bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges of analysing stochastic gene expression in bacteria using single-cell time-lapse experiments
Authors: Hardo Georgeos , Bakshi Somenath 
Published: April 2021

Abstract
Stochastic gene expression causes phenotypic heterogeneity in a population of genetically identical bacterial cells. Such non-genetic heterogeneity can have important consequences for the population fitness, and therefore cells implement regulation strategies to either suppress or exploit such heterogeneity to adapt to their circumstances. By employing time-lapse microscopy of single cells, the fluctuation dynamics of gene expression may be analysed, and their regulatory mechanisms thus deciphered. However, a careful consideration of the experimental design and data-analysis is needed to produce useful data for deriving meaningful insights from them. In the present paper, the individual steps and challenges involved in a time-lapse experiment are discussed, and a rigorous framework for designing, performing, and extracting single-cell gene expression dynamics data from such experiments is outlined.
Functional annotation of lncRNA in high-throughput screening
Authors: Yip Chi Wai , Sivaraman Divya M. , Prabhu Anika V. , Shin Jay W. 
Published: April 2021

Abstract
Recent efforts on the characterization of long non-coding RNAs (lncRNAs) revealed their functional roles in modulating diverse cellular processes. These include pluripotency maintenance, lineage commitment, carcinogenesis, and pathogenesis of various diseases. By interacting with DNA, RNA and protein, lncRNAs mediate multifaceted mechanisms to regulate transcription, RNA processing, RNA interference and translation. Of more than 173000 discovered lncRNAs, the majority remain functionally unknown. The cell type-specific expression and localization of the lncRNA also suggest potential distinct functions of lncRNAs across different cell types. This highlights the niche of identifying functional lncRNAs in different biological processes and diseases through high-throughput (HTP) screening. This review summarizes the current work performed and perspectives on HTP screening of functional lncRNAs where different technologies, platforms, cellular responses and the downstream analyses are discussed. We hope to provide a better picture in applying different technologies to facilitate functional annotation of lncRNA efficiently.
Long non-coding RNAs and splicing
Authors: Staněk David 
Published: April 2021

Abstract
In this review I focus on the role of splicing in long non-coding RNA (lncRNA) life. First, I summarize differences between the splicing efficiency of protein-coding genes and lncRNAs and discuss why non-coding RNAs are spliced less efficiently. In the second half of the review, I speculate why splice sites are the most conserved sequences in lncRNAs and what additional roles could splicing play in lncRNA metabolism. I discuss the hypothesis that the splicing machinery can, besides its dominant role in intron removal and exon joining, protect cells from undesired transcripts.
Back to the future: lessons from past viral infections and the link with Parkinson’s disease
Authors: Dowd Eilis , McKernan Declan P. 
Published: April 2021

AbstractDuring the current coronavirus disease 2019 (COVID-19) pandemic, there has been noticeable increase in the reporting of neurological symptoms in patients. There is still uncertainty around the significance and long-term consequence of these symptoms. There are also many outstanding questions on whether the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) can directly infect the central nervous system (CNS). Given the long association between viral infections with neurodegenerative conditions such as Parkinson’s disease (PD), it seems timely to review this literature again in the context of the COVID-19 pandemic and to glean some useful information from studies on similar viruses. In this commentary, we will consider the current knowledge on viral infections in the brain. In addition, we review the link between viral infection and neurodegeneration in PD, and review the recent literature on SARS infections, the potential link with PD and the potential areas of study in the future.
Game theoretic vulnerability management for secondary frequency control of islanded microgrids against false data injection attacks
Authors: Liu Shichao , Li Qingyang , Chen Bo 
Published: April 2021

