bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-dependent soft and hard x-ray measurements using streak and x-ray diode array diagnostic systems
Authors: Shpilman Z. , Silberstein S. , Rubin D. , Ehrlich Y. , Oysher Z. , Ferber Y. , Levy I. 
Published: March 2021

High-temperature, high-density experiments require a simultaneous understanding of temporal and spectral regions. The spectral x-ray streak camera (SXSC) is a new high-temporal-resolution spectral x-ray diagnostic system that allows researchers to differentiate between soft and hard x-ray regions. The diagnostic offers three spectral channels with a wide spectral range, one direct channel that includes a filter and two indirect channels that include both mirrors and filters. The opto-mechanical design positions the filtered radiation at three different locations along the streak photo-cathode (PC) slit to provide time-dependent spectral channels with pico-second temporal resolution. A moderate spatial resolution (150–700 μm) is achieved using slits perpendicular to the PC slit, while the slit width is optimized according to the central channel wavelength (for each channel). The diagnostic system covers a spectral range of 30–500 eV for the mirror channels and &gt;1300 eV for the direct channel. The temporal and spatial axes of the streak camera are calibrated with respect to a sequence of x-ray pulses. The SXSC diagnostic system is tested and analyzed using Marshak-wave emission from an SiO2 foam that was heated by a laser-beam irradiated halfraum. The SXSC results are compared to measurements from an x-ray diode array with similar spectral channels.
A transmitted-beam diagnostic for the wavelength-tunable UV drive beam on OMEGA
Authors: Katz J. , Turnbull D. , Kruschwitz B. E. , Rigatti A. L. , Rinefierd R. , Froula D. H. 
Published: March 2021

A transmitted-beam diagnostic (P9TBD) was developed as part of a new experimental platform used to study laser–plasma interactions on OMEGA. Located in the opposing port to the wavelength-tunable (350 nm to 353 nm) UV drive beam, the P9TBD characterizes the beam after it propagates through an undersense plasma. The instrument consists of a large-aperture window that allows light to exit the target chamber and project onto a thin sheet of semi-transparent diffuser material. Light transmitted through the diffuser is recorded using a time-integrated camera and a fiber-optically coupled streaked spectrometer, providing measurements of the energy, power, fluence, polarization, and spectrum of the transmitted beam. The diagnostic enables direct observation of a variety of cross-beam energy transfer phenomena, such as wavelength detuning, polarization effects, and gain saturation.
Reconstructing 3D asymmetries in laser-direct-drive implosions on OMEGA
Authors: Mannion O. M. , Woo K. M. , Crilly A. J. , Forrest C. J. , Frenje J. A. , Johnson M. Gatu , Glebov V. Yu. , Knauer J. P. , Mohamed Z. L. , Romanofsky M. H. , Stoeckl C. , Theobald W. , Regan S. P. 
Published: March 2021

Three-dimensional reconstruction algorithms have been developed, which determine the hot-spot velocity, hot-spot apparent ion temperature distribution, and fuel areal-density distribution present in laser-direct-drive inertial confinement fusion implosions on the OMEGA laser. These reconstructions rely on multiple independent measurements of the neutron energy spectrum emitted from the fusing plasma. Measurements of the neutron energy spectrum on OMEGA are made using a suite of quasi-orthogonal neutron time-of-flight detectors and a magnetic recoil spectrometer. These spectrometers are positioned strategically around the OMEGA target chamber to provide unique 3D measurements of the conditions of the fusing hot spot and compressed fuel near peak compression. The uncertainties involved in these 3D reconstructions are discussed and are used to identify a new nTOF diagnostic line of sight, which when built will reduce the uncertainty in the hot-spot apparent ion temperature distribution from 700 to &lt;400 eV.
Noninvasive neuromagnetic single-trial analysis of human neocortical population spikes
Authors: Waterstraat Gunnar , Körber Rainer , Storm Jan-Hendrik , Curio Gabriel 
Published: March 2021

