bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study on the rapid establishment of the transonic gap flow field
Authors: Feng Wu-heng , Zhao Yu-xin , Wang Cheng-long , Wang Qian-cheng , Zhou Yong-yi
Published: January 2021

In turbine engines, there is a clearance between the rotating blade and the stationary casing. The flow in the tip gap, which is mostly transonic, has a significant impact on the overall thrust and safety performance of the engine. This study aims at elucidating the mechanism of flow establishment in a simplified tip gap model. In this study, the basic structure and pressure distribution of the transient flow field in the gap region are first determined via schlieren techniques and pressure measurements, respectively. Based on these results, we develop a rapid modeling technique of the flow field and analyze the similarities between gap flows with different aspect ratios. As demonstrated by this study, the gap flow can be established within 0.65 s and the entire process comprises five stages. The increase in the downstream pressure and relative fluid viscosity in the gap are found to significantly influence the shock wave structures. Similarities are observed between flow fields in different gaps when the width-to-height ratio is small. With a large width-to-height ratio, the viscosity of the fluid dominates and the corresponding flow fields exhibit no similarity.
Description of intermodulation generation of nonlinear responses beyond the validity of the power series expansion
Authors: Bergmann F. , Letz M. , Maune H. , Jakob G.
Published: January 2021

Weakly nonlinear responses are commonly described by a power series expansion. However, intermodulation distortion products that cannot be described by a power series have been observed in a variety of physical systems. As the power series description is only applicable within its radius of convergence, we choose an alternative approach based on Fourier coefficients to describe intermodulation levels beyond the convergence of the power series. The description over a wide power range allows us to make a decision about models and to determine previously inaccessible model parameters. We apply the approach to data obtained from the characterization of the nonlinear dielectric susceptibility of a glass ceramic in the microwave range. The data are accurately modeled by a saturable absorber's response. We obtain the absorber's linear contribution to the polarization (χ1=10−5) as well as its characteristic ratio of nonlinear and linear polarization (χ3/χ1=10−9 m2/V2). Due to the small contribution of the saturable absorber to the overall polarization, the material shows a highly linear response (χ3=10−14 m2/V2).
Experimental estimation of the spin diffusion length in undoped p-Ge on Fe3Si using vertical spin-valve devices
Authors: Yamada A. , Yamada M. , Shiihara T. , Ikawa M. , Yamada S. , Hamaya K.
Published: January 2021

Using vertical spin-valve devices, we experimentally investigate the room-temperature spin diffusion length in an undoped p-Ge layer grown on ferromagnetic Fe3Si. Because low-temperature molecular beam epitaxy techniques enable us to grow vertically stacked and all-epitaxial CoFe/Ge/Fe3Si trilayers on Si(111), we can intentionally vary the thickness (tGe) of the intermediate undoped p-Ge layer during the growth. With decreasing tGe, the magnitude of the spin signals gradually increases at room temperature. From the analysis based on the model by Fert and Jaffrès, the room-temperature spin diffusion length in the undoped p-Ge grown on Fe3Si is experimentally estimated to be ∼8.4 nm, much shorter than those reported in previous works on commercial p-Ge substrates.
Bubble formation from a submerged orifice in a thin liquid layer: Detachment and bursting
Authors: Zhou Yujia , Ji Bingqiang , Zhao Chenru , Bo Hanliang
Published: January 2021

Bubbles dispersed in thin liquid layers are ubiquitous and play important roles in the heat and mass transfer in nature and industrial processes including the energy, chemical, and biology engineering; thus, understanding the dynamics of bubbles confined in a liquid layer remains an important topic in multiphase flows. Here, we report the dynamics of bubble formation from a submerged orifice in a thin liquid layer with a thickness comparable to the bubble size. First, four flow regimes, detachment, jetting bursting, non-jetting bursting, and hole-opened bursting, are observed experimentally and their typical features are analyzed. Then, the evolutions of bubble size at different regimes are studied, and a quasi-static force model is proposed to predict the bubble size, which agrees well with the experimental results. We demonstrate the role of the capillary force exerted by the liquid film in the bubble cap and bubble geometry confined in the liquid layer in modulating the bubble size. Finally, a regime map regarding the liquid layer thickness and surface tension is provided and the criteria between different regimes are discussed based on the bubble geometry analysis and energy balance. Our experimental investigation and theoretical analysis provide insights into the formation and bursting dynamics of bubbles confined in a liquid layer.
Acoustofluidic phase microscopy in a tilted segmentation-free configuration
Authors: Mejía Morales Julián , Hammarström Björn , Lippi Gian Luca , Vassalli Massimo , Glynne-Jones Peter
Published: January 2021

A low-cost device for registration-free quantitative phase microscopy (QPM) based on the transport of intensity equation of cells in continuous flow is presented. The method uses acoustic focusing to align cells into a single plane where all cells move at a constant speed. The acoustic focusing plane is tilted with respect to the microscope’s focal plane in order to obtain cell images at multiple focal positions. As the cells are displaced at constant speed, phase maps can be generated without the need to segment and register individual objects. The proposed inclined geometry allows for the acquisition of a vertical stack without the need for any moving part, and it enables a cost-effective and robust implementation of QPM. The suitability of the solution for biological imaging is tested on blood samples, demonstrating the ability to recover the phase map of single red blood cells flowing through the microchip.
Transition-potential coupled cluster
Authors: Simons Megan , Matthews Devin A.
Published: January 2021

