bluuebunny/crossref_metadata_2025 huggingface dataset:
Supercharging Strategies for Prefabricated Flaps in a Rat Model
Authors: Xu Heng , Steinberger Zvi , Wo Yan , Li Ke , Kuo Chenghung , Tong Yun , Zhang Yixin
Published: May 2019

Background Limited survival area is an intractable problem in the clinical practice of prefabricated flaps. This study compared four strategies to find an effective method and to understand the potential mechanisms for supercharging.

Methods A prefabricated abdominal flap rodent model was prepared. Rats were randomly divided into five groups (n = 6/group). (A) Control group: prefabricated right side femoral vessels. Based on group A, various prefabricated vessels were added; (B) proximal venous supercharging group: right side superficial inferior epigastric vein (SIEV); (C) proximal arterial supercharging group: right side superficial inferior epigastric artery (SIEA); (D) distal venous supercharging group: left side SIEV; and (E) distal arterial supercharging group: left side SIEA. Macroscopic analysis, near-infrared fluorescence imaging, and microscopy were used to analyze the survival area, fluorescence area, and capillary density.

Results No significant differences in survival areas were found among supercharging groups (B–E), which were larger than in the control group. Near-infrared fluorescence imaging showed the areas of control and venous supercharging groups (A, B, and D) were smaller than in arterial groups (C and E). Capillary density areas in the right part of the flap in proximal supercharging groups (B and C) and left part of the flap in distal supercharging groups (D and E) were all greater than group A, with no significant differences among the other groups.

Conclusion Enhanced neovascularization is a useful supercharging strategy. Both arterial and venous vessel supercharging improved the survival area of prefabricated flaps.
On the nonlinearity of quantum dynamical entropy
Authors: Androulakis George , Wright Duncan
Published: May 2019

Linearity of a dynamical entropy means that the dynamical entropy of the n-fold composition of a dynamical map with itself is equal to n times the dynamical entropy of the map for every positive integer n. We show that the quantum dynamical entropy introduced by Słomczyński and Życzkowski is nonlinear in the time interval between successive measurements of a quantum dynamical system. This is in contrast to Kolmogorov-Sinai dynamical entropy for classical dynamical systems, which is linear in time. We also compute the exact values of quantum dynamical entropy for the Hadamard walk with varying Lüders-von Neumann instruments and partitions.
Dielectrophoretic buoyancy and heat transfer in a dielectric liquid contained in a cylindrical annular cavity
Authors: Kang Changwoo , Mutabazi Innocent
Published: May 2019

The effect of a thermoelectric body force on the flow of a dielectric fluid with a radial temperature gradient and an alternating electric voltage in a cylindrical annular cavity has been studied by a direct numerical simulation. The radial temperature gradient induces a vertical ascending flow near the hot surface and descending flow near the cold surface. A radial dielectrophoretic force with the electric field acting induces a thermoelectric convection in the form of columnar vortices that can transfer heat from the hot surface to the cold one. The heat transfer coefficient in the dielectric fluid significantly increases with the applied electric voltage.
Electroplasticity in AZ31B subjected to short-duration high-frequency pulsed current
Authors: Zhao Jingyi , Ren Zhencheng , Zhang Hao , Wang Guo-Xiang , Dong Yalin , Ye Chang
Published: May 2019

In this study, the plasticity behavior of an AZ31B magnesium alloy subjected to short-duration (100 μs), high-frequency (120–800 Hz) pulsed current was investigated using tensile tests. The key finding is that the effect of pulsed current on plastic deformation goes beyond the Joule heating effect. In our experiments, the frequency was adjusted to maintain a constant effective current density and, thus, the same Joule heating effect. A comparison with continuous current having the same Joule heating effect was made as well. It was observed that when the peak current density is higher than a critical value, a higher peak current density will yield a more significant reduction in flow stress even though the thermal heating effect is the same. This critical current density decreases with the increase in the effective current density. Pulsed current with a higher peak current density can more effectively reduce the dislocation density through electric-induced annealing, induce more severe grain rotation, and, thus, lower the resistance for dislocations to pass through barriers like grain boundaries, resulting in a more significant flow stress reduction. X-ray diffraction characterizations were also conducted for the deformed specimen to show that a higher peak current density induces more severe grain rotation and, thus, more effectively decreases dislocation density.
The laser shock station in the dynamic compression sector. I
Authors: Wang Xiaoming , Rigg Paulo , Sethian John , Sinclair Nicholas , Weir Nicholas , Williams Brendan , Zhang Jun , Hawreliak James , Toyoda Yoshimasa , Gupta Yogendra , Li Yuelin , Broege Douglas , Bromage Jake , Earley Robert , Guy Dale , Zuegel Jonathan
Published: May 2019

