bluuebunny/crossref_metadata_2025_split huggingface dataset:
From White to Black, from Darkness to Light: Species Delimitation and UNITE Species Hypothesis Testing in the Russula Albonigra Species Complex.
Authors: De Lange Ruben , Adamčík Slavomír , Adamčíkova Katarína , Asselman Pieter , Borovička Jan , Delgat Lynn , Hampe Felix , Verbeken Annemieke 
Published: December 2020

Abstract
Russula albonigra is considered a well-known species, morphologically delimited by the context of the basidiomata that is blackening without intermediate reddening, and the menthol-cooling taste of the lamellae. It is supposed to have a broad ecological amplitude and a large distribution area. A thorough molecular analysis based on four nuclear markers (ITS, LSU, RPB2 and TEF1-α) shows this traditional concept of R. albonigra s.l. represents a species complex consisting of at least five European, three North-American and one Chinese species. Morphological study shows traditional characters used to delimit R. albonigra are not always reliable. Therefore, a new delimitation of the R. albonigra lineage is proposed and a key to the described European species of R. subg. Compactae is presented. A lectotype and an epitype are designated for R. albonigra and three new European species are described: R. ambusta, R. nigrifacta and R. ustulata. UNITE species hypotheses at different thresholds were tested against the taxonomic data. The species hypotheses at the similarity threshold 0.5% give a perfect match to the phylogenetically defined species within the R. albonigra lineage. Publicly available sequence data can contribute to species delimitation and expand knowledge on ecology and distribution, but the pitfalls are short and low quality sequences. The importance of updating public taxonomic data and using correct sequence similarity thresholds is emphasised.
Increasing Rainfall and Runoff in Alpine Mountainous Areas Can't Completely Eliminate Drought Driven by Temperature Rise&nbsp;
Authors: Deng Yu , Guo Zhifeng , Ni Fuquan , Xue Lianqing , Wu Yiping , Deng Ouping , Zhou Man , Hu Jian , Zhang Ying , Bu Ruihan , Ma Jie , Nie Chao , Zhang Yang 
Published: December 2020

Abstract
Drought research under climate change is of great scientific significance. For Land Use and Land Cover Change (LUCC), temperature and rainfall in climate change, which factor has a greater impact on runoff change in alpine mountainous areas? Can the increase of rainfall in the alpine mountainous area completely eliminate the drought driven by temperature rise? This study takes the upper reaches of Heihe River basin (URHRB) as an example, the URHRB's Soil and Water Assessment Tool (SWAT) model is constructed. Based on 58 scenarios and The Budyko Framework, here we show that a)climate change has a greater contribution to runoff than LUCC, effect of increased rainfall greater than temperature rising on runoff in alpine mountainous area; b)the drought of 57.14% of UHRRB’s sub-basins have eased, 42.86% of the sub-basins is more serious, the increase in rainfall can't completely eliminate the drought driven by temperature rise. This study coupling SWAT simulation with Budyko Framework and other methods solves the problem of lack of data in alpine mountainous areas, and more accurately quantifies the impact of climate change, LUCC on runoff changes, realizing theoretical and method innovation. The results of this study provide a scientific paradigm for solving scientific problems in similar regions in China and other countries, and have important promotion value.
Numerical Simulation of Spiral Flow and Heat Transfer in Hydrate Pipeline With Long Twisted Band
Authors: Rao Yongchao , Li Lijun , Wang Shuli , Zhao Shuhua , Zhou Shidong 
Published: December 2020

