bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular ion abundances in the diffuse ISM: CF+, HCO+, HOC+, and C3H+
Authors: Gerin M. , Liszt H. , Neufeld D. , Godard B. , Sonnentrucker P. , Pety J. , Roueff E.
Published: November 2018

Aims.The transition between atomic and molecular hydrogen is associated with important changes in the structure of interstellar clouds, and marks the beginning of interstellar chemistry. Most molecular ions are rapidly formed (in ion–molecule reactions) and destroyed (by dissociative recombination) in the diffuse ISM. Because of the relatively simple networks controlling their abundances, molecular ions are usually good probes of the underlying physical conditions including, for instance the fraction of gas in molecular form or the fractional ionization. In this paper we focus on three possible probes of the molecular hydrogen column density, HCO+, HOC+, and CF+.

Methods.We presented high-sensitivity ALMA absorption data toward a sample of compact H IIregions and bright QSOs with prominent foreground absorption, in the ground-state transitions of the molecular ions HCO+, HOC+, and CF+and the neutral species HCN and HNC, and from the excited-state transitions of C3H+(4-3) and13CS(2-1). These data are compared withHerschelabsorption spectra of the ground-state transition of HF and p-H2O.

Results.We show that the HCO+, HOC+, and CF+column densities are well correlated with each other. HCO+and HOC+are tightly correlated with p-H2O, while they exhibit a different correlation pattern with HF depending on whether the absorbing matter is located in the Galactic disk or in the central molecular zone. We report new detections of C3H+confirming that this ion is ubiquitous in the diffuse matter, with an abundance relative to H2of ~7 × 10−11.

Conclusions.We confirm that the CF+abundance is lower than predicted by simple chemical models and propose that the rate of the main formation reaction is lower by a factor of about 3 than usually assumed. In the absence of CH or HF data, we recommend to use the ground-state transitions of HCO+, CCH, and HOC+to trace diffuse molecular hydrogen, with mean abundances relative to H2of 3 × 10−9, 4 × 10−8, and 4 × 10−11, respectively, leading to sensitivityN(H2)/ ∫τdvof 4 × 1020, 1.5 × 1021, and 6 × 1022cm−2/km s−1, respectively.
Predicted Equation for VO2 Based on a 20-Meter Multistage Shuttle Run Test for Children
Authors: Arsa Gisela , Lanza Fernanda , Cambri Lucieli , Antonio Ednei , Murad Neif , de Mello Marco , Santos Alexandra , de Tarso Camillo de Carvalho Paulo , Silva-Junior José , Bocalini Danilo , Mansano Barbara , Tucci Paulo , Serra Andrey
Published: November 2018

This study compared maximum oxygen consumption (VO2max) on a 20-meter multistage shuttle run test (20-Srt) with a cardiopulmonary exercise test (CPET) to determine a VO2max prediction equation for a 20-Srt in children aged 6–10 years. Eighty healthy children performed the CPET on a treadmill, while the 20-Srt took place on a sports court. Heart rate (HR) was measured and the expired gases were continuously measured breath-by-breath using a portable gas analyzer. The VO2max was lower (p<0.05) in CPET than 20-Srt for all, female, and male participants, respectively (46.3±7.9 vs. 48.7±4.6; 42.7±7.8 vs. 46.7±4.8; 49.3±6.8 vs. 50.4±3.9, mL·kg-1·min-1). The standard error estimates were between 3.0 and 3.6 and considered as not clinically relevant if less than 5 mL·kg-1·min-1. The intraclass correlation coefficient between the VO2 in CPET and in 20-Srt was 0.74 (CI95% 0.55–0.84) and considered moderately reliable. The linear multiple regression excluded sex, body mass index and fat-free mass and retained the maximum speed and age in the predictive equation. The 20-Srt estimates the VO2max with moderate reliability and the predictive equation was VO2maxpred=4.302+(maximum speed*5.613)–(age*1.523) for children aged 6–10 years.
Leitlinienadhärenz bei frustran verlaufenden Reanimationen mit automatischen Reanimationsgeräten
Authors: Ondruschka Benjamin , Baier Christina , Hartwig Thomas , Gräwert Stephanie , Böhm Lennert , Dreßler Jan , Bernhard Michael
Published: November 2018

Automatische externe Reanimationsgeräte, z. B. das LUCAS-Device, werden mehr und mehr im praktischen Alltag zur Sicherstellung einer dauerhaften Thoraxkompression verwendet. Ein besseres neurologisches Outcome oder höhere Überlebenschancen für Patienten mit einem prähospitalen Herz-Kreislauf-Stillstand im Vergleich zur manuellen Herzdruckmassage konnten bisher nicht gezeigt werden. Deswegen wird in den aktuellen nationalen und internationalen Leitlinien zur kardiopulmonalen Reanimation der standardisierte und unkritische Dauereinsatz von Reanimationshilfen nicht empfohlen. Die vorliegende Arbeit sollte an einem Obduktionskollektiv retrospektiv überprüfen, ob die 2015 formulierten Leitlinien zur Anwendung von automatischen externen Reanimationshilfen im Praxisalltag auch Verwendung finden. Grundsätzlich haben sich keine Unterschiede im Reanimationsregime für den Zeitraum vor (2014/2015) bzw. nach (2016/2017) Einführung der Anwendungsleitlinien hinsichtlich der demografischen und klinischen Daten der Patienten ergeben. Es fanden sich nur Einzelfälle mit Abweichungen von der Leitlinie, z. B. eine bereits primär bestehende Asystolie oder prähospitale Sterbefälle ohne Transportbeginn. Die primär korrekte Platzierung des LUCAS-Device am Thorax gelingt nicht permanent. Zusammenfassend kann festgestellt werden, dass für die Verwendung von LUCAS-Reanimationshilfen bei Patienten mit Herz-Kreislauf-Stillstand eine hohe Leitlinienadhärenz bestand und von den Empfehlungen nur in Einzelfällen abgewichen wurde.
Fetal Doppler Parameters at Term in Pregnancies Affected by Gestational Diabetes: Role in the Prediction of Perinatal Outcomes
Authors: Familiari Alessandra , Neri Caterina , Vassallo Chiara , Di Marco Giulia , Garofalo Serafina , Martino Carmelinda , Degennaro Valentina , Lanzone Antonio
Published: November 2018