The problem of orbital relaxation in computational core-hole spectroscopies, including x-ray absorption and x-ray photoionization, has long plagued linear response approaches, including equation-of-motion coupled cluster with singles and doubles (EOM-CCSD). Instead of addressing this problem by including additional electron correlation, we propose an explicit treatment of orbital relaxation via the use of “transition potential” reference orbitals, leading to a transition-potential coupled cluster (TP-CC) family of methods. One member of this family, in particular, TP-CCSD(12), is found to essentially eliminate the orbital relaxation error and achieve the same level of accuracy for the core-hole spectra as is typically expected of EOM-CCSD in the valence region. These results show that very accurate x-ray absorption spectra for molecules with first-row atoms can be computed at a cost essentially the same as that for EOM-CCSD.
From National Drought Policy to National Drought Agreement: the evolution of Australia’s drought response
Authors: Botterill Linda Courtenay
Published: January 2021

Australia has had a formal National Drought Policy for nearly three decades. Over that time, the policy has morphed, with the programs that make up the policy being revised and replaced as it has sought to address both the concerns of the farm business and the welfare needs of farm families. The stated principles underpinning the policy have remained relatively stable, focusing on farmer self-reliance and risk management. The most recent iteration, embodied in a December 2018 National Drought Agreement, is very similar in stated intent to the original 1992 policy. Despite attempts to focus on risk management, however, the policy remains to a large extent crisis driven, with changes to the policy, particularly big-ticket spending, frequently announced during severe drought. As a result of the tension between the political imperative to respond during drought events and the desire to promote self-reliance and drought preparedness among farmers, the original policy’s ambition of avoiding ad hoc reactions has not been achieved, and the risk management/self-reliance theme is reflected more rhetorically than in policy substance. These tensions reflect the challenge of juggling the conflicting values around drought support, between broad community sympathy for farmers which is activated during drought, and aspirations of a risk management approach which requires longer term thinking and the avoidance of ad hoc policy making.
Measuring the subcellular compartmentalization of viral infections by protein complementation assay
Authors: Fernandez Juliette , Hassen-Khodja Cédric , Georget Virginie , Rose Thierry , Jacob Yves , Janin Yves L. , Nisole Sébastien , Vidalain Pierre-Olivier , Arhel Nathalie J.
Published: January 2021

Significance

The COVID-19 pandemic has highlighted the need to develop assays that can measure specific steps of viral replication on a large scale. Here we describe an innovative assay called αCentauri that uses fluorescence- or bioluminescence-based protein complementation assays to quantify the subcellular compartmentalization of viruses. As proof of concept, the Centauri fragment was tethered to the nuclear pore complex or sequestered in the nucleus, while the complementary α fragment was attached to the integrase proteins of infectious HIV-1. Thereupon the trafficking of HIV to the nucleus efficiently reconstituted superfolder green fluorescent protein and NanoLuc αCentauri reporters. This technology offers a robust readout of specific steps of viral infection in a multiwell format that is compatible for high-throughput screening.
Placental trophoblast syncytialization potentiates macropinocytosis via mTOR signaling to adapt to reduced amino acid supply
Authors: Shao Xuan , Cao Guangming , Chen Dunjin , Liu Juan , Yu Bolan , Liu Ming , Li Yu-Xia , Cao Bin , Sadovsky Yoel , Wang Yan-Ling
Published: January 2021

Significance

The appropriate allocation of nutrients between the mother and the fetus during pregnancy is predominantly governed by the syncytiotrophoblast lining at the outer surface of the placental villi. To date the advantages of such an extensively multinucleated cellular structure in substance exchange remains poorly understood. In this study, we discovered that differentiation of trophoblasts toward syncytium triggers an endocytosis strategy, macropinocytosis, to uptake large extracellular molecules. The unique uptake machinery is strikingly boosted via inhibition of mammalian target of rapamycin signaling under amino acid shortage conditions, which is essential for fetal survival. The findings highlight an adaptive mechanism of syncytiotrophoblast that senses nutrient status and support fetal survival under nutrient deprivation.
Parameters of clitic combination
Authors: Colomina M. Pilar
Published: January 2021

This chapter presents the restrictions and
alterations that object clitics show when they are combined (forming
a ‘clitic cluster’) in different varieties of Spanish, Catalan and
Aragonese. As it is well-known, the combination of a third person
accusative clitic and a third person dative clitic is rejected [in
these varieties]. The relevant point that I will explore is that
there is, in fact, variation in the way that languages avoid these
ungrammatical sequences. To show this, I consulted different
databases that describe this combination (grammars, atlases and
corpora). Furthermore, I offer a proposal that accounts for these
restrictions, building on the conclusions presented in Colomina (2020).
Suppression of thermal nanoplasma emission in clusters strongly ionized by hard x-rays
Authors: Kumagai Yoshiaki , Jurek Zoltan , Xu Weiqing , Saxena Vikrant , Fukuzawa Hironobu , Motomura Koji , Iablonskyi Denys , Nagaya Kiyonobu , Wada Shin-ichi , Ito Yuta , Takanashi Tsukasa , Yamada Shuhei , Sakakibara Yuta , Hiraki Toshiyuki Nishiyama , Umemoto Takayuki , Patanen Minna , Bozek John D , Dancus Ioan , Cernaianu Mihail , Miron Catalin , Bauer Tobias , Mucke Melanie , Kukk Edwin , Owada Shigeki , Togashi Tadashi , Tono Kensuke , Yabashi Makina , Son Sang-Kil , Ziaja Beata , Santra Robin , Ueda Kiyoshi
Published: January 2021

