bluuebunny/crossref_metadata_2025 huggingface dataset:
Graphene oxide interlayered in binder-free sulfur vapor deposited cathode for lithium–sulfur battery
Authors: Hakimi Mahdieh , Sanaee Zeinab , Ghasemi Shahnaz , Mohajerzadeh Shams
Published: January 2022

The main drawback of lithium–sulfur (Li–S) batteries which leads to a short lifetime, is the shuttle effect during the battery operation. One of the solutions to mitigate the shuttle effect is the utilization of interlayers. Herein, graphene oxide (GO) paper as an interlayer has been implemented between the sulfur cathode fabricated by the vapor deposition process as a binder-free electrode and a separator in a Li–S battery in order to gain a sufficient capacity. The morphological characteristics and electrochemical performance of the fabricated electrode have been investigated. The fabricated battery demonstrates an initial discharge capacity of 1265.46 mAh g−1 at the current density of 100 mA g−1. The coulombic efficiency is obtained to be 88.49% after 40 cycles. The remained capacity for the battery is 44.70% after several cycles at different current densities. The existence of the GO interlayer improves the electrochemical properties of the battery compared to the one with a pure sulfur cathode. The obtained results indicate that after 40 cycles, the capacity retention is 2.1 times more than that of the battery without the GO implementation.
Double-atom catalysts for energy-related electrocatalysis applications: a theoretical perspective
Authors: Wu Donghai , He Bingling , Wang Yuanyuan , Lv Peng , Ma Dongwei , Jia Yu
Published: January 2022

Due to the excellent activity, selectivity, and stability, atomically dispersed metal catalysts with well-defined structures have attracted intensive research attention. As the extension of single-atom catalyst, double-atom catalyst (DAC) featuring with the metal dimer anchored on a suitable substrate has recently emerged as a research focus for the energy-related electrocatalysis reactions. Due to the flexible dual-metal sites and the synergetic effect between the two metal atoms in DACs, there are more possibilities to adjust their geometrical configurations and electronic structures. The wide tunability of the active sites could offer more opportunities to optimize the binding strength of the reaction intermediates and thus the catalytic activity and/or selectivity of chemical reactions. Moreover, the neighboring metal sites provide a platform to perform more complex electrocatalysis reaction involving the chemical bond coupling. This review aims to summarize the recent advance in theoretical research on DACs for diverse energy-related electrocatalytic reactions. It starts with a brief introduction to DACs. Then an overview of the main experimental synthesis strategies of DACs is provided. Emphatically, the catalytic performance together with the underlying mechanism of the different electrocatalytic reactions, including nitrogen reduction reaction, carbon dioxide reduction reaction, oxygen reduction reaction, and oxygen and hydrogen evolution reactions, are highlighted by discussing how the outstanding attributes mentioned above affect the reaction pathway, catalytic activity, and product selectivity. Finally, the opportunities and challenges for the development of DACs are prospected to shed fresh light on the rational design of more efficient catalysts at the atomic scale in the future.
Antisite disorder and phase segregation in Mn2NiSn
Authors: Malik S V , Dias E T , Nigam A K , Priolkar K R
Published: January 2022

A systematic study of crystal structure, local structure, magnetic and transport properties in quenched and temper annealed Ni

2
−
x

Mn

1
+
x

Sn alloys indicate the formation of Mn3Sn type structural defects caused by an antisite disorder between Mn and Sn occupying the Y and Z sublattices of X2YZ Heusler structure. The antisite disorder is caused by the substitution of Ni by Mn at the X sites. On temper annealing, these defects segregate and phase separate into

L

2
1

Heusler and

D

0

19

Mn3Sn type phases.
Thermodynamics, static properties and transport behaviour of fluids with competing interactions
Authors: Perdomo-Pérez Román , Martínez-Rivera Jaime , Palmero-Cruz Norma C , Sandoval-Puentes Miguel A , Gallegos Javier A S , Lázaro-Lázaro Edilio , Valadez-Pérez Néstor E , Torres-Carbajal Alexis , Castañeda-Priego Ramón
Published: January 2022

Competing interaction fluids have become ideal model systems to study a large number of phenomena, for example, the formation of intermediate range order structures, condensed phases not seen in fluids driven by purely attractive or repulsive forces, the onset of particle aggregation under in- and out-of-equilibrium conditions, which results in the birth of reversible and irreversible aggregates or clusters whose topology and morphology depend additionally on the thermodynamic constrictions, and a particle dynamics that has a strong influence on the transport behaviour and rheological properties of the fluid. In this contribution, we study a system of particles interacting through a potential composed by a continuous succession of a short-ranged square-well (SW), an intermediate-ranged square-shoulder and a long-ranged SW. This potential model is chosen to systematically analyse the contribution of every component of the interaction potential on the phase behaviour, the microstructure, the morphology of the resulting aggregates and the transport phenomena of fluids described by competing interactions. Our results indicate that the inclusion of a barrier and a second well leads to new and interesting effects, which in addition result in variations of the physical properties associated to the competition among interactions.
Anharmonic lattice dynamics and thermal transport in type-I inorganic clathrates
Authors: Godse Shravan , Srivastava Yagyank , Jain Ankit
Published: January 2022