Significance
Evolution has shaped the human brain as a “single-trial” processor reacting fast and reliably to environmental threats. The noninvasive analysis of its electrical activity commonly draws on electroencephalography/magnetoencephalography (EEG/MEG) with a millisecond time resolution suitable even for short-lived neuronal output spikes. However, while standard EEG/MEG can detect very small evoked population spikes, it does so only after averaging over hundreds of trials. Here, MEG based on an ultralow-noise superconducting quantum interference device (SQUID) is shown to enable the first noninvasive single-trial characterization of human cortical population spikes, revealing amplitudes highly variable between trials and intertrial correlated response latencies. Thus, by expanding the scope of noninvasive neurotechnology, ultralow-noise MEG can support single-trial analyses of input–output characteristics in the human brain.
Super-resolution mapping of cellular double-strand break resection complexes during homologous recombination
Authors: Whelan Donna R. , Rothenberg Eli 
Published: March 2021

Significance
DNA resection is an initial, decisive step in the homologous recombination repair pathway of DNA double-strand breaks (DSBs). However, the individual roles and cross-talk of key proteins in this process remain unclear. To resolve the spatiotemporal dynamics of this intricate process, we applied multicolor single-molecule localization microscopy along with robust analytical approaches. Our data reveal the dynamic actions and interactions of MRE11, BRCA1, and CtIP both as a multimer and individually; the recruitment and spatial exclusion of 53BP1; the role of BLM helicase alongside EXO1 and DNA2 nucleases; and the inhibitory mechanisms of MRE11 exo-/endonuclease inhibition. Together, our findings describe important aspects of DNA DSB repair and highlight key differences between repair of clustered damage and sporadic endogenous breaks.
Role of intramolecular hydrogen bonds in promoting electron flow through amino acid and oligopeptide conjugates
Authors: Orłowski Rafał , Clark John A. , Derr James B. , Espinoza Eli M. , Mayther Maximilian F. , Staszewska-Krajewska Olga , Winkler Jay R. , Jędrzejewska Hanna , Szumna Agnieszka , Gray Harry B. , Vullev Valentine I. , Gryko Daniel T. 
Published: March 2021

Significance
Long-range electron transfer pervades biology, chemistry, and engineering, as it is critical for life-sustaining processes, chemical transformations, energy conversion, as well as electronic and photonic technologies. Elucidating the factors that control the rates of long-range electron transfer remains an outstanding challenge, owing in part to the complexity of proteins and other macromolecular structures that mediate such processes. We have found that short peptides linking electron donors and acceptors can assume folds with intramolecular hydrogen bond interactions that provide electronic-coupling pathways for ultrafast charge transfer. Our work will assist designs of donor–acceptor systems for efficient energy conversion and storage.
Impact of support material deformation in MEMS bulk micromachined diaphragm pressure sensors
Authors: Brace Eric , Ghaderian Sepideh , Ghannoum AbdulRahman , Nieva Patricia 
Published: March 2021

Abstract
In this work, experimental data and finite element analysis reveals deflection in diaphragm supporting material leading to non-linear pressure-reflection response. These results are contrary to the standard assumptions presented in literature, where modelling of deflection response in diaphragm pressure sensors is primarily carried out assuming a rigid supporting structure. An extrinsic fiber-optic Fabry–Perot pressure sensor, based on micro-electromechanical system, is developed and used to investigate optical deflection response. While the sensor is not novel, a series of experiments to validate support deflection phenomena are designed and carried out using a silicon membrane at gauge pressures from 0 to 1000 PSI in ambient temperature. The device is packaged with an industry standard stainless-steel housing typically used in plastic injection moulding. Sensor performance is compared to analytical and finite element modelling. Results suggest that the device is experiencing greater deflection than analytically predicted at pressures above 200 PSI, where a rigid support is assumed in existing literature. Based on these results, a modified analytical model is proposed to correct for this behaviour. The modified model is created through addition of a nonlinear component to an existing model, which is then fitted to the experimental data using least-square methods. Prediction of the experimental deflection results is improved from 81% error using a fixed-support analytical model to 4% error using the presented adjusted model. It is demonstrated that nonlinear effects are present and optically measurable in cases where deflection is lower than 1% of the membrane thickness. This work will aid in the implementation of high-resolution pressure sensors operating in harsh environment conditions.
The Fourier signatures of memristive hysteresis
Authors: Pershin Yuriy V , Chien Chih-Chun , Di Ventra Massimiliano 
Published: March 2021