Using electron and ion spectroscopy, we studied the electron and nuclear dynamics in ∼50 000-atom large krypton clusters, following excitation with an intense hard x-ray pulse. Beyond the single pulse experiment, we also present the results of a time-resolved, x-ray pump–near-infrared probe measurement that allows one to learn about the time evolution of the system. After core ionization of the atoms by x-ray photons, trapped Auger and secondary electrons form a nanoplasma in which the krypton ions are embedded, according to the already published scenario. While the ion data show expected features, the electron emission spectra miss the expected pump–probe delay-dependent enhancement except for a slight enhancement in the energy range below 2 eV. Theoretical simulations help to reveal that, due to the deep trapping potential of the ions during the long time expansion accompanied by electron–ion recombination, thermal emission from the transient nanoplasma becomes quenched.
Quantum fluctuation effects on the ordered moments in a two dimensional frustrated ferrimagnet
Authors: Majumdar Kingshuk , Mahanti Subhendra D
Published: January 2021

We propose a novel two-dimensional (2D) frustrated quantum spin-1/2 anisotropic Heisenberg model with alternating ferromagnetic and antiferromagnetic magnetic chains along one direction and antiferromagnetic interactions along the other. The (mean-field) ground state is ferrimagnetic in certain range of the interaction space. Spin-wave theory analysis of the reduction of ordered moments at inequivalent spin sites and the instability of the spin waves suggest a quantum phase transition which has the characteristics of both the frustrated 2D antiferromagnetic S = 1/2 (J
1, J
2) model and 1D S
1 = 1, S
2 = 1/2 quantum ferrimagnetic model.
Comment on ‘Two blocks connected by a string with variable tension: a dynamic case’
Authors: Mungan Carl E
Published: January 2021

An Atwood-type machine is investigated in which one block moving along a frictionless horizontal track is connected by a string over an ideal pulley to a hanging block. In the usual setup, the pulley is located at the corner between the end of the track on a tabletop and a vertical drop down to the floor. An alternative geometry analysed by Herrera-Suárez, Machado-Higuera, and Muñoz (Phys. Educ.
55 055022) raises the pulley above this corner, so that the portion of the string connecting the pulley to the horizontally moving block makes a nonzero angle relative to the track. Assuming the track extends beyond the edge of the table, both blocks are shown here to exhibit oscillations about the equilibrium configuration as the horizontal block passes under the pulley.
Reply to ‘Comment on “Two blocks connected by a string with variable tension: a dynamic case”’
Authors: Herrera-Suárez H J , Machado-Higuera M , Muñoz J H
Published: January 2021

In this short note is presented a reply to a comment made by Professor Carl E Mungan on the paper “Comment on ‘Two blocks connected by a string with variable tension: a dynamic case’".
Poloidally resolved measurements of the perpendicular propagation velocity of density fluctuations in ASDEX Upgrade L-mode plasmas
Authors: Höfler K , Happel T , Hennequin P , Stroth U , Cavedon M , Dux R , Fischer R , McDermott R M , Poli E , Schuster C U , Wolfrum E , Upgrade Team the ASDEX
Published: January 2021

Poloidal asymmetries of the propagation velocity of density fluctuations perpendicular to the magnetic field measured with Doppler reflectometry have been reported in several magnetic confinement plasma devices. Careful analysis of a large variety of different low confinement mode plasma scenarios performed at the ASDEX Upgrade tokamak does not reveal such an asymmetry outside the uncertainties of the evaluation process of the measurement data. The perpendicular velocity is investigated between mid-radius and the plasma edge and follows the poloidal dependence of the E × B drift velocity regardless of the probed turbulence structure size. Compared to measurements of a charge exchange recombination spectroscopy diagnostic this points towards a significantly smaller phase velocity than the E × B drift velocity. The analysis technique is presented in a representative discharge together with a sensitivity study of the impact of density, magneto hydrodynamic equilibrium and diagnostic alignment on the interpretation of the measured Doppler shift using ray tracing and thus on poloidal asymmetries. Three more highly different plasma scenarios with poloidally symmetric velocity profiles are shown.
Uncovering novel phase transitions in dense dry polar active fluids using a lattice Boltzmann method
Authors: Nesbitt David , Pruessner Gunnar , Lee Chiu Fan
Published: January 2021

The dynamics of dry active matter have implications for a diverse collection of biological phenomena spanning a range of length and time scales, such as animal flocking, cell tissue dynamics, and swarming of inserts and bacteria. Uniting these systems are a common set of symmetries and conservation laws, defining dry active fluids as a class of physical system. Many interesting behaviours have been observed at high densities, which remain difficult to simulate due to the computational demand. Here, we show how two-dimensional dry active fluids in a dense regime can be studied using a simple modification of the lattice Boltzmann method. We apply our method on a model that exhibits motility-induced phase separation, and an active model with contact inhibition of locomotion, which has relevance to collective cell migration. For the latter, we uncover multiple novel phase transitions: two first-order and one potentially critical. We further support our simulation results with an analytical treatment of the hydrodynamic equations obtained via a Chapman–Enskog coarse-graining procedure.
The timing residual patterns due to pulsar acceleration
Authors: Xie Yi , Wang Li-Chun
Published: January 2021

