bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract

Summary
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

Abstract
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

AbstractBackgroundPOEMS 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 summaryA 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.DiscussionWe 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.