through cyclization followed by intermolecular transfer of the alkoxycarbonylmethylene group.
Myofascial Pain
Authors: Comeau Douglas , Otis James , Weller Jason
Published: December 2018

Myofascial pain syndromes arise from acute and chronic musculoskeletal pain and often have a referred neuropathic component. It affects more than three quarters of the world's population and is one of the most important and overlooked causes of disability. The origins of pain are thought to reside anywhere between the motor end plate and the fibrous outer covering of the muscle, with involvement of microvasculature and neurotransmitters at the cellular level. Diagnosis is made by clinical examination for the presence of myofascial trigger points, though some ancillary tests may provide supportive evidence. The mainstay of treatment is regular physical therapy with the goal of restoration of normal muscle laxity and range of motion. Adjunct therapies including pharmacologic and nonpharmacologic interventions provide varying degrees of benefit in refractory cases, and onabotulinum toxin A injection has the most evidence of efficacy for these patients. Here, we discuss the epidemiology, pathophysiology, and diagnostic and therapeutic options for the evaluation and treatment of myofascial pain syndrome.
Radicular Pain Syndromes: Cervical, Lumbar, and Spinal Stenosis
Authors: Patel Ekta , Perloff Michael
Published: December 2018

Back pain is a top primary and urgent care complaint; radicular pain can be caused by herniation of the nucleus pulposus (intervertebral disc), spinal stenosis, or degenerative changes to the vertebrae. The focus of this clinical review will be the clinical approach and treatment of lumbar radicular pain, cervical radicular pain, and spinal stenosis. Usually localized through neurological history, exam, and imaging, specific signs and symptoms for lumbar radicular, spinal stenosis, and cervical radicular pain can help determine etiology. Once radicular back pain has been diagnosed, a multitude of treatment options are available from rest and physical therapy to medications, epidurals, and surgery. The most common and accepted are reviewed. With accurate diagnosis, safe and effective pain management can be employed to shorten radicular episodes and manage recurrent or chronic radicular syndromes. Using a step-wise approach from diagnosis to conservative therapy to potential surgery, radicular pain syndromes can improve or resolve, and patients may achieve a better functional status and quality of life.
Mechanical properties of bi- and poly-crystalline ice
Authors: Cao Pinqiang , Wu Jianyang , Zhang Zhisen , Fang Bin , Peng Li , Li Tianshu , Vlugt Thijs J. H. , Ning Fulong
Published: December 2018

A sound knowledge of fundamental mechanical properties of water ice is of crucial importance to address a wide range of applications in earth science, engineering, as well as ice sculpture and winter sports, such as ice skating, ice fishing, ice climbing, bobsleighs, and so on. Here, we report large-scale molecular dynamics (MD) simulations of mechanical properties of bi- and poly-crystalline hexagonal ice (Ih) under mechanical loads. Results show that bicrystals, upon tension, exhibit either brittle or ductile fracture, depending on the microstructure of grain boundaries (GBs), whereas they show ductile fracture by amorphization and crystallographic slips emitted from GBs under compression. Under shearing, the strength of bicrystals exhibits a characteristic plateau or sawtooth behavior drawn out the initial elastic strains. Nanograined polycrystals are destabilized by strain-induced amorphization and collective GB sliding. Their mechanical responses depend on the grain size. Both tensile and compressive strengths decrease as grain size decreases, showing inverse Hall-Petch weakening behavior. Large fraction of amorphous water structure in polycrystals with small grain size is mainly responsible for the inverse Hall-Petch softening. Dislocation nucleation and propagation are also identified in nanograined ice, which is in good agreement with experimental measurements. Beyond the elastic strain, a combination of GB sliding, grain rotation, amorphization and recrystallization, phase transformation, and dislocation nucleation dominate the plastic deformation in both bicrystals and polycrystals.
Epitaxial ferroelectric oxide thin films for optical applications
Authors: Sando D. , Yang Yurong , Paillard Charles , Dkhil B. , Bellaiche L. , Nagarajan V.
Published: December 2018