Objective The timing of delivery for women affected by gestational diabetes (GDM) is still controversial. Good clinical practice often suggests offering induction of labor at term in order to reduce the complications associated with this condition, while recent evidence supports expectant management. Fetal Doppler parameters represent a validated tool for testing fetal well-being at term and can select pregnancies that need increased surveillance. The aim of the present study was to evaluate the role of fetal Doppler parameters at term for the prediction of pregnancy outcomes in patients affected by GDM.

Methods Prospective cohort study in a single center. Evaluation of umbilical artery (UA) PI, middle cerebral artery (MCA) PI, cerebroplacental ratio (CPR) and umbilical-to-cerebral ratio (UCR) at > 37 weeks of gestation in singleton, morphologically normal pregnancies affected by GDM, was performed in order to estimate the association between ultrasound measurements at term and perinatal outcome. Regression linear analysis was used to estimate the association between fetal Doppler parameters and neonatal pH, neonatal Apgar score, neonatal weight and a composite adverse outcome. The receiver operating characteristic (ROC) curve was used to estimate the possible predictive value of the above association.

Results Our results on 130 women showed MCA PI to be the best predictor of perinatal outcomes in terms of low Apgar score at the 1st minute (p = 0.00), pH (p = 0.02) and composite adverse outcome (p = 0.05). UCR showed a significant correlation with neonatal pH (p = 0.02). No significant correlations for UA PI and CPR MoMs have been demonstrated in our population. However, the small sample size is a limitation of the study.

Conclusion Evaluation of MCA Doppler and eventually UCR at term can be a useful tool to discriminate pregnancies affected by GDM that can benefit from IOL before 41 weeks in order to reduce complications related to this condition.
Langzeitbeobachtung ehemaliger krebskranker Kinder und Jugendlicher
Authors: Langer Thorsten , Grabow Desiree , Kaatsch Peter , Creutzig Ursula , Eggert Angelika , Escherich Gabriele , Calaminus Gabriele
Published: November 2018

Krebskranke Kinder und Jugendliche überleben heute dank Heilungsraten von über 80% viel häufiger ihre Krebserkrankung als vor 40 Jahren. Etwa 33 000 geheilte ehemalige krebskranke Kinder und Jugendliche sind in der Langzeitbeobachtung über das Deutsche Kinderkrebsregister (DKKR) bundesweit erfasst. Heißt geheilt aber auch gesund? Beim Vergleich mit der Normalbevölkerung ist festzustellen, dass die Morbidität und Mortalität bei den ehemaligen Patienten deutlich erhöht ist. Die Krebserkrankungen und deren Behandlungen können bei zwei von drei Überlebenden 30 Jahre später zu therapiebedürftigen Spätfolgen führen, bei etwa einem Drittel werden sie als schwer eingestuft. Mittels einer strukturierten Nachbeobachtung können diese frühzeitig erkannt und bei Bedarf behandelt werden. Ziel dieses Positionspapiers ist eine Aktualisierung des ersten Positionspapiers aus dem Jahre 2007. Hierbei werden die aktuellen Entwicklungen beschrieben und dargestellt, wie geeignete Nachsorgestrukturen und Nachsorgeeinrichtungen – unter Berücksichtigung der bestehenden Strukturen und dem steigenden Bedarf – geplant werden sollten.
Training in Musculoskeletal Radiology in Europe: Philosophy, Challenges, and Practical Implementation
Authors: Eustace Stephen
Published: November 2018

This article provides an overview of the philosophy, mechanisms, and difficulties involved in the establishment of integrated training programs in medicine, radiology, and specifically musculoskeletal radiology across the European Union.
Outcome Evaluation of Patients with Burst Thoracolumbar Fractures: A Case Series
Authors: Jamali Mohammad , Goorakani Yashar , Solat Niloofar , Taheri Reza , Ghahramani Sulmaz
Published: November 2018

Objective The aim of the present study was to evaluate the outcome of short segment instrumentation in patients affected by burst thoracolumbar fractures.

Methods A total of 19 patients with unstable burst fractures of the thoracolumbar spine were eligible for short segment instrumentation. Their functional outcome (by using the Oswestry and Denis scales) and back pain (using the visual analog scale) were evaluated after 12 months.

Results The mean age of the patients was 30.7 years old, and most of them were male (n = 15). The mean hospital stay was 4.6 days. The mean ± standard deviation (SD) of the pain score according to the visual analog scale was 1.63 ± 1.25 after 12 months of surgery, and there were no patients classified with grades 4 or 5 on the Denis work scale. The average Oswestry disability index (ODI) was 17% during the follow-ups.