The form of timing residuals due to errors in pulsar spin period P and its derivative

P
˙

, in positions, as well as in proper motions, has been well presented for decades in the literature. However, the residual patterns due to errors in the pulsar acceleration have not been reported previously, while a pulsar in the Galaxy or a globular cluster (GC) will be unavoidably accelerated. The coupling effect of the pulsar transverse acceleration and the Römer delay on timing residuals is simulated in this work. The results demonstrate that the residuals due to the effect can be identified by the oscillation envelopes of the residuals. It is also shown that the amplitude of the residuals due to the effect is usually relatively small, however, it may probably be observable for pulsars distributed in the vicinity of the core of a nearby GC.
Optimization and growth in first-passage resetting
Authors: De Bruyne B , Randon-Furling J , Redner S
Published: January 2021

We combine the processes of resetting and first passage, resulting in first-passage resetting, where the resetting of a random walk to a fixed position is triggered by the first-passage event of the walk itself. In an infinite domain, first-passage resetting of isotropic diffusion is non-stationary, and the number of resetting events grows with time according to

t

. We analytically calculate the resulting spatial probability distribution of the particle, and also obtain the distribution by geometric-path decomposition. In a finite interval, we define an optimization problem that is controlled by first-passage resetting; this scenario is motivated by reliability theory. The goal is to operate a system close to its maximum capacity without experiencing too many breakdowns. However, when a breakdown occurs the system is reset to its minimal operating point. We define and optimize an objective function that maximizes reward for being close to the maximum level of operation and imposes a penalty for each breakdown. We also investigate extensions of this basic model, firstly to include a delay after each reset, and also to two dimensions. Finally, we study the growth dynamics of a domain in which the domain boundary recedes by a specified amount whenever the diffusing particle reaches the boundary, after which a resetting event occurs. We determine the growth rate of the domain for a semi-infinite line and a finite interval and find a wide range of behaviors that depend on how much recession occurs when the particle hits the boundary.
Non-probabilistic fermionic limit shapes
Authors: Bocini Saverio , Stéphan Jean-Marie
Published: January 2021

We study a translational invariant free fermions model in imaginary time, with nearest neighbor and next-nearest neighbor hopping terms, for a class of inhomogeneous boundary conditions. This model is known to give rise to limit shapes and arctic curves, in the absence of the next-nearest neighbor perturbation. The perturbation considered turns out to not be always positive, that is, the corresponding statistical mechanical model does not always have positive Boltzmann weights. We investigate how the density profile is affected by this nonpositive perturbation. We find that in some regions, the effects of the negative signs are suppressed, and renormalize to zero. However, depending on boundary conditions, new ‘crazy regions’ emerge, in which minus signs proliferate, and the density of fermions is not in [0, 1] anymore. We provide a simple intuition for such behavior, and compute exactly the density profile both on the lattice and in the scaling limit.
Entanglement entropy of excited states in the quantum Lifshitz model
Authors: Angel-Ramelli Juanfernando
Published: January 2021

In this work we calculate the entanglement entropy of certain excited states of the quantum Lifshitz model (QLM). The QLM is a 2 + 1-dimensional bosonic quantum field theory with an anisotropic scaling symmetry between space and time that belongs to the universality class of the quantum dimer model and its generalizations. The states we consider are constructed by exciting the eigenmodes of the Laplace–Beltrami operator on the spatial manifold of the model. We perform a replica calculation and find that, whenever a simple assumption is satisfied, the bipartite entanglement entropy of any such excited state can be evaluated analytically. We show that the assumption is satisfied for all excited states on the rectangle and for almost all excited states on the sphere and provide explicit examples in both geometries. We find that the excited state entanglement entropy obeys an area law and is related to the entanglement entropy of the ground state by two universal constants. We observe a logarithmic dependence on the excitation number when all excitations are put onto the same eigenmode.
Chloride load dynamics along channelized and intact reaches in a northeastern United States urban headwater stream
Authors: Slosson John R , Lautz Laura K , Beltran Julio
Published: January 2021

Sodium chloride has long been used for winter deicing, although its legacy use has resulted in rising chloride concentrations in urban watersheds. Persistently high chloride levels impair drinking water resources and threaten the health of aquatic life and vegetation. In urban areas, chloride fate and transport is impacted by human modification of the environment, including increased impervious surface cover and disconnection of stream corridors from riparian groundwater. We couple continuous streamflow records with weekly chloride concentration data over two water years to create continuous chloride load estimates at three locations along a degraded, urban stream in upstate New York with contrasting channelized and intact reaches. Our results show that degraded reaches characterized by channelized, armored banks and minimal groundwater connection deliver chloride loads closer to chloride application rates in the surrounding watershed. In contrast, stream–groundwater interactions in intact reaches adjacent to riparian floodplains, including surface water losses to subsurface flow paths, result in stream chloride loads that are 50% less than those delivered from upstream channelized reaches. These findings show that longitudinal chloride load estimates along a stream channel can be valuable in identifying the timing and magnitude of chloride sources and sinks, which may be common but less apparent in urban environments.
Effect of V2O5 addition on the structural and magnetic properties of Ni–Co–Zn ferrites
Authors: Ullah M Samir , Uddin M Firoz , Momin A A , Hakim M A
Published: January 2021