The Laser Shock Station in the Dynamic Compression Sector (DCS) [Advanced Photon Source (APS), Argonne National Laboratory] links a laser-driven shock compression platform with high energy x-ray pulses from the APS to achieve in situ, time-resolved x-ray measurements (diffraction and imaging) in materials subjected to well-characterized, high stress, short duration shock waves. This station and the other DCS experimental stations provide a unique and versatile facility to study condensed state phenomena subjected to shocks with a wide range of amplitudes (to above ∼350 GPa) and time-durations (∼10 ns–1 µs). The Laser Shock Station uses a 100 J, 5–17 ns, 351 nm frequency tripled Nd:glass laser with programmable pulse shaping and focal profile smoothing for maximum precision. The laser can operate once every 30 min. The interaction chamber has multiple diagnostic ports, a sample holder to expose 14 samples without breaking vacuum, can vary the angle between the x-ray and laser beams by 135°, and can translate to select one of the two types of x-ray beams. The x-ray measurement temporal resolution is ∼90 ps. The system is capable of reproducible, well-characterized experiments. In a series of 10 shots, the absolute variation in shock breakout times was less than 500 ps. The variation in peak particle velocity at the sample/window interface was 4.3%. This paper describes the entire DCS Laser Shock Station, including sample fabrication and diagnostics, as well as experimental results from shock compressed tantalum that demonstrate the facility’s capability for acquiring high quality x-ray diffraction data.
Oxygen vacancy induced electronic structure variation in the La0.2Sr0.8MnO3 thin film
Authors: Zhao Jiali , Liu Chen , Li Jinmei , Wu Rui , Wang Jiaou , Qian Haijie , Guo Haizhong , Li Jiankun , Ibrahim Kurash
Published: May 2019

Oxygen vacancy in different oxide systems shows up as a crucial parameter in modulation of the emerging application-oriented functionalities. A systematic exploration on the relation between oxygen vacancy and electronic structure of the La0.2Sr0.8MnO3 (LSMO) thin film has been carried out through sequential surface treatments followed by a series of wide scan XPS, O 1s XPS, O-K edge XAS, Mn-L edge XAS and work function measurements. Experimental results demonstrate mutual corroborative certifying evidences in between the different photoemission spectral measurements on the evolution and influence of the oxygen vacancy. Spectral characteristic features observed in the work are applicable using as justification fingerprint for the existence, modulation, or elimination of the oxygen vacancy in similar perovskite type oxide systems.
Ab initio predictions and laboratory validation for consistent ozone intensities in the MW, 10 and 5 μm ranges
Authors: Tyuterev Vl. G. , Barbe A. , Jacquemart D. , Janssen C. , Mikhailenko S. N. , Starikova E. N.
Published: May 2019

Reliable ozone spectral data consistent over several spectral ranges are a challenge for both experiment and theory. We present ab initio calculations for strong lines that lead to consistent results from the microwave to mid-infrared regions. The results agree well with established microwave line lists and our new measurements in the fundamental and first overtone regions of ozone at 5 and 10 μm. The calculations and their agreement to within 1% with measurements provide an important step toward consistent and accurate spectroscopic ozone data. The results imply that actual databases need to be corrected by about 3% in the corresponding mid-infrared spectral intervals. Appropriate recommendations for the consistency of strong line intensities of the ozone molecule in microwave, 10 and 5 μm ranges, in HITRAN (HIgh-resolution TRANsmittance and molecular apbsorption) and GEISA (Gestion et Etude des Informations Spectroscopiques Atmosphériques) databases are suggested.
An experimental study on the effect of swirl number on pollutant formation in propane bluff-body stabilized swirl diffusion flames
Authors: Jalalatian Nafiseh , Tabejamaat Sadegh , Kashir Babak , EidiAttarZadeh Masoud
Published: May 2019

The combustion characteristics of propane/air bluff-body stabilized swirl diffusion flames within the turbulent regime are studied experimentally to determine the effect of the swirl number on the flame dynamics and pollutant emissions. The investigated burner consists of a central bluff body with an annulus to introduce the tangential and axial air flows. Results show that in low annulus Reynolds numbers (ReS), the temperature distribution is more affected by the overall equivalence ratio (φo), which is calculated based on the flow rates of the air supplies and the fuel jet. However, by increasing ReS, the impact of swirl number becomes more apparent. Analysis of the combustion products demonstrates a reduction in CO concentration with increasing the geometric swirl number which becomes more evident in higher annulus Reynolds numbers. In addition, the trend of NO emission is strongly analogous to the temperature distribution which is an indication of thermal NO formation. Measurements demonstrate that in lower annulus Reynolds numbers, the dominant factor is the overall equivalence ratio, while with increasing the annulus Reynolds number, the swirl number represents more significance.
Atomic modeling of photoionization fronts in nitrogen gas
Authors: Gray William J. , Keiter P. A. , Lefevre H. , Patterson C. R. , Davis J. S. , Powell K. G. , Kuranz C. C. , Drake R. P.
Published: May 2019