Conclusions The outcome of the studied patients, including the clinical pain and the functional outcome of postsurgical patients, suggested that the short-segment instrumentation could be an appropriate method for patients with unstable thoracolumbar junction fractures. However, a long-term follow-up is recommended.
Cementless versus Cemented Fixation in Total Knee Arthroplasty: Usage, Costs, and Complications during the Inpatient Period
Authors: Gwam Chukwuweike U. , George Nicole E. , Etcheson Jennifer I. , Rosas Samuel , Plate Johannes F. , Delanois Ronald E.
Published: November 2018

Cemented fixation has been the gold standard in total knee arthroplasty (TKA). However, with younger and more active patients requiring TKA, cementless (press-fit) fixation has sparked renewed interest. Therefore, we investigated differences in (1) patient demographics, (2) inpatient costs, (3) short-term complications, and (4) discharge disposition between patients who underwent TKA with cemented and cementless fixation. The National Inpatient Sample database was queried for TKA patients with cement or cementless fixation between October 1 and December 31, 2015. Primary outcomes of interest included complications, length of stay (LOS), discharge disposition, and inpatient costs. Student's t-test and chi-square analysis were used to assess continuous and categorical data, respectively. Multivariable analysis evaluated the effects of fixation type on the continuous and categorical dependent variables. Patients who received cementless fixation were more often younger (63.5 vs. 65.9 years), male (47.4 vs. 40.3%), Black (10.7 vs. 7.7%), from the Northeast census region (29.1 vs. 17.1%), and under private insurance (49.2 vs. 40.3%; p < 0.001 for all). Cementless fixation involved higher inpatient hospital costs (US$17,357 vs. US$16,888) and charges (US$67,366 vs. US$64,190; p < 0.001 for both), lower mean LOS (2.63 vs. 2.71 days; p < 0.001), and higher odds of being discharged to home (odds ratio = 1.99; p = 0.002). This study revisited the outcomes of TKA with cementless fixation and demonstrated higher inpatient charges and costs, shorter mean LOS, and higher odds of being discharged home. Future studies should investigate patient outcomes and complications past the inpatient period, evaluate long-term survivorship and failure rates, and implement a prospective study design.
Numerical study of spheres settling in Oldroyd-B fluids
Authors: Pan Tsorng-Whay , Glowinski Roland
Published: November 2018

In order to simulate the motion of balls settling in Oldroyd-B fluids, we have generalized to three dimensions the distributed Lagrange multiplier based fictitious domain method we developed in the study by Hao et al. [“A fictitious domain/distributed Lagrange multiplier method for the particulate flow of Oldroyd-B fluids: A positive definiteness preserving approach,” J. Non-Newtonian Fluid Mech. 156, 95 (2009)] for viscoelastic particulate flow in two-dimensional channels. The effect of the fluid elastic number and that of the density ratio of the particle and fluid on the chaining of balls have been studied. For the cases of two balls released side-by-side at high elasticity numbers, the two balls attract each other first and then form a chain, and such a chain settles vertically. But at low elasticity numbers, the two balls either stay separate and interact periodically or attract each other, turn, and separate periodically. At high blockage ratios, a stronger wall effect enhances the formation of two ball chains. For the cases of three balls released side-by-side, the ball interaction is slightly more complicated due to its non-symmetrical initial configuration. At high elasticity numbers, either a three ball chain settles vertically or the leading two balls form a chain which leaves the third ball behind. But at low elasticity numbers considered in this article, only the leading two balls form a chain. For the vertical initial configuration, a three ball chain can be obtained at higher elasticity numbers and also the heavier balls can form a vertical chain easily.
Note: Double-layered polyimide film heater with low magnetic field generation
Authors: Yim S. H. , Kim Z. , Lee S. , Kim T. H. , Shim K. M.
Published: November 2018

We designed a double-layered polyimide film heater where the direction of the injection current of each layer is opposite to that of the other layer to reduce the magnetic field. The width of the heater is 0.125 mm and the resistance is 21.2 Ω. This specially designed heater successfully demonstrated temperature controllability within 10 mK for an atomic cell in an atom spin gyroscope while minimizing the generation of the magnetic field to within 1 nT.
The quantum mechanics-based polarizable force field for water simulations
Authors: Naserifar Saber , Goddard William A.
Published: November 2018

We report here a new force field for water based solely on quantum mechanics (QM) calculations with no empirical data. The QM was at a high level, coupled cluster single double triple, for all orientations and distances for water dimer plus X3LYP density functional theory (DFT) on 19 larger water clusters. In addition, we included charge and polarization based on the polarizable charge equilibration method and nonbond interactions from DFT-D3 calculations on the H2 and O2 crystal. This model, denoted as RexPoN, provides quite excellent agreement with experimental (expr) data for the solid and liquid phase of water: Tmelt = 273.3 K (expr = 273.15 K) and properties at 298 K: ΔHvap = 10.36 kcal/mol (expr = 10.52), density = 0.9965 gr/cm3 (expr = 0.9965), entropy = 68.4 (J/mol)/K (expr = 69.9), dielectric constant = 76.1 (expr = 78.4), and ln Ds (self-diffusion coef) = −10.08 (expr = −11.24). Such an accurate force field for water will, we believe, be useful for full solvent calculations of electrocatalysis, where we can restrict QM water to just the first one or two layers involving reactions, using RexPoN to provide the polarization for a more distant solvent. Also, RexPoN may provide a better description of the solvent for proteins, DNA, polymers, and inorganic systems for applications to biomolecular, pharma, electrocatalysis (fuel cells and water splitting), and batteries where interaction with explicit water molecules plays a significant role.
A self-consistent first order analytical model of plasma jets: A two fluids approach
Authors: Braga F. L. , Sternberg E. M. A. , Rodrigues N. A. S.
Published: November 2018