The effect of V2O5 addition on the structural and magnetic properties of Ni–Co–Zn ferrites having the compositions Ni0.62Co0.03Zn0.35Fe2O4 + xV2O5 (where x = 0.0, 0.5, 1.0 and 1.5 wt%) are reported. The samples were prepared by solid state reaction. The crystalline structure of all the samples showed cubic spinel structure. The microstructural study reveals that the grain growths of Ni–Co–Zn mixed ferrites are strongly depended on the amount of V2O5 contents. The saturation magnetization and coercivity were determined from the magnetic hysteresis loops, while Curie temperatures were estimated from the temperature dependence of magnetization. The saturation magnetization almost linearly decreased from 77 emu g−1 for x = 0.0 wt% V2O5 to 56 emu g−1 for x = 1.5 wt% V2O5. Curie temperatures for the studied samples decreased with increase of V2O5 addition. A general termed of permeability enhancement is clearly evidenced on V2O5 addition.
Salisbury screen absorbers using epsilon-near-zero substrate
Authors: Wulan Qiqige , He De , Zhang Tieyan , Peng Hao , Liu Lu , Medvedev Viacheslav V , Liu Zhijun
Published: January 2021

As a planar resonant structure, Salisbury screen offers a cost-effective way of manipulating electromagnetic waves for both fundamental studies and practical applications in optoelectronics. In this paper, we demonstrate Salisbury screen absorbers using epsilon-near-zero substrate, which reduces the spacer thickness below typical one quarter wavelength limit. Three-layered thin-film absorbers made of SiC substrate, ZnSe spacer layer and top NiCr film are designed and fabricated, which exhibit near-perfect absorption at 11.72 μm with spacer thickness of about half of a quarter-wavelength. For ideal zero-index material without optical loss, our proposed thin-film absorber simplifies to a two-layered structure even without the spacer layer in theory. These results suggest that epsilon-near-zero materials provide an alternative approach in developing compact planar absorbing structures without involving lithographic patterning.
Material design of intelligent plastic products with sound generation function due to snap-through buckling
Authors: Hachisuka Ryosuke , Noda Reona , Yamaguchi Masayuki
Published: January 2021

Audible sound generation due to snap-through buckling during bending deformation was studied using an injection-molded product with a hinge. The sound was clearly generated in a rigid plastic product with a specific shape of the hinge that was markedly deformed. The large elastic energy stored in the hinge by the bending deformation, which was suddenly released during buckling deformation, was responsible for the increased sound pressure. This phenomenon may be exploited as a sensor to control the maximum deformation at bending in intelligent plastic products.
Drought-induced reduction in flower size and abundance correlates with reduced flower visits by bumble bees
Authors: Kuppler J , Wieland J , Junker R R , Ayasse M
Published: January 2021

Reduced water availability can cause physiological stress in plants that affects floral development leading to changes in floral morphology and traits that mediate interactions with pollinators. As pollinators can detect small changes in trait expressions, drought-induced changes in floral traits could affect pollinator visitations. However, the linkage between changes in floral traits and pollinator visitations under drought conditions is not well explored. We, therefore, tested whether drought-induced changes in floral morphology and abundance of flowers are linked to changes in pollinator visitations. We conducted flight cage experiments with a radio frequency identification system for automated visitation recordings with bumble bees (Bombus terrestris) and common charlock (Sinapis arvensis) as the model system. In total, we recorded interactions for 31 foraging bumble bees and 6569 flower visitations. We found that decreasing soil moisture content correlated with decreasing size of all measured morphological traits except stamen length and nectar tube width. The reductions in floral size, petal width and length, nectar tube depth and number of flowers resulted in decreasing visitation rates by bumble bees. These decreasing visitations under lower soil moisture availability might be explained by lower numbers of flowers and thus a reduced attractiveness and/or by increased difficulties experienced by bumble bees in handling smaller flowers. Whether these effects act additively or synergistically on pollinator behaviour and whether this leads to changes in pollen transfer and to different selectionp ressures require further investigation.
Benchmarking network-based gene prioritization methods for cerebral small vessel disease
Authors: Zhang Huayu , Ferguson Amy , Robertson Grant , Jiang Muchen , Zhang Teng , Sudlow Cathie , Smith Keith , Rannikmae Kristiina , Wu Honghan
Published: January 2021