Abstract
The DPM model (discrete phase model) considering the motion of solid particles was used to simulate the complex spiral flow characteristics of hydrate in the pipe spinning up with long twisted band. The deposition and heat transfer characteristics of gas hydrate particles in the pipe spiral flow were studied. The velocity distribution, pressure drop distribution, heat transfer characteristics and particle settling characteristics of the flow field in the pipeline were investigated. The numerical results show that, compared with the straight flow of light pipe without twisted band, two obvious eddies are formed in the flow field under the spinning action of twisted band, and the velocities are maximum at the center of the eddies. Along the direction of the pipe, the two vortices move towards the pipe wall from near the twisted band, which can effectively carry the hydrate particles deposited on the pipe wall. With the same Reynolds number, the greater the twist ratio, the weaker the spiral strength, the smaller the tangential velocity of the spiral flow, and the smaller the pressure drop of the pipe. Therefore, the pressure loss can be reduced as much as possible while ensuring the spinning effect of the spiral flow. In a straight light pipe flow, the Nusser number is in a parabolic shape with the opening downwards. At the center of the pipe, the Nusser number gradually decreases towards the pipe wall at the maximum, and at the near wall, the attenuation gradient of Nu is large. For spiral flow, the curve presented by Nusserr number shows a trough at the center of the pipe and a peak at 1/2 of the pipe diameter. With the reduction of twist rate, the Nussel number becomes larger and larger. Therefore, the spiral flow can make the temperature distribution in the flow field in the pipeline more even, and prevent the large temperature difference resulting in the mass formation of hydrate particles in the pipeline wall. Spiral flow has a good carrying effect. Under the same working condition, the spiral flow carries hydrate particles at a distance about 3-4 times that of the straight flow.
Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry
Authors: Ito Sosuke , Ashida Keita , Aoki Kazuhiro 
Published: December 2020

Abstract
Chemical reactions are responsible for information processing in living cells, and their accuracy and speed have been discussed from a thermodynamic viewpoint. The recent development in stochastic thermodynamics enables evaluating the thermodynamic cost of information processing. However, because experimental estimation of the thermodynamic cost based on stochastic thermodynamics requires a sufficient number of samples, it is only estimated in simple living systems, such as RNA folding and F1-ATPase. Therefore, it is challenging to estimate the thermodynamic cost of information processing by chemical reactions in living cells. Here, we evaluated the thermodynamic cost and its efficiency of information processing in living systems at the single-cell level for the first time by establishing an information-geometric method to estimate them with a relatively small number of samples. We evaluated the thermodynamic cost of the extracellular signal-regulated kinase (ERK) phosphorylation from the time series of the fluorescence imaging data by calculating the intrinsic speed in information geometry. We also evaluated a thermodynamic efficiency based on the thermodynamic speed limit, and thus this paper reports the first experimental test of thermodynamic uncertainty relations in living systems. Our evaluation revealed the change of the efficiency under the conditions of different cell densities and its robustness to the upstream pathway perturbation. Because our approach is widely applicable to other signal transduction pathways, such as the G-protein coupled receptor pathways for sensation, it would clarify efficient mechanisms of information processing in such a living system.
Early life stress induces age-dependent epigenetic changes in p11 gene expression
Authors: Seo Mi Kyoung , Lee Jung Goo , Park Sung Woo 
Published: December 2020

Abstract
Early life stress (ELS) causes long-lasting changes in depression-like behaviors through epigenetic mechanisms. However, little is known about the effects of ELS in adulthood, specifically across different age groups. In this study, the epigenetic modifications of p11 expression in adult mice subjected to ELS were investigated in different stages of adulthood. Pups experienced maternal separation (MS) for 3 h daily from postnatal day 1 to 21. At young and middle adulthood, behavior phenotypes, hippocampal p11 expression levels, and levels of histone acetylation and methylation and DNA methylation at the hippocampal p11 promoter were measured. Middle-aged, but not young adult, MS mice exhibited depression-like behavior in the forced swimming test. Concurrent with reduced hippocampal p11 levels, mice in both age groups showed decreases in histone acetylation and activating histone methylation as well as increases in repressive histone methylation at the p11 promoter. The extent of the reduction in gene expression and histone acetylation was much higher in middle than in young adulthood. Moreover, DNA methylation analysis of the p11 promoter revealed increased CpG methylation in middle-aged MS mice only. The results highlight the age-dependent deleterious effects of ELS on depression-like behavior and on the epigenetic modifications of p11 transcription.
Exploring Ichnofacies Distribution in Ancient Seaways: The Late Miocene Rifian Corridor as a Natural Laboratory
Authors: de Weger Wouter , Rodríguez-Tovar Francisco , Miguez-Salas Olmo 
Published: December 2020