Laser ablation processes have applications from thin film deposition to isotope separation, through plasma plume generation, which suggests mass and charge separation of species as the plume evolves. However, they do not have a theoretical model that takes into account equilibrium configurations. The present work is dedicated to build a simplified non-neutral self-consistent two fluid model, based on a few parameters for the first and fast analysis of morphological and statistical features for typical experimental plasma plumes. The velocity field, density profiles, and normalized histograms for the velocity module associated with the species were determined. The electrostatic potential field was also depicted. The model was validated for laser-ablated plasma plumes and found to be in good agreement with the experimental molybdenum plasma jet generated by the interaction of the Nd:YAG nanosecond pulsed laser with the solid target expanding in air at atmospheric pressure.
Probing drug-DNA interactions using super-resolution force spectroscopy
Authors: Jia Haina , Tsai Te-Wei , Xu Shoujun
Published: November 2018

Atomic magnetometry and ultrasound, as individual techniques, have been used extensively in various physical, chemical, and biomedical fields. Their combined application, however, has been rare. We report that super-resolution force spectroscopy, which is based on the integration of the two techniques, can find unique biophysical applications in studying drug-DNA interactions. The precisely controlled ultrasound generates acoustic radiation force on the biological systems labeled with magnetic microparticles. A decrease in the magnetic signal, measured by an automated atomic magnetometer, indicates that the acoustic radiation force equals the binding force of the biological system. With 0.5 pN force resolution, we were able to precisely resolve three small molecules binding with two DNA sequences and quantitatively reveal the effect of a single hydrogen bond. Our results indicate that the increases in DNA binding force caused by drug binding correlate with the enthalpy instead of free energy, thus providing an alternative physical parameter for optimizing chemotherapeutic drugs.
Mode-locked dysprosium fiber laser: Picosecond pulse generation from 2.97 to 3.30 μm
Authors: Woodward R. I. , Majewski M. R. , Jackson S. D.
Published: November 2018

Mode-locked fiber laser technology to date has been limited to sub-3 μm wavelengths despite significant application-driven demand for compact picosecond and femtosecond pulse sources at longer wavelengths. Erbium-doped and holmium-doped fluoride fiber lasers incorporating a saturable absorber are emerging as promising pulse sources for 2.7–2.9 μm, yet it remains a major challenge to extend this coverage. Here, we propose a new approach using a dysprosium-doped fiber with frequency shifted feedback (FSF). Using a simple linear cavity with an acousto-optic tunable filter, we generate ∼33 ps pulses with up to 2.7 nJ energy and 330 nm tunability from 2.97 to 3.30 μm (∼3000–3400 cm−1)—the first mode-locked fiber laser to cover this spectral region and the most broadly tunable pulsed fiber laser to date. Numerical simulations show excellent agreement with experiments and also offer new insights into the underlying dynamics of FSF pulse generation. This highlights the remarkable potential of both dysprosium as a gain material and FSF for versatile pulse generation, opening new opportunities for mid-IR laser development and practical applications outside the laboratory.
Anharmonic stabilization and lattice heat transport in rocksalt β-GeTe
Authors: Xia Yi , Chan Maria K. Y.
Published: November 2018

Peierls-Boltzmann transport equation, coupled with third-order anharmonic lattice dynamics calculations, has been widely used to model lattice thermal conductivity (κl) in bulk crystals. However, its application to materials with structural phase transition at relatively high temperature is fundamentally challenged by the presence of lattice instabilities (imaginary phonon modes). Additionally, its accuracy suffers from the absence of higher-than-third-order phonon scattering processes, which are important near/above the Debye temperature. In this letter, we present an effective scheme that combines temperature-induced anharmonic phonon renormalization and four-phonon scattering to resolve these two theoretical challenges. We apply this scheme to investigate the lattice dynamics and thermal transport properties of GeTe, which undergoes a second-order ferroelectric phase transition from rhombohedral α-GeTe to rocksalt β-GeTe at about 700 K. Our results on the high-temperature phase β-GeTe at 800 K confirm the stabilization of β-GeTe by temperature effects. We find that considering only three-phonon scattering leads to significantly overestimated κl of 3.8 W/mK at 800 K, whereas including four-phonon scattering reduces κl to 1.7 W/mK, a value comparable with experiments. To explore the possibility to further suppress κl, we show that alloying β-GeTe with heavy cations such as Pb and Bi can effectively reduce κl to about 1.0 W/mK, whereas particle size needs to be around 10 nm through nanostructuring to achieve a comparable reduction in κl.
Low frequency vibrational anharmonicity and nuclear spin effects of Cl–(H2) and Cl–(D2)
Authors: Spieler Steffen , Dinu Dennis F. , Jusko Pavol , Bastian Björn , Simpson Malcolm , Podewitz Maren , Liedl Klaus R. , Schlemmer Stephan , Brünken Sandra , Wester Roland
Published: November 2018