Network-based gene prioritization algorithms are designed to prioritize disease-associated genes based on known ones using biological networks of protein interactions, gene–disease associations (GDAs) and other relationships between biological entities. Various algorithms have been developed based on different mechanisms, but it is not obvious which algorithm is optimal for a specific disease. To address this issue, we benchmarked multiple algorithms for their application in cerebral small vessel disease (cSVD). We curated protein–gene interactions (PGIs) and GDAs from databases and assembled PGI networks and disease–gene heterogeneous networks. A screening of algorithms resulted in seven representative algorithms to be benchmarked. Performance of algorithms was assessed using both leave-one-out cross-validation (LOOCV) and external validation with MEGASTROKE genome-wide association study (GWAS). We found that random walk with restart on the heterogeneous network (RWRH) showed best LOOCV performance, with median LOOCV rediscovery rank of 185.5 (out of 19 463 genes). The GenePanda algorithm had most GWAS-confirmable genes in top 200 predictions, while RWRH had best ranks for small vessel stroke-associated genes confirmed in GWAS. In conclusion, RWRH has overall better performance for application in cSVD despite its susceptibility to bias caused by degree centrality. Choice of algorithms should be determined before applying to specific disease. Current pure network-based gene prioritization algorithms are unlikely to find novel disease-associated genes that are not associated with known ones. The tools for implementing and benchmarking algorithms have been made available and can be generalized for other diseases.
xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery
Authors: Gorla Aditya , Jew Brandon , Zhang Luke , Sul Jae Hoon
Published: January 2021

Motivation

Since the first human genome was sequenced in 2001, there has been a rapid growth in the number of bioinformatic methods to process and analyze next-generation sequencing (NGS) data for research and clinical studies that aim to identify genetic variants influencing diseases and traits. To achieve this goal, one first needs to call genetic variants from NGS data, which requires multiple computationally intensive analysis steps. Unfortunately, there is a lack of an open-source pipeline that can perform all these steps on NGS data in a manner, which is fully automated, efficient, rapid, scalable, modular, user-friendly and fault tolerant. To address this, we introduce xGAP, an extensible Genome Analysis Pipeline, which implements modified GATK best practice to analyze DNA-seq data with the aforementioned functionalities.

Results

xGAP implements massive parallelization of the modified GATK best practice pipeline by splitting a genome into many smaller regions with efficient load-balancing to achieve high scalability. It can process 30× coverage whole-genome sequencing (WGS) data in ∼90 min. In terms of accuracy of discovered variants, xGAP achieves average F1 scores of 99.37% for single nucleotide variants and 99.20% for insertion/deletions across seven benchmark WGS datasets. We achieve highly consistent results across multiple on-premises (SGE & SLURM) high-performance clusters. Compared to the Churchill pipeline, with similar parallelization, xGAP is 20% faster when analyzing 50× coverage WGS on Amazon Web Service. Finally, xGAP is user-friendly and fault tolerant where it can automatically re-initiate failed processes to minimize required user intervention.

Availability and implementation

xGAP is available at https://github.com/Adigorla/xgap.

Supplementary information

Supplementary data are available at Bioinformatics online.
MEWpy: a computational strain optimization workbench in Python
Authors: Pereira Vítor , Cruz Fernando , Rocha Miguel
Published: January 2021

Metabolic Engineering aims to favour the overproduction of native, as well as non-native, metabolites by modifying or extending the cellular processes of a specific organism. In this context, Computational Strain Optimization (CSO) plays a relevant role by putting forward mathematical approaches able to identify potential metabolic modifications to achieve the defined production goals. We present MEWpy, a Python workbench for metabolic engineering, which covers a wide range of metabolic and regulatory modelling approaches, as well as phenotype simulation and CSO algorithms.

Availability and implementation

MEWpy can be installed from PyPi (pip install mewpy), the source code being available at https://github.com/BioSystemsUM/mewpy under the GPL license.
Temperature Effects on Oviposition by Rhagoletis indifferens (Diptera: Tephritidae) Vary in Different Developmental Stages of Sweet Cherry
Authors: Yee Wee
Published: January 2021

Fruit developmental stage affects oviposition responses by tephritid fruit flies, but the role temperature plays in these responses to different fruit stages remains largely unknown. Here, temperature effects on oviposition rates of western cherry fruit fly, Rhagoletis indifferens Curran, in different stages of Bing sweet cherry (Prunus avium L.) were determined in no-choice experiments. Stage 1 (green), stage 2 (green-yellow to orange red), stage 3 (yellow-orange to red), and stage 4 cherries (red to burgundy) were exposed to flies at 15.6, 21.1, 26.7, and 32.2°C for 3 h and oviposition recorded. Oviposition was lower at 15.6°C than at all other test temperatures within all four cherry stages. Regression analysis using the three higher temperatures indicated there were significant cherry stage and temperature effects and a significant cherry stage × temperature interaction. The oviposition–temperature relationship was best explained by linear or curvilinear equations, depending on cherry stage. Oviposition in stage 1 cherries was lowest of the four stages and was not or linearly related to temperature. Oviposition in stage 2 cherries was greater and was related to temperature in a linear or curvilinear response. Oviposition was greatest in stage 3 and 4 cherries, with curvilinear and linear equations, respectively, best explaining oviposition–temperature relationships. Results suggest that temperatures and cherry stage together rather than cherry stage alone may have selected for behaviors leading to oviposition responses in R. indifferens.
Left ventricular systolic dysfunction with concomitant bradyarrhythmia in a patient with POEMS syndrome: a case report
Authors: Tan Joo Hor , Yew Min Sen , Huang Wenjie , Tan Kenny
Published: January 2021

Background

POEMS syndrome (PS) is a paraneoplastic disorder from plasma cell dyscrasia, characterized by polyneuropathy, organomegaly, endocrinopathy, monoclonal protein, and skin changes. Vascular endothelial growth factors (VEGFs)-driven fluid extracellular matrix expansion plays a key role in this condition. Associated cardiac involvement has been sparsely reported thus far.

