Miracle-dz/UniFAR-FTUs huggingface dataset:
De novo assembly of Amorpha fruticosa L. transcriptome in response to drought stress provides insight into the tolerance mechanisms

Background Amorpha fruticosa L. is a deciduous shrub that is native to North America and has been introduced to China as an ornamental plant. In order to clarify the drought resistance characteristics of Amorpha fruticosa L. and excavate the related genes involved in drought resistance regulation pathway, the mechanism of drought resistance stress of Amorpha fruticosa L. was revealed by the changes of transcriptome of Amorpha fruticosa L. under drought stress.Through the changes of the transcriptome of Amorpha fruticosa L. under drought stress, the mechanism of anti-stress of Amorpha fruticosa L. could be revealed. Methods Different concentrations of polyethylene glycol-6000 (PEG-6000) was used to simulate drought stress, and transcriptomic analysis was used to reveal the changes of gene expression patterns in Amorpha fruticosa L. seedlings. Results Results showed that Amorpha fruticosa L. seedlings were seriously affected by PEG-6000. As for the differently expressed genes (DEGs), most of them were up-regulated. The additional Go and KEGG analysis results showed that DEGs were functionally enriched in cell wall, signal transduction and hormonal regulation related pathways. DEGs like AfSOD, AfHSP, AfTGA, AfbZIP and AfGRX play roles in response to drought stress. Conclusion In conclusion, Amorpha fruticosa L. seedlings were sensitive to drought, which was different from Amorpha fruticosa L. tree, and the genes functions in drought stress responses via ABA-independent pathways. The up-regulation of Salicylic acid signal related DEGs (AfTGA and AfPR-1) indicated that Salicylic acid play a key role in response to drought stress in Amorpha fruticosa L.
Spatiotemporal dynamics of habitat suitability for the Ethiopian staple crop, Eragrostis tef (teff), under changing climate

Teff (Eragrostis tef (Zucc.) Trotter) is a staple, ancient food crop in Ethiopia. Its growth is affected by climate change, so it is essential to understand climatic effects on its habitat suitability in order to design countermeasures to ensure food security. Based on the four Representative Concentration Pathway emission scenarios (i.e., RCP2.6, RCP4.5, RCP6.0 and RCP8.5) set by the Intergovernmental Panel on Climate Change (IPCC), we predicted the potential distribution of teff under current and future scenarios using a maximum entropy model (Maxent). Eleven variables were selected out of 19, according to correlation analysis combined with their contribution rates to the distribution. Simulated accuracy results validated by the area under the curve (AUC) had strong predictability with values of 0.83–0.85 for current and RCP scenarios. Our results demonstrated that mean temperature in the coldest season, precipitation seasonality, precipitation in the cold season and slope are the dominant factors driving potential teff distribution. Proportions of suitable teff area, relative to the total study area were 58% in current climate condition, 58.8% in RCP2.6, 57.6% in RCP4.5, 59.2% in RCP6.0, and 57.4% in RCP8.5, respectively. We found that warmer conditions are correlated with decreased land suitability. As expected, bioclimatic variables related to temperature and precipitation were the best predictors for teff suitability. Additionally, there were geographic shifts in land suitability, which need to be accounted for when assessing overall susceptibility to climate change. The ability to adapt to climate change will be critical for Ethiopia’s agricultural strategy and food security. A robust climate model is necessary for developing primary adaptive strategies and policy to minimize the harmful impact of climate change on teff.
Two hours in Hollywood: A manually annotated ground truth data set of eye movements during movie clip watching