Low frequency combination bands of 35Cl–(H2) and 35Cl–(D2) have been measured in the region between 600 and 1100 cm−1 by infrared predissociation spectroscopy in a cryogenic 22-pole ion trap using a free electron laser at the FELIX Laboratory as a tunable light source. The 35Cl–(H2) (35Cl–(D2)) spectrum contains three bands at 773 cm−1 (620 cm−1), 889 cm−1 (692 cm−1), and 978 cm−1 (750 cm−1) with decreasing intensity toward higher photon energies. Comparison of the experimentally determined transition frequencies with anharmonic vibrational self-consistent field and vibrational configuration interaction calculations suggests the assignment of the combination bands v1 + v2, 2v1 + v2, and 3v1 + v2 for 35Cl–(H2) and 2v1 + v2, 3v1 + v2, and 4v1 + v2 for 35Cl–(D2), where v1 is the 35Cl–⋯H2 stretching fundamental and v2 is the Cl–(H2) bend. The observed asymmetric temperature dependent line shape of the v1 + v2 transition can be modeled by a series of ∑+-∏ ro-vibrational transitions, when substantially decreasing the rotational constant in the vibrationally excited state by 35%. The spectrum of 35Cl–(D2) shows a splitting of 7 cm−1 for the strongest band which can be attributed to the tunneling of the ortho/para states of D2.
A theoretical investigation of the glide dislocations in the sphalerite ZnS
Authors: Huang Lili , Wang Shaofeng
Published: November 2018

The 90° and 30° partial glide dislocations in ZnS are investigated theoretically in the framework of the fully discrete Peierls model and first-principles calculation. It is found that there are four types of equilibrium cores for each kind of partial glide dislocation, which are named as the O-Zn-core, the B-Zn-core, the O-S-core, and the B-S-core, according to their geometrical feature and atomic ingredient at the core. For the 90° partial dislocation, the O-Zn-core (double-period core) and the B-S-core (single-period core) are stable. The Peierls barrier heights of the O-Zn-core and the B-S-core are about 0.03 eV/Å and 0.01 eV/Å, respectively. For the 30° partial dislocation, the O-Zn-core (double-period core) and the B-Zn-core (single-period core) are stable and their Peierls barrier heights are approximately the same as that of the O-Zn-core of the 90° partial dislocation. The Peierls stress related to the barrier height is about 800 MPa for the 90° partial dislocation with the B-S-core. The existence of unstable equilibrium cores enables us to introduce the concept of the partial kink. Based on the concept of the partial kink, a minimum energy path is proposed for the formation and migration of kinks. It is noticed that the step length in kink migration is doubled due to the core reconstruction.
Kinetic bandgap analysis of plasma photonic crystals
Authors: Trieschmann Jan , Mussenbrock Thomas
Published: November 2018

The dispersion relation of plasma and plasma-dielectric photonic multilayer structures is approached in terms of a one-dimensional Particle-in-Cell simulation. For several plasma-dielectric configurations, the system response is obtained using a pulsed excitation and a subsequent two-dimensional frequency analysis. It is first shown that the dispersion relation of a single, homogeneous plasma slab is well described by the cold-plasma model even at a low pressure of 1 Pa. The study is extended to the simulation of plasma photonic crystals with a variety of configurations based on the work of Hojo and Mase [J. Plasma Fusion Res. 80, 89 (2004)]. Considering a one-dimensional plasma photonic crystal made from alternating layers of dielectric and homogeneous plasma slabs, it is shown that the assumption of a cold-plasma description is well justified also in this case. Moreover, in this work, the results are reformatted and analyzed in a band diagram representation, in particular, based on the lattice constant a. Based on these considerations, a scaling invariant representation is presented, utilizing a generalized set of parameters. The study is completed with an exemplary comparison of three plasma-dielectric photonic crystal configurations and their corresponding band diagrams.
First vibrational investigations of N2O–H2O, N2O–(H2O)2, and (N2O)2–H2O complexes from the far to the near-infrared spectral region by neon matrix isolation and ab initio calculations
Authors: Soulard P. , Goubet M. , Tremblay B.
Published: November 2018

We present for the first time the investigation of water molecules complexed with dinitrogen monoxide, two abundant molecules in atmosphere, in solid neon using Fourier transform infrared (IR) spectroscopy. We identify at least three complexes from concentration effects, N2O–H2O, N2O–(H2O)2, and (N2O)2–H2O, by observation of new absorption bands close to the monomer fundamental modes from the far to the near IR region. We highlight the presence of isomers for the N2O–H2O complex with the help of theoretical calculations at second order Møller-Plesset (MP2) and coupled-cluster single double triple-F12a/aug-cc-pVTZ levels. The observed frequencies for the N2O–(H2O)2 and (N2O)2–H2O complexes are compared with MP2/aug-cc-pVTZ harmonic data. Anharmonic coupling constants have been derived from the observations of overtones and combination bands.
A spectrometer for ultrashort gamma-ray pulses with photon energies greater than 10 MeV
Authors: Behm K. T. , Cole J. M. , Joglekar A. S. , Gerstmayr E. , Wood J. C. , Baird C. D. , Blackburn T. G. , Duff M. , Harvey C. , Ilderton A. , Kuschel S. , Mangles S. P. D. , Marklund M. , McKenna P. , Murphy C. D. , Najmudin Z. , Poder K. , Ridgers C. P. , Sarri G. , Samarin G. M. , Symes D. , Warwick J. , Zepf M. , Krushelnick K. , Thomas A. G. R.
Published: November 2018