Case summary

A 55-year-old woman with PS presented with a pleural effusion and respiratory failure requiring mechanical ventilation. Transthoracic echocardiogram revealed left ventricular (LV) systolic dysfunction with a moderate pericardial effusion. She developed intermittent complete heart block and ventricular standstill, requiring temporary transcutaneous pacing. Further evaluation revealed no significant coronary stenosis on coronary angiogram and cardiac magnetic resonance (CMR) showed elevated T1 and extracellular volume suggestive of myocardial oedema with possible early cardiac infiltration. She had a dual-chamber permanent pacemaker implanted in view of recurrent high-grade heart block. She was initiated on a daratumumab-based chemotherapy regimen prior to discharge. She recovered well subsequently with a promising clinical response to chemotherapy.

Discussion

We describe the first case of LV systolic dysfunction with concomitant significant bradyarrhythmia in a patient with PS. CMR revealed evidence suggestive of LV myocardial oedema and/or possible early infiltration. VEGF overexpression could explain oedema-related LV dysfunction which reversed with adequate diuresis, as well as damage to the conduction system. Early cardiac amyloidosis, which can be associated with PS, is an important differential diagnosis. Pacemaker implantation, adequate diuresis, and definitive chemotherapy are key to the management of concomitant ventricular myocardial and electrical dysfunction in such rare case.
Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion
Authors: Wyka Stephen A , Mondo Stephen J , Liu Miao , Dettman Jeremy , Nalam Vamsi , Broders Kirk D
Published: January 2021

The genus Claviceps has been known for centuries as an economically important fungal genus for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, morphological, and metabolic features (Claviceps sects. Citrinae, Paspalorum, Pusillae, and Claviceps). The first three sections are additionally characterized by narrow host range, whereas section Claviceps is considered evolutionarily more successful and adaptable as it has the largest host range and biogeographical distribution. However, the reasons for this success and adaptability remain unclear. Our study elucidates factors influencing adaptability by sequencing and annotating 50 Claviceps genomes, representing 21 species, for a comprehensive comparison of genome architecture and plasticity in relation to host range potential. Our results show the trajectory from specialized genomes (sects. Citrinae and Paspalorum) toward adaptive genomes (sects. Pusillae and Claviceps) through colocalization of transposable elements around predicted effectors and a putative loss of repeat-induced point mutation resulting in unconstrained tandem gene duplication coinciding with increased host range potential and speciation. Alterations of genomic architecture and plasticity can substantially influence and shape the evolutionary trajectory of fungal pathogens and their adaptability. Furthermore, our study provides a large increase in available genomic resources to propel future studies of Claviceps in pharmacology and agricultural research, as well as, research into deeper understanding of the evolution of adaptable plant pathogens.
DEFECTIVE HISTONE TRANSITION DURING SPERMIOGENESIS IN HETEROZYGOUS SEGREGATION DISTORTER MALES OF DROSOPHILA MELANOGASTER
Authors: Hauschteck-Jungen Elizabeth , Hartl Daniel L
Published: January 2021

Males of Drosophila melanogaster that are heterozygous for the segregation distorter (SD) chromosome produce a gross excess of SD-bearing offspring because most of the non-SD-bearing sperm are dysfunctional. These dysfunctional sperm exhibit abnormalities in chromatin condensation and compaction during spermiogenesis. Use of the fluorescent dye sulfoflavine, which is specific for basic proteins, has now revealed that the dysfunctional sperm are also defective in the normal transition from somatic to spermatid-specific histones.
INTERACTIONS BETWEEN FUSED AND ENGRAILED, TWO MUTATIONS AFFECTING PATTERN FORMATION IN DROSOPHILA MELANOGASTER
Authors: Fausto-Sterling Anne , Smith-Schiess Heidi
Published: January 2021

In this paper we demonstrate that the severity of the engrailed phenotype is greatly increased when engrailed is combined with the X-linked mutation fused. The secondary sex combs of fu;en flies contain from two to four times more setae than do those of en siblings. The number of transverse rows of bristles on the metatarsus of the metathoracic leg is reduced by a factor of one and a half to two in fu;en flies when compared to their en siblings, while the frequency of reversed bract polarity, bristle abnormalities and misshapen metatarsi increases greatly. In addition, fu;en flies express the en wing phenotype more completely than their siblings and have a much higher frequency of wing vein abnormalities—some of which we have interpreted as triplications of the third and first longitudinal wing veins. We briefly discuss the significance of the fused-engrailed gene interaction.
ON THE CONTROL OF THE DISTRIBUTION OF MEIOTIC EXCHANGE IN DROSOPHILA MELANOGASTER
Authors: Carpenter Adelaide T C , Baker Bruce S
Published: January 2021

The effects of eight recombination-defective meiotic mutants on crossing over within the X heterochromatin were examined. Since none permit substantial frequencies of exchange within heterochromatin although six lessen or abolish constraints on the location of exchanges within euchromatin, the systems that prohibit exchange within heterochromatin and that govern where exchanges will occur in euchromatin are under separate genetic control.—A minor component of the effects of mei-218 is the production of nonhomologous exchanges; of mei-9 is the recovery of deleted chromatids; and of mei-41 is the recovery of deleted chromatids and/or a low frequency of heterochromatic exchanges.
UNEXPECTED BEHAVIOR IN TWO LOCUS GENETIC SYSTEMS: AN ANALYSIS OF MARGINAL UNDERDOMINANCE AT A STABLE EQUILIBRIUM
Authors: Hastings Alan
Published: January 2021