The anharmonic phonon properties of type-I filled inorganic clathrates Ba8Ga16Ge30 and Sr8Ga16Ge30 are obtained from the first-principles calculations by considering the temperature-dependent sampling of the potential energy surface and quartic phonon renormalization. Owing to the weak binding of guest atoms with the host lattice, the obtained guest modes undergo strong renormalization with temperature and become stiffer by up to 50% at room temperature in Sr8Ga16Ge30. The calculated phonon frequencies and associated thermal mean squared displacements are comparable with experiments despite the on-centering of guest atoms at cage centers in both clathrates. Lattice thermal conductivities are obtained in the temperature range of 50–300 K accounting for three-phonon scattering processes and multi-channel thermal transport. The contribution of coherent transport channel is significant at room temperature (13% and 22% in Ba8Ga16Ge30 and Sr8Ga16Ge30) but is insufficient to explain the experimentally observed glass-like thermal transport in Sr8Ga16Ge30.
Methodological developments and practice in characterisation of unconventional and legacy waste
Authors: Strand Per , Jefferies Nick , Koma Yoshikazu , Plyer Jo
Published: January 2022

Radioactive waste management requires planned and systematic actions to provide confidence that the entire system, processes and final products will satisfy given requirements for quality. The characterisation process is dependent on setting clear characterisation objectives and gathering the right information to underpin the decisions that need to be taken to manage the waste safely. This paper reviews experience of characterisation of waste generated from past nuclear activities that were not conducted in compliance consistent with current criteria, or from unexpected situations that were not planned for. This experience shows that the development of a reliable and efficient characterisation and categorisation methodology is a common challenge for such wastes, referred to here as unconventional and legacy (UL) waste. Through the activites of the Nuclear Energy Agency Expert Group on the Characterisation of Unconventional and Legacy Waste, consideration has been given to widely used waste stream characterisation procedures and methods that were originally developed primarily for application in conventional decommissioning work. Although they provide a substantial basis for characterisation, there are various additional factors that commonly need to be taken into account in the case of UL waste. By analysing the challenges and lessons learned from a variety of case studies and other international experience, it has been possible to identify opportunities for adaptations and enhancements to these characterisation methologies, and these are set out and explained. The need for integration of waste characterisation with other aspects of strategic planning for UL waste management is discussed, including characterisation to address any non-radiological hazards. The analysed case studies have also highlighted the importance of developing a robust legislative and regulatory framework in parallel with an appropriate waste infrastructure to treat, store and dispose of UL waste. Finally, the basic features of a UL waste characterisation roadmap are presented, including the interactions within a wider UL waste management programme and key areas for further consideration and possible development. It is anticipated such work can be supported by continued international cooperation.
Embedded growth of colorful CsPbX3 (X = Cl, Br, I) nanocrystals in metal-organic frameworks at Room Temperature
Authors: Chen Chen , Nie Lei , Huang Yizhe , Xi Shuang , Liu Xingyue , Zhang Xiwen , Shi Tielin , Liao Guanglan , Liu Shiyuan , Tang Zirong
Published: January 2022

Herein, we develop a novel strategy for preparing all-inorganic cesium lead halide (CsPbX3, X = Cl, Br, I) perovskite nanocrystals (NCs)@Zn-based metal-organic framework (MOF) composites through interfacial synthesis. The successful embedding of fluorescent perovskite NCs in Zn-MOFs is due to the in situ confined growth, which is attributed to the re-nucleation of water-triggered phase transformation from Cs4PbBr6 to CsPbBr3. The controllable synthesis of mixed-halide based composites with various emission wavelength can be achieved by adding the desired amount of halide (Cl or I) salts in the re-nucleation process. More importantly, the anion exchange reaction is inhibited among various composites with different halogen atoms by being trapped in MOFs. Besides, a white light-emitting diode (WLED) is produced using a blue LED chip with the green-emitting and red-emitting composites, which has a color coordinate of (0.3291, 0.3272) and a wide color gamut. This work provides a novel route to achieving perovskite NCs growth in MOFs, which also can be extended to the other NCs embedded in frames as well.
Artificially created interfacial states enabled van der Waals heterostructure memory device
Authors: Xiang Du , Cao Yi , Wang Kun , Han Zichao , Liu Tao , Chen Wei
Published: January 2022