Ferroelectrics are non-centrosymmetric crystalline materials that possess a spontaneous polarization that can be switched by an electric field. The electric-field-dependent optical response of these materials makes them important for optical devices, such as modulators or beam deflectors. In the inexorable drive to miniaturization, the concept of integrated thin film optical devices has led to the incorporation of ferroelectric thin films on single-crystal substrates. These structures have appealing electro-optic modulation characteristics, interesting strain-dependent bandgaps and refractive index, as well as promising possibilities for solar harvesting. Here, we review the work on epitaxial ferroelectric (FE) films for optical applications. We first show that FE thin film materials are attractive for integrated electro-optic modulators and then show that epitaxial strain can be used to enhance the FE and optical functionality of films. Next, we describe some of the photovoltaic functionality of FE thin film materials' systems and conclude the review by highlighting some thin-film devices that exploit the aforementioned optical effects.
Frustration and relaxation of antiferromagnetic domains reversed by magneto-electric field cooling in a Pt/Co/Au/Cr2O3/Pt-stacked film
Authors: Shiratsuchi Yu , Watanabe Shunsuke , Yonemura Shogo , Shibata Tatsuo , Nakatani Ryoichi
Published: December 2018

Using magnetic domain observations, we investigated the reversal process of the perpendicular exchange bias polarity resulting from the antiferromagnetic Cr2O3 domain reversal driven by magneto-electric field cooling (MEFC). The exchange bias polarity changed from negative to positive with increasing electric field during MEFC. The relevant change in the magnetic domain revealed the stochastic appearance of the reversed magnetic domains that exhibit the positive exchange bias. The local magnetization curves suggest that the antiferromagnetic domain state after MEFC was frustrated because of energy competition between the interfacial exchange coupling and the bulk magneto-electric effect. The frustrated nature of the magnetic domain structure is supported by the training effect of the exchange bias after MEFC.
Fast sweeping probe system for characterization of spokes in E × B discharges
Authors: Skoutnev V. , Dourbal P. , Rodríguez E. , Raitses Y.
Published: December 2018

We have developed a rapidly swept, back-to-back 100 kHz Langmuir probe system using a tunable compensating network to study the temporal evolution of low frequency oscillations in Penning discharges, Hall Thrusters, and other E × B discharges. Experimental validation of the probe system is performed at low and high sweeping frequencies in a stable Penning discharge. Then application of the probe system to measurements of plasma parameter fluctuations in a low frequency (4 kHz) rotating spoke and an analysis method using the Hilbert transform are shown. We find that the rotating spoke oscillation conducts approximately a third of the cross field current in our Penning device.
The direct bandgap of gray α-tin investigated by infrared ellipsometry
Authors: Carrasco Rigo A. , Zamarripa Cesy M. , Zollner Stefan , Menéndez José , Chastang Stephanie A. , Duan Jinsong , Grzybowski Gordon J. , Claflin Bruce B. , Kiefer Arnold M.
Published: December 2018

Using Fourier-transform infrared ellipsometry, the authors provide spectroscopic evidence about the valence band (VB) structure of diamond-like α-tin. The mid-infrared dielectric function of α-tin grown pseudomorphically on InSb or CdTe by molecular beam epitaxy shows a strong E¯0 peak near 0.41 eV. This peak is assigned to allowed intravalence band transitions from the Γ7− (electron-like) VB to the Γ8+v heavy hole VB and/or interband transitions from Γ7− to the Γ8+c light “hole” conduction band. The strength of this peak requires a hole density in the mid-1018 cm−3 range at room temperature, which might be caused by unintentional doping, by thermal electron-hole pair generation, or by the possibility that the L6+ conduction band might have an energy slightly lower than the Γ8+ VB maximum. Alternatively, this E¯0 peak might be enhanced by the M-shape of the Γ7− VB caused by interactions with the Γ7+ split-off hole VB. A sum-rule analysis of the dielectric function between 0.16 and 6.5 eV is consistent with a high-frequency dielectric constant of 24, which has at most a weak temperature dependence between 100 and 300 K.
Comparison of discharge mechanism of negative corona between hyperboloid and hemispherical electrodes
Authors: Lu B. X. , Zhu J. J.
Published: December 2018

