bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen bonded capsules by layer-by-layer assembly of tannic acid and poly(2-n-propyl-2-oxazoline) for encapsulation and release of macromolecules
Authors: Paramasivam Gokul , Vergaelen Maarten , Ganesh Munuswamy-Ramanujam , Hoogenboom Richard , Sundaramurthy Anandhakumar
Published: October 2017

We report hydrogen bonded capsules with the built-in ability to release loaded bioactive molecules at a physiological temperature of 37 °C.
Neurochemical characterization of nerve fibers in the porcine gallbladder wall under physiological conditions and after the administration ofSalmonella enteritidislipopolysaccharides (LPS)
Authors: Makowska Krystyna , Mikolajczyk Anita , Calka Jaroslaw , Gonkowski Slawomir
Published: October 2017

Lipopolysaccharides (LPS, bacterial endotoxin) are a component of the cellular membrane of Gram-negative bacteria, which is known as an important pathological factor.
The mechanism of all-trans retinoic acid in the regulation of apelin expression in vascular endothelial cells
Authors: Shi Hongyun , Yuan Lanhui , Yang Huibin , Zang Aimin
Published: October 2017

The apelin gene can promote vascular endothelial cell (VEC) proliferation, migration, and angiogenesis. However, the molecular mechanism for regulation of the apelin gene is still unknown. Real-time PCR and Western blotting analysis were employed to detect the effect of all-trans retinoic acid (ATRA) in up-regulating apelin expression in human umbilical vein endothelial cells (HUVECs). Furthermore, the in vivo study also indicated that ATRA could increase apelin expression in balloon-injured arteries of rats, which is consistent with the results from the cultured HUVECs. To ensure whether retinoic acid receptor (RAR) α (RARα) could be induced by ATRA in regulating apelin, the expression of RARα was tested with a siRNA method to knock down RARα or adenovirus vector infection to overexpress RARα. The results showed that ATRA could up-regulate apelin expression time- and dose- dependently in HUVECs. ATRA could induce a RARα increase; however, the expression of RARβ and RARγ were unchanged. The blocking of RARα signaling reduced the response of apelin to ATRA when HUVECs were treated with RARα antagonists (Ro 41-5253) or the use of siRNA against RARα (si-RARα) knockdown RARα expression before using ATRA. In addition, induction of RARα overexpression by infection with pAd-GFP-RARα further increased the induction of apelin by ATRA. These results suggested that ATRA up-regulated apelin expression by promoting RARα signaling.
Stepped θ‐QAM for high‐order modulation
Authors: Lee Jaeyoon , Hong Heejin , Yoon Dongweon
Published: October 2017

M‐ary stepped θ‐QAM (θ‐QAM) for M = 22l, l ≥ 3 based on square QAM is proposed. The signal constellation of stepped θ‐QAM and the coordinates of the symbols generalised for modulation order M are presented. Then analyse the symbol error rate (SER) performance, and the optimum value of θ in terms of minimum SER for stepped θ‐QAM in additive white Gaussian noise and fading channels. Through computer simulations, the theoretical results are validated and show that stepped θ‐QAM offers better error performance than θ‐QAM.
Voltage stability constrained multi‐objective optimisation model for long‐term expansion planning of large‐scale wind farms
Authors: Nikkhah Saman , Rabiee Abbas
Published: October 2017

This study proposes a new model for long‐term planning of large‐scale wind farms (WFs) considering voltage stability constraints. The proposed model is a multi‐objective optimisation problem which aims to maximise the profit of WF investor from wind energy procurement and to minimise the overall power generation cost. By performing modal analysis on the reduced power flow Jacobian matrix, proper locations for installation of WFs are determined. Moreover, the impact of voltage stability constraints on the capacity of WFs is investigated. In comparison with other studies, the main contributions of this study are: (i) to propose a new methodology for determination of the best locations for WFs, (ii) to study the impact of voltage stability as an important security constraint in long‐term planning of wind energy. The proposed voltage stability constrained multi‐objective wind power planning (VSC‐MOWPP) model is solved via ɛ ‐constraint method in General Algebraic Modelling System optimisation package environment. The compromise solution of Pareto optimal set is selected using fuzzy satisfying approach. The proposed VSC‐MOWPP model is examined on the IEEE 39‐bus standard test system. The numerical investigations substantiate the suitability of the proposed model for multi‐year planning of WFs at the presence of long‐term voltage stability constraints.
Search for gamma-ray emission from Galactic novae with the Fermi -LAT
Authors: Franckowiak A. , Jean P. , Wood M. , Cheung C. C. , Buson S.
Published: October 2017

Context. A number of novae have been found to emit high-energy gamma rays (>100 MeV). However, the origin of this emission is not yet understood. We report on the search for gamma-ray emission from 75 optically detected Galactic novae in the first 7.4 years of operation of the Fermi  Large Area Telescope using the Pass 8 data set.

Aims. We compile an optical nova catalog including light curves from various resources and estimate the optical peak time and optical peak magnitude in order to search for gamma-ray emission to determine whether all novae are gamma-ray emitters.

Methods. We repeated the analysis of the six novae previously identified as gamma-ray sources and developed a unified analysis strategy that we then applied to all novae in our catalog. We searched for emission in a 15 day time window in two-day steps ranging from 20 days before to 20 days after the optical peak time. We performed a population study with Monte Carlo simulations to set constraints on the properties of the gamma-ray emission of novae.