Abstract
Oceanic gateways have modulated ocean circulation and have influenced climatic variations throughout the Earth´s history. During the Late Miocene (7.8 - 7.35 Ma), the Atlantic Ocean and the Mediterranean Sea were connected through the Rifian Corridor (Morocco). This gateway is one of the few examples of deep ancient seaways with a semi-continuous sedimentary record. Deposits comprise turbidites intercalated between deep-sea fine grain sediments (i.e., hemipelagites and drift deposits), channelized sandstone contourite facies, and shallow marine sandstones. Herein an ichnological analysis was conducted in these upper Miocene sediments to improve characterisation of palaeoenvironmental conditions. In addition, ichnofacies were analysed to elucidate how bottom currents control ichnofacies distribution and can modified their attributes. Turbidite deposits are typified by vertical trace fossils (i.e., Ophiomorpha), conforming the Ophiomorpha rudis ichnosubfacies. Contouritic sandstones exhibit high density and low diverse trace fossil assemblage, with predominant Macaronichnus and Scolicia, resembling a proximal expression of Cruziana ichnofacies. Shallow marine environments are dominated by vertical trace fossils (e.g., Conichnus, Ophiomorpha and Skolithos), allowing an assignation to Skolithos ichnofacies. This study reveals energy to be a major controlling factor determining ichnofacies attributes and distribution in ancient deep seaways. Within these seaways, highly energetic conditions typical of shallower settings are present in deeper environments (i.e., slope), contributing to ichnodiversity impoverishment in ichnofacies.
Depth of Anaesthesia Assessment Based on Spectral Entropy
Authors: Ra Jee Sook , Li Tianning , Li Yan 
Published: December 2020

Abstract
Anaesthesia is a state of temporary controlled loss of awareness induced for medical purposes. An accurate assessment of the depth of anaesthesia (DoA) has always been required. However, the current DoA algorithms have limitations such as inaccuracy or inflexibility. In this study, for more reliable DoA assessment, pre-denoised electroencephalograph (EEG) signals are divided into ten frequency bands (α, β1, β2, β3, β4, β, βγ, γ, δ and θ), and the basic complexity measure is done by using spectral entropy (SE). SE from beta-gamma frequency band (21.5 - 38.5 Hz) and SE from beta frequency band show the highest R squared value (0.8458 and 0.7312, respectively) with currently the most popular DoA index, bispectral index (BIS). A new DoA index is developed based on these two SE values for monitoring the DoA and evaluated by comparing with the BIS index. The highest Pearson correlation coefficient is 0.918, and the average is 0.80. In addition, the proposed index shows an earlier reaction than BIS index when the patient from deep anaesthesia to moderate anaesthesia, and the consistency in the case of poor signal quality (SQ) while the BIS Index exhibits inflexibility with cases of poor SQ.
Photocurrent-driven transient symmetry breaking in the Weyl semimetal TaAs
Authors: Sirica Nicolas , Orth Peter , Scheurer Matthias , Dai Yaomin , Lee Min-Cheol , Padmanabhan Prashant , Mix LaMoyne , Teitelbaum Samuel , Trigo Mariano , Zhao Lingxiao , Chen Genfu , Xu Bing , Yang Run , Shen Bing , Hu Chaowei , Lee Chi-Cheng , Lin Hsin , Cochran Tyler , Trugman Stuart , Zhu Jian-Xin , Hasan M , Ni Ni , Qiu Xianggang , Taylor Antoinette , Yarotski Dmitry , Prasankumar Rohit 
Published: December 2020

Abstract
Symmetry plays a central role in conventional and topological phases of matter, making the ability to optically drive symmetry changes a critical step in developing future technologies that rely on such control. Topological materials, like the newly discovered topological semimetals, are particularly sensitive to a breaking or restoring of time-reversal and crystalline symmetries, which affect both bulk and surface electronic states. While previous studies have focused on controlling symmetry via coupling to the crystal lattice, we demonstrate here an all-electronic mechanism based on photocurrent generation. Using second-harmonic generation spectroscopy as a sensitive probe of symmetry changes, we observe an ultrafast breaking of time-reversal and spatial symmetries following femtosecond optical excitation in the prototypical type-I Weyl semimetal TaAs. Our results show that optically driven photocurrents can be tailored to explicitly break electronic symmetry in a generic fashion, opening up the possibility of driving phase transitions between symmetry protected states on ultrafast time scales.
Effect of Shape on the Magnitude of the Delboeuf Illusion
Authors: Li Shujie , Zhang Xiaolin , Yin Keli 
Published: December 2020

