Miracle-dz/UniFAR-FTUs huggingface dataset:
Meeting the communication needs of students on the autism spectrum in Australian classrooms: Adjustments reported by educators and specialists

Abstract Purpose The purpose of this study was to examine educators’ and specialists’ provision of communication adjustments for students on the autism spectrum in mainstream and supported education settings. Method Secondary analysis of data collected from educators and specialists in the Australian Autism Educational Needs Analysis was undertaken. Thematic analysis of adjustment descriptions identified 11 categories. The use of the 11 specific adjustment categories with reference to (a) participant group (educator versus specialists), and (b) setting (mainstream versus supported) were described and associations investigated using Chi-square analyses. Result Only 32% of the 381 educators and specialists reported using adjustments. Of the adjustments reported, those categorised as “Multimodal Communication”, “Structured Teaching”, and “Assistive Technology” were frequently included by both groups. Significant associations were apparent between groups and the use of specific adjustments including naturalistic communication strategies. Significant differences were evident in the proportion of specific adjustments used by participants in supported as opposed to mainstream settings. Conclusion Possible reasons for the differences in the adjustments reported by educators and specialists and the role that setting may play in these are discussed. These include resourcing, the choice of adjustment being driven by school setting rather than student need, and possible differences between professionals in describing the adjustments made.
Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana.

Vernalization accelerates flowering after prolonged winter cold. Transcriptional and epigenetic changes are known to be involved in the regulation of the vernalization response. Despite intensive applications of next-generation sequencing in diverse aspects of plant research, genome-wide transcriptome and epigenome profiling during vernalization response has not been conducted. In this work, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, resulting in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway.
Schwann cell reprogramming into repair cells increases miRNA-21 expression in exosomes promoting axonal growth

ABSTRACT Functional recovery after peripheral nerve damage is dependent on the reprogramming of differentiated Schwann cells (dSCs) into repair Schwann cells (rSCs), which promotes axonal regeneration and tissue homeostasis. Transition into a repair phenotype requires expression of c-Jun and Sox2, which transcriptionally mediates inhibition of the dSC program of myelination and activates a non-cell-autonomous repair program, characterized by the secretion of neuronal survival and regenerative molecules, formation of a cellular scaffold to guide regenerating axons and activation of an innate immune response. Moreover, rSCs release exosomes that are internalized by peripheral neurons, promoting axonal regeneration. Here, we demonstrate that reprogramming of Schwann cells (SCs) is accompanied by a shift in the capacity of their secreted exosomes to promote neurite growth, which is dependent on the expression of c-Jun (also known as Jun) and Sox2 by rSCs. Furthermore, increased expression of miRNA-21 is responsible for the pro-regenerative capacity of rSC exosomes, which is associated with PTEN downregulation and PI3-kinase activation in neurons. We propose that modification of exosomal cargo constitutes another important feature of the repair program of SCs, contributing to axonal regeneration and functional recovery after nerve injury. Highlighted Article: Schwann cells reprogrammed to a repair phenotype produce exosomes with increased expression of miRNA-21. These exosomes promote neurite growth through downregulation of PTEN and activation of PI3-kinase in receiving neurons.
Gene Expression of Metallothioneins in Barley during Senescence and Heavy Metal Treatment

Despite their ubiquitous distribution, the exact functions of metallothloneins (MTs) are still not known. We analyzed the expression of four novel barley (Hordeum vulgare L.) genes coding for MTs, comparing two different situations: (i) leaf senescence, and (ii) heavy metal stress. Physiological analysis of chlorophyll content and photosystem II efficiency revealed similar stress response during natural leaf senescence and short-term heavy metal treatment with toxic concentrations of Cu and Cd. Gene expression patterns of the newly identified MTs (HvMT-1a, HvMT-2a, HvMT-2b and HvMT-3a) clearly vary under these different conditions, suggesting specific roles for the barley MTs during leaf senescence and heavy metal stress. While HvMT-1a is induced during leaf senescence and after heavy metal treatment but not during metal deficiency, expression of HvMT-2a is not affected under any of conditions tested. The MT HvMT-3a is only induced in response to Cu deficiency and HvMT-2b is downregulated in response to Cd stress.
Parametric Investigation of Particle Swarm Optimization to Improve the Performance of the Adaptive Neuro-Fuzzy Inference System in Determining the Buckling Capacity of Circular Opening Steel Beams

