bluuebunny/crossref_metadata_2025_split huggingface dataset:
Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species
Authors: Zhong Yan , Chen Zhao , Cheng Zong-Ming 
Published: January 2022

AbstractIn this study, genome-wide identification, phylogenetic relationships, duplication time and selective pressure of the NBS-LRR genes, an important group of plant disease-resistance genes (R genes), were performed to uncover their genetic evolutionary patterns in the six Prunus species. A total of 1946 NBS-LRR genes were identified; specifically, 589, 361, 284, 281, 318, and 113 were identified in Prunus yedoensis, P. domestica, P. avium, P. dulcis, P. persica and P. yedoensis var. nudiflora, respectively. Two NBS-LRR gene subclasses, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (non-TNL), were also discovered. In total, 435 TNL and 1511 non-TNL genes were identified and could be classified into 30/55/75 and 103/158/191 multi-gene families, respectively, according to three different criteria. Higher Ks and Ka/Ks values were detected in TNL gene families than in non-TNL gene families. These results indicated that the TNL genes had more members involved in relatively ancient duplications and were affected by stronger selection pressure than the non-TNL genes. In general, the NBS-LRR genes were shaped by species-specific duplications, and lineage-specific duplications occurred at recent and relatively ancient periods among the six Prunus species. Therefore, different duplicated copies of NBS-LRRs can resist specific pathogens and will provide an R-gene library for resistance breeding in Prunus species.
Shared decision-making and the lessons learned about decision regret in cancer patients
Authors: Chichua Mariam , Brivio Eleonora , Mazzoni Davide , Pravettoni Gabriella 
Published: January 2022

AbstractThe commentary presents reflections on the literature on post-treatment cancer patient regret. Even though a lot of effort has been made to increase patient satisfaction by engaging them in medical decisions, patient regret remains present in clinical settings. In our commentary, we identify three main aspects of shared decision-making that previously have been shown to predict patient regret. Based on these findings, we provide recommendations for physicians involved in the shared decision-making process. In addition, we make methodological suggestions for future research in the field.
Semi-discrete optimal transport methods for the semi-geostrophic equations
Authors: Bourne David P. , Egan Charlie P. , Pelloni Beatrice , Wilkinson Mark 
Published: January 2022

AbstractWe give a new and constructive proof of the existence of global-in-time weak solutions of the 3-dimensional incompressible semi-geostrophic equations (SG) in geostrophic coordinates, for arbitrary initial measures with compact support. This new proof, based on semi-discrete optimal transport techniques, works by characterising discrete solutions of SG in geostrophic coordinates in terms of trajectories satisfying an ordinary differential equation. It is advantageous in its simplicity and its explicit relation to Eulerian coordinates through the use of Laguerre tessellations. Using our method, we obtain improved time-regularity for a large class of discrete initial measures, and we compute explicitly two discrete solutions. The method naturally gives rise to an efficient numerical method, which we illustrate by presenting simulations of a 2-dimensional semi-geostrophic flow in geostrophic coordinates generated using a numerical solver for the semi-discrete optimal transport problem coupled with an ordinary differential equation solver.
On the definition of solution to the total variation flow
Authors: Kinnunen Juha , Scheven Christoph 
Published: January 2022

AbstractWe show that the notions of weak solution to the total variation flow based on the Anzellotti pairing and the variational inequality coincide under some restrictions on the boundary data. The key ingredient in the argument is a duality result for the total variation functional, which is based on an approximation of the total variation by area-type functionals.
Equivariant Yamabe problem with boundary
Authors: Ho Pak Tung , Shin Jinwoo 
Published: January 2022

AbstractAs a generalization of the Yamabe problem, Hebey and Vaugon considered the equivariant Yamabe problem: for a subgroupGof the isometry group, find aG-invariant metric whose scalar curvature is constant in a given conformal class. In this paper, we study the equivariant Yamabe problem with boundary.
Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis)
Authors: Barrett Kimberley G. , Amaral Geneviève , Elphinstone Melanie , McAdie Malcolm L. , Davis Corey S. , Janes Jasmine K. , Carnio John , Moehrenschlager Axel , Gorrell Jamieson C. 
Published: January 2022

AbstractCaptive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.
From Full Day Learning to 30 Minutes a Day: A Descriptive Study of Early Learning During the First COVID-19 Pandemic School Shutdown in Ontario
Authors: Spadafora Natalie , Reid-Westoby Caroline , Pottruff Molly , Wang Jade , Janus Magdalena 
Published: January 2022

