bluuebunny/crossref_metadata_2025 huggingface dataset:
Charge-transfer selectivity and quantum interference in real-time electron dynamics: Gaining insights from time-dependent configuration interaction simulations
Authors: Ramakrishnan Raghunathan
Published: May 2020

Many-electron wavepacket dynamics based on time-dependent configuration interaction (TDCI) is a numerically rigorous approach to quantitatively model electron transfer across molecular junctions. TDCI simulations of cyanobenzene thiolates—para- and meta-linked to an acceptor gold atom—show donor states conjugating with the benzene π-network to allow better through-molecule electron migration in the para isomer compared to the meta counterpart. For dynamics involving non-conjugating states, we find electron injection to stem exclusively from distance-dependent non-resonant quantum mechanical tunneling, in which case the meta isomer exhibits better dynamics. The computed trend in donor-to-acceptor net-electron transfer through differently linked azulene bridges agrees with the trend seen in low-bias conductivity measurements. Disruption of π-conjugation has been shown to be the cause of diminished electron injection through 1,3-azulene, a pathological case for a graph-based diagnosis of the destructive quantum interference. Furthermore, we demonstrate the quantum interference of many-electron wavefunctions to drive para-vs-meta selectivity in the coherent evolution of superposed π(CN)- and σ(NC–C)-type wavepackets. Analyses reveal that in the para-linked benzene, σ and π MOs localized at the donor terminal are in-phase, leading to the constructive interference of electron density distribution, while the phase-flip of one of the MOs in the meta isomer results in the destructive interference. These findings suggest that a priori detection of orbital phase-flip and quantum coherence conditions can aid in molecular device design strategies.
Parametric study of the phase diffusion process in a gain-switched semiconductor laser for randomness assessment in quantum random number generator
Authors: Septriani Brigitta , de Vries Oliver , Steinlechner Fabian , Gräfe Markus
Published: May 2020

The quantum phase noise in a pulsed semiconductor laser is studied thoroughly in the context of its utilization as a quantum entropy source in a quantum random number generator (QRNG) device. We performed a numerical analysis of the phase diffusion process for a semiconductor laser in the continuous-wave operation mode and gain-switched (GS) mode. The result demonstrates the amplification of randomness in the GS mode, which is gauged physically by the variance VarΔϕ. The variance value, which is mathematically related to the temporal distance between the laser pulses used in the experimental setup, also determines the stability of the setup. Furthermore, we show how the QRNG probability distribution is influenced by several experimental factors such as the quality of the interference process and the noise in the detection system.
A standardised monitoring protocol for the black caiman (Melanosuchus niger)
Authors: Naveda-Rodríguez Adrián , Utreras B. Víctor , Zapata-Ríos Galo
Published: May 2020

Abstract
ContextEstimating population abundance can be plagued by the violation of methodological assumptions, which can be overcome with standardised protocols. The black caiman (BC) is considered a conservation-dependent species, and previous abundance estimates are surrounded by uncertainty and flaws in the survey (e.g. different survey design and efforts) and analytical approach used (e.g. relative abundance index, which ignores imperfect detection). Its conservation status assessment demands the implementation of a standardised monitoring protocol.
AimsThe protocol provides guidelines to collect and analyse data in a consistent manner to survey BC. Besides accounting for imperfect detection to produce reliable abundance estimates, the protocol aimed to be easily implemented by park rangers, and to fit field observations into a hierarchical modelling approach to assess how environmental variables affects detectability and abundance.
MethodsThe protocol subdivides a 20-km transect into 10 2-km segments; each transect is surveyed four consecutive nights, starting at 1900 hours and finishing when the 20km are completed. For each caiman detected, the observers estimated head size to classify the individual by age. We tested the protocol in Ecuador during January and December 2017, and field data were analysed using N-mixture models. We compared abundance estimates derived with this protocol with commonly used relative abundance indexes.
Key resultsWe surveyed 460km that resulted in 177 detections. Percentage of moonlight and distance from human settlement best explained detectability and abundance respectively. Mean detection probability was 0.14 (95% BCI: 0.1–0.18), whereas absolute abundance was 196 (95% BCI: 147–370). The overall adult to immature ratio was 1:1.3.
ConclusionsThis is the first estimate of detectability and absolute abundance for BC by using a standardised survey with a clearly defined and repeatable survey and analysis methods. Relative abundance indexes did not reflect absolute abundance estimates. We recommend the use of this protocol in future surveys across the Amazon region to effectively evaluate BC conservation status.
ImplicationsPopulation size cannot be estimated from relative abundance indexes; they lead to bias estimates for ignoring imperfect detection. We discourage the use of relative abundance indexes to evaluate the conservation status of this species.
Protein phosphatase 2A promotes stomatal development by stabilizing SPEECHLESS in
Arabidopsis
Authors: Bian Chao , Guo Xiaoyu , Zhang Yi , Wang Lu , Xu Tongda , DeLong Alison , Dong Juan
Published: May 2020