Photoionization fronts play a dominant role in many astrophysical environments but remain difficult to achieve in a laboratory experiment. Recent papers have suggested that experiments using a nitrogen medium held at ten atmospheres of pressure which is irradiated by a source with a radiation temperature of TR ∼ 100 eV can produce viable photoionization fronts. We present a suite of one-dimensional numerical simulations using the Helios multimaterial radiation hydrodynamics code that models these conditions and the formation of a photoionization front. We study the effects of varying the atomic kinetics and radiative transfer model on the hydrodynamics and ionization state of the nitrogen gas, finding that more sophisticated physics, in particular, a multi-angle long characteristic radiative transfer model and a collisional-radiative atomics model, dramatically changes the atomic kinetic evolution of the gas. A photoionization front is identified by computing the ratios between the photoionization rate, the electron impact ionization rate, and the total recombination rate. We find that due to the increased electron temperatures found using more advanced physics that photoionization fronts are likely to form in our nominal model. We report the results of several parameter studies. In one of these, the nitrogen pressure is fixed at ten atmospheres and the source radiation temperature is varied, while in another, the temperature is fixed at 100 eV and the nitrogen pressure is varied. Lower nitrogen pressures increase the likelihood of generating a photoionization front while varying the peak source temperature has little effect.
Analysis of sponsor hearings on health technology assessment decision making
Authors: Flowers Melinda , Lybrand Sean , Wonder Michael
Published: May 2019

Objective
The aim of this study was to get a better understanding of the frequency of Pharmaceutical Benefits Advisory Committee (PBAC) hearings, the factors that influence a sponsor’s decision to proceed with a hearing and to assess the impact hearings may have had on PBAC decision making.

Methods
All public summary documents (PSDs) from March 2014 to November 2016 PBAC meetings, obtained from the Pharmaceutical Benefits Scheme (PBS) website, were examined to identify major submissions for which sponsor hearings were conducted. Each PSD was analysed to determine the topics discussed at the sponsor hearing and the ‘usefulness’ of a sponsor hearing from the PBAC’s perspective.

Results
During the study period there were 472 PSDs. 74 sponsor hearings (28% of major submissions) were conducted during the study period. A clinician external to the sponsor presented at the majority of the hearings (78%) and accordingly, the main topics presented related to clinical positioning/use and clinical benefit/use.

Conclusion
The PBAC considered approximately 45% of sponsor hearings to be informative or moderately informative whereas 18% were classed as uninformative.

What is known about the topic?
Although the sponsors of medicines being considered by the Pharmaceutical Benefits Advisory Committee (PBAC) for public subsidy have been able to give a 10 min presentation to the Committee at the time of decision making for several years, it is unknown whether these hearings are beneficial.

What does this paper add?
We present what is believed to be the results of the first analysis of PBAC sponsor hearings.

What are the implications for practitioners?
All stakeholders should consider the findings of our research and associated recommendations to ensure that future sponsor hearings enhance PBAC decision making and promote good public health policy.
Influence of capping ligands on the assembly of quantum dots and their properties
Authors: Al-Alwani Ammar J. , Shinkarenko O. A. , Chumakov A. S. , Pozharov M. V. , Begletsova N. N. , Kolesnikova Anna S. , Sevostyanova V. P. , Glukhovskoy E. G.
Published: May 2019

In order to understand the effect of capping ligand on optical and electrical properties of semiconductor quantum dots (QDs), we have added liquid crystal (8CB) to the CdSe/CdS/ZnS QDs monolayer formed via the Langmuir Blodgett technique And studied emission spectra and conducting properties of resulting QDs. The assembly of QDs monolayer modified by liquid crystal (8CB) can be tuned by varying the temperature. The mechanism of the influence of capping ligands on the gap energy, dipole moment and charge distribution within (CdSe)13 cluster was studied via quantum chemical calculations, i.e. we have used density functional theory to systematically investigate the equilibrium configuration of QDs passivated by oleic acid and liquid crystal ligands.

GRAPHICAL ABSTRACT
The structure solution of the F-type i-ZnMgHf from the X-ray diffraction
Authors: Buganski Ireneusz , Toyonaga Kotoba , Takakura Hiroyuki , Yamada Tsunetomo , de Boissieu Marc , Perez Olivier , Fertey Pierre , Wolny Janusz
Published: May 2019

We report a successful growth of the ZnMgHf F-type icosahedral quasicrystal in the form of faceted single grains. By varying the heat treatment parameters we were able to obtain single crystals with a quality suitable for a single crystal X-ray diffraction which was conducted in a synchrotron facility. Ab initio structure solution by a charge flipping algorithm manifests the existence of two types of Bergman clusters. Clusters are differentiated by the preferential occupation of the high-symmetry positions by hafnium in a rhombic triacontahedron, being the outer shell of the atomic cluster.

This paper is part of a Thematic Issue on The Crystallographic Aspects of Metallic Alloys.
Moderate‐intensity exercise performed in the evening does not impair sleep in healthy males
Authors: Miller D. J. , Sargent C. , Roach G. D. , Scanlan A. T. , Vincent G. E. , Lastella M.
Published: May 2019