In this short article we present our manual annotation of the eye movement events in a subset of the large-scale eye tracking data set Hollywood2. Our labels include fixations, saccades, and smooth pursuits, as well as a noise event type (the latter representing either blinks, loss of tracking, or physically implausible signals). In order to achieve more consistent annotations, the gaze samples were labelled by a novice rater based on rudimentary algorithmic suggestions, and subsequently corrected by an expert rater. Overall, we annotated eye movement events in the recordings corresponding to 50 randomly selected test set clips and 6 training set clips from Hollywood2, which were viewed by 16 observers and amount to a total of approximately 130 minutes of gaze data. In these labels, 62.4% of the samples were attributed to fixations, 9.1% – to saccades, and, notably, 24.2% – to pursuit (the remainder marked as noise). After evaluation of 15 published eye movement classification algorithms on our newly collected annotated data set, we found that the most recent algorithms perform very well on average, and even reach human-level labelling quality for fixations and saccades, but all have a much larger room for improvement when it comes to smooth pursuit classification. The data set is made available at https://gin.g-node.org/ioannis.agtzidis/hollywood2_em.
Interaction between image and text during the process of biblical art reception

In our exploratory study, we ask how naive observers, without a distinct religious background, approach biblical art that combines image and text. For this purpose, we choose the book ‘New biblical figures of the Old and New Testament’ published in 1569 as source of the stimuli. This book belongs to the genre of illustrated Bibles, which were very popular during the Reformation. Since there is no empirical knowledge regarding the interaction between image and text during the process of such biblical art reception, we selected four relevant images from the book and measured the eye movements of participants in order to characterize and quantify their scanning behavior related to such stimuli in terms of i) looking at text (text usage), ii) text vs. image interaction measures (semantic or contextual relevance of text), and iii) narration. We show that texts capture attention early in the process of inspection and that text and image interact. Moreover, semantics of texts are used to guide eye movements later through the image, supporting the formation of the narrative.
Evaluating Age-Related Variations of Gaze Behavior for a Novel Digitized-Digit Symbol Substitution Test

Analysis of cognitive functioning from gaze behavior might serve as an early indicator of age related decline of cognitive functions. Standard psychological tests like the digit-symbol substitution test or the symbol-digit modalities test is used exclusively in this regard. In this paper, we have designed and developed a digitized version of the digit symbol substitution test. Three different versions have been designed in order to derive deeper insights of the user behavior. The test-retest validation of the versions reveals good correlation across sessions. Further, the difference in gaze behavior which might be used as an indicator of cognitive functions is tested for two different age groups (13 participants <30 years and 11 participants >40 years). It is seen that the designed digitized version along with the usage of physiological markers like eye tracking bestows additional information and is sensitive to age related factors which might be used for the assessment as well as for the training purpose in rehabilitation systems. Results show that the performance can be analyzed using gaze and pupillometric features in addition to the conventional test performance metrics. We derived an index to measure the performance related to visuo-spatial functioning on one of the designed versions of the test. Results of this index on the number of fixations for two age groups are found to be separated in a statistically significant (p<0.05) manner. The age related difference (p<0.05) is also evident in the pupillometric responses obtained.
Improving Eye–Computer Interaction Interface Design: Ergonomic Investigations of the Optimum Target Size and Gaze-triggering Dwell Time

Interactive feedback of interface elements and low level of spatial accuracy are two main key points for the interaction research in the Eye-computer interaction system. This study tried to solve these two problems from the perspective of human–computer interactions and ergonomics. Two experiments were conducted to explore the optimum target size and gaze-triggering dwell time of the eye–computer interaction (ECI) system. Experimental Series 1 was used as the pre-experiment to identify the size that has a greater task completion rate. Experimental Series 2 was used as the main experiment to investigate the optimum gaze-triggering dwell time by using a comprehensive evaluation of the task completion rate, reaction time, and NASA-TLX (Task Load Index). In Experimental Series 1, the optimal element size was determined to be 256 × 256p x 2. The conclusion of Experimental Series 2 was that when the dwell time is set to 600 ms, the efficiency of the interface is the highest, and the task load of subjects is minimal as well. Finally, the results of Experiment Series 1 and 2 have positive effects on improving the usability of the interface. The optimal control size and the optimal dwell time obtained from the experiments have certain reference and application value for interface design and software development of the ECI system.
Task-Dependent Eye-Movement Patterns in Viewing Art