We present a design for a pixelated scintillator based gamma-ray spectrometer for non-linear inverse Compton scattering experiments. By colliding a laser wakefield accelerated electron beam with a tightly focused, intense laser pulse, gamma-ray photons up to 100 MeV energies and with few femtosecond duration may be produced. To measure the energy spectrum and angular distribution, a 33 × 47 array of cesium-iodide crystals was oriented such that the 47 crystal length axis was parallel to the gamma-ray beam and the 33 crystal length axis was oriented in the vertical direction. Using an iterative deconvolution method similar to the YOGI code, modeling of the scintillator response using GEANT4 and fitting to a quantum Monte Carlo calculated photon spectrum, we are able to extract the gamma ray spectra generated by the inverse Compton interaction.
Multi-Segment Indexes of Arterial Stiffness Show Lower Repeatability Than Carotid–Femoral Pulse Wave Velocity or Systolic Blood Pressure
Authors: Beltrami Fernando G , Mzee David , Spengler Christina M
Published: November 2018

BACKGROUND

We investigated the inter-day repeatability of newly proposed indexes of cardiovascular health based on the absolute (PWVABS) or relative (PWVRATIO) difference in pulse wave velocity (PWV) between the carotid–femoral (PWVCF) and carotid–radial (PWVCR) segments compared with PWVCF alone and with systolic blood pressure (BPSYST) over multiple days.

METHODS

All variables were measured in triplicates in a group of 16 young, healthy individuals (8 men/8 women, body mass 66 ± 14 kg, height 1.7 ± 0.1 m, age 27 ± 3 years old, all mean ± SD) on 6 different occasions, always at the same time of the day (± 1 hour) and with at least 48 hours between assessments.

RESULTS

Values did not differ significantly over the 6 different visits for any of the parameters (all Ps > 0.08). Intraclass coefficients (ICCs) ranged from 0.52 (PWVRATIO) to 0.8 (PWVCF). The ICC 95% confidence interval of PWVRATIO (0.30–0.77) and PWVABS (0.33–0.78) did not overlap with that of PWVCF (0.79–0.95), indicating lower repeatability. The coefficient of variation (CV) of PWVABS was over 5-fold larger than the next largest one (46.7 vs. 8.1% for PWVABS and PWVRATIO, respectively), whereas PWVCF and BPSYST showed the lowest CVs (4.6 and 4.0%, respectively).

CONCLUSION

Between PWVABS and PWVRATIO, the relative method showed better repeatability and might be more sensitive to longitudinal changes in patients. Nonetheless, indexes of arterial stiffness-based PWV gradients between different segments show lower inter-day repeatability compared with PWVCF or BPSYST, suggesting that the latter are still preferable in clinical practice.
Which Features of Accent affect Understanding? Exploring the Intelligibility Threshold of Diverse Accent Varieties
Authors: Kang Okim , Thomson Ron I , Moran Meghan
Published: November 2018

With the ascendency of English as a global lingua franca, a clearer understanding of what constitutes intelligible speech is needed. However, research systematically investigating the threshold of intelligibility has been very limited. In this article, we provide a brief summary of the literature as it pertains to intelligible and comprehensible speech, and then report on an exploratory study seeking to determine what specific features of accented speech make it difficult for global listeners to process. Eighteen speakers representing six English varieties were recruited to provide speech stimuli for two English listening tests. Sixty listeners from the same six English varieties took part in the listening tests, and their scores were then assessed against measurable segmental, prosodic, and fluency features found in the speech samples. Results indicate that it is possible to identify particular features of English speech varieties that are most likely to lead to a breakdown in communication, and that the number of such features present in a particular speakers’ speech can predict intelligibility.
Measurement error and variant-calling in deep Illumina sequencing of HIV
Authors: Howison Mark , Coetzer Mia , Kantor Rami
Published: November 2018

Motivation

Next-generation deep sequencing of viral genomes, particularly on the Illumina platform, is increasingly applied in HIV research. Yet, there is no standard protocol or method used by the research community to account for measurement errors that arise during sample preparation and sequencing. Correctly calling high and low-frequency variants while controlling for erroneous variants is an important precursor to downstream interpretation, such as studying the emergence of HIV drug-resistance mutations, which in turn has clinical applications and can improve patient care.

Results

We developed a new variant-calling pipeline, hivmmer, for Illumina sequences from HIV viral genomes. First, we validated hivmmer by comparing it to other variant-calling pipelines on real HIV plasmid datasets. We found that hivmmer achieves a lower rate of erroneous variants, and that all methods agree on the frequency of correctly called variants. Next, we compared the methods on an HIV plasmid dataset that was sequenced using Primer ID, an amplicon-tagging protocol, which is designed to reduce errors and amplification bias during library preparation. We show that the Primer ID consensus exhibits fewer erroneous variants compared to the variant-calling pipelines, and that hivmmer more closely approaches this low error rate compared to the other pipelines. The frequency estimates from the Primer ID consensus do not differ significantly from those of the variant-calling pipelines.

Availability and implementation

hivmmer is freely available for non-commercial use from https://github.com/kantorlab/hivmmer.

