bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fireshape: a shape optimization toolbox for Firedrake
Authors: Paganini Alberto , Wechsung Florian 
Published: February 2021

AbstractWe introduce Fireshape, an open-source and automated shape optimization toolbox for the finite element software Firedrake. Fireshape is based on the moving mesh method and allows users with minimal shape optimization knowledge to tackle with ease challenging shape optimization problems constrained to partial differential equations (PDEs).
Deep learning–based metal artefact reduction in PET/CT imaging
Authors: Arabi Hossein , Zaidi Habib 
Published: February 2021

Abstract
Objectives
The susceptibility of CT imaging to metallic objects gives rise to strong streak artefacts and skewed information about the attenuation medium around the metallic implants. This metal-induced artefact in CT images leads to inaccurate attenuation correction in PET/CT imaging. This study investigates the potential of deep learning–based metal artefact reduction (MAR) in quantitative PET/CT imaging.

Methods
Deep learning–based metal artefact reduction approaches were implemented in the image (DLI-MAR) and projection (DLP-MAR) domains. The proposed algorithms were quantitatively compared to the normalized MAR (NMAR) method using simulated and clinical studies. Eighty metal-free CT images were employed for simulation of metal artefact as well as training and evaluation of the aforementioned MAR approaches. Thirty 18F-FDG PET/CT images affected by the presence of metallic implants were retrospectively employed for clinical assessment of the MAR techniques.

Results
The evaluation of MAR techniques on the simulation dataset demonstrated the superior performance of the DLI-MAR approach (structural similarity (SSIM) = 0.95 ± 0.2 compared to 0.94 ± 0.2 and 0.93 ± 0.3 obtained using DLP-MAR and NMAR, respectively) in minimizing metal artefacts in CT images. The presence of metallic artefacts in CT images or PET attenuation correction maps led to quantitative bias, image artefacts and under- and overestimation of scatter correction of PET images. The DLI-MAR technique led to a quantitative PET bias of 1.3 ± 3% compared to 10.5 ± 6% without MAR and 3.2 ± 0.5% achieved by NMAR.

Conclusion
The DLI-MAR technique was able to reduce the adverse effects of metal artefacts on PET images through the generation of accurate attenuation maps from corrupted CT images.

Key Points
• The presence of metallic objects, such as dental implants, gives rise to severe photon starvation, beam hardening and scattering, thus leading to adverse artefacts in reconstructed CT images.
• The aim of this work is to develop and evaluate a deep learning–based MAR to improve CT-based attenuation and scatter correction in PET/CT imaging.
• Deep learning–based MAR in the image (DLI-MAR) domain outperformed its counterpart implemented in the projection (DLP-MAR) domain. The DLI-MAR approach minimized the adverse impact of metal artefacts on whole-body PET images through generating accurate attenuation maps from corrupted CT images.
Mind wandering increases linearly with text difficulty
Authors: Kahmann Rebecca , Ozuer Yesim , Zedelius Claire M. , Bijleveld Erik 
Published: February 2021

AbstractAlthough mind wandering during reading is known to be affected by text difficulty, the nature of this relationship is not yet fully understood. To examine this issue, we conducted an experiment in which participants read non-fiction texts that varied along five levels of difficulty under naturalistic conditions. Difficulty levels were determined based on Flesch–Kincaid Grade Levels and verified with Coh–Metrix indices. Mind wandering was measured with thought probes. We predicted that text difficulty and mind wandering have a U-shaped (i.e., quadratic) relationship. Contrary to our expectations, but in line with some prior studies, mind wandering linearly increased with text difficulty. Additionally, text interest moderated the effect of text difficulty on mind wandering. Finally, mind wandering was associated with worse performance on a comprehension test. Together, our findings extend previous work by showing that (a) a linear relationship between difficulty and mind wandering exists during common page-by-page reading of pre-existing texts and that (b) this relationship holds across a broad range of difficulty levels.
Long-term live cell cycle imaging of single Cyanidioschyzon merolae cells
Authors: Ichinose Takako M. , Iwane Atsuko H. 
Published: February 2021

