bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of inverse spin Hall devices based on the direct injection of carriers in L-valley of GaAs
Authors: Mudi Priyabrata , Khamari Shailesh K , Sharma T K
Published: February 2021

Numerical simulations are carried out to estimate the inverse spin Hall voltage (V
ISHE) as a function of applied electric field, dopant density and excitation energy for n-GaAs based opto-spintronic devices. Adopting a three valley rate equation model, an expression is derived for the density of spin polarized electrons accumulated in different valleys of conduction band. It is noted that an external electric field can be used to enhance the magnitude of V
ISHE significantly, however the shape of curve depends upon the choice of excitation energy. A significant rise of V
ISHE is noted beyond a critical value of electric field when the carriers are injected into Γ-valley of GaAs. On the other hand, a peak like behaviour is observed when hot electrons are injected into Γ-valley. A dual slope behaviour of V
ISHE with applied electric field is noticed when carriers are injected directly into L-valley of GaAs, where a reasonable value of V
ISHE can be predicted even for a modest value of electric field. Further, a peak like behaviour of V
ISHE with dopant density is predicted irrespective of the choice of excitation energy. The optimum dopant density of n-GaAs based Inverse spin Hall devices is found to be ∼4 × 1016 cm−3. Theoretical predictions made in this work are critically important for the realization of next generation inverse spin Hall devices involving L-valley electrons.
Processing CdS- and CdSe-containing window layers for CdTe solar cells
Authors: Çiriş Ali , Başol Bülent M , Atasoy Yavuz , Karaca Abdullah , Tomakin Murat , Küçükömeroğlu Tayfur , Bacaksız Emin
Published: February 2021

The influence of heat treatment steps on the characteristics of (CdS, CdSe) junction partners and on solar cell performance was studied. CdS films were obtained by chemical bath deposition, and CdSe layers were evaporated. Structural and compositional properties of CdS/CdSe bilayer stacks did not change upon heat treatment at 400 °C up to 10 min, whereas heat treatment in the presence of CdCl2 for 10 min caused formation of a CdSSe alloy with a bandgap value of about 2.05 eV. Originally, the cubic structure of the stack was also transformed into a hexagonal structure during this treatment. CdSe–CdTe interdiffusion was also studied using CdS/CdSe/CdTe triple layer stacks. CdTe films were deposited using a close-spaced sublimation method. Limited CdSe–CdTe interdiffusion was seen when CdTe was deposited over the as-deposited CdSe layer at 580 °C. However, such interdiffusion was not detected for samples where CdTe deposition was carried out on CdS/CdSe stacks pre-annealed in the presence of CdCl2. This suggests that partial crystallization of the CdS/CdSe bilayer stack by CdCl2 reduced such an interaction. Solar cells with CdSe/CdTe, CdS/CdTe and CdS/CdSe/CdTe structures with efficiencies of 8.39%, 10.12% and 11.47% were fabricated using 4.5–5 µm thick CdTe layers and a final CdCl2 treatment. Quantum efficiency measurements demonstrated the benefit of CdSe–CdTe alloying during the final CdCl2 treatment in improving the short circuit current values.
Pressure-induced electrides and metallic phases in the Y–Cl system
Authors: Yu Hulei , Chen Yue
Published: February 2021

Pressure can profoundly change the electronic structure, leading to the formation of new phases and materials with exotic properties. Herein, using evolutionary algorithms and density functional theory, we systematically investigate the behaviour of materials in the yttrium–chlorine binary system under pressure. Electrons are found to be spatially confined at low pressures in yttrium chlorides and tend to form new electrides. In particular, a novel yttrium chloride, Y3Cl2, is predicted to be thermodynamically and lattice dynamically stable at approximately 10 GPa. Further analyses of the electron localization function and partial charge density identify trigonal Y3Cl2 as a new 2D high-pressure electride with partially localized electrons contributing to the conduction. By further increasing the pressure, electrons in the yttrium–chlorine binary system tend to delocalize with the electrides decomposing into two new compounds (Y2Cl and YCl2) and a new YCl phase (space group P63/mmc) above 20 GPa. These newly discovered phases are all metallic in their stable pressure range according to band structure simulations without interstitial electron localization. The discovery of these unconventional yttrium chlorides may inspire strategies to search for low-pressure electrides in other rare-earth halogenide systems.
Strain effect on electronic structure and transport properties of zigzag α-T
3 nanoribbons: a mean-field theoretical study
Authors: Cheng Xing , Zhou Benhu , Zhou Benliang , Zhou Guanghui
Published: February 2021