The aim of this study was to examine the effect of single bouts of moderate‐intensity aerobic exercise and moderate‐intensity resistance exercise performed in the evening on the sleep of healthy young males. The study employed a repeated‐measures, counterbalanced, crossover design with three conditions (control, evening aerobic exercise, evening resistance exercise). Twelve male participants (mean ± SD; age: 21.9 ± 2.7 yr) attended the laboratory on three occasions separated by one day between each visit. Between 20:45 h and 21:30 h, participants completed either no exercise, 30 min of aerobic exercise at 75%HRmax, or 30 min of resistance exercise corresponding to 75% of 10‐repetition maximum. A 9‐h sleep opportunity was provided between 23:00 h and 08:00 h. Core body temperature was measured using ingestible temperature capsules and sleep was measured using polysomnography. Core body temperature was higher during the aerobic exercise and resistance exercise compared to control (p = 0.001). There was no difference in core body temperature at bedtime between the conditions. Sleep onset latency, total sleep time, slow‐wave sleep duration, REM sleep duration, wake after sleep onset and sleep efficiency were similar in each condition (p > 0.05). Single bouts of moderate‐intensity aerobic exercise or moderate‐intensity resistance exercise performed in the evening did not impact subsequent night‐time sleep. Core body temperature increased during both forms of exercise, but returned to pre‐exercise levels in the 90 min prior to bedtime. Healthy young males can engage in a single bout of moderate‐intensity aerobic exercise or moderate‐intensity resistance exercise ceasing 90 min before bed without compromising their subsequent sleep.
Psychometric evaluation of two instruments to assess connection to nature / Evaluación psicométrica de dos instrumentos que miden la conexión con la naturaleza
Authors: Chew Peter K. H.
Published: May 2019

The biophilia hypothesis states that human beings have an innate tendency to connect with nature. The current study aimed to examine the psychometric properties of the full and short versions of both the Environmental Identity Scale (EID) and the Nature Relatedness Scale (NR). Participants were 209 Singaporean undergraduate students (67.9% females) from a medium-sized university in Singapore. Exploratory factor analyses revealed a unidimensional structure for the Full EID and the Short EID. Acceptable internal consistency coefficients of .96 and .92 were found for the two instruments, respectively. Exploratory factor analyses revealed a three-factor structure for the Full NR: (a) NR-Self; (b) NR-Experience; and (c) NR-Perspective. However, two items were removed, and there are differences in the items that load on each factor. In addition, the NR-Perspective is unreliable, with an internal consistency coefficient of .62. Exploratory factor analyses revealed a unidimensional structure for the Short NR. An acceptable internal consistency coefficient of .82 was found. Taken together, the current study provided support for the use of the Full and Short EID and the Short NR as psychometrically valid instruments among Singapore undergraduate students.
Who plays the ferryman: ATG2 channels lipids into the forming autophagosome
Authors: Ktistakis Nicholas T.
Published: May 2019

Expansion of the autophagosomal membrane requires a mechanism to supply lipids while excluding most membrane proteins. In this issue, Valverde et al. (2019. J. Cell Biol. https://doi.org/10.1083/jcb.201811139) identify ATG2, a member of the autophagy-related protein family, as a lipid transfer protein and provide important novel insights on how autophagosomes grow.
Hlf marks the developmental pathway for hematopoietic stem cells but not for erythro-myeloid progenitors
Authors: Yokomizo Tomomasa , Watanabe Naoki , Umemoto Terumasa , Matsuo Junichi , Harai Ryota , Kihara Yoshihiko , Nakamura Eri , Tada Norihiro , Sato Tomohiko , Takaku Tomoiku , Shimono Akihiko , Takizawa Hitoshi , Nakagata Naomi , Mori Seiichi , Kurokawa Mineo , Tenen Daniel G. , Osato Motomi , Suda Toshio , Komatsu Norio
Published: May 2019

Before the emergence of hematopoietic stem cells (HSCs), lineage-restricted progenitors, such as erythro-myeloid progenitors (EMPs), are detected in the embryo or in pluripotent stem cell cultures in vitro. Although both HSCs and EMPs are derived from hemogenic endothelium, it remains unclear how and when these two developmental programs are segregated during ontogeny. Here, we show that hepatic leukemia factor (Hlf) expression specifically marks a developmental continuum between HSC precursors and HSCs. Using the Hlf-tdTomato reporter mouse, we found that Hlf is expressed in intra-aortic hematopoietic clusters and fetal liver HSCs. In contrast, EMPs and yolk sac hematopoietic clusters before embryonic day 9.5 do not express Hlf. HSC specification, regulated by the Evi-1/Hlf axis, is activated only within Hlf+ nascent hematopoietic clusters. These results strongly suggest that HSCs and EMPs are generated from distinct cohorts of hemogenic endothelium. Selective induction of the Hlf+ lineage pathway may lead to the in vitro generation of HSCs from pluripotent stem cells.
CFTR gets together
Authors: Sedwick Caitlin
Published: May 2019

JGP study shows that pro-secretory agonists prompt CFTR to assemble into large lipid platforms.
Distillability of Sudden Death in Qutrit-Qutrit Systems under Global Mixed Noise*
Authors: Chai Bing-Bing , Guo Jin-Liang
Published: May 2019

Considering the influences of collective dephasing, multilocal qutrit-flip, local qutrit-flip, and the combination of global mixed noise, we study the dynamics of entanglement and the phenomenon of distillability of sudden death (DSD) in a qutrit-qutrit system under various decoherent noises. It is shown that the system always undergoes DSD when it interacts with multilocal and local qutrit-flip noise, and the time-determined bound entangled state is more dependent on different noises. Comparing with the cases of global mixed and collective dephasing noise, we conclude that the qutrit-flip noise is responsible for the DSD.
Multiple Soliton Solutions of Alice–Bob Boussinesq Equations*
Authors: Li Hui , Lou S. Y.
Published: May 2019