Two-dimensional (2D) interface plays a predominate role in determining the performance of a device that is configured as a van der Waals heterostructure (vdWH). Intensive efforts have been devoted to suppressing the emergence of interfacial states during vdWH stacking process, which facilitates the charge interaction and transfer between the heterostructure layers. However, the effective generation and modulation of the vdWH interfacial states could give rise to a new design and architecture of 2D functional devices. Here, we report a 2D non-volatile vdWH memory device enabled by the artificially created interfacial states between hexagonal boron nitride (hBN) and molybdenum ditelluride (MoTe2). The memory originates from the microscopically coupled optical and electrical responses of the vdWH, with the high reliability reflected by its long data retention time over 104 s and large write-erase cyclic number exceeding 100. Moreover, the storage currents in the memory can be precisely controlled by the writing and erasing gates, demonstrating the tunability of its storage states. The vdWH memory also exhibits excellent robustness with wide temperature endurance window from 100 K to 380 K, illustrating its potential application in harsh environment. Our findings promise interfacial-states engineering as a powerful approach to realize high performance vdWH memory device, which opens up new opportunities for its application in 2D electronics and optoelectronics.
A nanographene disk rotating a single molecule gear on a Cu(111) surface
Authors: Lin H-H , Croy A , Gutierrez R , Joachim C , Cuniberti G
Published: January 2022

On Cu(111) surface and in interaction with a single hexa-tert-butylphenylbenzene molecule-gear, the rotation of a graphene nanodisk was studied using the large-scale atomic/molecular massively parallel simulator molecular dynamics simulator. To ensure a transmission of rotation to the molecule-gear, the graphene nanodisk is functionalized on its circumference by tert-butylphenyl chemical groups. The rotational motion can be categorized underdriving, driving and overdriving regimes calculating the locking coefficient of this mechanical machinery as a function of external torque applied to the nanodisk. The rotational friction with the surface of both the phononic and electronic contributions is investigated. For small size graphene nanodisks, the phononic friction is the main contribution. Electronic friction dominates for the larger disks putting constrains on the experimental way of achieving the transfer of rotation from a graphene nanodisk to a single molecule-gear.
Improving a high-power laser-based relativistic electron source: the role of laser pulse contrast and gas jet density profile
Authors: Grigoriadis A , Andrianaki G , Fitilis I , Dimitriou V , Clark E l , Papadogiannis N A , Benis E P , Tatarakis M
Published: January 2022

A relativistic electron source based on high power laser interaction with gas jet targets has been developed at the Institute of Plasma Physics and Lasers of the Hellenic Mediterranean University. Initial measurements were conducted using the ‘Zeus’ 45 TW laser with peak intensities in the range of 1018–1019 W cm−2 interacting with a He pulsed gas jet having a 0.8 mm diameter nozzle. A significant improvement of the electron signal was measured after using an absorber to improve the laser pulse contrast from 10−10 to 10−11. A high stability quasi-mono-energetic electron beam of about 50 MeV was achieved and measured using a magnetic spectrometer for pulsed gas jet backing pressure of 12 bar. Supplementary studies using a 3 mm diameter nozzle for backing pressures in the range of 35–40 bar showed electron beam production with energies spread in the range from 50 to 150 MeV. The pulsed jet density profile was determined using interferometric techniques. Particle-in-cell simulations, at the above experimentally determined conditions, support our experimental findings.
The influences of radiation effects on DC/RF performances of L
g = 22 nm gate-all-around nanosheet field-effect transistor
Authors: Ma Yue , Bi Jinshun , Majumdar Sandip , Mehmood Safdar , Ji Lanlong , Sun Yichao , Zhang Chenrui , Fan Linjie , Zhao Biyao , Wang Hanbin , Shen Lizhi , Han Tingting
Published: January 2022

In this paper, we carried out detailed technology computer aided design simulations to investigate the radiation effects, e.g. total ionizing dose (TID) and single-event effects (SEEs), on direct current (DC) and radio frequency (RF) characteristics of the gate-all-around (GAA) nanosheet field-effect transistor (FET). The simulation model used is composed of seven-layer stacked GAA nanosheet FET with L
g = 22 nm, which was implemented in this study. The open current and the drain-induced barrier lowering of the device are ∼3 mA μm−1 and 47 mV V−1, respectively. The results indicate that the TID have little influence on the DC and RF characteristics when the transistor is working in an open state. During the SEEs simulation, we considered three incident directions for the high energy particle, including the lateral direction of the channels, the vertical direction of the channels and the top of the channels. The influence of the particle injecting along the lateral and vertical directions of the channels shows stronger relation with the distance from the incident point compared to the influence of the particle from the top. Besides, the general influence of the particle injecting along the lateral directions of the channels is higher than the other two directions. The total injected charge of the particle injecting along the lateral direction, along the vertical direction and from the top are 3 fC, 1.4 fC and 2.1 fC, respectively. As compared to the fin FET, the GAA nanosheet has superior RF performances and less sensitivity to TID effect. This work can provide a guideline for the GAA nanosheet devices in aerospace and avionic RF applications.
DC characterization of advanced fine-filamentary MgB2 superconducting wires
Authors: Kováč P , Melišek T , Kováč J , Búran M , Hušek I , Rindfleisch M , Tomsic M
Published: January 2022