Electrostatic precipitators based on corona discharge are a research hotspot in recent years. It is of great significance to investigate the characteristics of corona discharge under different system parameters for improving the dust removal efficiency. In this manuscript, the continuity equations coupled with Poisson’s equation are solved by the finite element method (FEM) to explore the different mechanisms of the generation of Trichel pulses when hyperboloid and hemispherical electrodes are used in negative corona discharges for a needle-plate configuration under atmospheric pressure. The fitting curve of the Trichel pulse frequency versus systematic macro parameters, including the applied voltage, the needle tip radius and the needle-plate distance, are given and their mechanisms are analyzed. Subsequently, the features of the Trichel pulses of the hyperboloid electrode and the hemispherical electrode at similar power are compared. From precipitation point of view, the hemispherical electrode is obviously better than hyperboloid electrode.
Physical nature of electrically detected magnetic resonance through spin dependent trap assisted tunneling in insulators
Authors: Anders M. A. , Lenahan P. M. , Cochrane C. J. , van Tol Johan
Published: December 2018

We show that electrically detected magnetic resonance (EDMR), through spin dependent trap assisted tunneling (SDTT) in amorphous SiC, exhibits approximately equal amplitudes at very high (8.5 T) and very low (0.013 T) magnetic fields at room temperature. This result strongly supports an SDTT/EDMR model in which spins at two nearby sites involved in a tunneling event are coupled for a finite time in circumstances somewhat analogous to spin pair coupling in the spin dependent recombination/EDMR model of Kaplan, Solomon, and Mott (KSM) [Kaplan, Solomon, and Mott, J. Phys. Lett. 39, 51 (1978)]. Since a comparable near zero magnetic field change in resistance is also observed in these samples, our results support the idea that this magnetoresistance response is also the result of a KSM-like mechanism involving SDTT. Additionally, we observe a large enhancement in SDTT/EDMR at high field (8.5 T) for temperatures below 50 K, which suggests the potential utility of SDTT in spin based quantum computation and other spintronic applications.
Studying rare nonadiabatic dynamics with transition path sampling quantum jump trajectories
Authors: Schile Addison J. , Limmer David T.
Published: December 2018

We present a method to study rare nonadiabatic dynamics in open quantum systems using transition path sampling and quantum jump trajectories. As with applications of transition path sampling to classical dynamics, the method does not rely on prior knowledge of transition states or reactive pathways and thus can provide mechanistic insight into ultrafast relaxation processes in addition to their associated rates. In particular, we formulate a quantum path ensemble using the stochastic realizations of an unravelled quantum master equation, which results in trajectories that can be conditioned on starting and ending in particular quantum states. Because the dynamics rigorously obeys detailed balance, rate constants can be evaluated from reversible work calculations in this conditioned ensemble, allowing for branching ratios and yields to be computed in an unbiased manner. We illustrate the utility of this method with three examples: energy transfer in a donor-bridge-acceptor model, and models of photo-induced proton-coupled electron transfer and thermally activated electron transfer. These examples demonstrate the efficacy of path ensemble methods and pave the way for their use in studying complex reactive quantum dynamics.
Atomically stepped, pseudomorphic, corundum-phase (Al1-xGax)2O3 thin films (0 ≤ x < 0.08) grown on R-plane sapphire
Authors: Lorenz Michael , Hohenberger Stefan , Rose Eduard , Grundmann Marius
Published: December 2018

Atomically smooth, pseudomorphic (Al1−xGax)2O3 thin films were grown for 0 ≤ x < 0.08 on R-plane sapphire (01.2) by pulsed laser deposition at growth temperatures up to 1000 °C. Films up to 720 nm thickness show atomically stepped surfaces with monolayer terraces, similar to the substrates prior to growth, in wide ranges of growth pressure and temperature. A careful analysis of 13 symmetric, skew-symmetric, and asymmetric X-ray peaks agrees quite well with the continuum elastic strain theory of pseudomorphic distortion in corundum heterostructures by M. Grundmann [J. Appl. Phys. 124, 185302 (2018)]. The Ga-contents x and weak deviations from the expected ratios of rhombohedral c/a lattice constants are obtained from the best fits of the spacing of the (02.4), (04.8), and (00.6), (00.12) film and substrate reflections, in reasonable agreement with chemical energy dispersive X-ray spectrometry analyses. In addition, the measured tilts of the asymmetric film lattice planes corroborate the elastic theory.
Effect of soluble sugar content in silique wall on seed oil accumulation during the seed-filling stage in Brassica napus
Authors: Ni Fei , Liu Jiahuan , Zhang Jing , Khan Mohammad Nauman , Luo Tao , Xu Zhenghua , Hu Liyong
Published: December 2018