In art schools and classes for art history students are trained to pay attention to different aspects of an artwork, such as art movement characteristics and painting techniques. Experts are better at processing style and visual features of an artwork than nonprofessionals. Here we tested the hypothesis that experts in art use different, task-dependent viewing strategies than nonprofessionals when analyzing a piece of art. We compared a group of art history students with a group of students with no art education background, while viewing 36 paintings under three discrimination tasks. Participants were asked to determine the art movement, the date and the medium of the paintings. We analyzed behavioral and eye-movement data of 27 participants. Our observers adjusted their viewing strategies according to the task, resulting in longer fixation durations and shorter saccade amplitudes for the medium detection task. We found higher task accuracy and subjective confidence, less congruence and higher dispersion in fixation locations in experts. Expertise also influenced saccade metrics, biasing it towards larger saccade amplitudes, advocating a more holistic scanning strategy of experts in all three tasks.
The complete mitochondrial genome of a cave-dwelling loach Triplophysa baotianensis (Teleostei: Nemacheilidae)

Abstract Triplophysa baotianensis belong to the genus Triplophysa (Teleostei, Nemacheilidae), endemic to Guizhou Province, Southwestern China. In this study, the complete mitochondrial genome of T. baotianensis was sequenced and reported for the first time. The circular mitogenome was 16,576 bp in length and consisted of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding control region. The overall base composition was 30.79% A, 27.62% T, 25.46% C, and 16.13% G with 41.59% GC content. Phylogenetic analysis using mitochondrial genomes of 40 species showed that all Triplophysa species clustered as one monophyletic clade, and T. baotianensis was the closest to (T. nasobarbatula + (T. rosa + T. xiangxiensis)).
Radiological differences in computed tomography findings and texture analysis between cystic lymph node metastases of human papillomavirus-positive oropharyngeal cancer and second branchial cysts

Purpose The study aimed to analyse radiological differences in computed tomography (CT) findings and texture analysis between cystic lymph node metastases (CNM) in human papillomavirus (HPV)-positive oropharyngeal cancer (OPC) and second branchial cleft cysts (2nd BC). Material and methods Patients with pathological evidence of CNM-HPV-OPC and 2nd BC, who underwent contrast-enhanced CT, were retrospectively evaluated. The evaluated characteristics include age, sex, and CT findings. CT findings included the maximum and minimum transverse diameters, maximum caudal diameter, thickness of the peripheral wall, presence of internal septation, presence of surrounding fat stranding, location, and 40 texture parameters. Results A total of 13 patients had CNM-HPV-OPC (19 lesions), while 20 patients had 2nd BC (20 lesions). Patients with 2nd BC were significantly younger than those with CNM-HPV-OPC (p < 0.001). In terms of diameter, 2nd BC lesions were significantly larger than the CNM-HPV-OPC lesions (p < 0.001). CNM-HPV OPC lesions had significantly thicker walls than 2nd BC lesions (p < 0.001). CNM-HPV-OPC lesions had significantly higher association with internal septations than 2nd BC lesions (p < 0.001). Second BC lesions were significantly less common at level III than CNM-HPV-OPC lesions (p = 0.047). Among the 40 texture parameters measured, 8 had significant differences (p ≤ 0.001). Conclusions There were significant differences in CT findings and textural parameters between CNM-HPV-OPC and 2nd BC lesions. These results may help in differentiating one from the other.
A taxonomically detailed and large-scale view of the factors affecting the distribution and abundance of tree species planted in private gardens of Christchurch city, New Zealand