The α-T
3 lattice, a minimal model that presents flat bands, has sparked much interest in research but the finite-size effect and interaction has been rarely involved. Here we theoretically study the electronic structure and transport properties of zigzag-edge α-T
3 nanoribbons (ZαT
3NRs) with and without uniaxial strain, where the exemplary widths N = 40 and 41 for two series are considered. By adopting the mean-field Hubbard model combined with the nonequilibrium Green’s function method, we show that the spin-degenerate dispersionless flat band at the Fermi energy for the pristine ribbons is split into spin-up and -down flat bands under electron–electron Coulomb interaction. Specifically, the two bands are shifted toward in an opposite direction and away from the Fermi energy, which leads to an energy gap opening in the case of α ≠ 1. All three series of ZαT
3NRs with width N = 3n, 3n + 1, 3n + 2 (where n is a positive integer) exhibit an energy gap. This differs from the simple tight-binding calculations without considering electron–electron Coulomb interaction, for which the gap is always zero in the case of N = 3n + 1. Here, the origin of the energy gap for N = 3n + 1 arises from Coulomb repulsion between electrons. Importantly, the energy gap can be effectively manipulated by an uniaxial strain and Coulomb interaction if α ≠ 1. The gap linearly increases (decreases) when a tensile (compressive) strain increases, and it also monotonously increases as enhancing Coulomb interaction. Interestingly, a ground state of antiferromagnetic to ferromagnetic transition occurs when α increases from 0.8 to 1, leading to a semiconductor to metallic transition. Besides, the α-, strain- and interaction-dependent conductance is also explored. The findings here may be of importance in the band gap engineering and electromechanical applications of α-T
3 nanoribbon-based devices.
Total finite element tearing and interconnection method for computationally efficient micromechanical analysis
Authors: Kulkarni Nagesh H , Gautham B P , Kulkarni Salil S
Published: February 2021

Micromechanical analysis of a representative volume element (RVE) is commonly performed to estimate the material’s effective/homogenized properties in a multiscale analysis of deformation of materials. Typically numerical analysis techniques such as the finite element (FE) method are used for such an analysis. A highly refined FE mesh is required to capture microstructure features accurately for the analysis of RVE. However, this increases the number of degrees of freedom and affects computational time adversely. In this contribution a total finite element tearing and interconnection (TFETI) domain decomposition method based approach is presented for a computationally efficient micromechanical analysis. Two critical aspects of the micromechanical analysis, namely, a) computationally efficient solution of the boundary value problem and b) ease of computation of effective properties, are addressed in this work. This work focuses on the displacement driven micromechanical analysis where the boundary conditions are available in terms of displacements over the entire boundary. Two types of displacement boundary conditions, viz uniform or proportional displacements and periodic displacements corresponding to the state of uniaxial extension and simple shear are considered. The performance of the adapted TFETI with commonly used preconditioners, namely Dirichlet and lumped, for such displacement driven analysis is investigated. An efficient algorithm that exploits the structure of the TFETI method is proposed to calculate the effective properties. The proposed method’s efficacy is demonstrated by analyzing some representative model problems of composite materials. It is observed that the method’s performance depends on various problem parameters such as volume fraction, the shape of inclusion, the distance between the inclusions, and the contrast between the material properties of matrix and inclusion. The performance also depends on the numerical method parameters, such as the number of subdomains, shape of subdomains, and preconditioners. Therefore, a systematic study is carried out to study the influence of these parameters on the method’s performance.
Transition from elastic to plastic strain release in core−shell nanowires revealed by in-plane x-ray diffraction
Authors: Al Hassan Ali , Salehi Waheed A , Lewis Ryan B , Anjum Taseer , Sternemann Christian , Geelhaar Lutz , Pietsch Ullrich
Published: February 2021

We investigate the strain evolution and relaxation process as function of increasing lattice mismatch between the GaAs core and surrounding In
x
Ga1−x
As shell in core–shell nanowire heterostructures grown on Si(111) substrates. The dimensions of the core and shell are kept constant whereas the indium concentration inside the shell is varied. Measuring the

22

4
¯

and

2

2
¯

0

in-plane Bragg reflections normal to the nanowire side edges and side facets, we observe a transition from elastic to plastic strain release for a shell indium content x > 0.5. Above the onset of plastic strain relaxation, indium rich mounds and an indium poor coherent shell grow simultaneously around the GaAs core. Mound formation was observed for indium contents x = 0.5 and 0.6 by scanning electron microscopy. Considering both the measured radial reflections and the axial 111 Bragg reflection, the 3D strain variation was extracted separately for the core and the In
x
Ga1−x
As shell.
Numerical simulation of dielectric barrier discharge with asymmetrical electrode in atmospheric helium
Authors: Wang Jing , Li Jing , Lei Bingying , Ran Shuang , Xu Boping , Liu Yinghua , Li Xinzhong , Wang Yishan , Tang Jie , Zhao Wei , Duan Yixiang
Published: February 2021

The characteristics of the dielectric barrier discharge (DBD) equipped with asymmetrical electrode (ring electrode on the upper and disk electrode on the lower) in atmospheric helium are investigated by a two-dimensional self-consistent fluid model. Simulation results show that as the applied voltage increases, the discharge enhances and the onset of discharge advances, which is similar to the results of traditional DBD. However, with the applied voltage increasing, the symmetry of the discharge current pulses in the positive and negative half cycles disappears because of the asymmetric electrode configuration. In addition, only the spatial distribution of the electron density at the peak moments of the first and second current pulses satisfies the complementary characteristics, while the spatial distribution at other peak moments does not meet the complementary characteristics. Moreover, the electric field, near the upper dielectric barrier surface, presents a curtain-like distribution with considerable radial electric field components, which results from the non-uniform radial surface charge distribution and the ring electrode configuration. The relative variation of the radial distribution of surface charge density is largely determined by the geometry of the opposite electrode.
Next generation electronics on the ultrawide-bandgap aluminum nitride platform
Authors: Hickman Austin Lee , Chaudhuri Reet , Bader Samuel James , Nomoto Kazuki , Li Lei , Hwang James C M , Grace Xing Huili , Jena Debdeep
Published: February 2021