Soluble sugar content in silique wall and seeds of rapeseed (Brassica napus L.) has significant effects on seed oil formation and accumulation. We studied the relationship between soluble sugar content in B. napus seeds and silique wall and oil concentration under field conditions in two cropping seasons, and examined changes in soluble sugar content in seeds and silique wall under different nitrogen (N) levels. Two commercialised Chinese rapeseed varieties, HZ9 and HZ62, with high seed yield and different N responses were used. Our results indicated that carbon (C):N ratio and soluble sugar content in silique wall had the greater effect on seed oil concentration. When C:N ratio and soluble sugar content in silique wall were within 5–15% and 10–25%, respectively, plants had relatively well coordinated C and N metabolism, facilitating oil accumulation. During 25–35 days of silique development, when C:N ratio and soluble sugar content in silique wall were within 10–15 and 15–25%, respectively, oil synthesis was fastest; the highest accumulation rate was 3.8% per day. When they were each <5%, seeds tended to mature, and oil synthesis gradually decreased, ceased or degraded. During the early stage of silique development, if C:N ratio and soluble sugar content in silique wall were >15% and 30%, there was no apparent tendency for oil accumulation, probably because of adverse environmental conditions. When N application increased from 0 to 270kg ha–1, final oil concentration in seeds decreased by 0.024%. In summary, C:N ratio and soluble sugar content in silique wall are important in regulating seed oil concentration, whereas excessive N application significantly reduced seed oil concentration. Therefore, appropriate reduction of N application would save resources, provide environment benefits and increase rapeseed oil production with no substantial reduction in seed yield, through coordinated seed yield and oil concentration.
Breeding for improved blanchability in peanut: phenotyping, genotype × environment interaction and selection
Authors: Wright G. C. , Borgognone M. G. , O Connor D. J. , Rachaputi R. C. N. , Henry R. J. , Furtado A. , Anglin N. L. , Freischfresser D. B.
Published: December 2018

Breeding for improved blanchability—the propensity of the testa (skin) to be removed from the kernel following rapid heat treatment—is a priority for improvement in the Australian Peanut Breeding Program (APBP). Easy removal of the testa by blanching is required for processing of peanuts into peanut butter and various other confectionary products. Thus, blanchability is an economically important trait in any newly released cultivar in Australia. A better understanding of the range of genetic variation, nature of inheritance and genotype×environment (G×E) interactions, and the development of a low-cost method to phenotype in early generations, could speed up breeding for this trait. Studies were conducted to develop a low-cost, rapid method utilising minimal amounts of seed to phenotype in early generations, along with an assessment of G×E interactions over a range of years and environments to derive optimal selection protocols. Use of a smaller kernel sample size than standard (50 vs 200g) was effective for accurately assessing blanchability in breeding lines and could allow selection in early generations (e.g. in seed produced from a single F2 plant where seed supply is adequate). G×E interaction for blanchability was shown to be very low. Genotypic variance explained 62–100% of the total variance for blanchability, assessed in two diverse germplasm pools including 107 accessions in the USA mini-core over three environments and multiple APBP breeding lines grown over nine different years–environments. Genotypic correlations between all environments were very high (~0.60–0.96), with heritability for the blanchability trait estimated to be very high (0.74–0.97) across the 13 trials. The results clearly demonstrate that effective selection for improved blanchability can be conducted in early generations and in a limited number of contrasting environments to ensure consistency of results.
Quantitative conformational profiling of kinase inhibitors reveals origins of selectivity for Aurora kinase activation states
Authors: Lake Eric W. , Muretta Joseph M. , Thompson Andrew R. , Rasmussen Damien M. , Majumdar Abir , Faber Erik B. , Ruff Emily F. , Thomas David D. , Levinson Nicholas M.
Published: December 2018

Significance

Many drugs trigger changes to the structure of their target receptor upon binding. These conformational effects are thought to be an essential part of molecular recognition but have proven challenging to quantify. Using a high-throughput method for tracking structural changes in a protein kinase in solution, we discovered that many clinically important cancer drugs trigger substantial structural changes to their target protein kinase Aurora A, and that these effects systematically account for the ability of the drugs to differentiate between different biochemical forms of Aurora A. The results provide insight into mechanisms of drug selectivity and suggest strategies for tailoring inhibitors to target certain cancers in which Aurora A has been dysregulated in different ways.
Dengue type 1 viruses circulating in humans are highly infectious and poorly neutralized by human antibodies
Authors: Raut Rajendra , Corbett Kizzmekia S. , Tennekoon Rashika N. , Premawansa Sunil , Wijewickrama Ananda , Premawansa Gayani , Mieczkowski Piotr , Rückert Claudia , Ebel Gregory D. , De Silva Aruna D. , de Silva Aravinda M.
Published: December 2018