A city’s planted trees, the great majority of which are in private gardens, play a fundamental role in shaping a city’s wild ecology, ecosystem functioning, and ecosystem services. However, studying tree diversity across a city’s many thousands of separate private gardens is logistically challenging. After the disastrous 2010–2011 earthquakes in Christchurch, New Zealand, over 7,000 homes were abandoned and a botanical survey of these gardens was contracted by the Government’s Canterbury Earthquake Recovery Authority (CERA) prior to buildings being demolished. This unprecedented access to private gardens across the 443.9 hectares ‘Residential Red Zone’ area of eastern Christchurch is a unique opportunity to explore the composition of trees in private gardens across a large area of a New Zealand city. We analysed these survey data to describe the effects of housing age, socio-economics, human population density, and general soil quality, on tree abundance, species richness, and the proportion of indigenous and exotic species. We found that while most of the tree species were exotic, about half of the individual trees were local native species. There is an increasing realisation of the native tree species values among Christchurch citizens and gardens in more recent areas of housing had a higher proportion of smaller/younger native trees. However, the same sites had proportionately more exotic trees, by species and individuals, amongst their larger planted trees than older areas of housing. The majority of the species, and individuals, of the larger (≥10 cm DBH) trees planted in gardens still tend to be exotic species. In newer suburbs, gardens in wealthy areas had more native trees than gardens from poorer areas, while in older suburbs, poorer areas had more native big trees than wealthy areas. In combination, these describe, in detail unparalleled for at least in New Zealand, how the tree infrastructure of the city varies in space and time. This lays the groundwork for better understanding of how wildlife distribution and abundance, wild plant regeneration, and ecosystem services, are affected by the city’s trees.
The role that composition plays in determining how a viewer looks at landscape art

Viewing artworks may be subject to the same processes as everyday scene selection in respect of gaze behaviour. However, artists may employ carefully constructed composition in their paintings to lead the eyes of viewers along a predetermined path. This paper investigates whether composition is successful through comparison of expected scanpaths (constructed using the known intention of the artist) and actual scanpaths (as captured using an eye-tracker) based on a loci and sequence similarity index. The findings suggest that composition is successful in leading the eye, although the order of fixations can vary. It could thus be concluded that composition is largely successful in terms of salient elements, but less so for guiding elements. Furthermore, using Cognitive Linguistics theories and applying it to the paintings with reference to the statistical results, the Art Creation Continuum that captures the role of composition on a spectrum is proposed.
An electrochemical sensor for p-aminophenol based on the mesoporous silica modified carbon paste electrode

A mesoporous silica was synthesised and used to modify the surface of carbon paste electrode (CPE). The electrochemical behaviours of p-aminophenol were investigated. Compared to the unmodified CPE, the mesoporous silica-modified CPE obviously lowers the oxidation potential of p-aminophenol, and remarkably increases its oxidation peak current. The effects of pH value, amount of mesoporous silica, accumulation potential and time were examined. As a result, a sensitive, rapid and convenient electroanalytical method was developed for p-aminophenol. The linear range is from 0.025 mg L−1 to 3 mg L−1, and the limit of detection is 0.01 mg L−1 after 2-min accumulation. Finally, the method was successfully used to determine p-aminophenol in water samples.
Efflux and assimilation of xylem-transported CO2 in stems and leaves of tree species with different wood anatomy.

Determining the fate of CO2 respired in woody tissues is necessary to understand plant respiratory physiology and to evaluate CO2 recycling mechanisms. An aqueous 13 C-enriched CO2 solution was infused into the stem of 3-4 m tall trees to estimate efflux and assimilation of xylem-transported CO2 via cavity ring down laser spectroscopy and isotope ratio mass spectrometry, respectively. Different tree locations (lower stem, upper stem and leafy shoots) and tissues (xylem, bark and leaves) were monitored in species with tracheid, diffuse- and ring- porous wood anatomy (cedar, maple and oak, respectively). Radial xylem CO2 diffusivity and xylem [CO2 ] were lower in cedar relative to maple and oak trees, thereby limiting label diffusion. Part of the labeled 13 CO2 was assimilated in cedar (8.7 %) and oak (20.6 %) trees, mostly in xylem and bark tissues of the stem, while limited solution uptake in maple trees hindered detection of label assimilation. Little label reached foliar tissues, suggesting substantial label loss along the stem-branch transition following reductions in the radial diffusive pathway. Differences in respiration rates and radial xylem CO2 diffusivity (lower in conifer relative to angiosperm species) might reconcile discrepancies in efflux and assimilation of xylem-transported CO2 so far observed between taxonomic clades. This article is protected by copyright. All rights reserved.
Unmasking coupling between channel gating and ion permeation in the muscle nicotinic receptor