AbstractWhile most existing works ignore securing the communication of control signals in microgrids' centralized secondary frequency control, here, a stochastic game between the microgrid control centre (MGCC) and the attacker for enhancing the vulnerability of the MGCC to false data injection (FDI) attack (wireless spoof attack) is proposed. The vulnerability to wireless spoof attack is assessed based on the controllability Gramian when the FDI attack is modelled as the malicious control input that aims to drive the microgrid state to undesired values. In the formulated zero‐sum two‐player Markov game, the state is uniquely associated with the vulnerability index defined by the trace of the controllability Gramian with respect to the attack input. Moreover, the utility function of the stochastic game includes not only the costs related to conducting spoof attack and encryption actions but also the possible remedy costs associated with the resulted vulnerability levels. In turn, the potential impacts of the cyber‐layer action choices on the performance of the physical power system are considered when designing the optimal attack and defence strategies. A distribution feeder system with four distributed generators (DGs) is used for simulation studies. The vulnerability assessment results show that the vulnerability level increases when the attacker compromises more on the communication links between the MGCC and DGs. In the simulated game, mixed stationary attack and defence strategies are predominate when considering the uncertainty of the other player.
N-body simulations of planet formation via pebble accretion
Authors: Matsumura Soko , Brasser Ramon , Ida Shigeru 
Published: April 2021

Aims. The connection between initial disc conditions and final orbital and physical properties of planets is not well-understood. In this paper, we numerically study the formation of planetary systems via pebble accretion and investigate the effects of disc properties such as masses, dissipation timescales, and metallicities on planet formation outcomes.
Methods. We improved the N-body code SyMBA that was modified for our Paper I by taking account of new planet–disc interaction models and type II migration. We adopted the ‘two-α’ disc model to mimic the effects of both the standard disc turbulence and the mass accretion driven by the magnetic disc wind.
Results. We successfully reproduced the overall distribution trends of semi-major axes, eccentricities, and planetary masses of extrasolar giant planets. There are two types of giant planet formation trends, depending on whether or not the disc’s dissipation timescales are comparable to the planet formation timescales. When planet formation happens fast enough, giant planets are fully grown (Jupiter mass or higher) and are distributed widely across the disc. On the other hand, when planet formation is limited by the disc’s dissipation, discs generally form low-mass cold Jupiters. Our simulations also naturally explain why hot Jupiters (HJs) tend to be alone and how the observed eccentricity-metallicity trends arise. The low-metallicity discs tend to form nearly circular and coplanar HJs in situ, because planet formation is slower than high-metallicity discs, and thus protoplanetary cores migrate significantly before gas accretion. The high-metallicity discs, on the other hand, generate HJs in situ or via tidal circularisation of eccentric orbits. Both pathways usually involve dynamical instabilities, and thus HJs tend to have broader eccentricity and inclination distributions. When giant planets with very wide orbits (“super-cold Jupiters”) are formed via pebble accretion followed by scattering, we predict that they belong to metal-rich stars, have eccentric orbits, and tend to have (~80%) companions interior to their orbits.
Simulating observable structures due to a perturbed interstellar medium in front of astrospheric bow shocks in 3D MHD
Authors: Baalmann L. R. , Scherer K. , Kleimann J. , Fichtner H. , Bomans D. J. , Weis K. 
Published: April 2021

Context. While the shapes of many observed bow shocks can be reproduced by simple astrosphere models, more elaborate approaches have recently been used to explain differing observable structures.
Aims. By placing perturbations of an otherwise homogeneous interstellar medium in front of the astrospheric bow shock of the runaway blue supergiant λ Cephei, the observable structure of the model astrosphere is significantly altered, providing insight into the origin of perturbed bow shock images.
Methods. Three-dimensional single-fluid magnetohydrodynamic (MHD) models of stationary astrospheres were subjected to various types of perturbations and simulated until stationarity was reached again. As examples, simple perturbations of the available MHD parameters (number density, bulk velocity, temperature, and magnetic field) as well as a more complex perturbation were chosen. Synthetic observations were generated by line-of-sight integration of the model data, producing Hα, 70 μm dust emission, and bremsstrahlung maps of the perturbed astrosphere’s evolution.
Results. The resulting shock structures and observational images differ strongly depending on the type of the injected perturbation and the viewing angles, forming arc-like protrusions or bifurcations of the bow shock structure, as well as rings, arcs, and irregular structures detached from the bow shock.
β-Ga2O3 on Si (001) grown by plasma-assisted MBE with γ-Al2O3 (111) buffer layer: Structural characterization
Authors: Hadamek Tobias , Posadas Agham B. , Al-Quaiti Fatima , Smith David J. , McCartney Martha R. , Demkov Alexander A. 
Published: April 2021