Significance

Due to difficulty in obtaining relevant samples and low levels of dengue virus (DENV) present in patients, it has been difficult to characterize the properties of virions circulating in humans. We characterized DENV1 directly from early acute primary dengue samples and from their cell culture isolates. We observed that virions in humans are more infectious and mature as compared with their cell culture isolates. DENV1 cell culture isolates were hypersensitive to neutralization by human antibodies. Cross-reactive fusion loop antibodies and heterotypic immune sera poorly neutralized plasma DENV1. Identical genome sequences showed that the phenotypic differences are due to the differences in maturation state. The observed structural variation is a significant advance applicable to understanding vaccine failure and designing future vaccine strategies.
Calditol-linked membrane lipids are required for acid tolerance inSulfolobus acidocaldarius
Authors: Zeng Zhirui , Liu Xiao-Lei , Wei Jeremy H. , Summons Roger E. , Welander Paula V.
Published: December 2018

Significance

It is thought that the distinct ether lipid membranes of archaea allow them to thrive in environmental extremes. However, it has been difficult to demonstrate this physiological role directly. Here, we identify a protein required for the biosynthesis of a unique archaeal lipid head group, calditol, whose production was considered to be restricted to a subset of archaeal thermoacidophiles. We show that deletion of this protein inSulfolobus acidocaldariusprevents production of calditol-linked membrane lipids and, in turn, inhibits cell growth at extremely low pH. Our findings also suggest that archaea more broadly, like bacteria, employ radicalS-adenosylmethionine proteins to modify membrane lipids in ways that confer protective effects when environmental conditions, such as pH, fluctuate significantly.
Sarcomere length–dependent effects on Ca2+-troponin regulation in myocardium expressing compliant titin
Authors: Li King-Lun , Methawasin Mei , Tanner Bertrand C.W. , Granzier Henk L. , Solaro R. John , Dong Wen-Ji
Published: December 2018

Cardiac performance is tightly regulated at the cardiomyocyte level by sarcomere length, such that increases in sarcomere length lead to sharply enhanced force generation at the same Ca2+ concentration. Length-dependent activation of myofilaments involves dynamic and complex interactions between a multitude of thick- and thin-filament components. Among these components, troponin, myosin, and the giant protein titin are likely to be key players, but the mechanism by which these proteins are functionally linked has been elusive. Here, we investigate this link in the mouse myocardium using in situ FRET techniques. Our objective was to monitor how length-dependent Ca2+-induced conformational changes in the N domain of cardiac troponin C (cTnC) are modulated by myosin–actin cross-bridge (XB) interactions and increased titin compliance. We reconstitute FRET donor- and acceptor-modified cTnC(13C/51C)AEDANS-DDPM into chemically skinned myocardial fibers from wild-type and RBM20-deletion mice. The Ca2+-induced conformational changes in cTnC are quantified and characterized using time-resolved FRET measurements as XB state and sarcomere length are varied. The RBM20-deficient mouse expresses a more compliant N2BA titin isoform, leading to reduced passive tension in the myocardium. This provides a molecular tool to investigate how altered titin-based passive tension affects Ca2+-troponin regulation in response to mechanical stretch. In wild-type myocardium, we observe a direct association of sarcomere length–dependent enhancement of troponin regulation with both Ca2+ activation and strongly bound XB states. In comparison, measurements from titin RBM20-deficient animals show blunted sarcomere length–dependent effects. These results suggest that titin-based passive tension contributes to sarcomere length–dependent Ca2+-troponin regulation. We also conclude that strong XB binding plays an important role in linking the modulatory effect of titin compliance to Ca2+-troponin regulation of the myocardium.
Agricultural Economics as a Poster Child of Applied Economics: Big Data & Big Issues1
Authors: Zilberman David
Published: December 2018