Significance

The innovation of stomatal pores in plant evolution enables the success and diversification of land plants over the past 400 million years. The production and patterning of stomata are regulated by a group of deeply conserved bHLH transcription factors in land plants, with the founding member SPEECHLESS (SPCH) playing a pivotal role in the initiation of stomatal lineage. The protein stability and function of SPCH are tightly regulated by protein phosphorylation mediated by multiple kinases in
Arabidopsis
. Here, we establish the highly conserved PP2A protein phosphatases as positive regulators of SPCH and thus stomatal production, underscoring a key function of PP2A in fine-tuning stomatal development, a highly plastic biological process that influences many plant responses to changing environmental conditions.
Caring for the future can turn tragedy into comedy for long-term collective action under risk of collapse
Authors: Barfuss Wolfram , Donges Jonathan F. , Vasconcelos Vítor V. , Kurths Jürgen , Levin Simon A.
Published: May 2020

We will need collective action to avoid catastrophic climate change, and this will require valuing the long term as well as the short term. Shortsightedness and uncertainty have hindered progress in resolving this collective action problem and have been recognized as important barriers to cooperation among humans. Here, we propose a coupled social–ecological dilemma to investigate the interdependence of three well-identified components of this cooperation problem: 1) timescales of collapse and recovery in relation to time preferences regarding future outcomes, 2) the magnitude of the impact of collapse, and 3) the number of actors in the collective. We find that, under a sufficiently severe and time-distant collapse, how much the actors care for the future can transform the game from a tragedy of the commons into one of coordination, and even into a comedy of the commons in which cooperation dominates. Conversely, we also find conditions under which even strong concern for the future still does not transform the problem from tragedy to comedy. For a large number of participating actors, we find that the critical collapse impact, at which these game regime changes happen, converges to a fixed value of collapse impact per actor that is independent of the enhancement factor of the public good, which is usually regarded as the driver of the dilemma. Our results not only call for experimental testing but also help explain why polarization in beliefs about human-caused climate change can threaten global cooperation agreements.
CD5 signalosome coordinates antagonist TCR signals to control the generation of Treg cells induced by foreign antigens
Authors: Blaize Gaëtan , Daniels-Treffandier Hélène , Aloulou Meryem , Rouquié Nelly , Yang Cui , Marcellin Marlène , Gador Mylène , Benamar Mehdi , Ducatez Mariette , Song Ki-duk , Burlet-Schiltz Odile , Saoudi Abdelhadi , Love Paul E. , Fazilleau Nicolas , Gonzalez de Peredo Anne , Lesourne Renaud
Published: May 2020

CD5 is characterized as an inhibitory coreceptor with an important regulatory role during T cell development. The molecular mechanism by which CD5 operates has been puzzling and its function in mature T cells suggests promoting rather than repressing effects on immune responses. Here, we combined quantitative mass spectrometry and genetic studies to analyze the components and the activity of the CD5 signaling machinery in primary T cells. We found that T cell receptor (TCR) engagement induces the selective phosphorylation of CD5 tyrosine 429, which serves as a docking site for proteins with adaptor functions (c-Cbl, CIN85, CRKL), connecting CD5 to positive (PI3K) and negative (UBASH3A, SHIP1) regulators of TCR signaling. c-CBL acts as a coordinator in this complex enabling CD5 to synchronize positive and negative feedbacks on TCR signaling through the other components. Disruption of CD5 signalosome in mutant mice reveals that it modulates TCR signal outputs to selectively repress the transactivation ofFoxp3and limit the inopportune induction of peripherally induced regulatory T cells during immune responses against foreign antigen. Our findings bring insights into the paradigm of coreceptor signaling, suggesting that, in addition to providing dualistic enhancing or dampening inputs, coreceptors can engage concomitant stimulatory and inhibitory signaling events, which act together to promote specific functional outcomes.
As diversity increases, people paradoxically perceive social groups as more similar
Authors: Bai Xuechunzi , Ramos Miguel R. , Fiske Susan T.
Published: May 2020