Three Alice–Bob Boussinesq (ABB) nonlocal systems with shifted parity (

P
^

s

), delayed time reversal (

T
^

d

) and

P
^

s

T
^

d

nonlocalities are investigated. The multi-soliton solutions of these models are systematically found from the

P
^

s

,

T
^

d

and

P
^

s

T
^

d

symmetry reductions of a coupled local Boussinesq system. The result shows that for ABB equations with

P
^

s

and/or

T
^

d

nonlocality, an odd number of solitons is prohibited. The solitons of the

P
^

s

nonlocal ABB and

T
^

d

nonlocal ABB equations must be paired, while any number of solitons is allowed for the

P
^

s

T
^

d

nonlocal ABB system. t-breathers, x-breathers and rogue waves exist for all three types of nonlocal ABB system. In particular, different from classical local cases, the first-order rogue wave can have not only four leaves but also five and six leaves.
Polarization Conversion of Single Photon via Scattering by a Λ System in a Semi-Infinite Waveguide*
Authors: Yu Fu-Qiang , Cheng Mu-Tian , Li Shao-Ming , Ma Xiao-San , Zhu Zhi-Feng , Huang Xian-Shan
Published: May 2019

We theoretically investigate single-photon polarization conversion via scattering by an atom with Λ configuration coupled to a semi-infinite waveguide and discuss the two cases in which the Λ system is non-degenerated and degenerated. By applying the hard-wall boundary condition of the semi-infinite waveguide, it is found that single-photon polarization conversion can be realized with unit probability for both cases under the ideal condition. Together with the polarization conversion, the frequency conversion of a single photon can also be realized with unit probability in the ideal case if the Λ system is not degenerated.
Reduction of Electron Leakage in a Deep Ultraviolet Nitride Laser Diode with a Double-Tapered Electron Blocking Layer*
Authors: Wang Yi-Fu , Niass Mussaab I. , Wang Fang , Liu Yu-Huai
Published: May 2019

A double-tapered AlGaN electron blocking layer (EBL) is proposed to apply in a deep ultraviolet semiconductor laser diode. Compared with the inverse double-tapered EBL, the laser with the double-tapered EBL shows a higher slope efficiency, which indicates that effective enhancement in the transportation of electrons and holes is achieved. Particularly, comparisons among the double-tapered EBL, the inverse double-tapered EBL, the single-tapered EBL and the inverse single-tapered EBL show that the double-tapered EBL has the best performance in terms of current leakage.
Low-Temperature Properties of CePt3P Tuned by Magnetic Field*
Authors: Chen Jian , Lv Bai-Jiang , Zheng Shi-Yi , Li Yu-Ke
Published: May 2019

We present low-temperature magnetization, magnetoresistance and specific heat measurements on the Kondo lattice compound CePt3P under applied magnetic fields up to 9.0 T. At zero field, CePt3P exhibits a moderately enhanced Sommerfeld coefficient of electronic specific heat γ
Ce = 86 mJ/mol·K2 as well as two successive magnetic transitions of Ce 4f moments: an antiferromagnetic ordering at T
N1 = 3.0K and a spin reorientation at T
N2 = 1.9 K. The value of T
N1 shifts to lower temperature as magnetic field increases, and it is ultimately suppressed around B
c ∼ 3.0T at 1.5 K. No evidence of non-Fermi liquid behavior is observed around B
c down to the lowest temperature measured. Moreover, γ decreases monotonously with increasing the magnetic field. On the other hand, the electrical resistivity shows an anomalous temperature dependence ρ ∝ T

n
with the exponent n decreasing monotonously from ∼2.6 around B
c down to ∼1.7 for B = 9.0 T. The T–B phase diagram constructed from the present experimental results of CePt3P does not match the quantum criticality scenario of heavy fermion systems.
Dressed quantum trajectories: novel approach to the non-Markovian dynamics of open quantum systems on a wide time scale
Authors: Polyakov Evgeny A , Rubtsov Alexey N
Published: May 2019

A new approach to theory and simulation of the non-Markovian dynamics of open quantum systems is presented. It is based on identification of a parameter which is uniformly bounded on wide time intervals: the occupation of the virtual cloud of quanta. By ‘virtual’ we denote those bath excitations which were emitted by the open system, but eventually will be reabsorbed before any measurement of the bath state. A useful property of the virtual cloud is that the number of its quanta is expected to saturate on long times, since physically this cloud is a (retarded) polarization of the bath around the system. Therefore, the joint state of open system and virtual cloud (we call it dressed state) can be accurately represented in a truncated basis of Fock states, on a wide time scale. At the same time, there can be an arbitrarily large number of the observable quanta (which survive up to measurement), especially if the open system is under driving. However, it turns out that the statistics of the bath-measurement outcomes is classical (in a suitable measurement basis): one can employ a Monte Carlo sampling of these outcomes. Therefore, it is possible to efficiently simulate the dynamics of the observable quantum field. In this work we consider the bath measurement with respect to the coherent states, which yields the Husimi function as the positive (quasi)probability distribution of the outcomes. The joint evolution of the dressed state and the corresponding outcome is called the dressed quantum trajectory. The Monte Carlo sampling of these trajectories yields a stochastic simulation method with promising convergence properties on wide time scales.
Structural studies of metastable and equilibrium vortex lattice domains in MgB2
Authors: Louden E R , Leishman A W D , Rastovski C , Kuhn S J , DeBeer-Schmitt L , Dewhurst C D , Zhigadlo N D , Eskildsen M R
Published: May 2019

