Miracle-dz/UniFAR-FTUs huggingface dataset:
Congruence and Plausibility, Not Presence: Pivotal Conditions for XR Experiences and Effects, a Novel Approach

Presence is often considered the most important quale describing the subjective feeling of being in a computer-generated and/or computer-mediated virtual environment. The identification and separation of orthogonal presence components, i.e., the place illusion and the plausibility illusion, has been an accepted theoretical model describing Virtual Reality (VR) experiences for some time. This perspective article challenges this presence-oriented VR theory. First, we argue that a place illusion cannot be the major construct to describe the much wider scope of virtual, augmented, and mixed reality (VR, AR, MR: or XR for short). Second, we argue that there is no plausibility illusion but merely plausibility, and we derive the place illusion caused by the congruent and plausible generation of spatial cues and similarly for all the current model’s so-defined illusions. Finally, we propose congruence and plausibility to become the central essential conditions in a novel theoretical model describing XR experiences and effects.
Pressure-driven wrinkling of soft inner-lined tubes

A simple equation modelling an inextensible elastic lining of an inner-lined tube subject to an imposed pressure difference is derived from a consideration of the idealised elastic properties of the lining and the pressure and soft-substrate forces. Two cases are considered in detail, one with prominent wrinkling and a second one in which wrinkling is absent and only buckling remains. Bifurcation diagrams are computed via numerical continuation for both cases. Wrinkling, buckling, folding, and mixed-mode solutions are found and organised according to system-response measures including tension, in-plane compression, maximum curvature and energy. Approximate wrinkle solutions are constructed using weakly nonlinear theory, in excellent agreement with numerics. Our approach explains how the wavelength of the wrinkles is selected as a function of the parameters in compressed wrinkling systems and shows how localised folds and mixed-mode states form in secondary bifurcations from wrinkled states. Our model aims to capture the wrinkling response of arterial endothelium to blood pressure changes but applies much more broadly.
Fatigued PageRank

Connections among entities are everywhere. From social media interactions to web page hyperlinks, networks are frequently used to represent such complex systems. Node ranking is a fundamental task that provides the strategy to identify central entities according to multiple criteria. Popular node ranking metrics include degree, closeness or betweenness centralities, as well as HITS authority or PageRank. In this work, we propose a novel node ranking metric, where we combine PageRank and the idea of node fatigue, in order to model a random explorer who wants to optimize coverage - it gets fatigued and avoids previously visited nodes. We formalize and exemplify the computation of Fatigued PageRank, evaluating it as a node ranking metric, as well as query-independent evidence in ad hoc document retrieval. Based on the Simple English Wikipedia link graph with clickstream transitions from the English Wikipedia, we find that Fatigued PageRank is able to surpass both indegree and HITS authority, but only for the top ranking nodes. On the other hand, based on the TREC Washington Post Corpus, we were unable to outperform the BM25 baseline, obtaining similar performance for all graph-based metrics, except for indegree, which lowered GMAP and MAP, but increased NDCG@10 and P@10.
Analysis of crucial genes, pathways and construction of the molecular regulatory networks in vascular smooth muscle cell calcification