Results. Two new novae candidates have been found at ~ 2σ global significance. Although these two novae candidates were not detected at a significant level individually, taking them together with the other non-detected novae, we found a sub-threshold nova population with a cumulative 3σ significance. We report the measured gamma-ray flux for detected sources and flux upper limits for novae without significant detection. Our results can be reproduced by several gamma-ray emissivity models (e.g., a power-law distribution with a slope of 2), while a constant emissivity model (i.e., assuming novae are standard candles) can be rejected.
Recollimation shocks and radiative losses in extragalactic relativistic jets
Authors: Bodo G. , Tavecchio F.
Published: October 2017

We present the results of state-of-the-art simulations of recollimation shocks induced by the interaction of a relativistic jet with an external medium, including the effect of radiative losses of the shocked gas. Our simulations confirm that – as suggested by earlier semi-analytical models – the post-shock pressure loss induced by radiative losses may lead to a stationary equilibrium state characterized by a very strong focusing of the flow, with the formation of quite narrow nozzles, with cross-sectional radii as small as 10-3 times the length scale of the jet. We also study the time-dependent evolution of the jet structure induced by a density perturbation injected at the flow base. The set-up and the results of the simulations are particularly relevant for the interpretation of the observed rapid variability of the γ-ray emission associated to flat spectrum radio quasars. In particular, the combined effects of jet focusing and Doppler beaming on the observed radiation make it possible to explain the sub-hour flaring events such as that observed in the flat specrum radio quasar PKS 1222+216 by MAGIC.
Family Planning for Sexual Minority Women
Authors: Stoffel Cynthia , Carpenter Emma , Everett Bethany , Higgins Jenny , Haider Sadia
Published: October 2017

The family planning needs of sexual minority women (SMW) are an understudied but growing area of research. SMW have family planning needs, both similar to and distinct from their exclusively heterosexual peers. Specifically, SMW experience unintended pregnancies at higher rates than their exclusively heterosexual peers, but factors that increase this risk are not well understood. Contraception use is not uncommon among SMW, but lesbian women are less likely to use contraception than bisexual or exclusively heterosexual women. High rates of unintended pregnancy suggest contraception is underused among SMW. Contraception counseling guidelines specific to SMW do not yet exist, but greater adoption of current best practices is likely to meet the needs of SMW. SMW may have unique needs for their planned pregnancies as well, for which obstetrics and gynecology (Ob/Gyn) providers should provide care and referrals. In general, understandings of the distinct family planning needs for SMW are limited and further research is needed, with particular attention to issues of overlapping health disparities related to status as a SMW and other factors such as race/ethnicity that may add additional layers of stigma and discrimination. Clinical resources are needed to help Ob/Gyns make their practice more welcoming to the needs of SMW.
Fetal Valproate Syndrome – Still a Problem Today!
Authors: Wiedemann Katharina , Stüber Tanja , Rehn Monika , Frieauff Eric
Published: October 2017

Introduction Fetal exposition to valproate can lead to a cluster of facial dysmorphism, congenital anomalies and neurodevelopmental retardation.

Case Report In this report we describe 2 cases of fetal valproate syndrome. In the first case, the gravida had a valproate medication before and during pregnancy with additional folic acid. She delivered a male premature infant at 25+2 weeks of gestation due to preterm labor and rupture of the membranes. Physical examination showed even in the premature infant typical signs of fetal valproate syndrome with trigonocephaly, epicanthal folds, broad root of the nose, low-set ears, thin upper lip and anteverted nares. In the second case, the gravida was under antiepileptic therapy with valproate and lamotrigine before and during pregnancy without any prophylaxis with folic acid. Sonographic examination during pregnancy diagnosed a spina bifida, Chiari II malformation and clubfeet. A female newborn was delivered at 39+4 weeks of gestation. Besides the prenatally detected anomalies, facial dysmorphism including microcephaly, low-set ears, thin upper lip and shallow philtrum were seen after birth.

Conclusion Valproate, a widely used anticonvulsant medication, is known for its teratogenic effects. The risk of congenital anomalies is even higher in combination with other antiepileptic drugs. Therefore, the avoidance of valproate or at least supplementation with a high dose prophylactic folic acid before and during pregnancy is highly recommended for women with epilepsy.
Fertility Preservation in Female Patients with Breast Cancer – a Current Overview
Authors: Guenther Veronika , Alkatout Ibrahim , Junkers Wiebe , Bauerschlag Dirk , Maass Nicolai , von Otte Soeren
Published: October 2017

Many premenopausal patients who develop breast cancer have not yet completed their family planning, so measures of fertility protection to preserve their fertile potential would be beneficial. Polychemotherapy causes irreversible damage to the ovarian follicles – irrespective of whether in a neoadjuvant or adjuvant setting – and this can sometimes result in permanent infertility. Depending on which cytostatic agents are used and on the age-related ovarian reserve of the woman, gonadotoxic risk must be classified as low, moderate or high. Options of fertility preservation include: a) cryopreservation of fertilised or unfertilised oocytes. After ovarian hyperstimulation, mature oocytes are retrieved by transvaginal follicle aspiration, after which they are cryopreserved, either unfertilised or on completion of IVF or ICSI treatment. During b) cryopreservation of ovarian tissue, about 50% of the ovarian cortex of one ovary is resected with the aid of a laparoscopic procedure and cryopreserved. The application of c) GnRH agonists as a medicinal therapy option is an attempt at endocrine ovarian suppression in order to protect oocytes, granulosa cells and theca cells from the cytotoxic effect of chemotherapy.
Wundversorgung des diabetischen Fuß-Ulkus (DFU) – Inkrementelle Kostenanalyse der mit einem Hämoglobinspray erweiterten Therapie der diabetisch-neuropathischen Fußläsion in Deutschland
Authors: Brüggenjürgen Bernd , Hunt Sharon D. , Eberlein Thomas
Published: October 2017