The phenomenon of marginal underdominance at a stable equilibrium in a two-locus-two-allele deterministic selection model is studied analytically using bifurcation theory. This technique and additional numerical studies indicate several new aspects of the phenomenon that are of biological importance. Marginal underdominance can occur at both loci simultaneously and can be present in a model with small fitness differentials. This can occur for a fitness scheme that is a one parameter generalization of the classical symmetric fitness model.
POLYCOMBLIKE: A GENE THAT APPEARS TO BE REQUIRED FOR THE NORMAL EXPRESSION OF THE BITHORAX AND ANTENNAPEDIA GENE COMPLEXES OF DROSOPHILA MELANOGASTER
Authors: Duncan Ian McKenzie
Published: January 2021

A newly identified gene is described that is required for the maintenance of normal identities in many of the body segments of the fly. The effects of mutants in this gene, which is called Polycomblike (Pcl), suggest that its wild-type allele functions in the regulation of the bithorax gene complex (BX-C) and the Antennapedia gene complex (ANT-C). Evidence in favor of this idea derives from (1) the close correspondence between segmental transformations caused by Pcl mutants and those caused by dominant gain-of-function mutants in the BX-C and ANT-C, (2) the interactions observed between Pcl mutants and mutants in these complexes, and (3) the dependence upon BX-C and ANT-C dosage of the severity of at least one of the transformations caused by Pcl mutants. Arguments are presented that the control of the BX-C and ANT-C by Pcl  + is negative in nature. The results of clonal analysis experiments indicate that, at least for the BX-C, Pcl  + exerts this control until late in development. Since the wild-type allele of another gene, called Polycomb (Pc), has previously been shown to have many of the same properties as Pcl  +, it appears that the BX-C and perhaps also the ANT-C are continuously regulated during development by at least two and probably several other genes.
LOCALIZATION OF MINUTES TO SPECIFIC POLYTENE CHROMOSOME BANDS BY MEANS OF OVERLAPPING DUPLICATIONS
Authors: Broderick David J , Roberts Paul A
Published: January 2021

Overlapping duplications recovered as suppressors of Minute loci have been used to localize M(2)z and M(3)w  124 to specific polytene bands 25A1(2) and 95A1(2). The surprising efficiency of M localization by duplication may result from the tendency of M suppressors to be at least a visible fraction of a polytene band in length.
PROPERTIES AND EVOLUTIONARY POTENTIAL OF NEWLY INDUCED TANDEM DUPLICATIONS IN DROSOPHILA MELANOGASTER
Authors: Roberts Paul A , Broderick David J
Published: January 2021

Most of some 33 X-ray-induced duplications recovered as Suppressors of Minute loci proved to be direct tandem duplications. When heterozygous, most duplications were crossover suppressors, and duplications of short to moderate size did not reduce the fitness of their bearers. Crossover suppression by tandem duplication may be attributed to intrastrand foldbacks of the type regularly seen in somatic polytene chromosomes. As a consequence, linkage disequilibrium between duplicated elements and normal chromosomes should be more profound than has been supposed. Tandem duplications appear to be predisposed by reason of frequency of generation, crossover suppression and fitness effects to serve as the primary source of new genes.
STUDIES ON THE SEX-SPECIFIC LETHALS OF DROSOPHILA MELANOGASTER. V. SEX TRANSFORMATION CAUSED BY INTERACTIONS BETWEEN A FEMALE-SPECIFIC LETHAL, Sxl
f#1, AND THE MALE-SPECIFIC LETHALS mle(3)132, msl-2
27, AND mle
Authors: Uenoyama T , Fukunaga A , Ioshi K
Published: January 2021

Interactions between a female-specific lethal mutant, Sxlf  #1, and each of three male-specific lethal mutants, mle(3)132, msl-2  27 and mle, of Drosophila melanogaster were observed to produce morphological changes in various sexually dimorphic external characters. Chromosomal females heterozygous for Sxlf  #1 and homozygous for any one of the male-specific lethals (and to a lesser degree heterozygous for male-specific lethals) sometimes had sex combs, male-type tergites, male-type sternites, male-type anal plates or male-type external genitalia. Penetrance was not high and expression was often incomplete; single individuals never had all the sexually dimorphic structures transformed. When mothers were homozygous for male-specific lethals, higher proportions of female progeny were affected than when mothers were heterozygous, suggesting a maternal effect.
THE REX GENE OF BACTERIOPHAGE λ IS REALLY TWO GENES
Authors: Matz Karen , Schmandt Margaret , Gussin Gary N
Published: January 2021

Complementation tests among previously isolated rex  - mutants of bacteriophage λ reveal that the mutants comprise two complementation groups, designated rexA and rexB. Because rexB  - mutants complement prm  - mutants, but rexA  - mutants do not, it appears that the rexA gene is coordinately controlled with the cI (repressor) gene under the direction of the PRM promoter, but that some other promoter is capable of directing the expression of rexB.