AbstractLive cell imaging by fluorescence microscopy is a useful tool for elucidating the localization and function of proteins and organelles in single cells. Especially, time-lapse analysis observing the same field sequentially can be used to observe cells of many organisms and analyze the dynamics of intracellular molecules. By single-cell analysis, it is possible to elucidate the characteristics and fluctuations of individual cells, which cannot be elucidated from the data obtained by averaging the characteristics of an ensemble of cells. The primitive red alga Cyanidioschyzon merolae has a very simple structure and is considered a useful model organism for studying the mechanism of organelle division, since the division is performed synchronously with the cell cycle. However, C. merolae does not have a rigid cell wall, and environmental changes such as low temperature or high pH cause morphological change and disruption easily. Therefore, morphological studies of C. merolae typically use fixed cells. In this study, we constructed a long-term time-lapse observation system to analyze the dynamics of proteins in living C. merolae cells. From the results, we elucidate the cell division process of single living cells, including the function of intracellular components.
High-resolution anoscopy, is there a benefit in proceeding directly to the operating room?
Authors: Moeckli B. , Canner J. , Najafian A. , Carbunaru S. , Cowell N. , Atallah C. , Paredes E. , Chudnovets A. , Fang S. H. 
Published: February 2021

Abstract
Background
The development of high-resolution anoscopy (HRA) has advanced our ability to detect anal dysplasia. Historically, HRA is performed in a clinical setting and subsequent ablation is performed in the clinical setting or operating room. The aim of this study was to determine the most effective venue for the performance of HRA.

Methods
Following institutional review board (IRB) approval, the correlation between anal cytology and HRA performed in the clinic versus in the operating room was evaluated. Data were extracted from our IRB-approved prospective HRA database over the time period of 2013–2017.

Results
One hundred twenty-eight HRAs were compared (101 in the clinical setting, 27 in the operating room). There was a statistically significant difference in the correlation between anal cytology and HRA pathology for procedures performed in the clinical setting (55% [56/101]) versus those performed in the operating room (82% [22/27]) (p = 0.014). More biopsies were obtained in the operating room than in the clinic setting (3 vs. 1, p < 0.0001). The majority of patients who had HRA in a clinical setting with subsequent HRA in the operating room stated that they preferred to have their HRAs performed in the operating room due to discomfort from the HRA procedure.

Conclusions
Detection rates for anal dysplasia on HRA, are significantly higher when performed in the operating room. To prevent discomfort in the clinical setting, patients with high-grade dysplasia on anal pap testing may benefit from proceeding directly to the operating room for concurrent HRA and ablation.
The social drift of trees. Consequence for growth trend detection, stand dynamics, and silviculture
Authors: Pretzsch Hans 
Published: February 2021

AbstractRecently, many studies worldwide tapped tree ring pattern for detection of growth events and trends caused by weather extremes and climate change. As long-term experiments with permanent survey of all trees are rare, growth trend analyses are mostly based on retrospective measurements of growth via increment coring or stem analyses of the remaining individual trees in older forest stands. However, the growth of the survivor trees in older stands may only unsufficiently represent the course of growth of the dominant trees throughout the stand development. Here, the more than 100 years survey data of the European beech (Fagus sylvaticaL.) thinning experiment Fabrikschleichach in South Germany are used to show the long-term changes in social ranking of trees and their consequences for growth trend detection by retrospective tree ring analyses, for stand dynamics and silvicultural management. Firstly, a significant social upwards drift of initially medium-sized trees till 2010 is shown based on the trees' percentiles in the stem diameter distribution in 1904 versus 2010. The social climbing is stronger on the thinned compared to the unthinned plots. Secondly, we show that 40–60% of the 100 tallest trees in 1904 were replaced by social climbers and down-ranked below the 100 tallest trees till 2010. Linear mixed model analyses reveal that the long-term trend of the diameter growth of the 100 dominant survivors in 2010 was on average by 23% steeper than the trend of the 100 tallest starters in 1904. This indicates that the survivors had a steeper and longer lasting growth than the originally dominant trees. Thirdly, the diameter growth trend in the last 20 years, from 1990 to 2010, is analyzed in dependency on the current and past social position. A linear model shows that early subdominance or suppression can significantly steepen the growth trend a century later and vice versa.Finally, we discuss the implications of the social drift for the survivor-based growth trend analyses, for the stand dynamics, and silvicultural management.
Imaging of pediatric bone and growth disorders: Of diagnostic workhorses and new horizons
Authors: Mehany Sarah N. , Patsch Janina M. 
Published: February 2021