Zielsetzung Die Behandlung des diabetischen Fuß-Ulkus (DFU) ist klinisch problematisch und mit hohen Kosten verbunden. Die ergänzende
topische Applikation des Hämoglobinsprays Granulox® zusätzlich zum etablierten Therapiestandard der lokalen Wundversorgung
erreicht einen schnelleren und häufigeren Wundverschluss insbesondere bei stagnierender Wundheilung. Die Auswirkung der zusätzlichen Gabe
des Hämoglobinsprays auf die Kosten aus Sicht der Krankenversicherung soll untersucht werden.

Methodik Auf Basis von klinischen Studiendaten wurde ein 28-Wochen-Markov-Modell mit den Modellzuständen „unterbrochene Wundheilung“,
„normale Wundheilung“, „infizierte Wunde“, „Amputation“, „verstorben“ und „geheilt“ programmiert. Die inkrementellen Kosten-Unterschiede
wurden analysiert und mit einer Sensitivitätsanalyse überprüft.

Ergebnisse Patienten in der Standardtherapie des DFU verursachten über 28 Wochen Durchschnittskosten in Höhe von 1737 €, für
DFU-Patienten mit zusätzlicher Gabe von Hämoglobin-Spray fielen Gesamtkosten in Höhe von 1028 € an. Behandlungspflege war der größte
Kostenfaktor mit durchschnittlich 806 € in der Standardversorgung und 474 € in der um den Hämoglobin-Spray erweiterten Behandlungsstrategie.
Die Kostenreduktion von insgesamt durchschnittlich 709 € bestätigte sich in dieser Größenordnung auch bei der Variation der Modellannahmen
in der Sensitivitätsanalyse.

Schlussfolgerung Durch eine zusätzliche Gabe des Hämoglobinsprays Granulox® können beträchtliche Kosteneinsparungen aus
Sicht der Krankenversicherung im Rahmen der Wundversorgung des diabetischen Fuß-Ulkus in Deutschland erreicht werden.
Born radicals? Prevent, positivism, and ‘race-thinking’
Authors: Sian Katy
Published: October 2017

In the contemporary Western climate, counter-terrorism discourse dealing with so-called Islamic extremism appears to be obsessed with trying to understand the motives behind what prompts somebody to turn to terrorism. This paper will argue that attempts to locate extremist motives in such a way can be seen to reinforce earlier iterations of positivist criminology and race-thinking. Through a critical examination of the works of criminologist Cesare Lombroso, this paper will tease out the interconnections between his ‘criminal types’ thesis, and the British government’s current Prevent policy that seeks to identify ‘extremist types.’ By developing a rich critique of these positivist approaches, the paper will go on to question how we might think beyond the essentialism, reductivism, and racism/Islamophobia inherent within such frameworks. In this way, the paper raises a series of conceptual implications for criminology and terrorism studies, while at the same time, develops a contribution to critical race and ethnicity studies.
Advanced magneto-optical Kerr effect measurements of superconductors at low temperatures
Authors: Stahl Claudia , Gräfe Joachim , Ruoß Stephen , Zahn Patrick , Bayer Jonas , Simmendinger Julian , Schütz Gisela , Albrecht Joachim
Published: October 2017

Magneto-optical Kerr-effect (MOKE) measurements of superconducting films with soft-magnetic coatings are performed at low temperatures using a laser-based MOKE set-up. An elaborate measurement scheme with internal reference allows the quantitative comparison of the temperature dependent Kerr-amplitude with the magnetic field generated by supercurrents. For this purpose, an amorphous CoFeB thin film exhibiting a large Kerr-signal is deposited directly on top of the YBCO superconductor acting as field sensing layer. It is shown that the resulting magnetic hysteresis loops of the soft-magnetic film can be used to reconstruct the electric properties of the superconductor.
Effect of gas mixing on physical properties of warm collisional helicon plasmas
Authors: Kabir M. , Niknam A. R.
Published: October 2017

The effect of inert gas mixing on the physical properties of a helicon plasma source with a Nagoya type III antenna is analytically investigated by taking into account the thermal and collisional effects. The dielectric permittivity tensor of this mixed gas plasma is obtained by using the Bhatnagar–Gross– Krook kinetic theory. Considering the dielectric tensor of mixed gas plasma and solving the electromagnetic field equations, the profiles of electromagnetic fields and plasma resistance are plotted and discussed. The results show that the plasma resistance peaks decrease with increasing Xe fraction in Ar–Xe plasma, and increase with the He fraction in Ar–He plasma. It is also shown that by increasing the xenon filling fraction, the electromagnetic field amplitudes are lowered, and by increasing the helium filling fraction, they are increased.
Electrical and thermoelectric transport by variable range hopping in reduced graphene oxide
Authors: Park Min , Hong Sung Ju , Kim Kyung Ho , Kang Hojin , Lee Minwoo , Jeong Dae Hong , Park Yung Woo , Kim Byung Hoon
Published: October 2017