Abstract
While resistors with memory, sometimes called memristive elements (such as ReRAM cells), are often studied under conditions of periodic driving, little attention has been paid to the Fourier features of their memory response (hysteresis). Here we demonstrate experimentally that the hysteresis of memristive systems can be unambiguously distinguished from the linear or non-linear response of systems without hysteresis by the values of certain Fourier series coefficients. We also show that the Fourier series convergence depends on driving conditions, and introduce a measure of hysteresis. These results may be used to quantify the memory content of resistive memories, and tune their Fourier spectrum according to the excitation signal.
An antisymmetric neural network to predict free energy changes in protein variants
Authors: Benevenuta S , Pancotti C , Fariselli P , Birolo G , Sanavia T 
Published: March 2021

Abstract
The prediction of free energy changes upon protein residue variations is an important application in biophysics and biomedicine. Several methods have been developed to address this problem so far, including physical-based and machine learning models. However, most of the current computational tools, especially data-driven approaches, fail to incorporate the antisymmetric basic thermodynamic principle: a variation from wild-type to a mutated form of the protein structure (

X

W

→

X

M

) and its reverse process (

X

M

→

X

W

) must have opposite values of the free energy difference:

Δ
Δ

G

W
M

=
−
Δ
Δ

G

M
W

. Here, we build a deep neural network system that, by construction, satisfies the antisymmetric properties. We show that the new method (ACDC-NN) achieved comparable or better performance with respect to other state-of-the-art approaches on both direct and reverse variations, making this method suitable for scoring new protein variants preserving the antisymmetry. The code is available at: https://github.com/compbiomed-unito/acdc-nn.
Thermal oxidation of Ru(0001) to RuO2(110) studied with ambient pressure x-ray photoelectron spectroscopy
Authors: Diulus J Trey , Tobler Benjamin , Osterwalder Jürg , Novotny Zbynek 
Published: March 2021

Abstract
The thermal oxidation of Ru(0001) has been extensively studied in the surface science community to determine the oxidation pathway towards ruthenium dioxide (RuO2(110)), improving the knowledge of Ru(0001) surface chemistry. Using time-lapsed ambient-pressure x-ray photoelectron spectroscopy (APXPS), we investigate the thermal oxidation of single-crystalline Ru(0001) films toward rutile RuO2(110) in situ. APXPS spectra were continuously collected while the Ru(0001) films were exposed to a fixed O2 partial pressure of 10−2 mbar and the sample temperature was increased stepwise from room temperature to 400 °C. We initially observe the removal of adventitious carbon and subsequent formation of a chemisorbed oxygen overlayer at 250 °C. Further annealing to 300 °C leads to an increase in thickness of the oxide layer and a shift in the Ru–O component of the Ru 3d spectra, indicating the presence of a metastable O–Ru–O trilayer structure. A rapid formation of the RuO2 rutile phase with an approximate thickness of at least 2.6 nm is formed about four minutes after stabilizing the temperature at 350 °C and subsequent annealing to 400 °C, signaled by a distinct binding energy shift in both the Ru 3d and O 1s spectra, as well as quantitative analysis of XPS intensities. This observed autocatalytic oxidation process agrees well with previous theoretical models and experimental studies, and the data provide the unambiguous spectral identification of one proposed metastable precursor required for full oxidation to rutile RuO2(110). Further ex situ characterization of the grown oxide with x-ray photoelectron diffraction confirms the presence of three rotated domains of rutile RuO2(110) and reveals their orientation relative to the substrate lattice.
Multiple magnetic states of CoPc molecule on a two-dimensional layer of NbSe2
Authors: Montero Ana M , Guimarães Filipe S M , Lounis Samir 
Published: March 2021