Supplementary information

Supplementary data are available at Bioinformatics online.
An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein–monosaccharide complexes
Authors: Blanco Capurro Juan I , Di Paola Matias , Gamarra Marcelo Daniel , Martí Marcelo A , Modenutti Carlos P
Published: November 2018

Unraveling the structure of lectin–carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging due to their low affinity, hydrophilic nature and ligand conformational diversity. In the last decade several strategies, such as the inclusion of glycan conformation specific scoring functions or our developed solvent-site biased method, have improved carbohydrate docking performance but significant challenges remain, in particular, those related to receptor conformational diversity. In the present work we have analyzed conventional and solvent-site biased autodock4 performance concerning receptor conformational diversity as derived from different crystal structures (apo and holo), Molecular Dynamics snapshots and Homology-based models, for 14 different lectin–monosaccharide complexes. Our results show that both conventional and biased docking yield accurate lectin–monosaccharide complexes, starting from either apo or homology-based structures, even when only moderate (45%) sequence identity templates are available. An essential element for success is a proper combination of a middle-sized (10–100 structures) conformational ensemble, derived either from Molecular dynamics or multiple homology model building. Consistent with our previous works, results show that solvent-site biased methods improve overall performance, but that results are still highly system dependent. Finally, our results also show that docking can select the correct receptor structure within the ensemble, underscoring the relevance of joint evaluation of both ligand pose and receptor conformation.
Maximum norm error estimates for Neumann boundary value problems on graded meshes
Authors: Apel Thomas , Rogovs Sergejs , Pfefferer Johannes , Winkler Max
Published: November 2018

This paper deals with a priori pointwise error estimates for the finite element solution of boundary value problems with Neumann boundary conditions in polygonal domains. Due to the corners of the domain, the convergence rate of the numerical solutions can be lower than in the case of smooth domains. As a remedy, the use of local mesh refinement near the corners is considered. In order to prove quasi-optimal a priori error estimates, regularity results in weighted Sobolev spaces are exploited. This is the first work on the Neumann boundary value problem where both the regularity of the data is exactly specified and the sharp convergence order $h^{2} \lvert \ln h \rvert $ in the case of piecewise linear finite element approximations is obtained. As an extension we show the same rate for the approximate solution of a semilinear boundary value problem. The proof relies in this case on the supercloseness between the Ritz projection to the continuous solution and the finite element solution.
Extending the unified transform: curvilinear polygons and variable coefficient PDEs
Authors: Colbrook Matthew J
Published: November 2018

We provide the first significant extension of the unified transform (also known as the Fokas method) applied to elliptic boundary value problems, namely, we extend the method to curvilinear polygons and partial differential equations (PDEs) with variable coefficients. This is used to solve the generalized Dirichlet-to-Neumann map. The central component of the unified transform is the coupling of certain integral transforms of the given boundary data and of the unknown boundary values. This has become known as the global relation and, in the case of constant coefficient PDEs, simply links the Fourier transforms of the Dirichlet and Neumann boundary values. We extend the global relation to PDEs with variable coefficients and to domains with curved boundaries. Furthermore, we provide a natural choice of global relations for separable PDEs. These generalizations are numerically implemented using a method based on Chebyshev interpolation for efficient and accurate computation of the integral transforms that appear in the global relation. Extensive numerical examples are provided, demonstrating that the method presented in this paper is both accurate and fast, yielding exponential convergence for sufficiently smooth solutions. Furthermore, the method is straightforward to use, involving just the construction of a simple linear system from the integral transforms, and does not require knowledge of Green’s functions of the PDE. Details on the implementation are discussed at length.
Managers’ perceptions of the effects of a national mandatory accreditation program in Danish hospitals. A cross-sectional survey
Authors: Nicolaisen A , Bogh S B , Churruca K , Ellis L A , Braithwaite J , von Plessen C
Published: November 2018

Objective

This study aimed to examine and compare middle and senior hospital managers’ perceptions of the effects of a mandatory accreditation program in Denmark, the Danish Healthcare Quality Program (Den Danske Kvalitetsmodel [DDKM]) after it was terminated in 2015.

Design

A cross-sectional online questionnaire survey.

Setting

All 26 somatic and psychiatric public hospitals in Denmark.

Participants

All senior and middle managers.

Methods

A questionnaire with open and closed response (five-point Likert scale) questions. Quantitative data were analyzed descriptively and through ordered logistic regression by management level. Qualitative data were subjected to a software-assisted content analysis.

Results

The response rate was 49% (533/1059). In both the qualitative and quantitative data sets, participants perceived the DDKM as having: led to an increased focus on registration, documentation and additional and unnecessary procedures. While the DDKM was perceived as increasing a focus on quality, the time required for accreditation was at the expense of patient care. There were significant differences by management level, with middle managers having more negative perceptions of the DDKM related to time spent on documentation and registration.

Conclusion

While the DDKM had some perceived benefits for quality improvement, it was ultimately considered time-consuming and outdated or having served its purpose. Including managers, particularly middle managers, in refinements to the new quality improvement model could capitalize on the benefits while redressing the problems with the terminated accreditation program.
The phrenological collection of Gama Machado in the Science Museum, University of Coimbra
Authors: Pereira Helena
Published: November 2018

José Joaquim da Gama Machado was a devotee of the doctrine of phrenology. The theory, formulated by the physician Franz Gall c.1792–93, postulated a biological basis for human behaviour, locating the different mental faculties within the cerebral cortex. Machado was among the founders of the Phrenological Society of Paris. In order to conduct his investigations, he gathered an extensive collection of plaster casts moulded from heads, which he bequeathed to the University of Coimbra in 1861. After more than a century and a half, we investigate what is known about its founder, the man and the collector; the historical and scientific context in which the collection originated; and the paths it travelled within the university. In tracing the life of the collection, we identify also the fortuitous and idiosyncratic nature of its long journey from its formation to the present day.
Diagnostic accuracy of the 1,3-β-D-glucan test for pneumocystis pneumonia in a tertiary university hospital in Denmark: A retrospective study
Authors: Engsbro Anne Line , Najat Sara , Jørgensen Karin Meinike , Kurtzhals Jørgen A L , Arendrup Maiken Cavling
Published: November 2018