Gallium nitride high-electron-mobility transistors (GaN HEMTs) are at a point of rapid growth in defense (radar, SATCOM) and commercial (5G and beyond) industries. This growth also comes at a point at which the standard GaN heterostructures remain unoptimized for maximum performance. For this reason, we propose the shift to the aluminum nitride (AlN) platform. AlN allows for smarter, highly-scaled heterostructure design that will improve the output power and thermal management of III-nitride amplifiers. Beyond improvements over the incumbent amplifier technology, AlN will allow for a level of integration previously unachievable with GaN electronics. State-of-the-art high-current p-channel FETs, mature filter technology, and advanced waveguides, all monolithically integrated with an AlN/GaN/AlN HEMT, is made possible with AlN. It is on this new AlN platform that nitride electronics may maximize their full high-power, high-speed potential for mm-wave communication and high-power logic applications.
A coupling method of the superconducting devices modeled by finite element method with the lumped parameters electrical circuit
Authors: dos Santos G , Martins F G R , Sass F , Dias D H N , Sotelo G G , Morandi A
Published: February 2021

Superconducting devices have been widely studied over these years. Their application can be found in cables for electric power transmission, energy storage systems, magnetic levitation, electric machines, and fault current limiters. The literature presents some formulations to model the superconductors’ behavior using the finite element method (FEM), such as the H, the AV, and the T formulations, among others. Many superconducting devices have been simulated and designed using some of these formulations. However, none method available offers a coupling between an electric power system, simulated using electrical lumped parameters, to the superconducting FEM model. In this context, this work introduces a methodology for coupling superconducting devices in FEM to lumped parameters composing the power system. Here, a case study with a Saturated Iron Core Superconducting Fault Current Limiter was presented to apply the proposed methodology. This research analyzes the influence of the self and external fields in the superconducting coil on its critical current density. Moreover, it investigates the DC-biased coil voltage drop and the superconducting resistance. Besides, the paper presents the simulations of short circuits for various DC currents applied to the superconducting coil. Short-circuit tests were performed for validating the simulation results, and it showed a maximum error of 15% for the compared points.
Determination of Si(Li) detector efficiency by experimental and Monte Carlo simulation methods
Authors: Zadehrafi M , Luca A , Ioan M-R
Published: February 2021

In this study, a Si(Li) detector was modeled by MCNP (Monte Carlo n-particle) code and its efficiency was estimated by Monte Carlo simulation in the photon energy range of 5.9–59.54 keV. Experimental measurements using 55Fe, 57Co, and 241Am radioactive standard sources were performed for validation of the applied simulation code. The primary results of the simulation were compared with the experimental ones and considerable discrepancies were observed, especially in the low energy region. Since the dead layers’ thicknesses are not always precisely provided by the manufacturer and even can change during detector aging, they were assumed as the cause of these discrepancies (front dead layer’s thickness being a critical parameter for low energy photons). After adjusting the thicknesses of the front and rear dead layers in a step-by-step procedure, a reasonable agreement was achieved between the simulated and experimental results. The results of this study indicate that if performing an experiment by the detector is difficult for any reason in some energies, one can rely on the MCNP code as an operational tool by interpolation or extrapolation of the available experimental efficiency data (in low energy region).
Influence of Brownian motion and thermophoresis parameters on silver-based Di-Hydrogen CNTs between two stretchable rotating disks
Authors: Shah Zahir , Dawar Abdullah , Islam Saeed
Published: February 2021

The magnetohydrodynamic flow of Silver (Ag) based carbon nanotubes (SWCNTs and MWCNTs) nanofluid between two stretchable rotating disks is presented in this article. The magnetic field is functioned in the tangential direction. The modeled equations are attempted with the homotopy analysis approach. The convergence of the applied approach is shown through figures and tables. The performance of influential factors on velocity (radial, axial and tangential), thermal, and concentration profiles for both CNTs are portrayed through figures. Also, the performance of influential parameters on physical quantities of interests for both CNTs is numerically examined through tables. The velocities along the radial, axial, and tangential directions are intensified with nanoparticles volume fraction CNTs nanoparticles, Reynolds number, and magnetic parameter. The heightening volume fraction of CNTs nanoparticles, thermophoresis, and Brownian motion parameters increased the thermal profile. The concentration profile is escalated with the thermophoresis parameter and Lewis number.
Pressure induced superconducting state in ideal topological insulator BiSbTe3
Authors: Gangwar Vinod K , Kumar Shiv , Singh Mahima , Ghosh Labanya , Zhang Yufeng , Shahi Prashant , Muntwiler Matthias , Patil Swapnil , Shimada Kenya , Uwatoko Yoshiya , Sau Jyotirmoy , Kumar Manoranjan , Chatterjee Sandip
Published: February 2021