With globalization and immigration, societal contexts differ in sheer variety of resident social groups. Social diversity challenges individuals to think in new ways about new kinds of people and where their groups all stand, relative to each other. However, psychological science does not yet specify how human minds represent social diversity, in homogeneous or heterogenous contexts. Mental maps of the array of society’s groups should differ when individuals inhabit more and less diverse ecologies. Nonetheless, predictions disagree on how they should differ. Confirmation bias suggests more diversity means more stereotype dispersion: With increased exposure, perceivers’ mental maps might differentiate more among groups, so their stereotypes would spread out (disperse). In contrast, individuation suggests more diversity means less stereotype dispersion, as perceivers experience within-group variety and between-group overlap. Worldwide, nationwide, individual, and longitudinal datasets (
n
= 12,011) revealed a diversity paradox: More diversity consistently meant less stereotype dispersion. Both contextual and perceived ethnic diversity correlate with decreased stereotype dispersion. Countries and US states with higher levels of ethnic diversity (e.g., South Africa and Hawaii, versus South Korea and Vermont), online individuals who perceive more ethnic diversity, and students who moved to more ethnically diverse colleges mentally represent ethnic groups as more similar to each other, on warmth and competence stereotypes. Homogeneity shows more-differentiated stereotypes; ironically, those with the least exposure have the most-distinct stereotypes. Diversity means less-differentiated stereotypes, as in the melting pot metaphor. Diversity and reduced dispersion also correlate positively with subjective wellbeing.
The αvβ6 integrin in cancer cell‐derived small extracellular vesicles enhances angiogenesis
Authors: Krishn Shiv Ram , Salem Israa , Quaglia Fabio , Naranjo Nicole M. , Agarwal Ekta , Liu Qin , Sarker Srawasti , Kopenhaver Jessica , McCue Peter A. , Weinreb Paul H. , Violette Shelia M. , Altieri Dario C. , Languino Lucia R.
Published: May 2020

Prostate cancer (PrCa) cells crosstalk with the tumour microenvironment by releasing small extracellular vesicles (sEVs). sEVs, as well as large extracellular vesicles (LEVs), isolated via iodixanol density gradients from PrCa cell culture media, express the epithelial‐specific αvβ6 integrin, which is known to be induced in cancer. In this study, we show sEV‐mediated protein transfer of αvβ6 integrin to microvascular endothelial cells (human microvascular endothelial cells 1 – HMEC1); we demonstrate that de novo αvβ6 integrin expression is not caused by increased mRNA levels. Incubation of HMEC1 with sEVs isolated from PrCa PC3 cells that express the αvβ6 integrin results in a highly significant increase in the number of nodes, junctions and tubules. In contrast, incubation of HMEC1 with sEVs isolated from β6 negative PC3 cells, generated by shRNA against β6, results in a reduction in the number of nodes, junctions and tubules, a decrease in survivin levels and an increase in a negative regulator of angiogenesis, pSTAT1. Furthermore, treatment of HMEC1 with sEVs generated by CRISPR/Cas9‐mediated down‐regulation of β6, causes up‐regulation of pSTAT1. Overall, our findings suggest that αvβ6 integrin in cancer sEVs regulates angiogenesis during PrCa progression.
Retrieval of attosecond pulse ensembles from streaking experiments using mixed state time-domain ptychography
Authors: Witting Tobias , Furch Federico J , Kornilov Oleg , Osolodkov Mikhail , Schulz Claus P , Vrakking Marc J J
Published: May 2020

The electric field of attosecond laser pulses can be retrieved from laser-dressed photoionisation measurements, where electron wavepackets that result from single-photon ionisation by the attosecond pulse in the presence of a dressing field are produced. In case of fluctuating dressing laser and/or attosecond pulses, e.g. due to pulse-to-pulse fluctuations of the carrier envelope phase of the infrared laser pulse, commonly applied retrieval algorithms result in the erroneous extraction of the pulse fields. We present a mixed state time-domain ptychography algorithm for the retrieval of pulse ensembles from attosecond streaking experiments.
Iteration of semiconductor Bloch equations for ultrashort laser pulse propagation
Authors: Pfeiffer Adrian N
Published: May 2020

The numerical propagation of intense laser pulses through bulk material requires the recurrent calculation of the nonlinear material response. To describe the optical Kerr effect and the current in the conduction band for macroscopic propagation distances, very simplified models are typically used. Recent studies of the response of dielectrics to intense few-cycle pulses have revealed that ionization does not accumulate monotonically, but conduction bands are populated both irreversibly and reversibly during a laser cycle. The reversible (or transient or virtual) population of the conduction bands is not captured by simple response models. Here, an efficient iteration based on the semiconductor Bloch equations for three bands is developed, which consistently captures the laser cycle resolved interband polarization and intraband current. The full calculation of the nonlinear material response at each propagation step is avoided, instead only the incremental modification of the previous propagation step is calculated. The iteration is particularly well-suited for very short pulses and can be applied for intensities above the critical value at which perturbation theory does not converge. Furthermore, it is shown that virtual currents and dynamic Bloch oscillations are mechanisms which are missing in the Drude model, but these two mechanisms prevail for short intense pulses. Therefore, a generalized Drude model is derived from the SBEs, which is capable to account for arbitrary band shapes and both real and virtual ionization.
Trace moisture measurement in natural gas mixtures with a single calibration for nitrogen background gas
Authors: Takeda N , Carroll P , Tsukahara Y , Beardmore S , Bell S , Yamanaka K , Akao S
Published: May 2020