MgB2 wires with 114, 192 and 342 filaments of size 14–19 µm manufactured by HyperTech Research, Inc. have been subjected to low-temperature DC measurements. R(T), I–V characteristics, critical currents, stress and strain tolerances of these wires differing by filament architecture and filament size sheathed by resistive CuNi alloys were measured and compared with the literature data. It was found that these fine-filamentary wires have high engineering current densities not reduced by twisting up to 10 mm, sufficient strain tolerances and therefore are promising for future applications where minimized AC losses are required due to resistive sheaths, thin MgB2 filaments and short twist pitches.
Atomic-scale observation of spontaneous hole doping and concomitant lattice instabilities in strained nickelate films
Authors: Lin I C , Lee M H , Wu P C , Lin S C , Chen J W , Li C-C , Guo G Y , Chu Y-H , Sankar R , Chu M-W
Published: January 2022

Thin oxide films are of vast opportunities for modern electronics and can facilitate emergent phenomena by factors absent in the bulk counterparts, such as the ubiquitous epitaxial strain and interfacial charge doping. Here, we demonstrate the twisting of intended bulk-metallic phases in 10-unit-cell LaNiO3, PrNiO3, and NdNiO3 films on (001)-oriented SrTiO3 into distinct charge-lattice entangled states by epitaxial strains. Using atomically-resolved electron microscopy and spectroscopy, the interfacial electron doping into SrTiO3 in the conventional context of band alignments are discounted. Instead, spontaneously doped holes that are localized and at the order of 1013 cm−2 are atomically unraveled across all three heterointerfaces and associated with strain mitigations by the accompanied atomic intermixing with various ionic radii. The epitaxial strains also lead to condensations of monoclinic-C2/c lattice instabilities, which are hidden to the bulk phase diagram. The group-theoretical analysis of characteristic transition pathways unveils the strain resurrection of the hidden C2/c symmetry. While this strain-induced monoclinic phase in LaNiO3 remains metallic at room temperature, those in PrNiO3 and NdNiO3 turn out to be insulating. Such strain-induced monoclinic lattice instabilities and parasitic localized holes go beyond the classical elastic deformations of films upon epitaxial strains and hint on plausible hidden orders in versatile oxide heterostructures with unexpected properties, of which the exploration is only at the infancy and full of potentials.
Structure of spherically symmetric objects: a study based on structure scalars
Authors: Yousaf Z
Published: January 2022

The aim of this paper is to explore the consequences of extra curvature terms mediated from f(R, T, Q) (where Q ≡ R

μ
ν

T

μ
ν
) theory on the formation of scalar functions and their importance in the study of populations who are crowded with regular relativistic objects. For this purpose, we model our system comprising of non-rotating spherical geometry formed due to gravitation of locally anisotropic and radiating sources. After considering a particular f(R, T, Q) model, we form a peculiar relation among Misner-Sharp mass, tidal forces, and matter variables. Through structure scalars, we have modeled shear, Weyl, and expansion evolutions equations. The investigation for the causes of the irregular distribution of energy density is also performed with and without constant curvature conditions. It is deduced that our computed one of the f(R, T, Q) structure scalars (Y

T
) has a vital role to play in understanding celestial mechanisms in which gravitational interactions cause singularities to emerge.
An ab-initio study of electronic and optical properties of RhXO3 (X = Ga, Ag) perovskites
Authors: Rouf Syed Awais , Hussain Muhammad Iqbal , Mumtaz Umair , Masood Hafiz Tariq , Albalawi Hind , Majeed Abdul Mannan , Khalil R M Arif , Mahmood Q
Published: January 2022

The ab-initio computations were performed to study the electronic and optoelectronic properties of

RhXO

3

(
X
=
Ga
,

Ag
)

perovskites using WIEN2k code. The

RhGaO

3

has band gap of 2.29 eV, and the behavior of

RhAgO

3

is metallic. The sub-TDOS of the studied materials revealed that rhodium and oxygen atoms have significant contributions in the valence band and conduction band formation of both materials. The silver cation is responsible for the reasonable peaks appearing at the Fermi level of

RhAgO

3

,

which demonstrated the conducting nature of

RhAgO

3

.

The dielectric functions, optical conductivity, energy loss function, absorption coefficient, refractive index, extinction coefficient, and reflectivity are computed for these materials to understand the optical behavior of the studied materials. The analysis of optical properties ensure the

RhGaO

3

is a promising material for optoelectronics while

RhAgO

3

has metallic nature.
Effects of La2O3 contents on microstructure and properties of laser-cladded 5 wt% CaB6/HA bioceramic coating
Authors: Liu Jinjing , Long Xin , Zhu Hongmei , Zhu Weihua , Chen Zhiyong , He Dong , Song Nini , Wang Xinlin
Published: January 2022