SummaryChildren and adolescents with bone and growth disorders require interdisciplinary care from various specialists including pediatric radiologists with a focus on musculoskeletal disorders. This article covers routine topics, differential diagnoses, and selected research imaging in children with osteogenesis imperfecta (OI), X‑linked hypophosphatemic rickets (XLH), achondroplasia, and other bone and growth disorders from the standpoint of a tertiary referral center.
Landrace added value and accessibility in Europe: what a collection of case studies tells us
Authors: Raggi L. , Caproni L. , Negri V. 
Published: February 2021

AbstractIn the actual climate change scenario, in situ conservation of plant genetic resources for food and agriculture can significantly contribute broadening the diversity of our food system as well as increasing its resilience; nevertheless, landrace cultivation has been dramatically reduced in the last decades all over Europe. One of the most effective approaches to counteract the loss of landrace diversity in situ is facilitating its use. Aims of this study were to (i) describe how in situ maintenance of landraces occurs in different agro-environmental conditions in Europe and (ii) identify the main factors influencing landrace added values and accessibility as means to increase their adoption by new farmers. To the purpose, a collection of 95 case studies of both garden and open field landraces maintained in situ was analysed. A first description was obtained by classifying the information into 18 purposely defined categories. Data on landraces added values and accessibility were further transformed into weighted variables; the derived quantitative scores were then used as dependent variables in univariate and multivariate analyses. Results showed that farmers alone are still the main actors maintaining landraces in situ across different European biogeographical regions, mainly carrying out their activity under organic or low-input conditions, often in marginal areas. Results of the multivariate analysis showed that (i) type of actor involved in the multiplication, (ii) the main use of the product and (iii) presence of promotion actions significantly affect garden landraces added value and accessibility; presence of promotion actions was the only factor affecting added value of open field entries. Evidence arising from this work can contribute to the establishment of a fruitful ground of discussion for future European policies and strategies to protect and increase landrace use.
Disentangling Turbulent Gas Diffusion from Non-diffusive Transport in the Boundary Layer
Authors: Kowalski Andrew S. , Serrano-Ortiz Penélope , Miranda-García Gabriela , Fratini Gerardo 
Published: February 2021

AbstractAn analysis based on the law of linear momentum conservation demonstrates unequivocally that the mass fraction is the scalar whose gradient determines gas diffusion, both molecular and turbulent. It illustrates sizeable errors in previous micrometeorological definitions of the turbulent gas flux based on fluctuations in other scalars such as the mixing ratio or density. In deference to conservation law, we put forth a new definition for the turbulent gas flux. Net gas transport is then defined as the sum of this turbulent flux with systematic transport by the mean flow. This latter, non-diffusive flux is due to the net upward boundary-layer momentum, a Stefan flow forced by evaporation, which is the dominant surface gas exchange. A comparison with the traditional methodology shows exact agreement between the two methods regarding the net flux, but with the novelty of partitioning gas transport according to distinct physical mechanisms. The non-diffusive flux is seen to be non-negligible in general, and to dominate turbulent transport under certain conditions, with broad implications for boundary-layer meteorology.
Development of antibacterial and UV protective cotton fabrics using plant food waste and alien invasive plant extracts as reducing agents for the in-situ synthesis of silver nanoparticles
Authors: Čuk Nina , Šala Martin , Gorjanc Marija 
Published: February 2021