Abstract
Three experiments to discuss the applicability of the contour attraction and the parallel attraction to different shapes in the Delboeuf illusion. The contour attraction suggests that the contours of the test figure and the inducer have an effect of interattraction in the Delboeuf illusion, and the parallel attraction suggests that the attraction between non-intersecting contours was maximal when they were parallel. In Experiment 1, the shape of the test figures and the inducers changed simultaneously and formed parallel lines. In Experiment 2, the test figures remained circles while the inducers changed shape. Experiment 3 was identical to Experiment 2 except that the areas of the inducers remained equal. The results demonstrated that the illusion is influenced by shape. Importantly, the effect of shape on the magnitude of the Delboeuf illusion is based on the contour attraction and the parallel attraction. Configurations with circles or shapes more similar to a circle were related more to the contour attraction, whereas shapes that were dissimilar to a circle were related more to the parallel attraction. We suggest that the contour attraction may be a circular modality of the parallel attraction.
A Zero-field Nuclear Magnetic Resonance Spectroscopy Study on the Structure Property Relationship in Co thin Films
Authors: Fritsch Patrizia , Lucassen Juriaan , Swagten Henk , Büchner Bernd , Lavrijsen Reinoud , Wurmehl Sabine 
Published: December 2020

Abstract
The interfacial Dzyaloshinskii-Moriya interaction (iDMI) was investigated in Co thin-films with different combinations of seeding and capping layers in previous works. The variations in the local magnetic out-of-plane (oop) anisotropy K as a function of film thickness t lead to additional contributions that make the quantification of the iDMI more challenging. These additional contributions were specifically attributed to the transition of fcc Co to hcp Co at a critical thickness tcr. In this work we clarify this issue by investigating the local structure and local magnetic stiffness and their contribution to the oop anisotropy K in two Pt/Co(t)/Ir film stacks with t = 10 nm and t = 25 nm. Zero-field nuclear magnetic resonance spectroscopy (ZF NMR) is the method of choice as it is a non-destructive and sensitive probe to examine structure and magnetic properties of nano-sized samples. We describe the evolution of the Co allotropes (fcc & hcp) and stacking fault disorder with the increase of t and illustrate the structure-property relationship between the local environments of Co and their respective magnetic stiffness.
Conversion and Validation of Rectal Constraints for Prostate Carcinoma Receiving Hypofractionated Carbon-ion Radiotherapy With a Local Effect Model
Authors: Wang Weiwei , Li Ping , Sheng Yinxiangzi , Huang Zhijie , Zhao Jingfang , Hong Zhengshan , Shahnazi Kambiz , Jiang Guoliang , Zhang Qing 
Published: December 2020

Abstract
Purpose: The study objective was to convert the microdosimetric kinetic model (MKM) rectum constraints for 16-fraction carbon-ion radiotherapy (CIRT) to local effect model (LEM) constraints for 12-fraction, 8-fraction, and 4-fraction CIRT for prostate carcinoma patients (PCAs).Methods: Two strategies were employed. To understand the fractionation effects, MKM linear-quadric (LQ) strategy first converted MKM rectum constraints for 16-fraction CIRT to 12-fraction, 8-fraction, and 4-fraction CIRT. To examine the differences in the biophysical models, MKM constraints were converted to LEM constraints using an RBE-conversion model. The LEM LQ strategy first converted MKM rectum constraints for 16-fraction CIRT to LEM constraints using the RBE-conversion model. Then, the LEM constraints converted the 16-fraction constraints to the rectum constraints for 12-fraction, 8-fraction, and 4-fraction CIRT using the LQ model. The LEM rectum constraints for 16 and 12-fraction CIRTs were compared to the rectum doses and the clinical follow-ups in 40 patients.Results: The 16-fraction NIRS rectum constraint Dmax < 60.8 Gy(RBE) and CNAO rectum constraint D1cc < 66.00 Gy(RBE) were converted by MKM LQ strategy to LEM constraints 58.01 and 55.97 Gy(RBE) (12fx), 45.47 and 43.97 Gy(RBE) (8fx), and 29.64 and 28.67 Gy(RBE) (4fx) and by LEM LQ strategy to 61.73 and 59.69 Gy(RBE) (12fx), 53.03 and 51.33 Gy(RBE) (8fx), and 40.10 and 38.88 Gy(RBE) (4fx). Differences of 36.13% were found. No late rectum complications were reported.Conclusions: The LEM rectum constraints from MKM LQ strategy were more conservative and can be used as the reference constraints for starting the hypofractionated CIRT.
Foot Arch Posture Development in Children and Adolescents aged 6 to 19 Years: A Cross-sectional Descriptive Study
Authors: Mahmoudzadeh Yousef , Alipour Roghayyeh 
Published: December 2020