Structural, pressure-dependent resistivity, angle resolved photoemission spectroscopy (ARPES), x-ray photoelectron diffraction (XPD) and band structure by DFT calculation have been investigated for BiSbTe3 Topological insulator. It has been demonstrated that the Dirac point of the topological surface state (TSS) located exactly at the Fermi level. Additionally, superconductivity emerges under pressure of 8 GPa with a critical temperature of ∼2.5 K. With further increase of pressure, the superconducting transition temperature (Tc) increases and at 14 GPa it shows the maximum Tc (∼3.3 K). It has also been shown that the surface state remains unchanged under pressure and has been suggested that the origin of the superconductivity is due to the bulk state. The investigation indicates that the BiSbTe3 has robust surface states and becomes superconductor under pressure.
Systematic map of determinants of buildings’ energy demand and CO2 emissions shows need for decoupling
Authors: Mata É , Wanemark J , Cheng S H , Ó Broin E , Hennlock M , Sandvall A
Published: February 2021

Buildings are responsible for a major share of global final energy consumption and carbon dioxide (CO2) emissions. An analysis of the worldwide observed drivers of demand can highlight the policy actions most suited to drive the decarbonization of the building sector. To contribute to such an analysis, we carry out a mapping of the literature on determinants of energy demand and CO2 emissions from buildings. The work includes a list and classification of relevant studies in an on-line geographical map, a description of trends and gaps, and a narrative review. We identify 4080 articles in the Scopus and the Web of Science databases, of which 712 are relevant after screening at the title and abstract level, and 376 are included for data extraction. The literature base mostly addresses electricity and water use, in North America and Europe (57% of the literature) and Asia (27%). Econometric modeling approaches using panel data to calculate demand elasticities, dominate. These findings highlight gaps in terms of the studied variables (only 5% focus on CO2 emissions while a mere 1% have a lifecycle perspective), geographical scope (only 5% of the articles focus on Africa, 7% on Latin America and the Caribbean, and 5% on Oceania), and methodological approach (only 5% use qualitative methods). We confirm that worldwide, income, energy price and outdoor temperature are unequivocal drivers of buildings energy demand and CO2 emissions, followed by other indicators of scale such as population or heated floor area. Our analysis makes it clear that decoupling from rising wealth levels has not been observed. This will continue to challenge reductions in energy use and CO2 emissions from buildings in line with climate targets. Macroeconomic policies focusing on the impacts of income, energy price, population and growing floor area are needed in combination with technical policy to reduce the impact of outdoor climate.
Emulating Target Trials to Improve Causal Inference From Agent-Based Models
Authors: Murray Eleanor J , Marshall Brandon D L , Buchanan Ashley L
Published: February 2021

Agent-based models are a key tool for investigating the emergent properties of population health settings, such as infectious disease transmission, where the exposure often violates the key “no interference” assumption of traditional causal inference under the potential outcomes framework. Agent-based models and other simulation-based modeling approaches have generally been viewed as a separate knowledge-generating paradigm from the potential outcomes framework, but this can lead to confusion about how to interpret the results of these models in real-world settings. By explicitly incorporating the target trial framework into the development of an agent-based or other simulation model, we can clarify the causal parameters of interest, as well as make explicit the assumptions required for valid causal effect estimation within or between populations. In this paper, we describe the use of the target trial framework for designing agent-based models when the goal is estimation of causal effects in the presence of interference, or spillover.
Molecular mechanisms and highly functional development for stress tolerance of the yeastSaccharomyces cerevisiae
Authors: Takagi Hiroshi
Published: February 2021

In response to environmental stress, microorganisms adapt to drastic changes while exerting cellular functions by controlling gene expression, metabolic pathways, enzyme activities, and protein–protein interactions. Microbial cells that undergo a fermentation process are subjected to stresses, such as high temperature, freezing, drying, changes in pH and osmotic pressure, and organic solvents. Combinations of these stresses that continue over long terms often inhibit cells’ growth and lead to their death, markedly limiting the useful functions of microorganisms (eg their fermentation ability). Thus, high stress tolerance of cells is required to improve productivity and add value to fermented/brewed foods and biofuels. This review focuses on stress tolerance mechanisms, including l-proline/l-arginine metabolism, ubiquitin system, and transcription factors, and the functional development of the yeast Saccharomyces cerevisiae, which has been used not only in basic science as a model of higher eukaryotes but also in fermentation processes for making alcoholic beverages, food products, and bioethanol.
Clinical and Laboratory Findings in Patients With Potential Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reinfection, May–July 2020
Authors: Lee James T , Hesse Elisabeth M , Paulin Heather N , Datta Deblina , Katz Lee S , Talwar Amish , Chang Gregory , Galang Romeo R , Harcourt Jennifer L , Tamin Azaibi , Thornburg Natalie J , Wong Karen K , Stevens Valerie , Kim Kaylee , Tong Suxiang , Zhou Bin , Queen Krista , Drobeniuc Jan , Folster Jennifer M , Sexton D Joseph , Ramachandran Sumathi , Browne Hannah , Iskander John , Mitruka Kiren
Published: February 2021

Background

We investigated patients with potential severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection in the United States during May–July 2020.