AbstractThe development of cellulose-based textiles that are functionalised with silver nanoparticles (AgNP), synthesised according to a green approach, and offer protection against ultraviolet (UV) radiation and pathogenic bacteria is very important today. In the present work we demonstrate the environmentally friendly approach to obtain such textile material by AgNP synthesis directly (in-situ) on cotton fabrics, using water extracts of plant food waste (green tea leaves, avocado seed and pomegranate peel) and alien invasive plants (Japanese knotweed rhizome, goldenrod flowers and staghorn sumac fruit) as reducing agents. The extracts were analysed for their total content of phenols and flavonoids and their antioxidant activity. The synthesised AgNP on cotton were round, of different size and amount depending on the reducing agent used. The highest amount of AgNP was found for samples where Japanese knotweed rhizome extract was used as reducing agent and the lowest where extracts of goldenrod flowers and green tea leaves were used. Regardless of the reducing agent used to form AgNP, all cotton samples showed excellent protection againstE. coliandS. aureusbacteria and against UV radiation with UV protection factor values above 50. The best results for UV protection even after the twelve repetitive washing cycles were found for the sample functionalized with AgNP synthesised with an extract of the Japanese knotweed rhizome. Due to the presence of AgNP on cotton, the air permeability and thermal conductivity decreased. AgNP had no effect on the change in breaking strength or elongation of fabrics.Graphic abstract
Internalizing Symptoms Among Youth in Foster Care: Prevalence and Associations with Exposure to Maltreatment
Authors: Moussavi Yasmin , Wergeland Gro Janne , Bøe Tormod , Haugland Bente Storm Mowatt , Larsen Marit , Lehmann Stine 
Published: February 2021

AbstractAmong youth in foster care (N = 303, aged 11–17 years), we investigated prevalence of internalizing symptoms; associations between symptom level and maltreatment types and numbers; and the interaction between gender and maltreatment, on internalizing symptoms. Youth completed Spence Children Anxiety Scale, Short Mood Feelings Questionnaire, and Child and Adolescent Trauma Screen. Compared to community samples, symptom levels above clinical cut-off was more frequent, with social- and generalized anxiety (ES = 0.78–0.88) being most prevalent among youth in foster care. Girls reported more internalizing symptoms (ES = 0.59–0.93). Sexual abuse and neglect were associated with a broader range of internalizing symptoms (ES = 0.35–0.64). Increased incidence of maltreatment was associated with increased levels of symptoms (ES = 0.21–0.22). Associations between maltreatment and symptom level were stronger for girls. This study stresses the importance of broad screening of maltreatment and internalizing symptoms to meet the needs of youth in foster care.
On the Kirchhoff-Love Hypothesis (Revised and Vindicated)
Authors: Ozenda Olivier , Virga Epifanio G. 
Published: February 2021

AbstractThe Kirchhoff-Love hypothesis expresses a kinematic constraint that is assumed to be valid for the deformations of a three-dimensional body when one of its dimensions is much smaller than the other two, as is the case for plates. This hypothesis has a long history checkered with the vicissitudes of life: even its paternity has been questioned, and recent rigorous dimension-reduction tools (based on standard$\varGamma $Γ-convergence) have proven to be incompatible with it. We find that an appropriately revised version of the Kirchhoff-Love hypothesis is a valuable means to derive a two-dimensional variational model for elastic plates from a three-dimensional nonlinear free-energy functional. The bending energies thus obtained for a number of materials also show to contain measures of stretching of the plate’s mid surface (alongside the expected measures of bending). The incompatibility with standard$\varGamma $Γ-convergence also appears to be removed in the cases where contact with that method and ours can be made.
Eye‐body allometry across biphasic ontogeny in anuran amphibians
Authors: Shrimpton Samuel J. , Streicher Jeffrey W. , Gower David J. , Bell Rayna C. , Fujita Matthew K. , Schott Ryan K. , Thomas Kate N. 
Published: February 2021

AbstractAnimals with biphasic lifecycles often inhabit different visual environments across ontogeny. Many frogs and toads (Amphibia: Anura) have free-living aquatic larvae (tadpoles) that metamorphose into adults that inhabit a range of aquatic and terrestrial environments. Ecological differences influence eye size across species, but these relationships have not yet been explored across life stages in an ontogenetic allometric context. We examined eye-body size scaling in a species with aquatic larvae and terrestrial adults, the common frog Rana temporaria, using a well-sampled developmental series. We found a shift in ontogenetic allometric trajectory near metamorphosis indicating prioritized growth in tadpole eyes. To explore the effects of different tadpole and adult ecologies on eye-body scaling, we expanded our taxonomic sampling to include developmental series of eleven additional anuran species. Intraspecific eye-body scaling was variable among species, with 8/12 species exhibiting a significant change in allometric slope between tadpoles and adults. Traits categorizing both tadpole ecology (microhabitat, eye position, mouth position) and adult ecology (habitat, activity pattern) across species had significant effects on allometric slopes among tadpoles, but only tadpole eye position had a significant effect among adults. Our study suggests that relative eye growth in the preliminary stages of biphasic anuran ontogenies is somewhat decoupled and may be shaped by both immediate ecological need (i.e. tadpole visual requirements) and what will be advantageous during later adult stages.
Green synthesis of silver, iron and gold nanoparticles of lycopene extracted from tomato: their characterization and cytotoxicity against COLO320DM, HT29 and Hella cell
Authors: Shejawal Kiran P. , Randive Dheeraj S. , Bhinge Somnath D. , Bhutkar Mangesh A. , Todkar Sachin S. , Mulla Anjum S. , Jadhav Namdeo R. 
Published: February 2021