Vascular calcification (VC) accompanies the trans-differentiation of vascular smooth muscle cells (VSMCs) into osteo/chondrocyte-like cells and resembles physiological bone mineralization. However, the molecular mechanisms underlying VC initiation and progression have remained largely elusive. The aim of the present study was to identify the genes and pathways common to VSMC and osteoblast calcification and construct a regulatory network of non-coding RNAs and transcription factors (TFs). To this end, the Gene Expression Omnibus dataset GSE37558 including mRNA microarray data of calcifying VSMCs (CVSMCs) and calcifying osteoblasts (COs) was analyzed. The differentially expressed genes (DEGs) were screened and functionally annotated and the microRNA (miRNA/mRNA)-mRNA, TF-miRNA and long non-coding RNA (lncRNA)-TF regulatory networks were constructed. A total of 318 DEGs were identified in the CVSMCs relative to the non-calcified VSMCs, of which 43 were shared with the COs. The CVSMC-related DEGs were mainly enriched in the functional terms cell cycle, extracellular matrix (ECM), inflammation and chemotaxis-mediated signaling pathways, of which ECM was enriched by the DEGs for the COs as well. The protein-protein interaction network of CVSMCs consisted of 281 genes and 3,650 edges. There were 30 hub genes in this network, including maternal embryonic leucine zipper kinase (MELK), which potentially regulates the differentially expressed TF (DETF) forkhead box (FOX)M1 and is a potential target gene of Homo sapiens miR-485-3p and miR-181d. The TF-miRNA network included 251 TFs and 60 miRNAs, including 10 DETFs such as FOXO1 and snail family transcriptional repressor 2 (SNAI2). Furthermore, the lncRNAs H19 imprinted maternally expressed transcript (H19) and differentiation antagonizing non-protein coding RNA (DANCR) were predicted as the upstream regulators of FOXO1 and SNAI2 in the lncRNA-TF regulatory network. DANCR, MELK and FOXM1 were downregulated, and H19, FOXO1 and SNAI2 were upregulated in the CVSMCs. Taken together, the CVSMCs and COs exhibited similar molecular changes in the ECM. In addition, the MELK-FOXM1, H19/DANCR-FOXO1 and SNAI2 regulatory pathways likely mediate VSMC calcification.
Classification of Rice Yield Using UAV-Based Hyperspectral Imagery and Lodging Feature

High-yield rice cultivation is an effective way to address the increasing food demand worldwide. Correct classification of high-yield rice is a key step of breeding. However, manual measurements within breeding programs are time consuming and have high cost and low throughput, which limit the application in large-scale field phenotyping. In this study, we developed an accurate large-scale approach and presented the potential usage of hyperspectral data for rice yield measurement using the XGBoost algorithm to speed up the rice breeding process for many breeders. In total, 13 japonica rice lines in regional trials in northern China were divided into different categories according to the manual measurement of yield. Using an Unmanned Aerial Vehicle (UAV) platform equipped with a hyperspectral camera to capture images over multiple time series, a rice yield classification model based on the XGBoost algorithm was proposed. Four comparison experiments were carried out through the intraline test and the interline test considering lodging characteristics at the midmature stage or not. The result revealed that the degree of lodging in the midmature stage was an important feature affecting the classification accuracy of rice. Thus, we developed a low-cost, high-throughput phenotyping and nondestructive method by combining UAV-based hyperspectral measurements and machine learning for estimation of rice yield to improve rice breeding efficiency.
SEPT6 drives hepatocellular carcinoma cell proliferation, migration and invasion via the Hippo/YAP signaling pathway

Septin 6 (SEPT6) is a member of the GTP-binding protein family that is highly conserved in eukaryotes and regulates various biological functions, including filament dynamics, cytokinesis and cell migration. However, the functional importance of SEPT6 in hepatocellular carcinoma (HCC) is not completely understood. The present study aimed to investigate the expression levels and roles of SEPT6 in HCC, as well as the underlying mechanisms. The reverse transcription quantitative PCR, western blotting and immunohistochemistry staining results demonstrated that SEPT6 expression was significantly elevated in HCC tissues compared with corresponding adjacent non-tumor tissues, which indicated that SEPT6 expression may serve as a marker of poor prognosis for HCC. By performing plasmid transfection and G418 treatment, stable SEPT6-knockdown and SEPT6-overexpression cell lines were established. The Cell Counting Kit-8, flow cytometry and Transwell assay results demonstrated that SEPT6 overexpression significantly increased HCC cell proliferation, cell cycle transition, migration and invasion compared with the Vector group, whereas SEPT6 knockdown displayed significant suppressive effects on HCC cell lines in vitro compared with the control group. Mechanistically, SEPT6 might facilitate F-actin formation, which induced large tumor suppressor kinase 1 dephosphorylation, inhibited Hippo signaling, upregulated yes-associated protein (YAP) expression and nuclear translocation, and upregulated cyclin D1 and matrix metallopeptidase 2 (MMP2) expression. Furthermore, YAP overexpression significantly reversed SEPT6 knockdown-induced inhibitory effects on HCC, whereas YAP knockdown significantly inhibited the oncogenic effect of SEPT6 overexpression on HCC. Collectively, the present study demonstrated that SEPT6 may promote HCC progression by enhancing YAP activation, suggesting that targeting SEPT6 may serve as a novel therapeutic strategy for HCC.
A Comparative Analysis of Quantitative Metrics of Root Architecture