Methods

We conducted case finding for patients with potential SARS-CoV-2 reinfection through the Emerging Infections Network. Cases reported were screened for laboratory and clinical findings of potential reinfection followed by requests for medical records and laboratory specimens. Available medical records were abstracted to characterize patient demographics, comorbidities, clinical course, and laboratory test results. Submitted specimens underwent further testing, including reverse transcription polymerase chain reaction (RT-PCR), viral culture, whole genome sequencing, subgenomic RNA PCR, and testing for anti-SARS-CoV-2 total antibody.

Results

Among 73 potential reinfection patients with available records, 30 patients had recurrent coronavirus disease 2019 (COVID-19) symptoms explained by alternative diagnoses with concurrent SARS-CoV-2 positive RT-PCR, 24 patients remained asymptomatic after recovery but had recurrent or persistent RT-PCR, and 19 patients had recurrent COVID-19 symptoms with concurrent SARS-CoV-2 positive RT-PCR but no alternative diagnoses. These 19 patients had symptom recurrence a median of 57 days after initial symptom onset (interquartile range: 47–76). Six of these patients had paired specimens available for further testing, but none had laboratory findings confirming reinfections. Testing of an additional 3 patients with recurrent symptoms and alternative diagnoses also did not confirm reinfection.

Conclusions

We did not confirm SARS-CoV-2 reinfection within 90 days of the initial infection based on the clinical and laboratory characteristics of cases in this investigation. Our findings support current Centers for Disease Control and Prevention (CDC) guidance around quarantine and testing for patients who have recovered from COVID-19.
Long, Interrupted Conversion Tracts Initiated by cog in Neurospora crassa
Authors: Yeadon P Jane , Catcheside David E A
Published: February 2021

Multiple polymorphisms distinguish Emerson and Lindegren strains of Neurospora crassa within the histidine-3 gene and in its distal flank. Restriction site and sequence length polymorphism in a set of 14 PCR products covering this 6.9-kb region were used to identify the parental origin of DNA sequence information in prototrophic progeny of crosses heterozygous for auxotrophic mutations in his-3 and the silent sequence differences. Forty-one percent of conversion tracts are interrupted. Where the absence of rec-2+ permits activity of the recombination hotspot cog, conversion appears to originate at cog and conversion tracts are up to 5.9 kb long. The chromosome bearing cog L, the dominant allele that confers a high frequency of recombination, is almost invariably the recipient of information. In progeny from crosses heterozygous rec-2/rec-2+, conversion tracts are much shorter, most are not initiated at cog and either chromosome seems equally likely to be converted. Although 32% of his-3 prototrophs have a crossover that may be associated with conversion, it is suggested that the apparent association between conversion and crossing over at this locus may be due to confounding of coincidental events rather than to a mechanistic relationship.
A Mutation in Paramecium tetraurelia Reveals Functional and Structural Features of Developmentally Excised DNA Elements
Authors: Mayer Kimberly M , Mikami Kazuyuki , Forney James D
Published: February 2021

The excision of internal eliminated sequences (IESs) from the germline micronuclear DNA occurs during the differentiation of a new macronuclear genome in ciliated protozoa. In Paramecium, IESs are generally short (28–882 bp), AT rich DNA elements that show few conserved sequence features with the exception of an inverted-terminal-repeat consensus sequence that has similarity to the ends of mariner/Tc1 transposons (Klobutcher and Herrick 1995). We have isolated and analyzed a mutant cell line that cannot excise a 370-bp IESs (IES2591) from the coding region of the 51A variable surface protein gene. A single micronuclear C to T transition within the consensus sequence prevents excision. The inability to excise IES2591 has revealed a 28-bp IES inside the larger IES, suggesting that reiterative integration of these elements can occur. Together, the consensus sequence mutation and the evidence for reiterative integration support the theory that Paramecium IESs evolved from transposable elements. Unlike a previously studied Paramecium IES, the presence of this IES in the macronucleus does not completely inhibit excision of its wild-type micronuclear copy through multiple sexual generations.
The Neurospora rca-1 Gene Complements an Aspergillus flbD Sporulation Mutant but Has No Identifiable Role in Neurospora Sporulation
Authors: Shen Wei-Chiang , Wieser Jenny , Adams Thomas H , Ebbole Daniel J
Published: February 2021

The Aspergillus nidulans flbD gene encodes a protein with a Myb-like DNA-binding domain that is proposed to act in concert with other developmental regulators to control initiation of conidiophore development. We have identified a Neurospora crassa gene called rca-1 (regulator of conidiation in Aspergillus) based on its sequence similarity to flbD. We found that N. crassa rca-1 can complement the conidiation defect of an A. nidulans flbD mutant and that induced expression of rca-1 caused conidiation in submerged A. nidulans cultures just as was previously observed for overexpression of flbD. Thus, the N. crassa gene appears to be a functional homologue of A. nidulans flbD and this is the first demonstration of functional complementation of an A. nidulans sporulation defect using a gene from an evolutionarily distant fungus. However, deletion of the rca-1 gene in N. crassa had no major effect on growth rate, macroconidiation, microconidiation, or ascospore formation. The only phenotype displayed by the rca-1 mutant was straight or counterclockwise hyphal growth rather than the clockwise spiral growth observed for wild type. Thus, if rca-1 is involved in N. crassa development, its role is subtle or redundant.
Marker-Assisted Selection Efficiency in Populations of Finite Size
Authors: Moreau Laurence , Charcosset Alain , Hospital Frédéric , Gallais André
Published: February 2021