β-Ga2O3 was deposited in thin film form by plasma-assisted molecular beam epitaxy at 670 °C and 630 °C onto a γ-Al2O3 (111) buffer layer grown at 840 °C by e-beam evaporation on a clean Si (001) surface. The β-Ga2O3 film was 66 nm thick, stoichiometric, and strongly textured, as determined by x-ray reflectivity, x-ray photoelectron spectroscopy, reflection high-energy electron diffraction, x-ray diffraction, and transmission electron microscopy, with three basal growth planes (2̄01), (101), and {310}, including one twin variant {31̄0}. The observed basal growth planes correspond to the close-packing planes of the distorted face-centered cubic oxygen sublattice of β-Ga2O3. Local structural ordering can be thought to occur due to a continuation of the oxygen sublattice from the γ-alumina buffer layer into the β-gallia film. Each β-Ga2O3 growth plane further gives rise to 12 symmetry-derived rotational in-plane variants, resulting in a total of 48 domain variants. Atomistic models of possible gallia–alumina interfaces are presented.
Study of a terahertz folded waveguide oscillator with sheet electron beam
Authors: Lu Fengying , Li Ke , Lei Zhixiong , Huang Ming , Qiao Wensheng 
Published: April 2021

High power vacuum electronic devices of the millimeter wave to terahertz regime are attracting extensive interest due to their potential applications in science and technologies. In this paper, a novel sheet beam (SB) folded waveguide (FWG) slow-wave structure (SWS) is applied and studied for enhanced output power of oscillators. Through the analysis of high-frequency characteristics of the SB FWG-SWS, the selection of an appropriate beam–wave interaction point on the dispersion curve and beam position is determined for an SB folded waveguide oscillator (FWO) operating near the 2π stopband point. The fundamental mode operation of the SB FWO was verified by the particle-in-cell simulation results, which also indicate that the SB FWO exhibits a better outstanding performance (84.6 W with a beam voltage and current of 25.1 kV and 200 mA, respectively) than the conventional circular beam FWO. The transmission stability of the SB was analyzed by observing the interception beam current in the FWO. The voltage and frequency tuning performance of the SB FWO were discussed in combination with clutter suppression. A preliminary experiment was conducted by fabricating a 220 GHz SB FWG-SWS and measuring the S parameter.
Hydrodynamic description of D meson production in high-energy heavy-ion collisions *
Authors: Ding Chi , Ke Wei-Yao , Pang Long-Gang , Wang Xin-Nian 
Published: April 2021

Abstract
The large values and constituent-quark-number scaling of the elliptic flow of low-

D mesons imply that charm quarks, initially produced through hard processes, might be partially thermalized through strong interactions with quark-gluon plasma (QGP) in high-energy heavy-ion collisions. To quantify the degree of thermalization of low-

charm quarks, we compare the

meson spectra and elliptic flow from a hydrodynamic model to experimental data as well as transport model simulations. We use an effective charm chemical potential at the freeze-out temperature to account for the initial charm quark production from hard processes and assume that they are thermalized in the local comoving frame of the medium before freeze-out.

mesons are sampled statistically from the freeze-out hyper-surface of the expanding QGP as described by the event-by-event (3+1)D viscous hydrodynamic model CLVisc. Both the hydrodynamic and transport models can describe the elliptic flow of

mesons at

GeV/c as measured in Au+Au collisions at

GeV. Though the experimental data on

spectra are consistent with the hydrodynamic result at small

GeV/c, they deviate from the hydrodynamic model at high transverse momentum,

GeV/c. The diffusion and parton energy loss mechanisms in the transport model can describe the measured spectra reasonably well within the theoretical uncertainty. Our comparative study indicates that charm quarks only approach local thermal equilibrium at small

, even though they acquire sizable elliptic flow comparable to light-quark hadrons at both small and intermediate