The vortex lattice (VL) in MgB2 is characterized by the presence of long-lived metastable states (MSs), which arise from cooling or heating across the equilibrium phase boundaries. A return to the equilibrium configuration can be achieved by inducing vortex motion. Here we report on small-angle neutron scattering studies of MgB2, focusing on the structural properties of the VL as it is gradually driven from metastable to equilibrium states (ESs) by an AC magnetic field. Measurements were performed using initial MSs obtained either by cooling or heating across the equilibrium phase transition. In all cases, the longitudinal correlation length remains constant and comparable to the sample thickness. Correspondingly, the VL may be considered as a system of straight rods, where the formation and growth of ES domains only occurs in the two-dimensional plane perpendicular to the applied field direction. Spatially resolved raster scans of the sample were performed with apertures as small as 80 μm, corresponding to only 1.2 × 106 vortices for an applied field of 0.5 T. These revealed spatial variations in the metastable and equilibrium VL populations, but individual domains were not directly resolved. A statistical analysis of the data indicates an upper limit on the average domain size of approximately 50 μm.
Thermal and structural properties of the martensitic transformations in Fe7Pd3 shape memory alloys: an ab initio-based molecular dynamics study
Authors: Holm Alexander , Mayr Stefan G
Published: May 2019

Ferromagnetic shape memory alloys, including the Fe7Pd3 system, constitute an upcoming class of functional materials, whose atomic-scale physical foundations are still insufficiently understood. The present work employs molecular dynamics simulations, based on ab initio derived embedded atom method potentials, to study martensitic transformations and twin variant reorientation. We address thermal and stress induced austenite-martensite transitions, twinning, as well as twin boundary mobility. While the predicted thermal properties are in accordance with experimental observations, we explore the detailed crystallography underlying transformation as well as twin boundary motion.
The symmetry energy and incompressibility constrained by the observations of glitching pulsars
Authors: Yan Yan
Published: May 2019

We investigate the masses of glitching pulsars in order to constrain their equation of state (EOS). The observations of glitches (sudden jumps in rotational frequency) may provide information on the interior physics of neutron stars. With the assumption that glitches are triggered by superfluid neutrons, the masses of glitching neutron stars can be estimated using observations of maximum glitches. Together with the observations of thermal emission from glitching pulsars Vela and J1709–4429, the slope of symmetry energy and incompressibility of nuclear matter at saturation density can be constrained. The slope of symmetry energy L should be larger than 67 MeV while the lower limit of incompressibility for symmetric nuclear matter K
0 is 215 MeV. We also obtain a relationship between L and K
0: 6.173 MeV + 0.283 K
0 ≤ L ≤ 7.729 MeV + 0.291 K
0. The restricted EOSs are consistent with the observations of 2-solar-mass neutron stars and gravitational waves from a binary neutron star inspiral.
Industrial symbiosis potential and urban infrastructure capacity in Mysuru, India
Authors: Chertow Marian , Gordon Matthew , Hirsch Peter , Ramaswami Anu
Published: May 2019

If the material intensive enterprises in an urban area of several million people shared physical resources that might otherwise be wasted, what environmental and public benefits would result? This study develops an algorithm based on lifecycle assessment tools for determining a city’s industrial symbiosis potential—that is, the sum of the wastes and byproducts from a city’s industrial enterprises that could reasonably serve as resource inputs to other local industrial processes. Rather than report, as do many previous papers, on private benefits to firms, this investigation focuses on public benefits to cities by converting the maximum quantity of resources recoverable by local enterprises into an estimate of the capacity of municipal infrastructure conserved in terms of landfill space and water demand. The results here test this novel approach for the district of Mysuru (Mysore), India. We find that the industrial symbiosis potential calculated based on analysis of the inputs and outputs of ∼1000 urban enterprises, translates into 84 000 tons of industrial waste, greater than 74 000 tons of CO2e, and 22 million liters per day of wastewater. The method introduced here demonstrates how industrial symbiosis links private production and public infrastructure to improve the resource efficiency of a city by creating an opportunity to extend the capacity of public infrastructure and generate public health co-benefits.
Multifaceted protein–protein interaction prediction based on Siamese residual RCNN
Authors: Chen Muhao , Ju Chelsea J -T , Zhou Guangyu , Chen Xuelu , Zhang Tianran , Chang Kai-Wei , Zaniolo Carlo , Wang Wei
Published: May 2019

Motivation

Sequence-based protein–protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Based on these features, statistical algorithms are learned to classify the PPIs. However, such explicit features are usually costly to extract, and typically have limited coverage on the PPI information.