In this paper, the main objectives are to investigate and select the most suitable parameters used in particle swarm optimization (PSO), namely the number of rules (nrule), population size (npop), initial weight (wini), personal learning coefficient (c1), global learning coefficient (c2), and velocity limits (fv), in order to improve the performance of the adaptive neuro-fuzzy inference system in determining the buckling capacity of circular opening steel beams. This is an important mechanical property in terms of the safety of structures under subjected loads. An available database of 3645 data samples was used for generation of training (70%) and testing (30%) datasets. Monte Carlo simulations, which are natural variability generators, were used in the training phase of the algorithm. Various statistical measurements, such as root mean square error (RMSE), mean absolute error (MAE), Willmott’s index of agreement (IA), and Pearson’s coefficient of correlation (R), were used to evaluate the performance of the models. The results of the study show that the performance of ANFIS optimized by PSO (ANFIS-PSO) is suitable for determining the buckling capacity of circular opening steel beams, but is very sensitive under different PSO investigation and selection parameters. The findings of this study show that nrule = 10, npop = 50, wini = 0.1 to 0.4, c1 = [1, 1.4], c2 = [1.8, 2], fv = 0.1, which are the most suitable selection values to ensure the best performance for ANFIS-PSO. In short, this study might help in selection of suitable PSO parameters for optimization of the ANFIS model.
Bootstrapping in EcosystemsInternal interactions largely determine productivity and stability in biological systems with strong positive feedback

ositive feedback is being increasingly recognized as an important component of tcosystem dynamics (DeAngelis et al. 1986, Gutierrez and Fey 1980, Pastor and Post 1988). Within the constraints of resource supply or other environmental factors, the biological system characterized by strong positive feedback among its components is in many respects self-generating-its productivity and stability determined largely through its internal interactions. "The idea of a system. generating [itself] in a self-consistent loop of explanation is reminiscent of the story of the boy who fell into a bog and hauled himself out by pulling on his own bootstraps, so. such modes of explanation [are called] 'bootstrapping' " (Davies 1983). A bootstrapping view, neither reductionist nor holistic in its basic orientation, can yield useful insights into ecosystem processes, particularly as they relate to stability and resilience. Systems characterized by strong, positive interactions among their components can be complex, productive, and quite stable under conditions to which they are adapted, but when key linkages are disrupted they are fragile and subject to threshold changes (DeAngelis et al. 1986). In this article we review recent Stable against normal disturbances, ecosystems based on close, mutual interactions may be quite vulnerable to foreign disturbances
Cytokine-Induced Killer (CIK) Cells, In Vitro Expanded under Good Manufacturing Process (GMP) Conditions, Remain Stable over Time after Cryopreservation

Cytokine-induced killer (CIK) cells are advanced therapy medicinal products, so their production and freezing process has to be validated before their clinical use, to verify their stability as a drug formulation according to the good manufacturing practice (GMP) guidelines. We designed a stability program for our GMP-manufactured CIK cells, evaluating the viability, identity and potency of cryopreserved CIK cells at varying time periods from freezing, and compared them with fresh CIK cells. We evaluated the effects of the cryopreservation method, transportation, and the length of time of different process phases (pre-freezing, freezing and post-thawing) on the stability of CIK cells. This included a worst case for each stage. The expanded CIK cells were viable for up to 30 min from the addition of the freezing solution, when transported on dry ice within 48 h once frozen, within 60 min from thawing and from 12 months of freezing while preserving their cytotoxic effects. The reference samples, cryopreserved simultaneously in tubes and following the same method, were considered representative of the batch and useful in the case of further analysis. Data obtained from this drug stability program can inform the accurate use of CIK cells in clinical settings.
A Novel Approach to 3D-DOA Estimation of Stationary EM Signals Using Convolutional Neural Networks

This paper proposes a novel three-dimensional direction-of-arrival (3D-DOA) estimation method for electromagnetic (EM) signals using convolutional neural networks (CNN) in a Gaussian or non-Gaussian noise environment. First of all, in the presence of Gaussian noise, four output covariance matrices of the uniform triangular array (UTA) are normalized and then fed into four neural networks for 1D-DOA estimation with identical parameters in parallel; then four 1D-DOA estimations of the UTA can be obtained, and finally, the 3D-DOA estimation could be obtained through post-processing. Secondly, in the presence of non-Gaussian noise, the array output covariance matrices are normalized by the infinity-norm and then processed in Gaussian noise environment; the infinity-norm normalization could effectively suppress impulsive outliers and then provide appropriate input features for the neural network. In addition, the outputs of the neural network are controlled by a signal monitoring network to avoid misjudgments. Comprehensive simulations demonstrate that in Gaussian or non-Gaussian noise environment, the proposed method is superior and effective in computation speed and accuracy in 1D-DOA and 3D-DOA estimations, and the signal monitoring network could also effectively control the neural network outputs. Consequently, we can conclude that CNN has better generalization ability in DOA estimation.
Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles

Wikipedia is the largest and most visited encyclopedia on the World Wide Web [1]. Wikipedia is frequently accessed as an educational resource in computational biology, with the articles on Bioinformatics and CRISPR being viewed 413,000 and 1.18 million times, respectively, in 2019 [2]. However, academics remain skeptical of Wikipedia as a reliable source of knowledge [3]. A common complaint by educators is the perceived lack of quality of information found on Wikipedia. Some educators also worry that the platform discourages deeper learner engagement, providing learners with a crutch instead of ways to engage in rigorous, secondary research within a discipline. Both of these concerns often overshadow the advantages of free and readily available knowledge. Given that Wikipedia is one of the most visited websites and an established platform for knowledge seekers, it makes sense to address these concerns and help learners make the most of what they would do anyway. Mentored contributions from students to open platforms like Wikipedia offer opportunities for improved rigor, quality, depth, and reliability of the information indexed and make it relatable to a wide audience. There have been stellar examples of such mentored contributions, resulting in well-curated additions to domain-specific knowledge amenable for consumption by both public and specialist audiences. For instance, educators around the world have mentored students to either improve or create Wikipedia articles and enter the annual International Society for Computational Biology (ISCB) Wikipedia Competition, a grassroots initiative designed to improve the coverage and depth of computational biology topics [4,5]. Entries are judged based on the quality of writing, figures, and depth of subject knowledge [6]. Winning entries have included important topics in computational biology, such as chromosome conformation capture [7], molecular phylogenetics [8], and the Ruzzo-Tompa algorithm [9]. Some educators have gone further, replacing the writing of traditional term papers with the rigorous editing or creation of new articles in Wikipedia, resulting in class assignments that enhance a vital, publicly accessible resource of field-specific information. Trainees at 24 United States universities participated in a pilot of the Wikipedia Education Program [10] during the 2010–2011 academic year. A 2012 article reviewed the experiences of four professors who participated, each assigning trainees to write Wikipedia articles on a course topic in place of a term paper [11]. Although each professor tailored assignments to her/his particular class, all found the assignments “extremely useful” in improving trainees’ learning. Similar positive outcomes have been reported in other studies, including larger introductory courses of over 100 PLOS COMPUTATIONAL BIOLOGY
Prognostic Value of Dynamic Contrast-Enhanced MRI-Derived Pharmacokinetic Variables in Glioblastoma Patients: Analysis of Contrast-Enhancing Lesions and Non-Enhancing T2 High-Signal Intensity Lesions

Objective To evaluate pharmacokinetic variables from contrast-enhancing lesions (CELs) and non-enhancing T2 high signal intensity lesions (NE-T2HSILs) on dynamic contrast-enhanced (DCE) magnetic resonance (MR) imaging for predicting progression-free survival (PFS) in glioblastoma (GBM) patients. Materials and Methods Sixty-four GBM patients who had undergone preoperative DCE MR imaging and received standard treatment were retrospectively included. We analyzed the pharmacokinetic variables of the volume transfer constant (Ktrans) and volume fraction of extravascular extracellular space within the CEL and NE-T2HSIL of the entire tumor. Univariate and multivariate Cox regression analyses were performed using preoperative clinical characteristics, pharmacokinetic variables of DCE MR imaging, and postoperative molecular biomarkers to predict PFS. Results The increased mean Ktrans of the CEL, increased 95th percentile Ktrans of the CELs, and absence of methylated O6-methylguanine-DNA methyltransferase promoter were relevant adverse variables for PFS in the univariate analysis (p = 0.041, p = 0.032, and p = 0.083, respectively). The Kaplan-Meier survival curves demonstrated that PFS was significantly shorter in patients with a mean Ktrans of the CEL > 0.068 and 95th percentile Ktrans of the CEL>0.223 (log-rank p = 0.038 and p = 0.041, respectively). However, only mean Ktrans of the CEL was significantly associated with PFS (p = 0.024; hazard ratio, 553.08; 95% confidence interval, 2.27–134756.74) in the multivariate Cox proportional hazard analysis. None of the pharmacokinetic variables from NE-T2HSILs were significantly related to PFS. Conclusion Among the pharmacokinetic variables extracted from CELs and NE-T2HSILs on preoperative DCE MR imaging, the mean Ktrans of CELs exhibits potential as a useful imaging predictor of PFS in GBM patients.
Drosophila Sas-6, Ana2 and Sas-4 self-organise into macromolecular structures that can be used to probe centriole and centrosome assembly