The efficiency of marker-assisted selection (MAS) based on an index incorporating both phenotypic and molecular information is evaluated with an analytical approach that takes into account the size of the experiment. We consider the case of a population derived from a cross between two homozygous lines, which is commonly used in plant breeding, and we study the relative efficiency of MAS compared with selection based only on phenotype in the first cycle of selection. It is shown that the selection of the markers included in the index leads to an overestimation of the effects associated with these markers. Taking this bias into account, we study the influence of several parameters, including experiment size and heritability, on MAS efficiency. Even if MAS appears to be most interesting for low heritabilities, we point out the existence of an optimal heritability (~0.2) below which the low power of quantitative trait loci detection and the bias caused by the selection of markers reduce the efficiency. In this situation, increasing the power of detection by using a higher probability of type I error can improve MAS efficiency. This approach, validated by simulations, gives results that are generally consistent with those previously obtained by simulations using a more sophisticated biological model than ours. Thus, though developed from a simple genetic model, our approach may be a useful tool to optimize the experimental means for more complex genetic situations.
Cell Cycle Arrest in cdc20 Mutants of Saccharomyces cerevisiae Is Independent of Ndc10p and Kinetochore Function but Requires a Subset of Spindle Checkpoint Genes
Authors: Tavormina Penny A , Burke Daniel J
Published: February 2021

The spindle checkpoint ensures accurate chromosome segregation by inhibiting anaphase onset in response to altered microtubule function and impaired kinetochore function. In this study, we report that the ability of the anti-microtubule drug nocodazole to inhibit cell cycle progression in Saccharomyces cerevisiae depends on the function of the kinetochore protein encoded by NDC10. We examined the role of the spindle checkpoint in the arrest in cdc20 mutants that arrest prior to anaphase with an aberrant spindle. The arrest in cdc20 defective cells is dependent on the BUB2 checkpoint and independent of the BUB1, BUB3, and MAD spindle checkpoint genes. We show that the lesion recognized by Bub2p is not excess microtubules, and the cdc20 arrest is independent of kinetochore function. We show that Cdc20p is not required for cyclin proteolysis at two points in the cell cycle, suggesting that CDC20 is distinct from genes encoding integral proteins of the anaphase promoting complex.
Approximate Analysis of QTL-Environment Interaction with No Limits on the Number of Environments
Authors: Korol Abraham B , Ronin Yefim I , Nevo Eviatar
Published: February 2021

An approach is presented here for quantitative trait loci (QTL) mapping analysis that allows for QTL × environment (E) interaction across multiple environments, without necessarily increasing the number of parameters. The main distinction of the proposed model is in the chosen way of approximation of the dependence of putative QTL effects on environmental states. We hypothesize that environmental dependence of a putative QTL effect can be represented as a function of environmental mean value of the trait. Such a description can be applied to take into account the effects of any cosegregating QTLs from other genomic regions that also may vary across environments. The conducted Monte-Carlo simulations and the example of barley multiple environments experiment demonstrate a high potential of the proposed approach for analyzing QTL × E interaction, although the results are only approximated by definition. However, this drawback is compensated by the possibility to utilize information from a potentially unlimited number of environments with a remarkable reduction in the number of parameters, as compared to previously proposed mapping models with QTL × E interactions.
The Homeobox Gene cut Interacts Genetically With the Homeotic Genes proboscipedia and Antennapedia
Authors: Johnston Laura A , Ostrow Bruce D , Jasoni Christine , Blochlinger Karen
Published: February 2021

The cut locus (ct) codes for a homeodomain protein (Cut) and controls the identity of a subset of cells in the peripheral nervous system in Drosophila. During a screen to identify ct-interacting genes, we observed that flies containing a hypomorphic ct mutation and a heterozygous deletion of the Antennapedia complex exhibit a transformation of mouthparts into leg and antennal structures similar to that seen in homozygous proboscipedia (pb) mutants. The same phenotype is produced with all heterozygous pb alleles tested and is fully penetrant in two different ct mutant backgrounds. We show that this phenotype is accompanied by pronounced changes in the expression patterns of both ct and pb in labial discs. Furthermore, a significant proportion of ct mutant flies that are heterozygous for certain Antennapedia (Antp) alleles have thoracic defects that mimic loss-of-function Antp phenotypes, and ectopic expression of Cut in antennal discs results in ectopic Antp expression and a dominant Antp-like phenotype. Our results implicate ct in the regulation of expression and/or function of two homeotic genes and document a new role of ct in the control of segmental identity.
Multigene Family of Ribosomal DNA in Drosophila melanogaster Reveals Contrasting Patterns of Homogenization for IGS and ITS Spacer Regions: A Possible Mechanism to Resolve This Paradox
Authors: Polanco Carlos , González Ana I , de la Fuente Álvaro , Dover Gabriel A
Published: February 2021

The multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) that underpin the process of molecular drive. The dynamics of spread of mutant repeats through a gene family, and ultimately through a sexual population, depends on the differences in rates of turnover within and between chromosomes. Our extensive molecular analysis of the intergenic spacer (IGS) and internal transcribed spacer (ITS) spacer regions within repetitive rDNA units, drawn from the same individuals in 10 natural populations of Drosophila melanogaster collected along a latitudinal cline on the east coast of Australia, indicates a relatively fast rate of X-Y and X-X interchromosomal exchanges of IGS length variants in agreement with a multilineage model of homogenization. In contrast, an X chromosome-restricted 24-bp deletion in the ITS spacers is indicative of the absence of X-Y chromosome exchanges for this region that is part of the same repetitive rDNA units. Hence, a single lineage model of homogenization, coupled to drift and/or selection, seems to be responsible for ITS concerted evolution. A single-stranded exchange mechanism is proposed to resolve this paradox, based on the role of the IGS region in meiotic pairing between X and Y chromosomes in D. melanogaster.
Bias in two-sample Mendelian randomization when using heritable covariable-adjusted summary associations
Authors: Hartwig Fernando Pires , Tilling Kate , Davey Smith George , Lawlor Deborah A , Borges Maria Carolina
Published: February 2021

Background

Two-sample Mendelian randomization (MR) allows the use of freely accessible summary association results from genome-wide association studies (GWAS) to estimate causal effects of modifiable exposures on outcomes. Some GWAS adjust for heritable covariables in an attempt to estimate direct effects of genetic variants on the trait of interest. One, both or neither of the exposure GWAS and outcome GWAS may have been adjusted for covariables.

Methods

We performed a simulation study comprising different scenarios that could motivate covariable adjustment in a GWAS and analysed real data to assess the influence of using covariable-adjusted summary association results in two-sample MR.

Results

In the absence of residual confounding between exposure and covariable, between exposure and outcome, and between covariable and outcome, using covariable-adjusted summary associations for two-sample MR eliminated bias due to horizontal pleiotropy. However, covariable adjustment led to bias in the presence of residual confounding (especially between the covariable and the outcome), even in the absence of horizontal pleiotropy (when the genetic variants would be valid instruments without covariable adjustment). In an analysis using real data from the Genetic Investigation of ANthropometric Traits (GIANT) consortium and UK Biobank, the causal effect estimate of waist circumference on blood pressure changed direction upon adjustment of waist circumference for body mass index.

Conclusions

Our findings indicate that using covariable-adjusted summary associations in MR should generally be avoided. When that is not possible, careful consideration of the causal relationships underlying the data (including potentially unmeasured confounders) is required to direct sensitivity analyses and interpret results with appropriate caution.
Feix–Kaledin Metric on the Total Spaces of Cotangent Bundles to Kähler Quotients
Authors: Abasheva Anna
Published: February 2021

In this paper, we study the geometry of the total space $Y$ of a cotangent bundle to a Kähler manifold $N$ where $N$ is obtained as a Kähler reduction from $\mathbb{C}^n$. Using the hyperkähler reduction, we construct a hyperkähler metric on $Y$ and prove that it coincides with the canonical Feix–Kaledin metric. This metric is in general non-complete. We show that the metric completion $\widetilde Y$ of the space $Y$ is equipped with a structure of a stratified hyperkähler space (in the sense of [ 31]). We give a necessary condition for the Feix–Kaledin metric to be complete using an observation of R. Bielawski. Pick a complex structure $J$ on $\widetilde Y$ induced from the quaternions. Suppose that $J\ne \pm I$ where $I$ is the complex structure whose restriction to $Y = T^{*}N$ is induced by the complex structure on $N$. We prove that the space $\widetilde{Y}_J$ admits an algebraic structure and is an affine variety.
Potential roles of G-quadruplex structures in RNA granules for physiological and pathological phase separation
Authors: Asamitsu Sefan , Shioda Norifumi
Published: February 2021

Cellular liquid–liquid phase separation is a physiologically inevitable phenomenon in molecularly crowded environments inside cells and serves to compartmentalize biomolecules to facilitate several functions, forming cytoplasmic and nuclear RNA granules. Abnormalities in the phase separation process in RNA granules are implicated in the onset of several neurodegenerative diseases; the initial liquid-like phase-separated droplets containing pathogenic proteins are prone to aberrantly mature into solid-like droplets. RNAs are involved in the maturation of physiological and pathological RNA granules and are essential for governing the fate of phase-transition processes. Notably, RNA G-quadruplex (G4RNA), which is the secondary structure of nucleic acids that are formed in guanine-rich sequences, appears to be an advantageous scaffold for RNA-derived phase separation because of its multivalent interactions with RNAs and RNA-binding proteins. Here, we summarize the properties of RNA granules in physiological and pathological phase separation and discuss the potential roles of G4RNA in granules.
Estimation of the Postmortem Interval Through the Use of Development Time of Two South American Species of Forensic Importance of the Genus Lucilia (Diptera: Calliphoridae)
Authors: Acosta Ximena , González-Reyes Andrea X , Corronca José A , Centeno Néstor D
Published: February 2021