Results

We present an end-to-end framework, PIPR (Protein–Protein Interaction Prediction Based on Siamese Residual RCNN), for PPI predictions using only the protein sequences. PIPR incorporates a deep residual recurrent convolutional neural network in the Siamese architecture, which leverages both robust local features and contextualized information, which are significant for capturing the mutual influence of proteins sequences. PIPR relieves the data pre-processing efforts that are required by other systems, and generalizes well to different application scenarios. Experimental evaluations show that PIPR outperforms various state-of-the-art systems on the binary PPI prediction problem. Moreover, it shows a promising performance on more challenging problems of interaction type prediction and binding affinity estimation, where existing approaches fall short.

Availability and implementation

The implementation is available at https://github.com/muhaochen/seq_ppi.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
scOrange—a tool for hands-on training of concepts from single-cell data analytics
Authors: Stražar Martin , Žagar Lan , Kokošar Jaka , Tanko Vesna , Erjavec Aleš , Poličar Pavlin G , Starič Anže , Demšar Janez , Shaulsky Gad , Menon Vilas , Lemire Andrew , Parikh Anup , Zupan Blaž
Published: May 2019

Motivation

Single-cell RNA sequencing allows us to simultaneously profile the transcriptomes of thousands of cells and to indulge in exploring cell diversity, development and discovery of new molecular mechanisms. Analysis of scRNA data involves a combination of non-trivial steps from statistics, data visualization, bioinformatics and machine learning. Training molecular biologists in single-cell data analysis and empowering them to review and analyze their data can be challenging, both because of the complexity of the methods and the steep learning curve.

Results

We propose a workshop-style training in single-cell data analytics that relies on an explorative data analysis toolbox and a hands-on teaching style. The training relies on scOrange, a newly developed extension of a data mining framework that features workflow design through visual programming and interactive visualizations. Workshops with scOrange can proceed much faster than similar training methods that rely on computer programming and analysis through scripting in R or Python, allowing the trainer to cover more ground in the same time-frame. We here review the design principles of the scOrange toolbox that support such workshops and propose a syllabus for the course. We also provide examples of data analysis workflows that instructors can use during the training.

Availability and implementation

scOrange is an open-source software. The software, documentation and an emerging set of educational videos are available at http://singlecell.biolab.si.
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
Authors: Nair Surag , Kim Daniel S , Perricone Jacob , Kundaje Anshul
Published: May 2019

Motivation

Genome-wide profiles of chromatin accessibility and gene expression in diverse cellular contexts are critical to decipher the dynamics of transcriptional regulation. Recently, convolutional neural networks have been used to learn predictive cis-regulatory DNA sequence models of context-specific chromatin accessibility landscapes. However, these context-specific regulatory sequence models cannot generalize predictions across cell types.

Results

We introduce multi-modal, residual neural network architectures that integrate cis-regulatory sequence and context-specific expression of trans-regulators to predict genome-wide chromatin accessibility profiles across cellular contexts. We show that the average accessibility of a genomic region across training contexts can be a surprisingly powerful predictor. We leverage this feature and employ novel strategies for training models to enhance genome-wide prediction of shared and context-specific chromatin accessible sites across cell types. We interpret the models to reveal insights into cis- and trans-regulation of chromatin dynamics across 123 diverse cellular contexts.

Availability and implementation

The code is available at https://github.com/kundajelab/ChromDragoNN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Selfish: discovery of differential chromatin interactions via a self-similarity measure
Authors: Ardakany Abbas Roayaei , Ay Ferhat , Lonardi Stefano
Published: May 2019

Motivation

High-throughput conformation capture experiments, such as Hi-C provide genome-wide maps of chromatin interactions, enabling life scientists to investigate the role of the three-dimensional structure of genomes in gene regulation and other essential cellular functions. A fundamental problem in the analysis of Hi-C data is how to compare two contact maps derived from Hi-C experiments. Detecting similarities and differences between contact maps are critical in evaluating the reproducibility of replicate experiments and for identifying differential genomic regions with biological significance. Due to the complexity of chromatin conformations and the presence of technology-driven and sequence-specific biases, the comparative analysis of Hi-C data is analytically and computationally challenging.

Results

We present a novel method called Selfish for the comparative analysis of Hi-C data that takes advantage of the structural self-similarity in contact maps. We define a novel self-similarity measure to design algorithms for (i) measuring reproducibility for Hi-C replicate experiments and (ii) finding differential chromatin interactions between two contact maps. Extensive experimental results on simulated and real data show that Selfish is more accurate and robust than state-of-the-art methods.

Availability and implementation

https://github.com/ucrbioinfo/Selfish
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework
Authors: Yang Hao , Chi Hao , Zeng Wen-Feng , Zhou Wen-Jing , He Si-Min
Published: May 2019

Motivation

De novo peptide sequencing based on tandem mass spectrometry data is the key technology of shotgun proteomics for identifying peptides without any database and assembling unknown proteins. However, owing to the low ion coverage in tandem mass spectra, the order of certain consecutive amino acids cannot be determined if all of their supporting fragment ions are missing, which results in the low precision of de novo sequencing.