ABSTRACT Centriole assembly requires a small number of conserved proteins. The precise pathway of centriole assembly has been difficult to study, as the lack of any one of the core assembly proteins [Plk4, Ana2 (the homologue of mammalian STIL), Sas-6, Sas-4 (mammalian CPAP) or Asl (mammalian Cep152)] leads to the absence of centrioles. Here, we use Sas-6 and Ana2 particles (SAPs) as a new model to probe the pathway of centriole and centrosome assembly. SAPs form in Drosophila eggs or embryos when Sas-6 and Ana2 are overexpressed. SAP assembly requires Sas-4, but not Plk4, whereas Asl helps to initiate SAP assembly but is not required for SAP growth. Although not centrioles, SAPs recruit and organise many centriole and centrosome components, nucleate microtubules, organise actin structures and compete with endogenous centrosomes to form mitotic spindle poles. SAPs require Asl to efficiently recruit pericentriolar material (PCM), but Spd-2 (the homologue of mammalian Cep192) can promote some PCM assembly independently of Asl. These observations provide new insights into the pathways of centriole and centrosome assembly. Highlighted Article: The lack of core centriole proteins leads to the absence of centrioles, making its assembly difficult to study. We use Sas-6 and Ana2 particles as a new model to probe this pathway.
Refining the life cycle of Plasmodiophora brassicae.

As a soil borne protist pathogen, Plasmodiophora brassicae causes the devastating clubroot disease on Brassicaeae crops worldwide. Due to its intracellular obligate biotrophic nature, the life cycle of P. brassicae is still not fully understood. Here, we use fluorescent probe-based confocal microscopy and TEM to investigate the infection process of P. brassicae on the susceptible host Arabidopsis under controlled conditions. We find that P. brassicae can initiate the primary infection in both root hairs and epidermal cells, producing the uninucleate primary plasmodium at 1 day post inoculation (dpi). After that, the developed multinucleate primary plasmodium underwent condensing and cytoplasm cleavage into uninucleate zoosporangia from one to four dpi. This was subsequently followed by the formation of multinucleate zoosporangia and the production of secondary zoospores within zoosporangium. Importantly, the secondary zoospores performed a conjugation in the root epidermal cells after their release. TEM revealed extensive uninucleate secondary plasmodium in cortical cells at 8 dpi, indicating the establishment of the secondary infection. The P. brassicae subsequently developed into binucleate, quadrinucleate and multinucleate secondary plasmodia from 10 to 15 dpi, during which, the clubroot symptoms appeared. The uninucleate resting spores were firstly observed in the cortical cells at 24 dpi, marking the completion of a life cycle. We also provide evidence that the secondary infection of P. brassicae may represent the diploid sexual life stage. From these findings, we propose a refined life cycle of P. brassicae which will contribute to understanding of the complicated infection biology of P. brassicae.
Current Status and Trends in Prophylaxis and Management of Anthrax Disease

Bacillus anthracis has been identified as a potential military and bioterror agent as it is relatively simple to produce, with spores that are highly resilient to degradation in the environment and easily dispersed. These characteristics are important in describing how anthrax could be used as a weapon, but they are also important in understanding and determining appropriate prevention and treatment of anthrax disease. Today, anthrax disease is primarily enzootic and found mostly in the developing world, where it is still associated with considerable mortality and morbidity in humans and livestock. This review article describes the spectrum of disease caused by anthrax and the various prevention and treatment options. Specifically we discuss the following; (1) clinical manifestations of anthrax disease (cutaneous, gastrointestinal, inhalational and intravenous-associated); (2) immunology of the disease; (3) an overview of animal models used in research; (4) the current World Health Organization and U.S. Government guidelines for investigation, management, and prophylaxis; (5) unique regulatory approaches to licensure and approval of anthrax medical countermeasures; (6) the history of vaccination and pre-exposure prophylaxis; (7) post-exposure prophylaxis and disease management; (8) treatment of symptomatic disease through the use of antibiotics and hyperimmune or monoclonal antibody-based antitoxin therapies; and (9) the current landscape of next-generation product candidates under development.
Commelinaceomyces, gen. nov., for four clavicipitaceous species misplaced in Ustilago that infect Commelinaceae

ABSTRACT A fungus causing false smut in the flowers of Murdannia keisak (Commelinaceae, Commelinales, Monocots) in Japan was morphologically identical to Ustilago aneilematis. The fungus infected ovaries of most flowers of host plants. Infected flowers were filled with yellow to orange thick-walled conidia that became olivaceous green at maturity. However, multilocus phylogenetic analysis of DNA sequences (18S, 28S, translation elongation factor 1α [TEF], the largest [RPB1] and the second largest [RPB2] subunit of RNA polymerase II) showed that the fungus belonged to the tribe Ustilaginoideae (Clavicipitaceae, Hypocreales, Ascomycota). Microscopic examination showed that the fungus developed conidia at the apex of conidiogenous cells, in contrast to other species in the Ustilaginoideae that develop conidia pleurogenously. A new genus, Commelinaceomyces, is formally proposed in the Ustilaginoideae to accommodate this fungus. Four species previously misplaced in Ustilago (Ustilaginales, Basidiomycota) are transferred to Commelinaceomyces, including the type of the genus, C. aneilematis, on Murdannia keisak. This is the first report of a clavicipitaceous species infecting host plants in the Commelinaceae.