The measurement and control of trace moisture is an important procedure to maintain and secure the quality and safety of pipeline systems for natural gas. The natural gas mix typically comprises methane, ethane, propane, some higher hydrocarbons, carbon dioxide and nitrogen. It is too impractical to perform additional calibrations of trace moisture measurement every time the combination of gas components in the natural gas mix is changed. This paper proposes a method to separate and compensate for the effect of the background gas composition from the trace moisture measurement by using two different frequencies in a trace moisture analyzer utilizing a ball surface acoustic wave (SAW) sensor. The experiment was performed by connecting the ball SAW trace moisture sensor to supplies of trace moisture in multiple background gases from the National Physical Laboratory (NPL) Multi-gas, Multi-pressure Standard Humidity Generator, and changing the composition of the background gases including N2, air, CH4, 80% CH4/20% C2H6, and 50% CH4/50% C2H6. At the nominal humidity frost-point values of −70 °C, −50 °C, −40 °C and −30 °C, the deviations due to the change of the background gases were within

±

1 °C in frost point.
Experimental observation of elevated heating in dynamically compressed CH foam
Authors: Falk K , Fontes C J , Fryer C L , Greeff C W , Holec M , Johns H M , Montgomery D S , Schmidt D W , Šmíd M
Published: May 2020

We present an experimental result of significantly increased heating in a laser-driven blastwave experiment carried out at the OMEGA laser facility. Abnormally high temperatures were observed in warm dense CH compared to older experiments and theoretical predictions. The higher temperatures in compressed CH were linked to an improved smoothness of the laser intensity profile, which resulted in better efficiency of the drive and coupling of more energy into the system compared to previous similar experiments. Fifteen beams with combined intensity of ∼7× 1014 W cm−2 and a square intensity profile with 2 ns duration were used to drive a strong shock, which subsequently developed to a blastwave travelling through low density CH foam creating warm dense matter. Multiple diagnostics were used to examine the thermodynamic conditions in the warm dense CH foam. Velocity interferometry (VISAR) and streaked pyrometry (SOP) observed increased blastwave velocities, while x-ray Thomson scattering (XRTS) measured elevated temperatures of 17.5 − 35 eV in compressed CH foam. The experimental results were compared to hydrodynamic simulations and a potential contribution from x-rays to the elevated temperatures in the dense material was considered.
Secondary CLIQ, a robust, redundant, and cost-effective means of protecting high-field accelerator magnets
Authors: Mentink M , Ravaioli E
Published: May 2020

Secondary CLIQ is a quench protection method for protecting high-field accelerator magnets that involves charged capacitors into secondary normal-conducting coils that are magnetically coupled to the superconducting coils. The resulting coupling losses quickly brings the magnet to normal state and safely discharges it.

No direct electrical or thermal link is required between the primary and secondary coils, and robust insulation is placed in between them. The two secondary circuits per magnet are galvanically insulated from the primary circuit, so that the tens to hundreds of CLIQ units needed to protect an accelerator circuit are galvanically insulated from one-another and from the superconducting magnets. The two secondary circuits per magnet each feature a CLIQ unit, and each CLIQ unit discharge is sufficient to bring the magnet to normal state over the entire operational current range. The coil geometry is such that the CLIQ discharge does not raise the voltage over the half-turns of the superconducting coils. After the superconducting coils develop resistance, a significant fraction of the stored magnetic energy is inductively transferred to and dissipated in the secondary coils. The resulting favourable adiabatic hot-spot temperature and voltage-to-ground enables the magnet designer to reduce the copper content of the superconducting coils, and thus lower the overall cost of the magnet.

Secondary CLIQ quench simulations were performed on a hypothetical 14 m variant of the HD2 Nb3Sn dipole with a bore field of 16 T. It is demonstrated that the Secondary CLIQ method protects the magnet over its entire operational current range even in the case where one of the two CLIQ units fails to discharge with an adiabatic hotspot temperature of 248 K and voltage-to-ground of 610 V under nominal protection conditions, and a worst-case adiabatic hot-spot temperature of 263 K and voltage-to-ground of 840 V under fault conditions.
Spurious ergodicity breaking in normal and fractional Ornstein–Uhlenbeck process
Authors: Mardoukhi Yousof , Chechkin Aleksei , Metzler Ralf
Published: May 2020

The Ornstein–Uhlenbeck process is a stationary and ergodic Gaussian process, that is fully determined by its covariance function and mean. We show here that the generic definitions of the ensemble- and time-averaged mean squared displacements fail to capture these properties consistently, leading to a spurious ergodicity breaking. We propose to remedy this failure by redefining the mean squared displacements such that they reflect unambiguously the statistical properties of any stochastic process. In particular we study the effect of the initial condition in the Ornstein–Uhlenbeck process and its fractional extension. For the fractional Ornstein–Uhlenbeck process representing typical experimental situations in crowded environments such as living biological cells, we show that the stationarity of the process delicately depends on the initial condition.
Bipolar and unipolar valley filter effects in graphene-based P/N junction
Authors: Lü Xiao-Long , Xie Hang
Published: May 2020