This study investigated the transport properties of single-layer reduced graphene oxides (rGOs). The rGOs were prepared by the bubble deposition method followed by thermal reduction. The crossover of the transport mechanism from Efros-Shklovskii (ES) variable range hopping (VRH) between the localized states to Mott-VRH was observed near 70 K using the temperature-dependent conductance. The ES-VRH conduction below 70 K is apparent in the electric field dependence of the field-driven hopping transport in the high-electric field regime. We also figure out that the thermoelectric power is consistent with the 2D Mott VRH above 70 K. We argue that the VRH conduction results from the topological disorders of rGO as confirmed by Raman spectroscopy. This infers that the average distance between defects is approximately 2.0 nm.
Substrate-emitting ring interband cascade lasers
Authors: Holzbauer Martin , Szedlak Rolf , Detz Hermann , Weih Robert , Höfling Sven , Schrenk Werner , Koeth Johannes , Strasser Gottfried
Published: October 2017

We demonstrate interband cascade lasers fabricated into ring-shaped cavities with vertical light emission through the substrate at a wavelength of λ ≈ 3.7 μm. The out-coupling mechanism is based on a metallized second-order distributed feedback grating. At room-temperature, a pulsed threshold current-density of 0.75 kA/cm2 and a temperature-tuning rate of 0.3 nm/°C are measured. In contrast to the azimuthal polarization of ring quantum cascade lasers, we observe a radial polarization of the projected nearfield of ring interband cascade lasers. These findings underline the fundamental physical difference between light generation in interband and intersubband cascade lasers, offering new perspectives for device integration.
Syngas production through biomass/CO2 gasification using granulated blast furnace slag as heat carrier
Authors: Yao Xin , Yu Qingbo , Xie Huaqing , Duan Wenjun , Han Zhengri , Liu Sihong , Qin Qin
Published: October 2017

The emerging technology of biomass/CO2 gasification to recover waste heat from granulated blast furnace (BF) slag for solving the energy crisis and relieving the greenhouse effect was proposed. The gasification performances of biomass/CO2 in granulated BF slag under different reaction temperatures and mole ratios of CO2 to fixed carbon in the biomass (CO2/C) were investigated, and the effects of granulated BF slag on the biomass/CO2 gasification reaction were illuminated. The results showed that with higher gas content, gas yield, and lower heating value (LHV) were obtained with higher reaction temperature. When CO2/C was up to 1, the maximum concentrations of CO and H2 were obtained, and the LHV was near maximum value. Granulated BF slag could promote biomass/CO2 gasification reactions to some degree and also could act as a catalyst in the reaction. Under the optimum conditions, a reaction temperature reaching 1000 °C, CO2/C of 1 and using granulated BF slag as a heat carrier, the maximum syngas concentrations of CO and H2 were 43.1% and 33.7%, and the gas yield and LHV were 1.453 m3/kg and 16.089 MJ/kg, respectively.
Mid-infrared two photon absorption sensitivity of commercial detectors
Authors: Boiko D. L. , Antonov A. V. , Kuritsyn D. I. , Yablonskiy A. N. , Sergeev S. M. , Orlova E. E. , Vaks V. V.
Published: October 2017

We report on broad-band two-photon absorption (TPA) in several commercially available MIR inter-band bulk semiconductor photodetectors with the spectral cutoff in the range of 4.5–6 μm. The highest TPA responsivity of 2 × 10−5 A·mm2/W2 is measured for a nitrogen-cooled InSb photovoltaic detector. Its performance as a two-photon detector is validated by measuring the second-order interferometric autocorrelation function of a multimode quantum cascade laser emitting at the wavelength of 8 μm.
Stability of the oxygen vacancy induced conductivity in BaSnO3 thin films on SrTiO3
Authors: Jaim H. M. Iftekhar , Lee Seunghun , Zhang Xiaohang , Takeuchi Ichiro
Published: October 2017

BaSnO3 (BSO) has emerged as a major candidate for exploration of a variety of functional device applications. In this letter, we report on the role of the oxygen vacancy concentration in the electronic states, the crystal structure, and the transport properties of BSO thin films grown on SrTiO3 substrates by pulsed laser deposition. We fabricated five BSO films systematically reducing the deposition oxygen pressure from 1 × 10−1 Torr to 5 × 10−3 Torr. The BSO films show gradual transition from an insulating one fabricated at 1 × 10−1 Torr to highly conducting ones with decreasing deposition oxygen pressure. X-ray photoelectron spectroscopy measurements show the increasing oxygen vacancy concentration as a function of the decreased deposition oxygen pressure. Films deposited at 5 × 10−3 Torr displayed the lowest room temperature resistivity (1.73 mΩ cm) and the highest concentration of oxygen vacancies. Temperature-dependent resistivity of the samples deposited at low oxygen pressures suggests the presence of shallow states near the conduction band. With decreasing oxygen pressure, the out-of-plane lattice parameter of BSO increases while the in-plane lattice parameter remains nearly the same. Oxygen deficient conducting BSO films with high oxygen vacancies exhibited excellent structural, electronic, and valence state stabilities when they were post-annealed at temperatures up to 760 °C.
Bi-SOC-states in one-dimensional random cellular automaton
Authors: Czechowski Zbigniew , Budek Agnieszka , Białecki Mariusz
Published: October 2017