Agricultural economists have embodied the notions of applied economics for a long time. They have used economic principles to address real‐world problems, integrating economics and scientific knowledge. Applied economics tends to be multidisciplinary and develop applied concepts, theories, and tools. Some, like human capital, diffusion of innovation, contingent valuation, and numerous numerical and econometric techniques have spread throughout economics. Agricultural economic research has been data intensive, and improved information technologies strengthen this tendency. Yet data without theory is of limited use and coevolution of theory and data are essential. Empirical analysis should incorporate quantitative information as well as narratives. We are challenged to understand the coevolution of business, supply chains, and technology, and how they are affected by policies and affect markets. Research should integrate agriculture, energy, and the environment and develop tools to analyze and regulate the emerging bio‐economy integrating biotech and infotech.
AStrap: identification of alternative splicing from transcript sequences without a reference genome
Authors: Ji Guoli , Ye Wenbin , Su Yaru , Chen Moliang , Huang Guangzao , Wu Xiaohui
Published: December 2018

Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features. We evaluated AStrap using collected AS events from reference genomes of rice and human as well as single-molecule real-time sequencing data from Amborella trichopoda. Results show that AStrap can identify much more AS events with comparable or higher accuracy than the competing method. AStrap also possesses a unique feature of predicting AS types, which achieves an overall accuracy of ∼0.87 for different species. Extensive evaluation of AStrap using different parameters, sample sizes and machine-learning models on different species also demonstrates the robustness and flexibility of AStrap. AStrap could be a valuable addition to the community for the study of AS in non-model organisms with limited genetic resources.

Availability and implementation

AStrap is available for download at https://github.com/BMILAB/AStrap.

Supplementary information

Supplementary data are available at Bioinformatics online.
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding
Authors: Shin Sunyoung , Hudson Rebecca , Harrison Christopher , Craven Mark , Keleş Sündüz
Published: December 2018

Understanding the regulatory roles of non-coding genetic variants has become a central goal for interpreting results of genome-wide association studies. The regulatory significance of the variants may be interrogated by assessing their influence on transcription factor binding. We have developed atSNP Search, a comprehensive web database for evaluating motif matches to the human genome with both reference and variant alleles and assessing the overall significance of the variant alterations on the motif matches. Convenient search features, comprehensive search outputs and a useful help menu are key components of atSNP Search. atSNP Search enables convenient interpretation of regulatory variants by statistical significance testing and composite logo plots, which are graphical representations of motif matches with the reference and variant alleles. Existing motif-based regulatory variant discovery tools only consider a limited pool of variants due to storage or other limitations. In contrast, atSNP Search users can test more than 37 billion variant-motif pairs with marginal significance in motif matches or match alteration. Computational evidence from atSNP Search, when combined with experimental validation, may help with the discovery of underlying disease mechanisms.

Availability and implementation

atSNP Search is freely available at http://atsnp.biostat.wisc.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.
Spatiotemporal Patterns and Risk Factors for Scrub Typhus From 2007 to 2017 in Southern China
Authors: Zheng Canjun , Jiang Dong , Ding Fangyu , Fu Jingying , Hao Mengmeng
Published: December 2018

Background

Substantial outbreaks of scrub typhus, coupled with the discovery of this vector-borne disease in new areas, suggest that the disease remains remarkably neglected. The objectives of this study were to map the contemporary and potential transmission risk zones of the disease and to provide novel insights into the health burden imposed by scrub typhus in southern China.

Methods

Based on the assembled data sets of annual scrub typhus cases and maps of environmental and socioeconomic correlates, a boosted regression tree modeling procedure was used to identify the environmental niche of scrub typhus and to predict the potential infection zones of the disease. Additionally, we estimated the population living in the potential scrub typhus infection areas in southern China.

Results

Spatiotemporal patterns of the annual scrub typhus cases in southern China between 2007 and 2017 reveal a tremendous, wide spread of scrub typhus. Temperature, relative humidity, elevation, and the normalized difference vegetation index are the main factors that influence the spread of scrub typhus. In southern China, the predicted highest transmission risk areas of scrub typhus are mainly concentrated in several regions, such as Yunnan, Guangxi, Guangdong, Hainan, and Fujian. We estimated that 162 684 million people inhabit the potential infection risk zones in southern China.

Conclusions

Our results provide a better understanding of the environmental and socioeconomic factors driving scrub typhus spread, and estimate the potential infection risk zones beyond the disease’s current, limited geographical extent, which enhances our capacity to target biosurveillance and help public health authorities develop disease control strategies.