AbstractOur study aimed at development of Silver, Iron and Gold nanoparticles of Lycopene isolated from tomato by using green synthesis technique and to evaluate its anticancer potential against colorectal and cervical cancer. Lycopene was extracted by benzene extraction method and the silver, iron and gold nanoparticles were developed by green synthesis method. 1% aqueous extract of isolated Lycopene was mixed with 1% solutions of AgNO3, FeCl3and HAuCl4solutions and incubated at ambient temperature for 3–4 h separately and observed for the color change which is an indicative of formation of the nanoparticles. The prepared nanoparticles were characterized by FTIR, SEM, XRD analysis and evaluated for their antimicrobial potential. The cytotoxicity studies were carried out by in vitro assay like MTT, SRB and Tryphan blue method against Colo 320 DM, HT 29, and Hella. SEM showed nanosized particles of 50–100 nm range, whereas no antimicrobial activity was exhibited by the prepared nanoparticles. In MTT assay the LyAgNP showed maximum 41.41 ± 0.4124% inhibition against COLO320DM, whereas LyGNP exhibited 41.47 ± 0.4469% inhibition against HT 29 and LyAgNP showed 40.9 ± 0.6908% inhibition against Hella cells. In SRB assay LyAgNP showed maximum 82.68 ± 1.1798% inhibition against COLO320DM, whereas LyGNP exhibited maximum 91.21 ± 0.2372% inhibition against HT29 and 87.98 ± 0.5878% inhibition against Hella cells. In tryphan blue assay against COLO320DM, HT29 and Hella cells, the maximum inhibition exhibited by the prepared nanoparticles were observed as LyGNP 83.45 ± 0.4694%, LyAgNP 88.05 ± 0.1870% and LyAgNP65.47 ± 0.4766%. We conclude that the developed nanoparticles of Lycopene exhibited potential anticancer activity against Colorectal and cervical cancer cell as compared with pure Lycopene.
Persistence of the spectral gap for the Landau–Pekar equations
Authors: Feliciangeli Dario , Rademacher Simone , Seiringer Robert 
Published: February 2021

AbstractThe Landau–Pekar equations describe the dynamics of a strongly coupled polaron. Here, we provide a class of initial data for which the associated effective Hamiltonian has a uniform spectral gap for all times. For such initial data, this allows us to extend the results on the adiabatic theorem for the Landau–Pekar equations and their derivation from the Fröhlich model obtained in previous works to larger times.
Choosing the Narrative: the Shadow Banking Crisis in Light of Covid
Authors: Miller Marcus 
Published: February 2021

AbstractCould experiencing a health pandemic aid in understanding the nature of financial crisis? It might, for example, help to discriminate between different narratives that claim to do so. In this spirit, two influential accounts of the near-collapse of shadow banking in the US financial crisis of 2008 are analysed: one developed by Mark Gertler and Nobuhiro Kiyotaki and the other presented by the Financial Crisis Inquiry Commission of the US Congress. Using a common two-sector framework, key features of these contrasting accounts of the market for banking services are presented, along with their corresponding diagnoses of what precipitated financial crisis. To see what the experience of Covid might imply about their relative credibility, four aspects of the current pandemic are considered: how it began from a small biological shock; how it gets spread by contagion; the significance of externalities; and how it may end with a vaccine. But the reader is left to form his or her own judgement.