Two statistically stationary states with power-law scaling of avalanches are found in a simple 1 D cellular automaton. Features of the fixed points, the spiral saddle and the saddle with index 1, are investigated. The migration of states of the automaton between these two self-organized criticality states is demonstrated during evolution of the system in computer simulations. The automaton, being a slowly driven system, can be applied as a toy model of earthquake supercycles.
Electroluminescence from silicon-based light-emitting devices with erbium-doped TiO2 films annealed at different temperatures
Authors: Chen Jinxin , Gao Zhifei , Jiang Miaomiao , Gao Yuhan , Ma Xiangyang , Yang Deren
Published: October 2017

We have previously developed silicon-based light-emitting devices (LEDs) with luminescent erbium (Er)-doped TiO2 (TiO2:Er) films [Yang et al., Appl. Phys. Lett. 100, 031103 (2012)]. In an LED therein, the TiO2:Er film is sandwiched between the ITO film and heavily boron-doped p-type silicon (p+-Si). In this work, we have investigated the electroluminescence (EL) from two LEDs with the TiO2:Er films annealed at 650 and 850 °C, respectively. It is revealed that between the TiO2:Er film and p+-Si, there is an intermediate silicon oxide (SiOx, x ≤ 2) layer and its thickness increases from ∼4 to 8 nm with the increase of annealing temperature from 650 to 850 °C. Interestingly, the thickness of the intermediate SiOx layer is found to exhibit a profound impact on the EL from the LED with the TiO2:Er film on p+-Si. The EL from the LED with the 650 °C-annealed TiO2:Er film is activated only under the forward bias with the positive voltage connecting to the p+-Si substrate. Such EL consists of the oxygen-vacancy-related emissions from TiO2 host and the characteristic visible and ∼1540 nm emissions from the Er3+ ions, while the EL from the LED with the 850 °C-annealed TiO2:Er film can only be enabled by the reverse bias with the negative voltage applied on the p+-Si substrate. Such EL features only the visible and ∼1540 nm emissions from the Er3+ ions. The difference in the EL behaviors of the two LEDs as mentioned above is found to be ascribed to the different electrical conduction mechanisms.
Terahertz particle-in-liquid sensing with spoof surface plasmon polariton waveguides
Authors: Ma Zhijie , Hanham Stephen M. , Arroyo Huidobro Paloma , Gong Yandong , Hong Minghui , Klein Norbert , Maier Stefan A.
Published: October 2017

We present a highly sensitive microfluidic sensing technique for the terahertz (THz) region of the electromagnetic spectrum based on spoof surface plasmon polaritons (SPPs). By integrating a microfluidic channel in a spoof SPP waveguide, we take advantage of these highly confined electromagnetic modes to create a platform for dielectric sensing of liquids. Our design consists of a domino waveguide, that is, a series of periodically arranged rectangular metal blocks on top of a metal surface that supports the propagation of spoof SPPs. Through numerical simulations, we demonstrate that the transmission of spoof SPPs along the waveguide is extremely sensitive to the refractive index of a liquid flowing through a microfluidic channel crossing the waveguide to give an interaction volume on the nanoliter scale. Furthermore, by taking advantage of the insensitivity of the domino waveguide’s fundamental spoof SPP mode to the lateral width of the metal blocks, we design a tapered waveguide able to achieve further confinement of the electromagnetic field. Using this approach, we demonstrate the highly sensitive detection of individual subwavelength micro-particles flowing in the liquid. These results are promising for the creation of spoof SPP based THz lab-on-a-chip microfluidic devices that are suitable for the analysis of biological liquids such as proteins and circulating tumour cells in buffer solution.
An experimental and theoretical study of the valence shell photoelectron spectra of 2-chloropyridine and 3-chloropyridine
Authors: Holland D. M. P. , Powis I. , Trofimov A. B. , Menzies R. C. , Potts A. W. , Karlsson L. , Badsyuk I. L. , Moskovskaya T. E. , Gromov E. V. , Schirmer J.
Published: October 2017

The valence shell photoelectron spectra of 2-chloropyridine and 3-chloropyridine have been studied both experimentally and theoretically. Synchrotron radiation has been employed to record angle resolved photoelectron spectra in the photon energy range 20–100 eV, and these have enabled anisotropy parameters and branching ratios to be derived. The experimental results have been compared with theoretical predictions obtained using the continuum multiple scattering Xα approach. This comparison shows that the anisotropy parameter associated with the nominally chlorine lone-pair orbital lying in the molecular plane is strongly affected by the atomic Cooper minimum. In contrast, the photoionization dynamics of the second lone-pair orbital, orientated perpendicular to the molecular plane, seem relatively unaffected by this atomic phenomenon. The outer valence ionization has been studied theoretically using the third-order algebraic-diagrammatic construction (ADC(3)) approximation scheme for the one-particle Green’s function, the outer valence Green’s function method, and the equation-of-motion (EOM) coupled cluster (CC) theory at the level of the EOM-IP-CCSD and EOM-EE-CC3 models. The convergence of the results to the complete basis set limit has been investigated. The ADC(3) method has been employed to compute the complete valence shell ionization spectra of 2-chloropyridine and 3-chloropyridine. The relaxation mechanism for ionization of the nitrogen σ-type lone-pair orbital (σN LP) has been found to be different to that for the corresponding chlorine lone-pair (σCl LP). For the σN LP orbital, π-π* excitations play the main role in the screening of the lone-pair hole. In contrast, excitations localized at the chlorine site involving the chlorine πCl LP lone-pair and the Cl 4p Rydberg orbital are the most important for the σCl LP orbital. The calculated photoelectron spectra have allowed assignments to be proposed for most of the structure observed in the experimental spectra. The theoretical work also highlights the formation of satellite states, due to the breakdown of the single particle model of ionization, in the inner valence region.
Time zero determination for FEL pump-probe studies based on ultrafast melting of bismuth
Authors: Epp S. W. , Hada M. , Zhong Y. , Kumagai Y. , Motomura K. , Mizote S. , Ono T. , Owada S. , Axford D. , Bakhtiarzadeh S. , Fukuzawa H. , Hayashi Y. , Katayama T. , Marx A. , Müller-Werkmeister H. M. , Owen R. L. , Sherrell D. A. , Tono K. , Ueda K. , Westermeier F. , Miller R. J. D.
Published: October 2017