High throughput phenotyping is important to bridge the gap between genotype and phenotype. The methods used to describe the phenotype therefore should be robust to measurement errors, relatively stable over time, and most importantly, provide a reliable estimate of elementary phenotypic components. In this study, we use functional-structural modeling to evaluate quantitative phenotypic metrics used to describe root architecture to determine how they fit these criteria. Our results show that phenes such as root number, root diameter, and lateral root branching density are stable, reliable measures and are not affected by imaging method or plane. Metrics aggregating multiple phenes such as total length, total volume, convex hull volume, and bushiness index estimate different subsets of the constituent phenes; they however do not provide any information regarding the underlying phene states. Estimates of phene aggregates are not unique representations of underlying constituent phenes: multiple phenotypes having phenes in different states could have similar aggregate metrics. Root growth angle is an important phene which is susceptible to measurement errors when 2D projection methods are used. Metrics that aggregate phenes which are complex functions of root growth angle and other phenes are also subject to measurement errors when 2D projection methods are used. These results support the hypothesis that estimates of phenes are more useful than metrics aggregating multiple phenes for phenotyping root architecture. We propose that these concepts are broadly applicable in phenotyping and phenomics.
Characterization of extracellular vesicles and synthetic nanoparticles with four orthogonal single‐particle analysis platforms

Abstract We compared four orthogonal technologies for sizing, counting, and phenotyping of extracellular vesicles (EVs) and synthetic particles. The platforms were: single‐particle interferometric reflectance imaging sensing (SP‐IRIS) with fluorescence, nanoparticle tracking analysis (NTA) with fluorescence, microfluidic resistive pulse sensing (MRPS), and nanoflow cytometry measurement (NFCM). EVs from the human T lymphocyte line H9 (high CD81, low CD63) and the promonocytic line U937 (low CD81, high CD63) were separated from culture conditioned medium (CCM) by differential ultracentrifugation (dUC) or a combination of ultrafiltration (UF) and size exclusion chromatography (SEC) and characterized by transmission electron microscopy (TEM) and Western blot (WB). Mixtures of synthetic particles (silica and polystyrene spheres) with known sizes and/or concentrations were also tested. MRPS and NFCM returned similar particle counts, while NTA detected counts approximately one order of magnitude lower for EVs, but not for synthetic particles. SP‐IRIS events could not be used to estimate particle concentrations. For sizing, SP‐IRIS, MRPS, and NFCM returned similar size profiles, with smaller sizes predominating (per power law distribution), but with sensitivity typically dropping off below diameters of 60 nm. NTA detected a population of particles with a mode diameter greater than 100 nm. Additionally, SP‐IRIS, MRPS, and NFCM were able to identify at least three of four distinct size populations in a mixture of silica or polystyrene nanoparticles. Finally, for tetraspanin phenotyping, the SP‐IRIS platform in fluorescence mode was able to detect at least two markers on the same particle, while NFCM detected either CD81 or CD63. Based on the results of this study, we can draw conclusions about existing single‐particle analysis capabilities that may be useful for EV biomarker development and mechanistic studies.
Sinomacrops bondei, a new anurognathid pterosaur from the Jurassic of China and comments on the group