AbstractWhen the COVID-19 pandemic was declared in March 2020, the lives of families all over the world were disrupted. Many adults found themselves working from home while their children were unable to go to school. To better understand the potential impact of these educational disruptions, it is important to establish what learning looked like during the first school shutdown in the spring of 2020, particularly for the youngest learners who may feel the longest lasting impacts from this pandemic. Therefore, the purpose of the current descriptive study was to gather information on how kindergarten teaching and learning occurred during this time, what the biggest barriers were, and what concerns educators had regarding returning in person to the classroom setting. The sample for the current study was 2569 kindergarten educators (97.6% female; 74.2% teachers, 25.8% early childhood educators) in Ontario, Canada. Participants completed a questionnaire consisting of both quantitative scales and qualitative open-ended questions. Educators reported that parents most often contacted them regarding technological issues or how to effectively support their child. The largest barrier to learning was the ability of both parents and educators to balance work, home life, and online learning/teaching. With regards to returning to school, educators were most concerned about the lack of ability of kindergarten aged children to do tasks independently and to follow safety protocols. Our findings highlight unique challenges associated with teaching kindergarten during the pandemic, contributing to our understanding of the learning that occurred in Ontario during the first COVID-19 shutdown.
Flexible scheduling of diagnostic tests in automotive manufacturing
Authors: König Simone , Reihn Maximilian , Abujamra Felipe Gelinski , Novy Alexander , Vogel-Heuser Birgit 
Published: January 2022

AbstractThe car of the future will be driven by software and offer a variety of customisation options. Enabling these customisation options forces modern automotive manufacturers to update their standardised scheduling concepts for testing and commissioning cars. A flexible scheduling concept means that every chosen customer configuration code must have its own testing procedure. This concept is essential to provide individual testing workflows where the time and resources are optimised for every car. Manual scheduling is complicated due to constraints on time, predecessor-successor relationships, mutual exclusion criteria, resources and status conditions on the car engineering and assembly line. Applied methods to handle the mathematical formulation for the corresponding industrial optimisation problem and its implementation are not yet available. This paper presents a procedure for automated and non-preemptive scheduling in the testing and commissioning of cars, which is built on a Boolean satisfiability problem on parallel and identical machines with temporal and resource constraints. The presented method is successfully implemented and evaluated on a variant assembly line of an automotive Original Equipment Manufacturer. This paper is the starting point for an automated workflow planning and scheduling process in automotive manufacturing.
Evolving cellular automata schemes for protein folding modeling using the Rosetta atomic representation
Authors: Varela Daniel , Santos José 
Published: January 2022

AbstractProtein folding is the dynamic process by which a protein folds into its final native structure. This is different to the traditional problem of the prediction of the final protein structure, since it requires a modeling of how protein components interact over time to obtain the final folded structure. In this study we test whether a model of the folding process can be obtained exclusively through machine learning. To this end, protein folding is considered as an emergent process and the cellular automata tool is used to model the folding process. A neural cellular automaton is defined, using a connectionist model that acts as a cellular automaton through the protein chain to define the dynamic folding. Differential evolution is used to automatically obtain the optimized neural cellular automata that provide protein folding. We tested the methods with the Rosetta coarse-grained atomic model of protein representation, using different proteins to analyze the modeling of folding and the structure refinement that the modeling can provide, showing the potential advantages that such methods offer, but also difficulties that arise.
An update on the ophthalmic features in hereditary haemorrhagic telangiectasia (Rendu-Osler-Weber syndrome)
Authors: Abdolrahimzadeh Solmaz , Formisano Martina , Marani Carla , Rahimi Siavash 
Published: January 2022

AbstractHereditary haemorrhagic telangiectasia (HHT) or Osler-Rendu-Weber syndrome is a rare autosomal dominant disease, characterised by systemic angiodysplasia. Dysfunction of the signalling pathway of β transforming growth factor is the main cause of HHT principally owing to mutations of the genes encoding for endoglin (ENG) and activin A receptor type II-like 1 (ACVRL1). Clinical manifestations can range from mucocutaneous telangiectasia to organ arterio-venous malformations and recurrent epistaxis. The early clinical manifestations may sometimes be subtle, and diagnosis may be delayed. The main ophthalmic manifestations historically reported in HHT are haemorrhagic epiphora, and conjunctival telangiectasia present in 45–65% of cases, however, imaging with wide-field fluorescein angiography has recently shown peripheral retinal telangiectasia in 83% of patients. Optimal management of HHT requires both understanding of the clinical presentations and detection of early signs of disease. Advances in imaging methods in ophthalmology such as wide-field fluorescein angiography, spectral domain optical coherence tomography, and near infrared reflectance promise further insight into the ophthalmic signs of HHT towards improved diagnosis and early management of possible severe complications.
Double perovskite Cs2AgBiBr6 radiation sensor: synthesis and characterization of single crystals
Authors: Murgulov Valeria , Schweinle Catherine , Daub Michael , Hillebrecht Harald , Fiederle Michael , Dědič Václav , Franc Jan 
Published: January 2022