A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T0)—the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T0 might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T0. In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T0 with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated). Our approach is potentially useful and applicable for fixed-target XFEL experiments, such as serial femtosecond crystallography, utilizing an optical pump pulse in the ultraviolet to near infrared spectral range and a pixelated 2D photon detector for recording crystallographic diffraction patterns in transmission geometry. In comparison to many other suitable approaches, our method is fairly independent of the pumping wavelength (UV–IR) as well as of the X-ray energy and offers a favorable signal contrast. The technique is exploitable not only for the determination of temporal characteristics of the experiment at the interaction point but also for investigating important conditions affecting experimental control such as spatial overlap and beam spot sizes.
Phase control with two-beam interferometry method in a terahertz dielectric wakefield accelerator
Authors: Wang Dan , Su Xiaolu , Yan Lixin , Du YingChao , Tian Qili , Liang Yifan , Niu Lujia , Huang Wenhui , Gai Wei , Tang Chuanxiang , Antipov Sergey
Published: October 2017

High-gradient, beam-driven wakefield acceleration in THz structures is a promising technology for future free electron lasers and colliders. In this scheme, the main beam is accelerated by the wakefield of the high current drive beam. The time separation between the main and drive beams has to be chosen carefully to ensure that the main beam is in an accelerating phase of the drive's wakefield. THz accelerating structures provide high gradient acceleration due to their small apertures, but their phase control is difficult due to the picosecond-scale period. Here, we report on a wakefield acceleration experiment in a 460 GHz dielectric wakefield accelerator (DWA). The optimum phase of the main beam during the experiment is determined with a two-beam wakefield interferometry (TBI) measurement. This is performed without the measurement of the main and drive beam bunch lengths or their separation. In TBI, the interference of the wakefields produced by the drive and main beams is measured with an integrating THz detector. The TBI signal, as a function of separation between the drive and main beams, exhibits a minimum due to destructive interference of these wakefields, which corresponds to maximum acceleration of the main beam as is confirmed by the energy spectrometer measurement. The maximum energy gain of 0.8 MeV and maximum energy loss of 1.2 MeV for the main beam have been measured, which agrees well with theoretical predictions.
Silicon clathrates for photovoltaics predicted by a two-step crystal structure search
Authors: Wu Juefei , Gao Hao , Xia Kang , Xing Dingyu , Sun Jian
Published: October 2017

Silicon in a cubic diamond structure currently plays a significant role in the photovoltaic industry. However, the intrinsic band structures of crystalline silicon restrict its sunlight conversion efficiency. Recently, a clathrate-like Si-24 has been successfully synthesized, which has a quasi-direct bandgap and sheds light on silicon-based photovoltaics. Here, we proposed a two-step crystal structure search method based on first-principles calculations and explored silicon clathrate structures extensively. First, the guest-host compounds were searched at high pressure, and then, the porous guest-free silicon clathrates were obtained by removing the guest atoms. Using potassium as the guest atom, we identified four metastable silicon clathrate structures, and some of them have bandgaps close to the optimal range of the Shockley-Queisser limit and have a better absorption rate than the cubic diamond silicon. These silicon clathrates may have promising value in photovoltaic applications.
The influence of parametric and external noise in act-and-wait control with delayed feedback
Authors: Wang Jiaxing , Kuske Rachel
Published: October 2017

We apply several novel semi-analytic approaches for characterizing and calculating the effects of noise in a system with act-and-wait control. For concrete illustration, we apply these to a canonical balance model for an inverted pendulum to study the combined effect of delay and noise within the act-and-wait setting. While the act-and-wait control facilitates strong stabilization through deadbeat control, a comparison of different models with continuous vs. discrete updating of the control strategy in the active period illustrates how delays combined with the imprecise application of the control can seriously degrade the performance. We give several novel analyses of a generalized act-and-wait control strategy, allowing flexibility in the updating of the control strategy, in order to understand the sensitivities to delays and random fluctuations. In both the deterministic and stochastic settings, we give analytical and semi-analytical results that characterize and quantify the dynamics of the system. These results include the size and shape of stability regions, densities for the critical eigenvalues that capture the rate of reaching the desired stable equilibrium, and amplification factors for sustained fluctuations in the context of external noise. They also provide the dependence of these quantities on the length of the delay and the active period. In particular, we see that the combined influence of delay, parametric error, or external noise and on-off control can qualitatively change the dynamics, thus reducing the robustness of the control strategy. We also capture the dependence on how frequently the control is updated, allowing an interpolation between continuous and frequent updating. In addition to providing insights for these specific models, the methods we propose are generalizable to other settings with noise, delay, and on-off control, where analytical techniques are otherwise severely scarce.
Large-scale Ising-machines composed of magnetic neurons
Authors: Mizushima Koichi , Goto Hayato , Sato Rie
Published: October 2017