1,3-β-D-glucan (BG), a cell-wall component of most fungi including Pneumocystis (PC), is recommended by international guidelines for screening for pneumocystis pneumonia (PCP) in hematologic patients. We retrospectively validated the BG test in our tertiary university hospital. Forty-five patients (median age 53 years, 33% female) tested for PC by polymerase chain reaction (PCR) and/or immunoflourescence (IF)-microscopy with a stored blood sample within ±5 days of the PC test were tested by the Fungitell (cutoff <60 and >80 pg/ml). Cases had symptoms and radiology compatible with PCP and positive IF-microscopy (proven PCP, n = 8) or positive PCR (probable PCP, n = 10). Controls had no compatible symptoms/radiology and negative tests for PC on conventional testing (no PCP, n = 24), or positive PCR/IF-microscopy (colonized, n = 3). Median BG-levels were 1108 pg/ml (proven PCP), 612 pg/ml (probable PCP), 29 pg/ml (colonized), and 48 pg/ml (controls, P < 0.001). Compared to the PCP case/control classification, the BG test showed sensitivities of 83–89% and specificities of 64–74%, positive likelihood ratio (LR) of 3.2 and negative LR of 0.23 at recommended cutoff and moderate agreement between tests. Optimal cutoff was ≥73 pg/ml. In PCR-positive cases, the agreement between the BG test and IF-microscopy was 78–89% with fair/moderate agreement. Elevated BG levels were seen in controls with probable invasive fungal infections (n = 4), hemodialysis, bacterial infections and/or betalactams. To conclude, 11% of patients with PCP would be missed if the BG test had been used for diagnosing PCP. Specificity was moderate. Among PCR-positive patients, the BG test identified more cases than IF-microscopy. BG testing is potentially helpful but sensitivity is insufficient to exclude PCP.
The magnetic propeller accretion regime of LkCa 15
Authors: Donati J-F , Bouvier J , Alencar S H , Hill C , Carmona A , Folsom C P , Ménard F , Gregory S G , Hussain G A , Grankin K , Moutou C , Malo L , Takami M , Herczeg G J ,   MaTYSSE Collaboration
Published: November 2018

We present a spectropolarimetric study of the classical T Tauri star (cTTS) LkCa 15 investigating the large-scale magnetic topology of the central star and the way the field connects to the inner regions of the accretion disc. We find that the star hosts a strong poloidal field with a mainly axisymmetric dipole component of 1.35 kG, whereas the mass accretion rate at the surface of the star is 10−9.2 M⊙  yr−1. It implies that the magnetic field of LkCa 15 is able to evacuate the central regions of the disc up to a distance of 0.07 au at which the Keplerian orbital period equals the stellar rotation period. Our results suggest that LkCa 15, like the lower mass cTTS AA Tau, interacts with its disc in a propeller mode, a regime supposedly very efficient at slowing down the rotation of cTTSs hosting strong dipolar fields.
On the possibility of detecting ultrashort period exoplanets with LISA
Authors: Wong Kaze W K , Berti Emanuele , Gabella William E , Holley-Bockelmann Kelly
Published: November 2018

Cunha, Silva & Lima recently reexamined the possibility of detecting gravitational waves from exoplanets, claiming that three ultrashort period systems would be observable by LISA. We revisit their analysis and conclude that the currently known exoplanetary systems are unlikely to be detectable, even assuming a LISA observation time Tobs = 4 yr. Conclusive statements on the detectability of one of these systems, GP Com b, will require better knowledge of the system’s properties, as well as more careful modelling of both LISA’s response and theG alactic confusion noise. Still, the possibility of exoplanet detection with LISA is interesting enough to warrant further study, as gravitational waves could yield dynamical properties that are difficult to constrain with electromagnetic observations.
Functional Comparison of a Pediatric Patient With Osteosarcoma and Limb-Sparing Distal Femoral Endoprosthesis With an Identical Twin
Authors: Ambler Steven B. , Highsmith M. Jason , Alvero Christine , Binitie Odion T.
Published: November 2018

Background/Objective:

In children, limb salvage techniques have been more slowly adopted because of concerns of complications from multiple surgical procedures, the sacrificing of the physis, and the leg-length discrepancy that can ensue. The purpose of this study was to compare gait and function between a pediatric patient with a distal femur replacement and his identical, healthy twin brother.

Methods:

Design: A single, case-control design was used.

Participants: A 13-year-old adolescent boy underwent a distal femoral resection and endoprosthetic reconstruction with a noninvasive extendible endoprosthesis. The control was the healthy, identical twin brother of the case patient.

Main Outcome Measure(s):

Functional movement testing consisting of 5× Sit-to-Stand Test, 10-m Walk Test, Timed Up and Go (TUG) test, and L-test. Spatiotemporal gait analysis was used to assess degree of asymmetry.

Results:

Comparisons were mixed across the functional movement testing, with the patient performing inferiorly on the 5× Sit-to-Stand Test and the 10-m Walk Test and superiorly on the TUG test and the L-test. Degree of asymmetry for step time, swing time, single support, and initial double support were all significantly different (P ≤ .05), with the patient being less symmetric in all measures.

Limitations:

This study is limited by its small sample size and a comparison with a single time point.

Conclusion:

Although the patient is doing well functionally, asymmetries remain compared with his twin. Future research should focus on more direct comparison of subjects who have undergone different treatment options for sarcoma.