Anurognathids are an elusive group of diminutive, potentially arboreal pterosaurs. Even though their monophyly has been well-supported, their intrarelationships have been obscure, and their phylogenetic placement even more. In the present work, we present a new genus and species from the Middle-Late Jurassic Tiaojishan Formation, the third nominal anurognathid species from the Jurassic of China. The new species provides new information concerning morphological diversity for the group. Furthermore, we provide a new phylogenetic analysis incorporating into a single data set characters from diverging phylogenetic proposals. Our results place them as the sister-group of Darwinoptera + Pterodactyloidea, as basal members of the Monofenestrata.
Revision of the Conwentzia Enderlein, 1905 (Neuroptera, Coniopterygidae) of China, combining morphological and molecular characters

Abstract The Chinese species of Conwentzia Enderlein are revised by integrating morphological characters and molecular data. Conwentzia yunguiana Liu & Yang, 1993 is proposed as a junior synonym of Conwentzia nietoi Monserrat, 1982, syn. nov. and Conwentzia orthotibia Yang, 1974 is proposed as a junior synonym of Conwentzia pineticola Enderlein, 1905, syn. nov. Moreover, a key to the adult males of the Conwentzia from China and DNA barcodes are provided.
Maternal depressive symptoms and early childhood development: the role of mother–child interactions among mother–child dyads in rural areas of Central and Western China

Background The associations among maternal depressive symptoms (MDS), mother–child interactions and early child development are poorly understood. This study aimed to explore the role of mother–child interactions on the associations between MDS and child development. Methods A cross-sectional study with a multistage sampling method was conducted in rural areas of Central and Western China. MDS, child development outcomes (communication, gross motor function, fine motor function, problem solving and personal social skills) and mother–child interactions were assessed by The Edinburgh Postpartum Depression Scale, the Chinese version of the Ages and Stages Questionnaires and the Multiple Indicator Cluster Surveys, respectively. Regression-based statistical mediation and moderation were conducted using the PROCESS macro for SPSS. Results A total of 2,548 participants (mothers: 1,274; children: 1,274) were included in our analyses. MDS was negatively associated with child development outcomes and mother–child interactions partly mediated these associations. The proportion of the mediating effect of mother–child interactions was 7.7% for communication, 8.2% for gross motor, 10.3% for fine motor, 10.1% for problem-solving and 9.5% for personal social domains. In addition, the interaction effects of MDS and mother–child interactions on the communication domain were significant (β = 0.070, 95% CI 0.016, 0.124; p = 0.011). The associations between MDS and child communication abilities were weaker at the high level (simple slope = −0.019, t = − 0.458, p = 0.647) of mother–child interactions than at the mean level (simple slope = −0.089, t = − 3.190, p = 0.002) and the low level (simple slope = −0.158, t = − 4.231, p < 0.001). Similar moderating effects were not observed in the other child development outcomes. Conclusion Our results suggest the important role of mother–child interactions on the associations between MDS and early childhood development. Due to the cross-sectional design of this study, these associations require further investigation in prospective studies.
Clinical significance of serum transforming growth factor-β1 and procollagen type I N-propeptide in post-tuberculosis tracheobronchial stenosis