We use the spin and valley degrees of freedom to design the bipolar and unipolar valley filter effects based on the graphene-based P/N junction. When the modified Haldane model and staggered potential are applied on the region P, while the off-resonant circularly polarized light and staggered ferromagnetic exchange field are applied on the region N, the unipolar valley filter effect emerges with the unidirectional spin–valley current. The direction and type of the unidirectional spin–valley current depend on the phase of the modified Haldane model and the direction of polarized light. Other types of the bipolar valley filter effects are also reported, such as the valley-mixed bipolar spin filter effect, valley-mixed bipolar filter effect, valley-locked bipolar spin filter effect and valley-locked bipolar filter effect. These bipolar filter effects have the similarity that the spin–valley currents flow bidirectionally. These types of the unipolar and bipolar valley filter effects can be also mutually switched by modulating the external fields. Moreover, these unipolar and bipolar valley filter effects are robust against a weak temperature. This work reveals that the graphene-based junction has the potential applications in designing the valley filter device and improving the reprogrammable spin logic.
Vegetation biomass change in China in the 20th century: an assessment based on a combination of multi-model simulations and field observations
Authors: Song Xiang , Li Fang , Harrison Sandy P , Luo Tianxiang , Arneth Almut , Forrest Matthew , Hantson Stijn , Lasslop Gitta , Mangeon Stephane , Ni Jian , Yue Chao , Hickler Thomas , Luo Yiqi , Sitch Stephen , Xu Xin , Zhu Zaichun
Published: May 2020

Vegetation biomass is a key and active component of the carbon cycle. Though China’s vegetation biomass in recent decades has been widely investigated, only two studies have quantitatively assessed its century-scale changes so far and reported totally opposite trends. This study provided the first multi-model estimates of China’s vegetation biomass change for the 20th century and its responses to historical changes in environmental and anthropogenic factors, based on simulations evaluated with the field observations from 3757 inventory plots in China and bias-corrected using machine learning (Gaussian process regression). A significant decline in vegetation biomass over the 20th century was shown by bias-corrected simulations from the six Dynamic Global Vegetation models (DGVMs) with trends ranging from −32.48 to −11.10 Tg C yr–1 and a mean trend of −17.74 Tg C yr–1. Land use and land cover change (LULCC) was primarily responsible for the simulated downward trend (−50.71 to −24.28 Tg C yr–1), while increasing atmospheric CO2 concentration lead to increased vegetation biomass (+9.27 to + 13.37 Tg C yr–1). Climate change had limited impacts on the long-term trend (−3.75 to + 5.06 Tg C yr–1). This study highlights the importance of LULCC for historical reconstruction and future projection of vegetation biomass over China. It also suggests that the incorrect change in China’s forest area for 1980–2000 in the LULCC dataset used as model input data of many existing and ongoing model intercomparison projects (MIPs) has likely led to inaccurate estimations of historical vegetation biomass changes in China.
Optimal spatial scales for seasonal forecasts over Africa
Authors: Young Matthew , Heinrich Viola , Black Emily , Asfaw Dagmawi
Published: May 2020

The availability of seasonal weather forecast information in Africa has potential to provide advanced early warning of rainfall variability, informing preparedness actions to minimise adverse impacts. Obtaining accurate forecast information for the spatial scales at which decisions are made is vital. Here we examine the impact of spatial scales on the utility of seasonal rainfall forecasts in Africa. Using observations alongside seasonal forecasts from the European Centre for Medium-Range Weather Forecasts (ECMWF), we combine measures of local representativity and skill to assess optimal spatial scales for anticipating local rainfall conditions. The results reveal regions where spatial aggregation of gridded forecast data improves the quality of information provided at the local scale, and regions where forecasts have useful skill without aggregation. More generally this study presents a novel approach for evaluating the utility of forecast information which is applicable both globally and at all timescales.
What goes up must come down: impacts of deposition in a sulfate geoengineering scenario
Authors: Visioni Daniele , Slessarev Eric , MacMartin Douglas G , Mahowald Natalie M , Goodale Christine L , Xia Lili
Published: May 2020

The problem of reducing the impacts of rising anthropogenic greenhouse gas on warming temperatures has led to the proposal of using stratospheric aerosols to reflect some of the incoming solar radiation back to space. The deliberate injection of sulfur into the stratosphere to form stratospheric sulfate aerosols, emulating volcanoes, will result in sulfate deposition to the surface. We consider here an extreme sulfate geoengineering scenario necessary to maintain temperatures at 2020 levels while greenhouse gas emissions continue to grow unabated. We show that the amount of stratospheric sulfate needed could be globally balanced by the predicted decrease in tropospheric anthropogenic SO2 emissions, but the spatial distribution would move from industrialized regions to pristine areas. We show how these changes would affect ecosystems differently depending on present day observations of soil pH, which we use to infer the potential for acid-induced aluminum toxicity across the planet.
Effects of the atmosphere and Mn doping on the electrical properties of Sr2Fe1−xMnxNbO6 and their mechanisms
Authors: Ge Ben , Sheng Jiaqi , Zhuang Yuan , Ma Jingtao , Yang Zhibin , Li Cunpu , Peng Suping
Published: May 2020