Abstract
Background: The arch height index (AHI) is a commonly used method for measuring foot arch posture. However, there are little studies have investigated the natural growth and normative values of the foot arch using the AHI. The objective of this study was to establish normative and cut-off values for foot arch posture and to identify factors influencing foot arch posture across childhood and adolescence. Methods: In this cross-sectional study, a sample of 3532 healthy children and adolescents (1804 boys, 1728 girls; aged 6 to 19 years) was recruited for the navicular height (NH) and AHI measurements and anthropometry assessment (weight, height, BMI and foot length). Data were explored descriptively and graphically, comparisons between groups used t-tests or ANOVA model as appropriate and a multiple regressions was conducted. The 95% and 68% prediction intervals were used as cut-off values. Results : approximately 69% had a normal AHI range, 12% low arched foot, 3% severely low arched, 14% high arched and 1.8% severely high arched foot. The mean (SD) AHI was 15.16 (2.61). Very little gender bias was found for AHI values, being higher in males 15.32 (2.54) than in females 15.0 (2.68) ( p = .019). Regression showed approximately 3%, 0.3% and 2% of the AHI change was explained by age, BMI and foot length, respectively. The mean NH significantly increased from the age of 6 (2.62 cm) to 19 (4.20 cm). Conclusions: This study confirms that the ‘flexible flatfoot’ or low arched foot decreases with age. Simultaneously, increase of high arched foot type and shift in foot posture towards more normal foot type are also confirmed. BMI does not seem to be an important determinant of children foot arch posture. Keywords: Foot posture, Navicular height, Arch height index, Normative values, Medial longitudinal arch, Foot arch development, Children, Adolescents
Systematic Identification and Characterization of Five Transcription Factors Mediating the Oxidative Stress Response in Candida Albicans
Authors: Cui YingChao , Wang DaoSheng , Nobile Clarissa J. , Dong Danfeng , Ni Qi , Su Tongxuan , Jiang Cen , Peng Yibing 
Published: December 2020

Abstract
BackgroundCandida albicans is an opportunistic human fungal pathogen that can cause both superficial and systemic infections, especially in immunocompromised individuals. In response to C. albicans infections, innate immune cells of the host produce and accumulate reactive oxygen species (ROS) that can lead to irreversible damage and apoptosis of fungal cells. Prior studies have identified several transcription factors involved in the oxidative stress response of C. albicans. However, a systematic study to identify transcription factors mediating the oxidative response had not been previously conducted. ResultsIn this study, we screened a comprehensive transcription factor mutant library consisting of 211 transcription factor deletion mutant strains in the presence and absence of H2O2, a potent inducer of ROS, and identified five transcription factors (Skn7, Dpb4, Cap1, Dal81 and Stp2) involved in the response to H2O2. Genome-wide transcriptional profiling revealed that H2O2 induced a discreet set of genes differentially regulated in common among the five transcription factor mutant strains identified. Functional enrichment analysis identified KEGG pathways pertaining to glycolysis/gluconeogenesis, amino sugar and nucleotide sugar metabolism, and ribosome synthesis as the most enriched pathways. Furthermore, among the most common differentially expressed genes, hexose catabolism and iron transport were the most enriched GO terms.ConclusionsOur study is the first to systematically identify and characterize transcription factors involved in the response to H2O2. Based on the transcription factors identified, we found that exposure to H2O2 modulates several downstream gene classes involved in fungal virulence. Overall, this study sheds new light on the metabolism, physiological functions and cellular processes involved in the H2O2-induced oxidative stress response in C. albicans.