Obtaining the specific development time of each species of forensic interest is crucial for the estimation of an accurate and reliable Minimum Postmortem Interval (PMImin). In Argentina, Lucilia ochricornis (Wiedemann) and Lucilia purpurascens (Walker) (Diptera: Calliphoridae) were masked under the name Lucilia cluvia (Walker) for a long time still in forensic expertise. For this reason, the objective of this work is to deepen the study of the development time of these species and utilize this relevant information in the generation of different associated methods that can be used in forensics to estimate the PMI. Immature stages of L. ochricornis and L. purpurascens were reared in a brood chamber according to the following temperature treatments: 13.4, 15.1, 22.3, and 23.6°C. The development time of each stage/state of these flies was recorded as well as the resulting accumulated degree-hours (ADH), to build isomorphen diagrams and thermal summation models for each species. The development time and ADH were different between both species and their development stages. On the other hand, the methods provided for estimating PMImin provide the forensic entomologist more tools to reach accurate and reliable estimates.
High Frequency of Recurrent Falls Among Prefrail and Frail Women With and Without HIV
Authors: Sharma Anjali , Hoover Donald R. , Shi Qiuhu , Gustafson Deborah R. , Plankey Michael , Tien Phyllis C , Weber Kathleen M. , Vance David E. , Floris-Moore Michelle , Bolivar Hector H. , Golub Elizabeth T. , Holstad Marcia M. , Yin Michael T.
Published: February 2021

Background:

Frailty may occur at younger ages among HIV+ populations. We evaluated associations of the frailty status with self-reported single and recurrent falls in the Women's Interagency HIV Study (WIHS).

Methods:

The frailty status was defined using the Fried Frailty Phenotype (FFP) among 897 HIV+ and 392 HIV− women; median age 53 years. Women were classified as robust (FFP 0), prefrail (FFP 1–2), and frail (FFP 3–5). Stepwise logistic regression models adjusting for the HIV status and study site were fit to evaluate associations of the FFP with self-reported single (1 vs. 0) and recurrent falls (≥2 vs. 0) over the prior 12 months.

Results:

HIV+ women were less likely to be frail (9% vs. 14% vs. P = 0.009), but frequency of falls did not differ by the HIV status. In multivariate analyses, recurrent falls were more common among prefrail [adjusted odds ratio (AOR) 2.23, 95% confidence interval (CI): 1.40 to 3.57, P = 0.0008] and frail (AOR 3.61, 95% CI: 1.90 to 6.89, P < 0.0001) than robust women. Among HIV+ women, single (AOR 2.88, 95% CI: 1.16 to 7.20, P = 0.023) and recurrent falls (AOR 3.50, 95% CI: 1.24 to 9.88, P = 0.018) were more common among those who were frail; recurrent, but not single falls, were more common among prefrail than robust HIV+ women (AOR 2.00, 95% CI: 1.03 to 3.91, P = 0.042).

Conclusions:

HIV+ women were less likely to be frail. Compared with robust women, prefrail and frail women with and without HIV were more likely to experience single or recurrent falls within a 12-month period. Additional studies are needed to develop interventions that decrease development of frailty and reduce risk of recurrent falls among HIV+ women.
AeroForm Tissue Expander
Authors: Huang Hao , Bogue Jarrod T. , Otterburn David M.
Published: February 2021

Background

Device-based reconstruction, the most common approach to breast reconstruction, typically occurs in 2 stages to allow for the breast envelope to be expanded serially before exchanging for a permanent implant. The AeroForm tissue expander is a carbon dioxide–based expansion system that allows for patient-initiated filling, and compared with the traditional saline expander, it has been shown to decrease the median time to full expansion and implant exchange. Furthermore, multiple changes have been incorporated into the newer V2.5 iteration resulting in reductions in device-related malfunctions, including overinflation.

Case Presentation

A 57-year-old woman who had a diagnosis of stage 1 ductal carcinoma in situ (T1c = 1.3 cm, ER/PR-negative, HER2-positive) underwent bilateral nipple-sparing mastectomy with sentinel lymph node biopsy and V2.5 AeroForm expander reconstruction. The procedure and subsequent postoperative follow-up visits were unremarkable without complications. However, once she entered an magnetic resonance imaging examination room for evaluation of an incidentally found meningioma, the carbon dioxide reservoir valve in both expanders was suddenly activated, releasing filling gas and maximally inflating the device to its 800-mL capacity. She elected to retain the expanders, and they were exchanged for permanent silicone implants 1 month later.

Conclusions

Although the V2.5 AeroForm expander is associated with a much lower rate of overinflation than its predecessor, our case suggests that autoexpansion remains of concern and likely occurs via a different mechanism when the device is subjected to clinical strength magnetic field. Clinicians should not order magnetic resonance imaging scans for women with AeroForm expanders due to the risk of unintended expansion.