Double-perovskite composite oxides (A2BB′O6) usually have excellent functional properties and are widely studied and applied. Its electrical, magnetic or other properties can be optimized by doping transition metal elements at its B or B′ site. In this paper, the effects of Mn doping and testing atmosphere on the crystal structures and the electrical conductivities of Sr2Fe1−xMnxNbO6(SFMN) were systematically investigated. The experimental results demonstrate that the conductivities of SFMN will increase in air while decrease under H2/H2O(g) atmosphere with Mn content rise. Doping Mn can enlarge the interplanar spacing of SFMN which increases the resistance of electron conduction across the crystal. First-principles calculations and XPS analysis results reveal that the chemical adsorption of H2 on the surface of SFMN is a key reason for its conductivity increase under H2/H2O(g) atmosphere. The forbidden band width of the reduced state of Sr2FeNbO6 (1.177 eV) is much smaller than that of the oxidation state (1.426 eV). The analysis results suggest that Fe 3d electron transition and exchange interaction between Mn–O–Mn are mainly two possible mechanisms contribute to the electrical conductivity of SFMN.
Toxicity assessment of laser-induced graphene by zebrafish during development
Authors: d’Amora Marta , Lamberti Andrea , Fontana Marco , Giordani Silvia
Published: May 2020

Laser-induced graphene (LIG) is a three-dimensional porous graphene-based material easily prepared by single or multiple laser direct writing on a polymeric or organic surface. It possesses impressive physical and chemical properties, including high surface area, hierarchical porosity, and good electrical conductivity. Here, we investigate the toxicological profile of LIG and its impact in zebrafish (Danio rerio) as in vivo biological models with high homology with humans. We evaluate the effect of LIG, administered in different concentrations to zebrafish embryos, on different biological parameters, including embryo viability and morphological changes. Our results show that LIG does not exhibit toxic effects and does not interfere with zebrafish development, even at high concentrations. Our findings provide direct evidence of the LIG biocompatibility and offer a promising avenue for its safe use in biological applications.
Implications of using two low-power continuous-wave lasers for polishing
Authors: Zhang Wenxuan , Wong Kiwan , Morales Miguel , Molpeceres Carlos , Arnold Craig B
Published: May 2020

Laser polishing is widely employed to reduce the surface roughness of products with complex geometries. Traditional laser polishing techniques use a single high-power Gaussian beam to melt and smooth a thin layer of surface material. However, the reliance on high power lasers can present practical challenges such as minimizing surface evaporation or reducing overall cost. In this work, we combined two identical low-power laser beams with a spatial offset in between them to construct an elliptical beam. By changing the spatial offset, combined beams with different lengths along the major axis can be created. We observe over 20% improvement in line roughness reduction using this approach compared to a single Gaussian laser beam with the same total power. Additionally, both experiment and simulation results suggest such improvement is because this dual-laser set-up can create a longer molten pool compared to a single laser.
Synthesis, microbial susceptibility and anti-cancerous properties of copper oxide nanoparticles- review
Authors: Sharma Manisha , Sharma Anurag , Majumder Sudip
Published: May 2020

Use of Nanoparticles in the diagnosis of cancer and treatment of Cancer is being rapidly studied and developed. The present cancer chemotherapy agents are not much selective in differentiating between cancer cells and normal cells and often lead to development of drug resistance and severe side effects. This has prompted the need to study other potential anticancer agents like metallic oxide nanoparticles, with emphasis on their synthesis and application s in the treatment of cancer by designing targeted delivery system to tumour and cancer cells [Vinardell and Mitjans 2015. Nanomaterials, 5, 1004–1021, Valodkar et al 2011. Mater Chem Phys, 128, 83–89]. In this review paper an attempt has been made to study various methods of preparation of Copper Oxide Nanoparticles, their characteristics and the detailed microbial activities and anti-cancerous properties of these differently synthesized Copper Oxide Nanoparticles.
Inverse scattering and soliton solutions of nonlocal reverse-spacetime nonlinear Schrödinger equations
Authors: Ma Wen-Xiu
Published: May 2020