Abstract
Molecular spintronics hinges on the detailed understanding of electronic and magnetic properties of molecules interfaced with various materials. Here we demonstrate with ab initio simulations that the prototypical Co-phthalocyanine (CoPc) molecule can surprisingly develop multi-spin states once deposited on the two-dimensional 2H–NbSe2 layer. Conventional calculations based on density functional theory (DFT) show the existence of low, regular and high spin states, which reduce to regular and high spins states once correlations are incorporated with a DFT + U approach. Depending on U, the ground state is either the low spin or high spin state with energy differences affected by the molecular orientation on top of the substrate. Our results are compared to recent scanning probe measurements and motivate further theoretical and experimental studies on the unveiled rich multi-magnetic behavior of CoPc molecule.
2D Nb2SiTe4 and Nb2GeTe4: promising thermoelectric figure of merit and gate-tunable thermoelectric performance
Authors: Wu Xuming , Gao Guoying , Hu Lei , Qin Dan 
Published: March 2021

Abstract
Recently, the experimentally synthesized Nb2SiTe4 was found to be a stable layered narrow-gap semiconductor, and the fabricated field-effect transistors (FETs) based on few-layers Nb2SiTe4 are good candidates for ambipolar devices and mid-infrared detection (Zhao et al 2019 ACS Nano
13 10705–10). Here, we use first-principles combined with Boltzmann transport theory and non-equilibrium Green’s function method to investigate the thermoelectric transport coefficients of monolayer Nb2XTe4 (X = Si, Ge) and the gate voltage effect on the thermoelectric performance of the FET based on monolayer Nb2SiTe4. It is found that both monolayers have large p-type Seebeck coefficients due to the ‘pudding-mold-type’ valence band structure, and they both exhibit anisotropic thermoelectric behavior with optimal thermoelectric figure of merit of 1.4 (2.2) at 300 K and 2.8 (2.5) at 500 K for Nb2SiTe4 (Nb2GeTe4). The gate voltage can effectively increase the thermoelectric performance for the Nb2SiTe4-based FET. The high thermoelectric figure of merit can be maintained in a wide temperature range under a negative gate voltage. Furthermore, the FET exhibits a good gate-tunable Seebeck diode effect. The present work suggests that Nb2XTe4 monolayers are promising candidates for 2D thermoelectric materials and thermoelectric devices.
Photolithographically-patterned C-MEMS graphene by carbon diffusion through nickel
Authors: Vaca Sveidy , Pilloni Oscar , Gómez Axel Rodríguez , Serkovic-Loli Laura N , Qureshi Naser , Oropeza-Ramos Laura 
Published: March 2021

Abstract
In recent years the most studied carbon allotrope has been graphene, due to the outstanding properties that this two-dimensional material exhibits; however, it turns out to be a difficult material to produce, pattern, and transfer to a device substrate without contamination. Carbon microelectromechanical systems are a versatile technology used to create nano/micro carbon devices by pyrolyzing a patterned photoresist, making them highly attractive for industrial applications. Furthermore, recent works have reported that pyrolytic carbon material can be graphitized by the diffusion of carbon atoms through a transition metal layer. In this work we take advantage of the latter two methods in order to produce multilayer graphene by improving the molecular ordering of photolithographically-defined pyrolytic carbon microstructures, through the diffusion (annealing) of carbon atoms through nickel, and also to eliminate any further transfer process to a device substrate. The allotropic nature of the final carbon microstructures was inspected by Raman spectroscopy (Average I
D/I
G of 0.2348 ± 0.0314) and TEM clearly shows well-aligned lattice planes of 3.34 Å fringe separation. These results were compared to measurements made on pyrolytic carbon (Average I
D/I
G of 0.9848 ± 0.0235) to confirm that our method is capable of producing a patterned multilayer graphene material directly on a silicon substrate.
Monte Carlo study on dose distributions from total skin electron irradiation therapy (TSET)
Authors: Ding George X , Osmundson Evan C , Shinohara Eric , Newman Neil B , Price Michael , Kirschner Austin N 
Published: March 2021