Results

In order to solve this problem, we developed pNovo 3, which used a learning-to-rank framework to distinguish similar peptide candidates for each spectrum. Three metrics for measuring the similarity between each experimental spectrum and its corresponding theoretical spectrum were used as important features, in which the theoretical spectra can be precisely predicted by the pDeep algorithm using deep learning. On seven benchmark datasets from six diverse species, pNovo 3 recalled 29–102% more correct spectra, and the precision was 11–89% higher than three other state-of-the-art de novo sequencing algorithms. Furthermore, compared with the newly developed DeepNovo, which also used the deep learning approach, pNovo 3 still identified 21–50% more spectra on the nine datasets used in the study of DeepNovo. In summary, the deep learning and learning-to-rank techniques implemented in pNovo 3 significantly improve the precision of de novo sequencing, and such machine learning framework is worth extending to other related research fields to distinguish the similar sequences.

Availability and implementation

pNovo 3 can be freely downloaded from http://pfind.ict.ac.cn/software/pNovo/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors
Authors: Sumanaweera Dinithi , Allison Lloyd , Konagurthu Arun S
Published: May 2019

The information criterion of minimum message length (MML) provides a powerful statistical framework for inductive reasoning from observed data. We apply MML to the problem of protein sequence comparison using finite state models with Dirichlet distributions. The resulting framework allows us to supersede the ad hoc cost functions commonly used in the field, by systematically addressing the problem of arbitrariness in alignment parameters, and the disconnect between substitution scores and gap costs. Furthermore, our framework enables the generation of marginal probability landscapes over all possible alignment hypotheses, with potential to facilitate the users to simultaneously rationalize and assess competing alignment relationships between protein sequences, beyond simply reporting a single (best) alignment. We demonstrate the performance of our program on benchmarks containing distantly related protein sequences.

Availability and implementation

The open-source program supporting this work is available from: http://lcb.infotech.monash.edu.au/seqmmligner.

Supplementary information

Supplementary data are available at Bioinformatics online.
PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors
Authors: Mourragui Soufiane , Loog Marco , van de Wiel Mark A , Reinders Marcel J T , Wessels Lodewyk F A
Published: May 2019

Motivation

Cell lines and patient-derived xenografts (PDXs) have been used extensively to understand the molecular underpinnings of cancer. While core biological processes are typically conserved, these models also show important differences compared to human tumors, hampering the translation of findings from pre-clinical models to the human setting. In particular, employing drug response predictors generated on data derived from pre-clinical models to predict patient response remains a challenging task. As very large drug response datasets have been collected for pre-clinical models, and patient drug response data are often lacking, there is an urgent need for methods that efficiently transfer drug response predictors from pre-clinical models to the human setting.

Results

We show that cell lines and PDXs share common characteristics and processes with human tumors. We quantify this similarity and show that a regression model cannot simply be trained on cell lines or PDXs and then applied on tumors. We developed PRECISE, a novel methodology based on domain adaptation that captures the common information shared amongst pre-clinical models and human tumors in a consensus representation. Employing this representation, we train predictors of drug response on pre-clinical data and apply these predictors to stratify human tumors. We show that the resulting domain-invariant predictors show a small reduction in predictive performance in the pre-clinical domain but, importantly, reliably recover known associations between independent biomarkers and their companion drugs on human tumors.

Availability and implementation

PRECISE and the scripts for running our experiments are available on our GitHub page (https://github.com/NKI-CCB/PRECISE).

Supplementary information

Supplementary data are available at Bioinformatics online.
Clinical Usefulness of Self-Rated Olfactory Performance—A Data Science-Based Assessment of 6000 Patients
Authors: Lötsch Jörn , Hummel Thomas
Published: May 2019

In clinical practice, with its time constraints, a frequent conclusion is that asking about the ability to smell may suffice to detect olfactory problems. To address this question systematically, 6049 subjects were asked about how well they can perceive odors, with 5 possible responses. Participants presented at a University Department of Otorhinolaryngology, where olfactory testing was part of the routine investigation performed in patients receiving surgery at the clinic (for various reasons). According to an odor identification test, 1227 subjects had functional anosmia and 3113 were labeled with normosmia. Measures of laboratory test performance were used to assess the success of self-estimates to capture the olfactory diagnosis. Ratings of the olfactory function as absent or impaired provided the diagnosis of anosmia at a balanced accuracy of 79%, whereas ratings of good or excellent indicated normosmia at a balanced accuracy of 64.6%. The number of incorrect judgments of anosmia increased with age, whereas false negative self-estimates of normosmia became rarer with increasing age. The subject’s sex was irrelevant in this context. Thus, when asking the question “How well can you smell odors?” and querying standardized responses, fairly accurate information can be obtained about whether or not the subject can smell. However, this has to be completed with the almost 30% (355 subjects) of anosmic patients who judged their ability to smell as at least “average.” Thus, olfactory testing using reliable and validated tests appears indispensable.