The paper presents nonlocal reverse-spacetime PT-symmetric multicomponent nonlinear Schrödinger (NLS) equations under a specific nonlocal group reduction, and generates their inverse scattering transforms and soliton solutions by the Riemann-Hilbert technique. The Sokhotski-Plemelj formula is used to determine solutions to a class of associated Riemann-Hilbert problems and transform the systems that generalized Jost solutions need to satisfy. A formulation of solutions is developed for the Riemann-Hilbert problems associated with the reflectionless transforms, and the corresponding soliton solutions are constructed for the presented nonlocal reverse-spacetime PT-symmetric NLS equations.
Anticanonical codes from del Pezzo surfaces with Picard rank one
Authors: Blache Régis , Couvreur Alain , Hallouin Emmanuel , Madore David , Nardi Jade , Rambaud Matthieu , Randriam Hugues
Published: May 2020

We construct algebraic geometric codes from del Pezzo surfaces and focus on the ones having Picard rank

1
1

and the codes associated to the anticanonical class. We give explicit constructions of del Pezzo surfaces of degree

4
4

,

5
5

, and

6
6

, compute the parameters of the associated anticanonical codes, and study their isomorphisms arising from the automorphisms of the surface. We obtain codes with excellent parameters, and some of them turn out to beat the best known codes listed on the database codetable.
Chemerin as a Driver of Hypertension: A Consideration
Authors: Ferland David J , Mullick Adam E , Watts Stephanie W
Published: May 2020

The protein chemerin (tazarotene-induced gene, TIG2; RARRES2) is a relatively new adipokine. Many studies support that circulating chemerin levels associate strongly and positively with body mass index, visceral fat, and blood pressure. Here, we focus on the specific relationship of chemerin and blood pressure with the goal of understanding whether and how chemerin drives (pathological) changes in blood pressure such that it could be interfered with therapeutically. We dissect the biosynthesis of chemerin and how current antihypertensive medications change chemerin metabolism. This is followed with a review of what is known about where chemerin is synthesized in the body and what chemerin and its receptors can do to the physiological function of organs important to blood pressure determination (e.g., brain, heart, kidneys, blood vessels, adrenal, and sympathetic nervous system). We synthesize from the literature our best understanding of the mechanisms by which chemerin modifies blood pressure, with knowledge that plasma/serum levels of chemerin may be limited in their pathological relevance. This review reveals several gaps in our knowledge of chemerin biology that could be filled by the collective work of protein chemists, biologists, pharmacologists, and clinicians.
Development of a Personal Aerosol Sampler for Monitoring the Particle–Vapour Fractionation of SVOCs in Workplaces
Authors: Dragan George C , Kohlmeier Vesta , Orasche Juergen , Schnelle-Kreis Juergen , Forbes Patricia B C , Breuer Dietmar , Zimmermann Ralf
Published: May 2020

Semi-volatile organic compounds (SVOCs), partitioned between particulates and vapours of an aerosol, require special attention. The toxicological effects caused by the inhalation of such aerosols may depend on the concentration and in which phase the organic compounds are found. A personal denuder-gas–particle separation aerosol sampler was developed to provide information about the partitioning of aerosols from organic compounds. The sampler was tested in a series of controlled laboratory experiments, which confirmed the capability and accuracy of the sampler to measure gas–particle mixtures. An average difference of 14.8 ± 4.8% was found between sampler and reference laboratory instruments. The obtained results showed that our sampler enables a more accurate measurement of the SVOC aerosols’ gas–particle fractionation, compared with that of conventional samplers.
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites
Authors: Liu Quanzhong , Chen Jinxiang , Wang Yanze , Li Shuqin , Jia Cangzhi , Song Jiangning , Li Fuyi
Published: May 2020

DNA N4-methylcytosine (4mC) is an important epigenetic modification that plays a vital role in regulating DNA replication and expression. However, it is challenging to detect 4mC sites through experimental methods, which are time-consuming and costly. Thus, computational tools that can identify 4mC sites would be very useful for understanding the mechanism of this important type of DNA modification. Several machine learning-based 4mC predictors have been proposed in the past 3 years, although their performance is unsatisfactory. Deep learning is a promising technique for the development of more accurate 4mC site predictions. In this work, we propose a deep learning-based approach, called DeepTorrent, for improved prediction of 4mC sites from DNA sequences. It combines four different feature encoding schemes to encode raw DNA sequences and employs multi-layer convolutional neural networks with an inception module integrated with bidirectional long short-term memory to effectively learn the higher-order feature representations. Dimension reduction and concatenated feature maps from the filters of different sizes are then applied to the inception module. In addition, an attention mechanism and transfer learning techniques are also employed to train the robust predictor. Extensive benchmarking experiments demonstrate that DeepTorrent significantly improves the performance of 4mC site prediction compared with several state-of-the-art methods.
Thymosin Alpha 1 Reduces the Mortality of Severe Coronavirus Disease 2019 by Restoration of Lymphocytopenia and Reversion of Exhausted T Cells
Authors: Liu Yueping , Pan Yue , Hu Zhenhong , Wu Ming , Wang Chenhui , Feng Zeqing , Mao Congzheng , Tan Yingjun , Liu Ying , Chen Li , Li Min , Wang Gang , Yuan Zilin , Diao Bo , Wu Yuzhang , Chen Yongwen
Published: May 2020

Background

Thymosin alpha 1 (Tα1) had been used in the treatment of viral infections as an immune response modifier for many years. However, clinical benefits and the mechanism of Tα1 treatment for COVID-19 patients are still unclear.