We propose Ising-machines composed of magnetic neurons, that is, magnetic bits in a recording track. In large-scale machines, the sizes of both neurons and synapses need to be reduced, and neat and smart connections among neurons are also required to achieve all-to-all connectivity among them. These requirements can be fulfilled by adopting magnetic recording technologies such as race-track memories and skyrmion tracks because the area of a magnetic bit is almost two orders of magnitude smaller than that of static random access memory, which has normally been used as a semiconductor neuron, and the smart connections among neurons are realized by using the read and write methods of these technologies.
Chirality effect on electron phonon relaxation, energy loss, and thermopower in single and bilayer graphene in BG regime
Authors: Ansari Meenhaz , Ashraf S. S. Z.
Published: October 2017

We investigate the energy dependent electron-phonon relaxation rate, energy loss rate, and phonon drag thermopower in single layer graphene (SLG) and bilayer graphene (BLG) under the Bloch-Gruneisen (BG) regime through coupling to acoustic phonons interacting via the Deformation potential in the Boltzmann transport equation approach. We find that the consideration of the chiral nature of electrons alters the temperature dependencies in two-dimensional structures of SLG and BLG from that shown by other conventional 2DEG system. Our investigations indicate that the BG analytical results are valid for temperatures far below the BG limit (∼TBG/4) which is in conformity with a recent experimental investigation for SLG [C. B. McKitterick et al., Phys. Rev. B 93, 075410 (2016)]. For temperatures above this renewed limit (∼TBG/4), there is observed a suppression in energy loss rate and thermo power in SLG, but enhancement is observed in relaxation rate and thermopower in BLG, while a suppression in the energy loss rate is observed in BLG. This strong nonmonotonic temperature dependence in SLG has also been experimentally observed within the BG limit [Q. Ma et al., Phys. Rev. Lett. 112, 247401 (2014)].
Low mortality rate in silver eels (Anguilla anguilla L.) passing through a small hydropower station
Authors: Bernaś Rafał , Dçbowski Piotr , Skóra Michał , Radtke Grzegorz , Morzuch Jacek , Kapusta Andrzej
Published: October 2017

In many regulated rivers, silver eels (Anguilla anguilla L.) experience significant mortality as they pass through small hydropower stations (HPS) during their downstream migration. There has been a huge collapse in the recruitment of this species, primarily because of the destruction of river–ocean connectivity with overfishing. The direct mortality caused by small hydro turbines varies between different places and depends on many factors. The aim of the present study was to assess the mortality rate of silvers eels passing through a small HPS equipped with a Francis turbine in a small Pomeranian river using acoustic telemetry. During the experiment, no direct mortality occurred as a result of passage through the HPS turbine. However, three individuals were believed to have suffered from injuries or passage trauma.
Speech audiometry test with picture-related sentence lists in Modern Greek for partially hearing children
Authors: Koloutsou Konstantina , Kikidis Dimitris , Spanoudakis George , Bibas Athanasios , Nikolopoulos Thomas
Published: October 2017

Objective:

The aim of this study was to develop Greek sentence-based speech audiometry test in quiet test for hearing-impaired (HI) children (G-SEBSAT).

Methods:

Seventy-six children were recruited following approval by the local ethics committee and after obtaining informed consent from their parents. The collection of vocabulary was based on showing pictures selected from popular reading materials in Greek to HI children. A grammatical content analysis was carried out to determine the average syntactic and morphological structures of the sentences used by the HI children. Ten picture-related sentence lists were developed based on the vocabulary and the grammatical analysis, and recorded by a male native speaker of standard Modern Greek. These were presented to both normal-hearing (NH) and HI children, and the average speech response threshold (SRT) as well as the slope of the SRT curve at the SRT level of 50% correct responses (S50) were recorded in both groups. Sentence lists were validated with respect to the variability of their difficulty within each group, as well the test-retest variability of the respective SRT scores.

Results:

The average SRT across all lists for HI children was 65.27 dB and the slope of the SRT curve at the SRT level of 50% correct responses was 3.11%/dB. The corresponding results across all lists for NH children were 17.66 dB and 9.7%/dB, respectively. The SRT of HI children were strongly positively correlated, in a statistically significant manner with the pure tone audiogram (PTA) in both the test and the retest sessions (test: r = 0.750, p < .0005; retest: r = 0.753, p < .0005). The Spearman’s correlation of the rankings of SRT values and the slope values was 0.998 and 0.997, respectively, for the HI and 0.939 and 0.88, for the NH group, indicating very low variability across the test and retest sessions. In addition, the analysis of variance (ANOVA) of the average SRT in NH children and the SRT residuals in the HI group indicated that the different sentences were of the same difficulty within each group. ((F(9,81) = 0.401, p = .930 and (F(9,93) = 2.241, p = .025, respectively).