Whether ion channel gating is independent of ion permeation has been an enduring, unresolved question. Here, applying single channel recording to the archetypal muscle nicotinic receptor, we unmask coupling between channel gating and ion permeation by structural perturbation of a conserved intramembrane salt bridge. A charge-neutralizing mutation suppresses channel gating, reduces unitary current amplitude, and increases fluctuations of the open channel current. Power spectra of the current fluctuations exhibit low- and high-frequency Lorentzian components, which increase in charge-neutralized mutant receptors. After aligning channel openings and closings at the time of transition, the average unitary current exhibits asymmetric relaxations just after channel opening and before channel closing. A theory in which structural motions contribute jointly to channel gating and ion conduction describes both the power spectrum and the current relaxations. Coupling manifests as a transient increase in the open channel current upon channel opening and a decrease upon channel closing.
Antioxidant and functional properties of cowhide collagen peptides.

In the present study, antioxidant activities and functional properties of cowhide collagen antioxidant peptides (CCAPs) with different molecular weight (MW) were investigated. The optimum preparation conditions of CCAPs were hydrolysis time of 1.53 hr, temperature of 54.9 °C, pH 7.38, and neutral enzyme to trypsin ratio of 0.048 g: 0.016 g according to single factor test and response surface methodology (RSM). Three fractions (CCAP-I, CCAP-II, and CCAP-III) were obtained by ultrafiltration and lyophilization. Antioxidant activities revealed that CCAP-III had high reducing power activity (0.323 ± 0.035) and scavenging effect on 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals (64.30 ± 5.99%), 2,2-azino-bis-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) radicals (75.25 ± 3.14%), and hydroxyl radicals (68.26 ± 6.74%) compared to the other fractions. In addition, LC-MS/MS analysis showed that Ala-Gly-Glu-Arg, Gly-Ile-Ala-Gly-Glu-Arg, Gly-Pro-Ala-Gly-Pro-Ala-Gly-Pro-Arg, Gly-Val-Val-Gly-Pro-Glu-Gly-Ala-Arg and Gly-Phe-Ser-Gly-Leu-Asp-Gly-Ala-Lys were the major peptides of CCAP-III. CCAP-III showed good hygroscopicity (HYG), water holding capacity (WHC), and oil holding capacity (OHC) when compared with CCAP-I and CCAP-II. However, CCAP-II has great emulsifying properties, and CCAP-I has excellent foaming properties. Therefore, CCAPs can be used as a promising source of functional peptides with antioxidant properties. PRACTICAL APPLICATION: This study demonstrated the peptides of cowhide collagen has superior antioxidant and functional properties. This study provided a scientific basis for the preparation of antioxidant peptides from cowhide collagen.
Revising the European Society of Gastrointestinal Endoscopy (ESGE) research priorities: a research progress update

Abstract Background One of the aims of the European Society of Gastrointestinal Endoscopy (ESGE) is to encourage high quality endoscopic research at a European level. In 2016, the ESGE research committee published a set of research priorities. As endoscopic research is flourishing, we aimed to review the literature and determine whether endoscopic research over the last 4 years had managed to address any of our previously published priorities. Methods As the previously published priorities were grouped under seven different domains, a working party with at least two European experts was created for each domain to review all the priorities under that domain. A structured review form was developed to standardize the review process. The group conducted an extensive literature search relevant to each of the priorities and then graded the priorities into three categories: (1) no longer a priority (well-designed trial, incorporated in national/international guidelines or adopted in routine clinical practice); (2) remains a priority (i. e. the above criterion was not met); (3) redefine the existing priority (i. e. the priority was too vague with the research question not clearly defined). Results The previous ESGE research priorities document published in 2016 had 26 research priorities under seven domains. Our review of these priorities has resulted in seven priorities being removed from the list, one priority being partially removed, another seven being redefined to make them more precise, with eleven priorities remaining unchanged. This is a reflection of a rapid surge in endoscopic research, resulting in 27 % of research questions having already been answered and another 27 % requiring redefinition. Conclusions Our extensive review process has led to the removal of seven research priorities from the previous (2016) list, leaving 19 research priorities that have been redefined to make them more precise and relevant for researchers and funding bodies to target.