In the present work, 5 wt% CaB6/hydroxyapatite (HA) bioceramic coatings with different La2O3 contents (0–0.6 wt%) have been fabricated by a laser cladding technique on Ti–6Al–4V. The effects of La2O3 contents on microstructure and properties of the laser-cladded 5 wt% CaB6/HA coatings have been carefully investigated. The results show that the microstructure is obviously refined, and the structure is relatively uniform after doping 0.2–0.4 wt% La2O3. As the La2O3 content increases, the corrosion resistance are found to increase firstly and then gradually decrease. The x-rays diffraction analysis confirms that the amount of HA and TCP (calcium phosphate) in the coating reaches maximum after doping 0.2 wt% La2O3. The La2O3-doped coatings show a significantly higher bone-like apatite precipitation after immersion in simulated body fluid compared with La2O3-free coating. In vitro experiment also shows that 5 wt% CaB6/HA bioceramic coatings with 0.2–0.4 wt% La2O3 are more suitable for the attachment and proliferation of MG63 cells, exhibiting superior bioactivity and biocompatibility.
Fibroblast growth factor 13 is involved in the pathogenesis of temporal lobe epilepsy
Authors: Shen Kai-Feng , Yue Jiong , Wu Zhi-Feng , Wu Ke-Fu , Zhu Gang , Yang Xiao-Lin , Wang Zhong-Ke , Wang Jing , Liu Shi-Yong , Yang Hui , Zhang Chun-Qing
Published: January 2022

Background

Temporal lobe epilepsy (TLE) is the most common drug-resistant epilepsy in adults, with pathological mechanisms remaining to be fully elucidated. Fibroblast Growth Factor 13 (FGF13) encodes an intracellular protein involved in microtubule stabilization and regulation of voltage-gated sodium channels (VGSCs) function. FGF13 mutation has been identified in patients with inherent seizure, suggesting a potential association between FGF13 and the etiology of TLE. Here, we set to explore the pathological role of FGF13 in the etiology of TLE.

Results

We found that the expression of FGF13 was increased in the cortical lesions and CA1 region of sclerotic hippocampus and correlated with the seizure frequency in TLE patients. Also, Fgf13 expression was increased in the hippocampus of chronic TLE mice generated by kainic acid (KA) injection. Furthermore, Fgf13 knockdown or overexpression was respectively found to attenuate or potentiate the effects of KA on axonal length, somatic area and the VGSCs-mediated current in the hippocampal neurons.

Conclusions

Taken together, these findings suggest that FGF13 is involved in the pathogenesis of TLE by modulating microtubule activity and neuronal excitability.
Individual variation in brain network topology is linked to course of illness in major depressive disorder
Authors: Sheng Wei , Cui Qian , Jiang Kexing , Chen Yuyan , Tang Qin , Wang Chong , Fan Yunshuang , Guo Jing , Lu Fengmei , He Zongling , Chen Huafu
Published: January 2022

Major depressive disorder (MDD) is a chronic and highly recurrent disorder. The functional connectivity in depression is affected by the cumulative effect of course of illness. However, previous neuroimaging studies on abnormal functional connection have not mainly focused on the disease duration, which is seen as a secondary factor. Here, we used a data-driven analysis (multivariate distance matrix regression) to examine the relationship between the course of illness and resting-state functional dysconnectivity in MDD. This method identified a region in the anterior cingulate cortex, which is most linked to course of illness. Specifically, follow-up seed analyses show this phenomenon resulted from the individual differences in the topological distribution of three networks. In individuals with short-duration MDD, the connection to the default mode network was strong. By contrast, individuals with long-duration MDD showed hyperconnectivity to the ventral attention network and the frontoparietal network. These results emphasized the centrality of the anterior cingulate cortex in the pathophysiology of the increased course of illness and implied critical links between network topography and pathological duration. Thus, dissociable patterns of connectivity of the anterior cingulate cortex is an important dimension feature of the disease process of depression.
Expectations, Wage Hikes and Worker Voice
Authors: Adhvaryu Achyuta , Molina Teresa , Nyshadham Anant
Published: January 2022

Enabling worker voice could improve worker retention and effort by providing workers the chance to improve their situation or an outlet to express discontent. We provide a test of this hypothesis via a randomised controlled trial in Indian garment factories. Just after what proved to be a disappointing wage hike, workers were chosen at random to participate in an anonymous survey in which they were asked for feedback on job conditions, supervisor performance and overall job satisfaction. Enabling voice in this manner reduced turnover and absenteeism after the hike, particularly for the most disappointed workers.
Characterisation of gluten-degrading prolyl endoprotease from Thermococcus kodakarensis
Authors: Shetty Radhakrishna , Bang-Berthelsen Claus Heiner , Ciurkot Klaudia Weronika , Vestergaard Mike , Hägglund Per Mårten , Prakash H S , Hobley Timothy John
Published: January 2022

There is increasing interest in gluten degrading enzymes for use during food and drink processing. The industrially available enzymes usually work best at low to ambient temperatures. However, food manufacturing is often conducted at higher temperatures. Therefore, thermostable gluten degrading enzymes are of great interest. We have identified a new thermostable gluten degrading proline specific prolyl endoprotease from the archaea Thermococcus kodakarensis. We then cloned and expressed it in Escherichia coli. The prolyl endoprotease was found to have a size of 70.1 kDa. The synthetic dipeptide Z-Gly-Pro-p-nitroanilide was used to characterise the prolyl endoprotease and it had maximum activity at pH 7 and 77°C. The VmaxKm and kcat values of the purified prolyl endoprotease were calculated to be 3.14 mM/s, 1.10 mM and 54 s–1 respectively. When the immunogenic gluten peptides PQPQLPYPQPQLPY (alpha-gliadin) and SQQQFPQPQQPFPQQP (gamma-hordein) were used as substrates, the prolyl endoprotease was able to degrade these. Furthermore, gluten in wort was reduced when the prolyl endoprotease was used during mashing of barley malt. The discoveries open up for new food processing possibilities and further the understanding of proline specific protease diversity.
The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2
Authors: Wassenaar Trudy M , Wanchai Visanu , Buzard Gregory , Ussery David W
Published: January 2022