Non-invasive strategies for monitoring post-tuberculosis (TB) tracheobronchial stenosis (PTTS) are clinically important but currently lacking. Transforming growth factor-β1 (TGF-β1) and procollagen type I N-propeptide (PINP) have been identified as markers of fibrosis. The present study aimed to investigate the clinical significance of serum TGF-β1 and PINP in PTTS. Serum samples were collected from 119 patients with tracheobronchial TB after the condition was treated for at least 6 months (59 patients with airway stenosis and 60 patients with no stenosis). Serum TGF-β1 and PINP levels were measured using ELISA and compared between the groups. Relationships between serum TGF-β1 and PINP levels and clinical characteristics, interventional bronchoscopy and outcomes of airway stenosis were analysed. The correlation between TGF-β1 and PINP, and their diagnostic efficacy for airway stenosis were also analysed. The TGF-β1 and PINP levels in the airway stenosis group were higher than those in the non-stenosis group. Furthermore, airway stenosis with atelectasis or mucus plugging was associated with higher TGF-β1 levels, and airway stenosis with atelectasis, mucus plugging, right main bronchus stenosis or severe airway tracheal stenosis was associated with higher PINP levels. In addition, TGF-β1 and PINP levels increased after interventional bronchoscopy therapy and airway stenosis with recurrent stenosis was associated with higher baseline levels of both markers. Finally, TGF-β1 levels were positively correlated with PINP levels in patients with airway stenosis. The area under the receiver operating characteristic curve of TGF-β1 and PINP for distinguishing airway stenosis from non-stenosis cases was 0.824 (95% CI: 0.748-0.900) and 0.863 (95% CI: 0.796-0.930), respectively. Therefore, TGF-β1 and PINP are potential biomarkers that may be useful for diagnosing and monitoring PTTS.
Sublethal fluazaindolizine doses inhibit development of the cyst nematode Heterodera schachtii during sedentary parasitism.

BACKGROUND Fluazaindolizine is a new compound for the control of plant-parasitic nematodes with an unknown and novel mode of action. This compound is very effective against important plant-parasitic nematodes. However, investigations elucidating the impact of sublethal fluazaindolizine doses on early nematode virulence and plant - nematode interaction parameters are lacking. RESULTS The effect of direct exposure of Heterodera schachtii juveniles to 50 ppm fluazaindolizine was negligible. Infection assays revealed a 57% reduction in adult females at 1.25 ppm and a 46% reduction in offspring at 40 ppm when juveniles were soaked in the compound for 48 hours and subsequently inoculated onto Arabidopsis thaliana. Pre-incubation of A. thaliana roots with fluazaindolizine was not effective against H. schachtii. Conversely, supplementing the plant growth medium with fluazaindolizine led to a significant reduction of adults (-35 %), females (-75 %) and female size at 1.25 ppm and nearly completely inhibited nematode parasitism at 5 ppm. The impact of fluazaindolizine on A. thaliana was dependent on plant age, compound concentration and duration of contact. Very low sublethal fluazaindolizine concentrations, 5 or 10 ppm, did not interfere with nematode mobility, host finding, penetration, and induction of the feeding site, but specifically inhibited sedentary nematode development inside the root in a concentration-dependent manner. CONCLUSION Fluazaindolizine does not have direct toxicity against infective juveniles, but has a clear effect on nematodes during sedentary development. The formation of females and the development of offspring are strongly reduced. It will be tempting to identify the underlying mechanism in the future.
Communication Campaigns to Support the Use of Nutritional Warnings: Different Messages for Different People?

Communication campaigns are expected to contribute to increase the efficacy of nutritional warnings. In this context, the aims of the present work were (a) to evaluate how citizens perceive different types of messages for a communication campaign and (b) to determine if personal characteristics such as gender, age, and educational level, as well socioeconomic and nutritional status, moderate how citizens perceive such campaign messages. A series of graphic pieces were designed for each of the following three types of messages: promotion of informed food choices; raising awareness of the negative health consequences of excessive consumption of sugar, fat, and sodium; and promotion of healthy food choices. An online study was conducted with 774 participants, who were randomly assigned to one of the three types of messages. The participants’ self-reported perception of the graphic pieces was evaluated using 7-point Likert-type scales. After completing the evaluation task, the participants proceeded to a series of choices. This was implemented to evaluate whether exposure to different types of messages affected hypothetical food choices. Results revealed that messages related to the promotion of healthy eating were perceived as the most adequate as part of a communication campaign and had the potential to encourage more healthful hypothetical choices in the experimental task. However, gender, age, and nutritional status moderated the influence of the type of message on the participants’ perception, meaning that different groups perceived different types of messages as the most adequate. The results from the present work stress the need to include different types of messages in a communication campaign to target individuals with different motivations and characteristics.