Abstract
Total skin electron therapy (TSET) has been used to treat mycosis fungoides since the 1950s. Practitioners of TSET rely on relatively crude, phantom-based point measurements for commissioning and treatment plan dosimetry. Using Monte Carlo simulation techniques, this study presents whole-body dosimetry for a patient receiving rotational, dual-field TSET. The Monte Carlo codes, BEAMnrc/DOSXYZnrc, were used to simulate 6 MeV electron beams to calculate skin dose from TSET. Simulations were validated with experimental measurements. The rotational dual-field technique uses extended source-to-surface distance with an acrylic beam degrader between the patient and incident beams. Simulations incorporated patient positioning: standing on a platform that rotates during radiation delivery. Resultant patient doses were analyzed as a function of skin depth-dose coverage and evaluated using dose-volume-histograms. Good agreement was obtained between simulations and measurements. For a cylinder with a 30 cm diameter, the depths that dose fell to 50% of the surface dose was 0.66 cm, 1.15 cm and 1.42 cm for thicknesses of 9 mm, 3 mm and without an acrylic scatter plate, respectively. The results are insensitive to cylinder diameter. Relatively uniform skin surface dose was obtained for skin in the torso area although large dose variations (>25%) were found in other areas resulting from partial beam shielding of the extremities. To achieve 95% mean dose to the first 5 mm of skin depth, the mean dose to skin depth of 5–10 mm and depth of 10–15 mm from the skin surface was 74% (57%) and 50% (25%) of the prescribed dose when using a 3 mm (9 mm) thickness scatter plate, respectively. As a result of this investigation on patient skin dose distributions we changed our patient treatments to use a 3 mm instead of a 9 mm thickness Acrylic scatter plate for clinically preferred skin depth dose coverage.
Loss of muscular force in isolated rat diaphragms is related to changes in muscle fibre size
Authors: Lieb Samuel , Schumann Stefan 
Published: March 2021

Abstract

Objective. Passivity of the diaphragm during prolonged mechanical ventilation can lead to ventilation-induced diaphragmatic dysfunction reasoned by a reduction of diaphragmatic muscle strength. Electrical stimulation may be utilised to modulate diaphragm muscle strength. Therefore we intended to investigate diaphragmatic muscle strength based on stimulation with electric impulses. Approach. Diaphragms of Wistar rats were excised, embedded in various incubation solutions and placed in a diaphragm force measurement device. Pressure amplitudes generated by the diaphragm in dependency of the embedding solution, stimulation frequency and time (360 min) were determined. Furthermore, the diaphragms were histologically evaluated. Main results. The ex vivo diaphragms evoked no pressure if embedded in incubation solutions with high potassium concentrations and up to >20 cmH2O if embedded in incubation solutions with extracellular potassium concentrations. Although vitality was well maintained after 360 min (78%) cultivation, the diaphragm’s force dropped by 90.8% after 240 min. The decline in the diaphragm’s force progressed faster if stimulation was performed every 20 min compared to every 120 min. The size of Type I muscle fibres was largest in diaphragms stimulated every 120 min. The fibre size of Type 2b/x muscle cells was lower in diaphragms after electrical stimulation compared to non-stimulated diaphragms. Significance. The force that the diaphragm can develop in ex vivo conditions depends on the incubation solution and the conditions of activation. Activity-related changes in the diaphragm’s muscular force are accompanied by specific changes in muscle fibre size.
AECG-DecompNet: abdominal ECG signal decomposition through deep-learning model
Authors: Rasti-Meymandi Arash , Ghaffari Aboozar 
Published: March 2021

Abstract

Objective. The accurate decomposition of a mother’s abdominal electrocardiogram (AECG) to extract the fetal ECG (FECG) is a primary step in evaluating the fetus’s health. However, the AECG is often affected by different noises and interferences, such as the maternal ECG (MECG), making it hard to evaluate the FECG signal. In this paper, we propose a deep-learning-based framework, namely ‘AECG-DecompNet’, to efficiently extract both MECG and FECG from a single-channel abdominal electrode recording. Approach. AECG-DecompNet is based on two series networks to decompose AECG, one for MECG estimation and the other to eliminate interference and noise. Both networks are based on an encoder-decoder architecture with internal and external skip connections to reconstruct the signals better. Main results. Experimental results show that the proposed framework performs much better than utilizing one network for direct FECG extraction. In addition, the comparison of the proposed framework with popular single-channel extraction techniques shows superior results in terms of QRS detection while indicating its ability to preserve morphological information. AECG-DecompNet achieves exceptional accuracy in the precision metric (97.4%), higher accuracy in recall and F
1 metrics (93.52% and 95.42% respectively), and outperforms other state-of-the-art approaches. Significance. The proposed method shows a notable performance in preserving the morphological information when the FECG within the AECG signal is weak.