The genomic diversity of SARS-CoV-2 is the result of a relatively low level of spontaneous mutations introduced during viral replication. With millions of SARS-CoV-2 genome sequences now available, we can begin to assess the overall genetic repertoire of this virus. We find that during 2020, there was a global wave of one variant that went largely unnoticed, possibly because its members were divided over several sublineages (B.1.177 and sublineages B.1.177.XX). We collectively call this Janus, and it was eventually replaced by the Alpha (B.1.1.7) variant of concern (VoC), next replaced by Delta (B.1.617.2), which itself might soon be replaced by a fourth pandemic wave consisting of Omicron (B.1.1.529). We observe that splitting up and redefining variant lineages over time, as was the case with Janus and is now happening with Alpha, Delta and Omicron, is not helpful to describe the epidemic waves spreading globally. Only ∼5% of the 30 000 nucleotides of the SARS-CoV-2 genome are found to be variable. We conclude that a fourth wave of the pandemic with the Omicron variant might not be that different from other VoCs, and that we may already have the tools in hand to effectively deal with this new VoC.
Simultaneous dissection of grain carotenoid levels and kernel color in biparental maize populations with yellow-to-orange grain
Authors: LaPorte Mary-Francis , Vachev Mishi , Fenn Matthew , Diepenbrock Christine
Published: January 2022

Maize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the US maize nested association mapping panel that have yellow to orange grain. Quantitative trait loci were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color quantitative trait loci ranging from 2.4% to 17.5%. These quantitative trait loci were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized ∼27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the α- or β-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with β-branch and total carotenoids and negligible correlations with α-branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.
The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster
Authors: Akiyama Noriyoshi , Sato Shoma , Tanaka Kentaro M , Sakai Takaomi , Takahashi Aya
Published: January 2022

The spatiotemporal regulation of gene expression is essential to ensure robust phenotypic outcomes. Pigmentation patterns in Drosophila are determined by pigments biosynthesized in the developing epidermis and the cis-regulatory elements of the genes involved in this process are well-characterized. Here, we report that the known primary epidermal enhancer is dispensable for the transcriptional activation of ebony (involved in light-colored pigment synthesis) in the developing epidermis of Drosophila melanogaster. The evidence was obtained by introducing an approximately 1 kbp deletion at the primary epidermal enhancer by genome editing. The effect of the primary epidermal enhancer deletion on pigmentation and on the endogenous expression pattern of a mCherry-fused ebony allele was examined in the abdomen. The expression levels of the mCherry-fused ebony in the primary epidermal enhancer-deleted strains were slightly higher than that of the control strain, indicating that the sequences outside the primary epidermal enhancer have an ability to drive an expression of this gene in the epidermis. Interestingly, the primary epidermal enhancer deletion resulted in a derepression of this gene in the dorsal midline of the abdominal tergites, where dark pigmentation is present in the wild-type individuals. This indicated that the primary epidermal enhancer fragment contains a silencer. Furthermore, the endogenous expression pattern of ebony in the 2 additional strains with partially deleted primary epidermal enhancer revealed that the silencer resides within a 351-bp fragment in the 5' portion of the primary epidermal enhancer. These results demonstrated that deletion assays combined with reporter assays are highly effective in detecting the presence of positively and negatively regulating sequences within and outside the focal cis-regulatory elements.
Citation needed? Wikipedia bibliometrics during the first wave of the COVID-19 pandemic
Authors: Benjakob Omer , Aviram Rona , Sobel Jonathan Aryeh
Published: January 2022

Background

With the COVID-19 pandemic’s outbreak, millions flocked to Wikipedia for updated information. Amid growing concerns regarding an “infodemic,” ensuring the quality of information is a crucial vector of public health. Investigating whether and how Wikipedia remained up to date and in line with science is key to formulating strategies to counter misinformation. Using citation analyses, we asked which sources informed Wikipedia’s COVID-19–related articles before and during the pandemic’s first wave (January–May 2020).

Results

We found that coronavirus-related articles referenced trusted media outlets and high-quality academic sources. Regarding academic sources, Wikipedia was found to be highly selective in terms of what science was cited. Moreover, despite a surge in COVID-19 preprints, Wikipedia had a clear preference for open-access studies published in respected journals and made little use of preprints. Building a timeline of English-language COVID-19 articles from 2001–2020 revealed a nuanced trade-off between quality and timeliness. It further showed how pre-existing articles on key topics related to the virus created a framework for integrating new knowledge. Supported by a rigid sourcing policy, this “scientific infrastructure” facilitated contextualization and regulated the influx of new information. Last, we constructed a network of DOI-Wikipedia articles, which showed the landscape of pandemic-related knowledge on Wikipedia and how academic citations create a web of shared knowledge supporting topics like COVID-19 drug development.