.
A hybrid method for real-time stimulation artefact removal during functional electrical stimulation with time-variant parameters
Authors: Bi Zheng-Yang , Zhou Yu-Xuan , Xie Chen-Xi , Wang Hai-Peng , Wang Hong-Xing , Wang Bi-Lei , Huang Jia , Lü Xiao-Ying , Wang Zhi-Gong 
Published: April 2021

Abstract

Objective. In this study, a hybrid method combining hardware and software architecture is proposed to remove stimulation artefacts (SAs) and extract the volitional surface electromyography (sEMG) in real time during functional electrical stimulations (FES) with time-variant parameters. Approach. First, an sEMG detection front-end (DFE) combining fast recovery, detector and stimulator isolation and blanking is developed and is capable of preventing DFE saturation with a blanking time of 7.6 ms. The fragment between the present stimulus and previous stimulus is set as an SA fragment. Second, an SA database is established to provide six high-similarity templates with the current SA fragment. The SA fragment will be de-artefacted by a 6th-order Gram–Schmidt (GS) algorithm, a template-subtracting method, using the provided templates, and this database-based GS algorithm is called DBGS. The provided templates are previously collected SA fragments with the same or a similar evoking FES intensity to that of the current SA fragment, and the lengths of the templates are longer than that of the current SA fragment. After denoising, the sEMG will be extracted, and the current SA fragment will be added to the SA database. The prototype system based on DBGS was tested on eight able-bodied volunteers and three individuals with stroke to verify its capacity for stimulation removal and sEMG extraction. Results. The average stimulus artefact attenuation factor, SA index and correlation coefficient between clean sEMG and extracted sEMG for 6th-order DBGS were 12.77 ± 0.85 dB, 1.82 ± 0.37 dB and 0.84 ± 0.33 dB, respectively, which were significantly higher than those for empirical mode decomposition combined with notch filters, pulse-triggered GS algorithm, 1st-order and 3rd-order DBGS. The sEMG-torque correlation coefficients were 0.78 ± 0.05 and 0.48 ± 0.11 for able-bodied volunteers and individuals with stroke, respectively. Significance. The proposed hybrid method can extract sEMG during dynamic FES in real time.
Impact of shaping on microstability in high-performance tokamak plasmas
Authors: Beeke O. , Barnes M. , Romanelli M. , Nakata M. , Yoshida M. 
Published: April 2021

Abstract
We have used the local-δf gyrokinetic code GS2 to perform studies of the effect of flux-surface shaping on two highly-shaped, low- and high-β JT-60SA-relevant equilibria, including a successful benchmark with the GKV code. We find that for a high-performance plasma, i.e. one with high plasma beta and steep pressure gradients, the turbulent outwards radial fluxes may be reduced by minimizing the elongation. We explain the results as a competition between the local magnetic shear and finite-Larmor-radius (FLR) stabilization. Electromagnetic studies indicate that kinetic ballooning modes are stabilized by increased shaping due to an increased sensitivity to FLR effects, relative to the ion-temperature-gradient instability. Nevertheless, at high enough β, increased elongation degrades the local magnetic shear stabilization that enables access to the region of ballooning second-stability.
Corrigendum: Effect of thermoelectric placement on the commercial waterblock to the liquid cooling system performance (2021 J. Phys.: Conf. Ser. 1763 012039)
Authors: Kennedy  , Anwar K , Muis A , Basri B , Ilhamsyah M 
Published: April 2021

Description of corrigendum:

Page 1:

“Azimi et al. [8] use the water is cooled by passing through a block which is on contact with the cold side of a thermoelectric in the liquid cooling garment, showed that temperature difference versus the number of fins and the block dimensions has increasing behavior.”

This should read:

“Azimi et al. [7] use the water is cooled by passing through a block which is on contact with the cold side of a thermoelectric in the liquid cooling garment, showed that temperature difference versus the number of fins and the block dimensions has increasing behavior.”