Conclusions:

A validated G-SEBSAT was created in Greek for the first time. SRT and S50 values for both NH and HI children are comparable to similar tests developed in other languages.
ndexr—an R package to interface with the network data exchange
Authors: Auer Florian , Hammoud Zaynab , Ishkin Alexandr , Pratt Dexter , Ideker Trey , Kramer Frank
Published: October 2017

Motivation

Seamless exchange of biological network data enables bioinformatic algorithms to integrate networks as prior knowledge input as well as to document resulting network output. However, the interoperability between pathway databases and various methods and platforms for analysis is currently lacking. The Network Data Exchange (NDEx) is an open-source data commons that facilitates the user-centered sharing and publication of networks of many types and formats.

Results

Here, we present a software package that allows users to programmatically connect to and interface with NDEx servers from within R. The network repository can be searched and networks can be retrieved and converted into igraph-compatible objects. These networks can be modified and extended within R and uploaded back to the NDEx servers.

Availability and implementation

ndexr is a free and open-source R package, available via GitHub (https://github.com/frankkramer-lab/ndexr) and Bioconductor (http://bioconductor.org/packages/ndexr/).

Supplementary information

Supplementary data are available at Bioinformatics online.
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data
Authors: Ravanmehr Vida , Kim Minji , Wang Zhiying , Milenković Olgica
Published: October 2017

Motivation

Chromatin immunoprecipitation sequencing (ChIP-seq) experiments are inexpensive and time-efficient, and result in massive datasets that introduce significant storage and maintenance challenges. To address the resulting Big Data problems, we propose a lossless and lossy compression framework specifically designed for ChIP-seq Wig data, termed ChIPWig. ChIPWig enables random access, summary statistics lookups and it is based on the asymptotic theory of optimal point density design for nonuniform quantizers.

Results

We tested the ChIPWig compressor on 10 ChIP-seq datasets generated by the ENCODE consortium. On average, lossless ChIPWig reduced the file sizes to merely 6% of the original, and offered 6-fold compression rate improvement compared to bigWig. The lossy feature further reduced file sizes 2-fold compared to the lossless mode, with little or no effects on peak calling and motif discovery using specialized NarrowPeaks methods. The compression and decompression speed rates are of the order of 0.2 sec/MB using general purpose computers.

Availability and implementation

The source code and binaries are freely available for download at https://github.com/vidarmehr/ChIPWig-v2, implemented in C ++.

Supplementary information

Supplementary data are available at Bioinformatics online.
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules
Authors: Sanchez-Pulido Luis , Ponting Chris P
Published: October 2017

The molecular functions of TMEM132 genes remain poorly understood and under-investigated despite their mutations associated with non-syndromic hearing loss, panic disorder and cancer. Here we show the full domain architecture of human TMEM132 family proteins solved using in-depth sequence and structural analysis. We reveal them to be five previously unappreciated cell adhesion molecules whose domain architecture has an early holozoan origin prior to the emergence of choanoflagellates and metazoa. The extra-cellular portions of TMEM132 proteins contain five conserved domains including three tandem immunoglobulin domains, and a cohesin domain homologue, the first such domain found in animals. These findings strongly predict a cellular adhesion function for TMEM132 family, connecting the extracellular medium with the intracellular actin cytoskeleton.

Supplementary information

Supplementary data are available at Bioinformatics online.
A comparison of the left thoracoabdominal and Ivor–Lewis esophagectomy
Authors: Davies A R , Zylstra J , Baker C R , Gossage J A , Dellaportas D , Lagergren J , Findlay J M , Puccetti F , El Lakis M , Drummond R J , Dutta S , Mera A , Van Hemelrijck M , Forshaw M J , Maynard N D , Allum W H , Low D , Mason R C
Published: October 2017

The purpose of this study was to assess the oncological outcomes of a large multicenter series of left thoracoabdominal esophagectomies, and compare these to the more widely utilized Ivor–Lewis esophagectomy. With ethics approval and an established study protocol, anonymized data from five centers were merged into a structured database. The study exposure was operative approach (ILE or LTE). The primary outcome measure was time to death. Secondary outcome measures included time to tumor recurrence, positive surgical resection margins, lymph node yield, postoperative death, and hospital length of stay. Cox proportional hazards models provided hazard ratios (HR) with 95% confidence intervals (CI) adjusting for age, pathological tumor stage, tumor grade, lymphovascular invasion, and neoadjuvant treatment. Among 1228 patients (598 ILE; 630 LTE), most (86%) had adenocarcinoma (AC) and were male (81%). Comparing ILE and LTE for AC patients, no difference was seen in terms of time to death (HR 0.904 95%CI 0.749–1.1090) or time to recurrence (HR 0.973 95%CI 0.768–1.232). The risk of a positive resection margin was also similar (OR 1.022 95%CI 0.731–1.429). Median lymph node yield did not differ between approaches (LTE 21; ILE 21; P = 0.426). In-hospital mortality was 2.4%, significantly lower in the LTE group (LTE 1.3%; ILE 3.6%; P = 0.004). Median hospital stay was 11 days in the LTE group and 14 days in the ILE group (P < 0.0001). In conclusion, this is the largest series of left thoracoabdominal esophagectomies to be submitted for publication and the only one to compare two different transthoracic esophagectomy strategies. It demonstrates oncological equivalence between operative approaches but possible short- term advantages to the left thoracoabdominal esophagectomy.