Conclusions

Understanding how scientific research interacts with the digital knowledge-sphere during the pandemic provides insight into how Wikipedia can facilitate access to science. It also reveals how, aided by what we term its “citizen encyclopedists,” it successfully fended off COVID-19 disinformation and how this unique model may be deployed in other contexts.
Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
Authors: Smolander Olli-Pekka , Blande Daniel , Ahola Virpi , Rastas Pasi , Tanskanen Jaakko , Kammonen Juhana I , Oostra Vicencio , Pellegrini Lorenzo , Ikonen Suvi , Dallas Tad , DiLeo Michelle F , Duplouy Anne , Duru Ilhan Cem , Halimaa Pauliina , Kahilainen Aapo , Kuwar Suyog S , Kärenlampi Sirpa O , Lafuente Elvira , Luo Shiqi , Makkonen Jenny , Nair Abhilash , de la Paz Celorio-Mancera Maria , Pennanen Ville , Ruokolainen Annukka , Sundell Tarja , Tervahauta Arja I , Twort Victoria , van Bergen Erik , Österman-Udd Janina , Paulin Lars , Frilander Mikko J , Auvinen Petri , Saastamoinen Marjo
Published: January 2022

Background

The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses.

Results

The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models.

Conclusions

The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.
Delayed Hopf Bifurcation and Space–Time Buffer Curves in the Complex Ginzburg–Landau Equation
Authors: Goh Ryan , Kaper Tasso J , Vo Theodore
Published: January 2022

In this article, the recently discovered phenomenon of delayed Hopf bifurcations (DHB) in reaction–diffusion partial differential equations (PDEs) is analysed in the cubic Complex Ginzburg–Landau equation, as an equation in its own right, with a slowly varying parameter. We begin by using the classical asymptotic methods of stationary phase and steepest descents on the linearized PDE to show that solutions, which have approached the attracting quasi-steady state (QSS) before the Hopf bifurcation remain near that state for long times after the instantaneous Hopf bifurcation and the QSS has become repelling. In the complex time plane, the phase function of the linearized PDE has a saddle point, and the Stokes and anti-Stokes lines are central to the asymptotics. The non-linear terms are treated by applying an iterative method to the mild form of the PDE given by perturbations about the linear particular solution. This tracks the closeness of solutions near the attracting and repelling QSS in the full, non-linear PDE. Next, we show that beyond a key Stokes line through the saddle there is a curve in the space-time plane along which the particular solution of the linear PDE ceases to be exponentially small, causing the solution of the non-linear PDE to diverge from the repelling QSS and exhibit large-amplitude oscillations. This curve is called the space–time buffer curve. The homogeneous solution also stops being exponentially small in a spatially dependent manner, as determined also by the initial data and time. Hence, a competition arises between these two solutions, as to which one ceases to be exponentially small first, and this competition governs spatial dependence of the DHB. We find four different cases of DHB, depending on the outcomes of the competition, and we quantify to leading order how these depend on the main system parameters, including the Hopf frequency, initial time, initial data, source terms, and diffusivity. Examples are presented for each case, with source terms that are a uni-modal function, a smooth step function, a spatially periodic function and an algebraically growing function. Also, rich spatio-temporal dynamics are observed in the post-DHB oscillations. Finally, it is shown that large-amplitude source terms can be designed so that solutions spend substantially longer times near the repelling QSS, and hence, region-specific control over the delayed onset of oscillations can be achieved.
Exploring the relation between clinician ratings and patient-reported experience and outcomes
Authors: Mendlovic Shlomo , Roe David , Markusfeld Geffen , Mainz Jan , Kristensen Solvejg , Goldzweig Gil
Published: January 2022

Background

Patient-reported outcome measures (PROMs) and patient-reported experience measures (PREMs) are increasingly recognized as important ways for patients to be more actively involved in their treatment and enhance shared decision-making.

Objective

The current study investigated the associations between PROMs, PREMs and various symptoms measures reported by clinicians and psychiatric patients.

Method

One hundred and twenty people admitted to a psychiatric hospital completed two PREMs, one PROM (the shortened version of the Manchester Short Assessment of Quality of Life scale) and Effects of Symptoms on Daily Functioning (the Sheehan Disability Scale), the Patient Clinical Global Impression and the Modified Colorado Symptom Index. Their psychiatrists rated them using the Global Assessment of Functioning scale, the Health of the Nation Outcome Scales and the Therapist Clinical Global Impression.

Results

There was a strong correlation between patient’s evaluation of their quality of life (PROM), experience of their care (PREM) and the overall severity of their condition and their progress. The pattern of correlation between patients’ and clinicians’ measures revealed a three-layer structure representing a continuum from inner experience to external presentation of experiences.