Page 3:

In the sub section 2.2, the following text appears:
““The performance of thermoelectric modules known from the amount of heat that is pumped by the Peltier effect, heat moves from the hot side to the cold side because of the thermal conductivity of the thermoelectric material, and a portion of the total Joule heating effect generated by the electric current to thermal resistance. From the energy equilibrium is obtained:”

This should read:

“The performance of thermoelectric modules known from the amount of heat that is pumped by the Peltier effect, heat moves from the hot side to the cold side because of the thermal conductivity of the thermoelectric material, and a portion of the total Joule heating effect generated by the electric current to thermal resistance. From the energy equilibrium is obtained [10]:”

Page 4:

In the Figure 3, the following figure appears:
This should be appeared:

Page 5:

The following figures (Figure 4, Figure 5 and Figure 6) appear:
This should be appeared:

Page 6:

In in the second line of the first paragraph, the following text appears:

“Observations through CFD were compared with experimental data to validate the simulation results. The simulation uses standard k- □ model turbulence, and boundary condition parameters are referred to the observed data.”

This should read:

“Observations through CFD were compared with experimental data to validate the simulation results. The simulation uses standard k-ε model turbulence, and boundary condition parameters are referred to the observed data.”
Regional Bouguer anomaly gravity data: 3-D modelling of subsurface structures of the Flores and Timor earthquake risk area
Authors: Minarto Eko , Santosa B J , Faridawati  , Azhari N Y , Widihartanti T , Titi Y L A 
Published: April 2021

Abstract
Regional anomaly gravity data are very useful for determining deep subsurface structures due correspond deep surface anomalies. This research aims at analyzing qualitatively to map the gravity anomaly of the island of Flores, modelling shallow surfaces, and interpret surface structures based on the gravity anomalies. In this research, the gravity method used was the secondary gravity data from the Bureau Gravimetric International (BGI) that would be applied using Upward Continuation techniques to interpret deep surfaces for 3D modelling of earthquake risk areas on the islands of Flores and Timor. The modelling was performed by an inversion technique applying the method of singular value decomposition (SVD) and Occam inversion. The result showed that the subsurface structure of the volcano area of the Flores island consists of sandstone, breccia, and andesite with density values of 2.42 g/cm3 - 2.62 g/cm3 and basaltic and lava with density values of 2.65 g/cm3 - 3.24 g/cm3. The most dominating rock in the study area was basaltic rocks with the average density of 2.73 g/cm3. Based on 3D models of regional Bouguer gravity anomalies, the Flores back arc fault was estimated at a depth of 30 km, the thickness of the earth’s crust in the Flores back arc fault zone was estimated to be up to 30 km while the thickness of the earth’s crust in the fore arc was estimated to be more than 60 km. The existence of magma chamber in the volcanic arc of Flores island was estimated at depth of 30 km in accordance with to the seismicity map Flores and Timor areas.
How is the serological diagnosis of hepatitis B and C in Brazil?
Authors: Folgueras-Flatschart A.V. , Pessoa M. C. F. , Flatschart R.B. 
Published: April 2021

Abstract
Hepatitis B and C are a serious public health problem that can be chronic and lead to cirrhosis or cancer. Their accurate diagnosis are important to allow proper treatment. In this work we seek, through analysis of data from Proficiency Testing rounds, to understand the performance of laboratories their serological tests. Considering the final interpretation of quantitative and qualitative assays, we observed at least 95% agreement on the results obtained in relation to those expected by the provider. This rate was higher in antibody detection assays, with a slight tendency to increased agreement and decreased dispersion over the period.
The primary measurement standard of ultrasonic power and radiation conductance at Inmetro
Authors: Alvarenga Andre V , Costa-Felix Rodrigo P B 
Published: April 2021

Abstract
In this work, the results of the measurement of the radiation conductance performed in the ultrasonic power measurement system of the Laboratory of Ultrasound (Labus) of Inmetro are presented. According to IEC 61161:2013, the Labus / Inmetro measurement system is considered a “primary measurement setup” since it took part in the BIPM Key Comparison CCAUV.U-K3.1, achieving satisfactory results. The measurements were carried out based on the primary measurement procedure for the determination of the radiation conductance, and the new results were compared with those previously obtained on the occasion of Key Comparison.