AbstractSingle crystals of lead-free halide double perovskite Cs2AgBiBr6 sensor material manifest a remarkable potential for application in radiation detection and imaging. In this study, the purity and crystallinity of solution-grown Cs2AgBiBr6 single crystals with cubic Fm$$\overline{3}$$

3
¯

m symmetry have been corroborated by powder XRD measurements, while the single crystal XRD patterns reveal the dominant {111} lattice planes parallel to the sample surfaces. A wider range of lower resistivity values (106–109 Ωcm) was obtained from the I-V measurements compared to the 1.55 × 109–6.65 × 1010 Ωcm values from the van der Pauw method, which is typically higher for the Ag than for the carbon paint electrodes. Charge-carrier mobility values estimated from the SCLC method for the carbon paint-Cs2AgBiBr6 (1.90–4.82 cm2V−1 s−1) and the Ag-Cs2AgBiBr6 (0.58–4.54 cm2V−1 s−1) including the density of trap states (109–1010 cm−3) are comparable. Similar values of 1.89 cm2V−1 s−1 and 2.36 cm2V−1 s−1 are derived from the Hall effect measurements for a sample with carbon and Ag electrodes, respectively. The key electrical parameters including the X-ray photoresponse measurements indicate that the Cs2AgBiBr6 samples synthesized in this study satisfy requirements for radiation sensors.
Graphical abstract
Stability Issues of Entropy-Stable and/or Split-form High-order Schemes
Authors: Gassner Gregor J. , Svärd Magnus , Hindenlang Florian J. 
Published: January 2022

AbstractThe focus of the present research is on the analysis of local energy stability of high-order (including split-form) summation-by-parts methods, with e.g. two-point entropy-conserving fluxes, approximating non-linear conservation laws. Our main finding is that local energy stability, i.e., the numerical growth rate does not exceed the growth rate of the continuous problem, is not guaranteed even when the scheme is non-linearly stable and that this may have adverse implications for simulation results. We show that entropy-conserving two-point fluxes are inherently locally energy unstable, as they can be dissipative or anti-dissipative. Unfortunately, these fluxes are at the core of many commonly used high-order entropy-stable extensions, including split-form summation-by-parts discontinuous Galerkin spectral element methods (or spectral collocation methods). For the non-linear Burgers equation, we further demonstrate numerically that such schemes cause exponential growth of errors during the simulation. Furthermore, we encounter a similar abnormal behaviour for the compressible Euler equations, for a smooth exact solution of a density wave. Finally, for the same case, we demonstrate numerically that other commonly known split-forms, such as the Kennedy and Gruber splitting, are also locally energy unstable.
RETRACTED ARTICLE: Anatomical adjustment of mature leaves of sycamore maple (Acer pseudoplatanus L.) to increased irradiance
Authors: Wyka Tomasz P. , Robakowski Piotr , Żytkowiak Roma , Oleksyn Jacek 
Published: January 2022

AbstractTrees regenerating in the understory respond to increased availability of light caused by gap formation by undergoing a range of morphological and physiological adjustments. These adjustments include the production of thick, sun-type leaves containing thicker mesophyll and longer palisade cells than in shade-type leaves. We asked whether in the shade-regenerating tree Acer pseudoplatanus, the increase in leaf thickness and expansion of leaf tissues are possible also in leaves that had been fully formed prior to the increase in irradiance, a response reported so far only for a handful of species. We acclimated potted seedlings to eight levels (from 1 to 100%) of solar irradiance and, in late summer, transferred a subset of them to full sunlight. Within 30 days, the shaded leaves increased leaf mass per area and became thicker mostly due to elongation of palisade cells, except for the most shaded individuals which suffered irreversible photo-oxidative damage. This anatomical acclimation was accompanied by partial degradation of chlorophyll and a transient decline in photosynthetic efficiency of PSII (Fv/FM). These effects were related to the degree of pre-shading. The Fv/FM recovered substantially within the re-acclimation period. However, leaves of transferred plants were shed significantly earlier in the fall, indicating that the acclimation was not fully effective. These results show that A. pseudoplatanus is one of the few known species in which mature leaves may re-acclimate anatomically to increased irradiance. This may be a potentially important mechanism enhancing utilization of gaps created during the growing season.
Can I show my skills? Affective responses to artificial intelligence in the recruitment process
Authors: Köchling Alina , Wehner Marius Claus , Warkocz Josephine 
Published: January 2022