Methods

We retrospectively reviewed the clinical outcomes of 76 severe COVID-19 cases admitted to 2 hospitals in Wuhan, China, from December 2019 to March 2020. The thymus output in peripheral blood mononuclear cells from COVID-19 patients was measured by T-cell receptor excision circles (TRECs). The levels of T-cell exhaustion markers programmed death-1 (PD-1) and T-cell immunoglobulin and mucin domain protein 3 (Tim-3) on CD8+ T cells were detected by flow cytometry.

Results

Compared with the untreated group, Tα1 treatment significantly reduced the mortality of severe COVID-19 patients (11.11% vs 30.00%, P = .044). Tα1 enhanced blood T-cell numbers in COVID-19 patients with severe lymphocytopenia. Under such conditions, Tα1 also successfully restored CD8+ and CD4+ T-cell numbers in elderly patients. Meanwhile, Tα1 reduced PD-1 and Tim-3 expression on CD8+ T cells from severe COVID-19 patients compared with untreated cases. It is of note that restoration of lymphocytopenia and acute exhaustion of T cells were roughly parallel to the rise of TRECs.

Conclusions

Tα1 treatment significantly reduced mortality of severe COVID-19 patients. COVID-19 patients with counts of CD8+ T cells or CD4+ T cells in circulation less than 400/μL or 650/μL, respectively, gained more benefits from Tα1. Tα1 reversed T-cell exhaustion and recovered immune reconstitution through promoting thymus output during severe acute respiratory syndrome–coronavirus 2 infection.
Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure
Authors: Jackman Shaun D , Coombe Lauren , Warren René L , Kirk Heather , Trinh Eva , MacLeod Tina , Pleasance Stephen , Pandoh Pawan , Zhao Yongjun , Coope Robin J , Bousquet Jean , Bohlmann Joerg , Jones Steven J M , Birol Inanc
Published: May 2020

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.
Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements
Authors: Hosseini Morteza , Pratas Diogo , Morgenstern Burkhard , Pinho Armando J
Published: May 2020

Background

The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer.

Results

We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image.

Conclusions

Tested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was ~1 GB, which makes Smash++ feasible to run on present-day standard computers.
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome
Authors: Marrano Annarita , Britton Monica , Zaini Paulo A , Zimin Aleksey V , Workman Rachael E , Puiu Daniela , Bianco Luca , Pierro Erica Adele Di , Allen Brian J , Chakraborty Sandeep , Troggio Michela , Leslie Charles A , Timp Winston , Dandekar Abhaya , Salzberg Steven L , Neale David B
Published: May 2020

Background

The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes.

Findings

Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars.

Conclusion

Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy
Authors: Lai Christopher K C , Ng Rita W Y , Wong Martin C S , Chong Ka Chun , Yeoh Yun Kit , Chen Zigui , Chan Paul K S
Published: May 2020

Background

Hong Kong (HK) is a densely populated city near the epicentre of the coronavirus disease 2019 (COVID-19) outbreak. Stringent border control together with aggressive case finding, contact tracing, social distancing and quarantine measures were implemented to halt the importation and spread of the virus.

Methods

We performed an epidemiological study using government information covering the first 100 confirmed cases to examine the epidemic curve, incidence, clusters, reproduction number (Rt), incubation period and time to containment.

Results

A total of 93 of the 100 cases were HK residents (6 infected in Mainland China, 10 on the Diamond Princess Cruise). Seven were visitors infected in Mainland China before entering HK. The majority (76%) were aged ≥45 years, and the incidence increased with age (P < 0.001). Escalation of border control measures correlated with a decrease in the proportion (62.5% to 0%) of cases imported from Mainland China, and a reduction in Rt (1.07 to 0.75). The median incubation period was 4.2 days [95% confidence interval (CI), 4.0–4.5; 5th and 95th percentiles: 1.3 and 14.0). Most clusters with identifiable epidemiological links were households involving 2–4 people. Three medium-spreading events were identified: two from New Year gatherings (6–11 people), and another from environmental contamination of a worship hall (12 people). Despite intensified contact tracing, containment was delayed in 78.9% of cases (mean = 5.96 days, range = 0–24 days). An unusual transmission in a multi-storey building via faulty toilet plumbing was suspected with >100 residents evacuated overnight. Our analysis indicated that faulty plumbing was unlikely to be the source of this transmission.

Conclusion

Timely stringent containment policies minimized the importation and transmission of COVID-19 in HK.