Conclusion

Together these findings help identify and emphasize various domains of subjective experiences and their relation to external ratings.
Young Software Engineer of the Year 2021
Authors: Hurst Mike
Published: January 2022

BCS-in-Scotland, a grouping of the BCS Branches and Specialist Groups in Scotland, continued its long-standing involvement with the annual ScotSoft event organised by ScotlandIS. Mike Hurst, Treasurer and Webmaster of the BCS Edinburgh Branch, reports.
EngRec
Authors: Wolfheart Olivia
Published: January 2022

This year, BCS was a strategic partner for EngRec: the virtual fair for early engineering careers. Olivia Wolfheart MBCS reports on the successful event.
Insight: AI
Authors: Smith Adam Leon
Published: January 2022

What is next for AI regulation? Senior Technologist Adam Leon Smith CITP FBCS explores the implications of the EU AI Act.
Relationship Building as a Strategy for Managing Referring Clinicians
Authors: Marshall Holly , Mehta Lina , Plecha Donna
Published: January 2022

The strength of a radiology practice depends on the strong relationships radiologists develop with referring clinicians. Solid relationships with referring clinicians can contribute to a satisfying work environment, and ultimately excellent patient care. There are several different ways that a radiologist can help improve relationships with clinicians. As a start, this includes a radiologist strengthening one’s emotional intelligence. Also, identifying the personality traits of others is key to successful interactions. Conflicts in the workplace are inevitable, and effective negotiation is helpful in building relationships with clinicians. Interacting with the referring clinicians is also key to a successful relationship. This includes all in-person communication, participating in tumor boards, community outreach events, and social functions outside of work. This article presents several tips to improve and manage relationships with referring clinicians.
The National Environmental Policy Act and the USDA Forest Service: Where We Agree, Where We Disagree, and Why
Authors: Fleischman Forrest , Struthers Cory , Arnold Gwen , Dockry Michael J , Scott Tyler
Published: January 2022

In this article, we respond to a critique of our earlier work examining the USDA Forest Service’s (USFS’s) planning processes. We appreciate that our critics introduce new data to the discussion of USFS planning. Further data integration is a promising path to developing a deeper understanding of agency activities. Our critics’ analysis largely supports our original claims. Our most important difference is in our conceptualization of the planning process’s relationship to agency goals. Although our critics conceive of the USFS’s legally prescribed planning processes as a barrier to land management activities, we believe that public comment periods, scientific analysis, and land management activities are tools the agency uses to achieve its goals of managing land in the public interest.

Study Implications: The USDA Forest Service’s current planning process has been critiqued as a barrier to accomplishing land management activities, but it is also an important tool for insuring science-based management and understanding public values and interests that the agency is legally bound to uphold.
MPK3 and MPK6 control salicylic acid signaling by up-regulatingNLRreceptors during pattern- and effector-triggered immunity
Authors: Lang Julien , Genot Baptiste , Bigeard Jean , Colcombet Jean
Published: January 2022

Arabidopsis thaliana mitogen-activated protein kinases 3 and 6 (MPK3/6) are activated transiently during pathogen-associated molecular pattern-triggered immunity (PTI) and durably during effector-triggered immunity (ETI). The functional differences between these two kinds of activation kinetics and how they coordinate the two layers of plant immunity remain poorly understood. Here, by suppressor analyses, we demonstrate that ETI-mediating nucleotide-binding domain leucine-rich repeat receptors (NLRs) and the NLR signaling components NDR1 and EDS1 can promote the salicylic acid sector of defense downstream of MPK3 activity. Moreover, we provide evidence that both sustained and transient MPK3/6 activities positively control the expression of several NLR genes, including AT3G04220 and AT4G11170. We further show that NDR1 and EDS1 contribute to the up-regulation of these two NLRs in both an ETI and a PTI context. Remarkably, whereas in ETI MPK3/6 activities are dependent on NDR1 and EDS1, they are not in PTI, suggesting crucial differences in the two signaling pathways. Finally, we demonstrate that expression of the NLR AT3G04220 is sufficient to induce expression of defense genes from the salicylic acid branch. Overall, this study expands our knowledge of MPK3/6 functions during immunity and provides new insights into the intricate interplay of PTI and ETI.
Evidence for anisotropic quenching in massive galaxy clusters at z ≈ 0.5
Authors: Stott John P
Published: January 2022

A recent observational result finds that the quenching of satellites in groups at z = 0.08 has an angular dependence relative to the semimajor axis of the central galaxy. This observation is described as ‘anisotropic quenching’ or ‘angular conformity’. In this paper, I study the variation in the colour of a mass-limited sample of satellite galaxies relative to their angle from the major axis of the brightest cluster galaxy in the CLASH clusters up to z ∼ 0.5, 4 Gyr further in lookback time. The same result is found: galaxies close to the major axis are more quenched than those along the minor axis. I also find that the star-forming galaxies tend to avoid a region ±45○ from the major axis. This quenching signal is thought to be driven by AGN outflows along the minor axis, reducing the density of the intergalactic medium and thus the strength of ram pressure. Here, I will discuss potential alternative mechanisms. Finally, I note that the advent of the Legacy Survey of Space and Time (LSST) and Euclid surveys will allow for a more detailed study of this phenomenon and its evolution.