AbstractCompanies increasingly use artificial intelligence (AI) and algorithmic decision-making (ADM) for their recruitment and selection process for cost and efficiency reasons. However, there are concerns about the applicant’s affective response to AI systems in recruitment, and knowledge about the affective responses to the selection process is still limited, especially when AI supports different selection process stages (i.e., preselection, telephone interview, and video interview). Drawing on the affective response model, we propose that affective responses (i.e., opportunity to perform, emotional creepiness) mediate the relationships between an increasing AI-based selection process and organizational attractiveness. In particular, by using a scenario-based between-subject design with German employees (N = 160), we investigate whether and how AI-support during a complete recruitment process diminishes the opportunity to perform and increases emotional creepiness during the process. Moreover, we examine the influence of opportunity to perform and emotional creepiness on organizational attractiveness. We found that AI-support at later stages of the selection process (i.e., telephone and video interview) decreased the opportunity to perform and increased emotional creepiness. In turn, the opportunity to perform and emotional creepiness mediated the association of AI-support in telephone/video interviews on organizational attractiveness. However, we did not find negative affective responses to AI-support earlier stage of the selection process (i.e., during preselection). As we offer evidence for possible adverse reactions to the usage of AI in selection processes, this study provides important practical and theoretical implications.
Frontal Recess Cells in International Frontal Sinus Anatomy Classification (IFAC); Prevalence, Infection Incidence, and Relation to Frontal Sinus Infection in Chronic Sinusitis Patients
Authors: Nofal Ahmed Abdelfattah Bayomy , El-Anwar Mohammad Waheed 
Published: January 2022

AbstractFrontal recess cells have many types with different sizes, arrangement, and extend. It plays an important role in successful functional endoscopic sinus surgery (FESS) as most causes of failure are related to it. Outline the prevalence of the frontal recess cells, pathological incidence of each cell regarding to frontal sinus pathology. Prospective study on 100 consecutive patients (200 sides) complaining from nasal and sinus symptoms which did not respond to medical management and indicated for FESS. Anterior group was infected in 30.8%; agger nasi cell (ANC) present in 97% (25.8% infected, 74.2% not infected), supra agger cell (SAC) present in 48% (39.6% infected, 60.4% not infected), supra agger frontal cell (SAFC) present in 11% (36.4% infected, 63.6% not infected). Posterior group was infected in 24.8%; supra bulla cell (SBC) present in 72% (30.6% infected, 69.4% not infected), supra bulla frontal cell (SBFC) present in 23% (17.4% infected, 82.6% not infected), supra orbital ethmoid cell (SOEC) present in 42% of cases (19% infected, 81% not infected). Medial group [frontal septal cell (FSC)] was present in 21% (33.3% infected, 66.7% not infected). FSC, SAC, SAFC, and SBC showed high infection rate in association with infected frontal sinus, while, the SOEC, ANC, and SBFC did not have such high infection rate. Frontal recess cells show no difference in their prevalence either if the frontal sinus infected or not, however their infection rate show significant difference.
Multiphysics coupling study of near-wellbore and reservoir models in ultra-deep natural gas reservoirs
Authors: Cheng Pengda , Shen Weijun , Xu Qingyan , Lu Xiaobing , Qian Chao , Cui Yue 
Published: January 2022

AbstractUnderstanding the changes of the near-wellbore pore pressure associated with the reservoir depletion is greatly significant for the development of ultra-deep natural gas reservoirs. However, there is still a great challenge for the fluid flow and geomechanics in the reservoir depletion. In this study, a fully coupled model was developed to simulate the near-wellbore and reservoir physics caused by pore pressure in ultra-deep natural gas reservoirs. The stress-dependent porosity and permeability models as well as geomechanics deformation induced by pore pressure were considered in this model, and the COMSOL Multiphysics was used to implement and solve the problem. The numerical model was validated by the reservoir depletion from Dabei gas field in China, and the effects of reservoir properties and production parameters on gas production, near-wellbore pore pressure and permeability evolution were discussed. The results show that the gas production rate increases nonlinearly with the increase in porosity, permeability and Young’s modulus. The lower reservoir porosity will result in the greater near-wellbore pore pressure and the larger rock deformation. The permeability changes have little effect on geomechanics deformation while it affects greatly the gas production rate in the reservoir depletion. With the increase in the gas production rate, the near-wellbore pore pressure and permeability decrease rapidly and tend to balance with time. The reservoir rocks with higher deformation capacity will cause the greater near-wellbore pore pressure.