Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex Evolution of Coronal Mass Ejections in the Inner Heliosphere as Revealed by Numerical Simulations and STEREO Observations: A Review

Abstract The transit of coronal mass ejections (CMEs) from the Sun to 1 AU lasts on average one to five days. As they propagate, CMEs interact with the solar wind and preceding eruptions, which modify their properties. In the past ten years, the evolution of CMEs in the inner heliosphere has been investigated with the help of numerical simulations, through the analysis of remote-sensing heliospheric observations, especially with the SECCHI suite onboard STEREO, and through the analysis of multi-spacecraft in situ measurements. Most studies have focused on understanding the characteristics of the magnetic flux rope thought to form the core of the CME. Here, we first review recent work related to CME propagation in the heliosphere, which point towards the need to develop more complex models to analyze CME observations. In the second part of this article, we review some recent studies of CME-CME interaction, which also illustrate the complexity of phenomena occurring in the inner heliosphere.
Angular modulation of single-molecule fluorescence by gold nanoparticles on DNA origami templates

Abstract We study the angular fluorescence intensity modulation of a single dye positioned near a spherical gold nanoparticle, induced by rotation of linearly polarized excitation light. Accurate positioning and alignment of nanoparticle and fluorophore with respect to each other and the incoming electric field is achieved by a three-dimensional, self-assembled DNA origami. An intensity map is obtained for a fixed distance and two different nanoparticle diameters, revealing polarization-dependent enhancement and quenching of fluorescence intensity in good agreement to numerical simulations.
Multi-frequency study of extragalactic supernova remnants and H II regions : sculptor group Sd galaxy NGC 300

We present a multi-frequency study of supernova remnants (SNRs) and $\ion{H}{ii }$ regions in the nearby Sculptor Group Sd galaxy NGC 300, based on new ATCA observations at the wavelengths of 13 and 20 cm, XMM-Newton observations, newly-processed ROSAT (PSPC/HRI; Read & Pietsch 2001) and VLA (20/6 cm) images of this galaxy. We have investigated the physical properties at the X-ray and radio wavelengths of the 28 optical SNRs found by Blair & Long (1997) and have expanded on the multi-wavelength work by Pannuti et al. (2000) on this same galaxy. From a total of 54 radio sources and 11 X-ray sources, we report 18 SNRs and three (3) SNR candidates (classified by spectral index alone) in NGC 300. Five of these 18 SNRs are associated with reported optical SNRs and three have X-ray counterparts. An additional 12 radio SNRs are seen in the Blair & Long (1997) [S II] images. We also investigate the luminosity function of our SNRs. Three background radio sources are confirmed and 12 other sources could represent additional background objects. Twenty two radio correlations with OB associations within NGC 300 correspond to either $\ion{H}{ii }$ regions or SNRs making them a good tracer of SNRs near star-forming regions. Additionally, two radio sources coincide with potential globular clusters of NGC 300 reported by Kim et al. (2002).
Disease severity of unvaccinated SARS-CoV-2 positive adults less than 65 years old without comorbidity, in the Omicron period and pre-Omicron periods

Background: The reduced severity and burden of COVID-19 in 2022 can largely be attributable to vaccination and a shift to Omicron predominance. However, millions of individuals remain unvaccinated. In the present study, we aimed to study disease severity in unvaccinated individuals without risk factors during the Omicron period, compared to pre-Omicron periods. Methods: This register-based study included all unvaccinated individuals in Sweden aged 18-64 years without comorbidity or care dependency who were SARS-CoV-2 positive between week 45 of 2020 and week 5 of 2022. Variant of concern (VOC) periods were periods with certain VOCs identified in [≥]92% of sequenced cases nationwide. Outcomes were hospitalization with a main discharge code of COVID-19; severe illness, defined as high-flow nasal oxygen treatment or intensive care unit admission; and death with COVID-19 as the underlying cause of death on the death certificate. Results: Among 788,895 individuals in the overall SARS-CoV-2 positive cohort, both hospitalization and death increased stepwise from the pre-VOC period to the Alpha and Delta periods, and decreased in the Omicron period. Among 15,179 patients hospitalized for COVID-19, the proportions with severe illness and death increased to the Delta period, but in the Omicron period, these outcomes returned to the level of the pre-VOC period. Conclusion: In the Omicron period, compared to pre-Omicron periods, unvaccinated SARS-CoV-2 positive adults <65 years old without comorbidity had reduced proportions of hospitalization and death overall, but similar proportion of severe illness among patients hospitalized for COVID-19. These results support continuous efforts to prevent hospitalizations for COVID-19.
Thai Sentiment Analysis via Bidirectional LSTM-CNN Model with Embedding Vectors and Sentic Features

Sentiment analysis is one of the most frequently performed tasks in Natural Language Processing that plays an important role in marketing research. It allows us to understand customer sentiment. The outcomes from this kind of analysis can be used to improve products and services. Recently, a Word2Vec model, a technique for word embedding (converting text into a number) has been developed and used successfully to a degree to get the sentiment of customers from the text responses that they provided. This work attempted to incorporate two more features-part-of-speech and sentic features-to make the analysis more accurate. The part-of-speech feature identifies the type of words that better convey various sentiments, while the sentic feature identifies the emotion underlying certain words. Combining Bidirectional Long Short-term Memory and Convolutional Neural Networks models with several combinations of the features mentioned, we performed a sentiment analysis of Thai children stories and found that the combination of all three features gave the best result at 78.89 % F1-score.
Defective Joint Development and Maintenance in GDF6‐Related Multiple Synostoses Syndrome

Multiple synostoses syndromes (SYNS) are a group of rare genetic bone disorders characterized by multiple joint fusions. We previously reported an SYNS4‐causing GDF6 c.1330 T > A (p.Tyr444Asn) mutation, which reduced Noggin‐induced GDF6 inhibition and enhanced SMAD1/5/8 signaling. However, the mechanisms by which GDF6 gain‐of‐function mutation alters joint formation and the comprehensive molecular portraits of SYNS4 remain unclear. Herein, we introduce the p.Tyr443Asn (orthologous to the human GDF6 p.Tyr444Asn) mutation into the mouse Gdf6 locus and report the results of extensive phenotype analysis, joint development investigation, and transcriptome profiling of Gdf6 p.Tyr443Asn limb buds. Gdf6 p.Tyr443Asn knock‐in mice recapitulated the morphological features of human SYNS4, showing joint fusion in the wrists, ankles, phalanges, and auditory ossicles. Analysis of mouse embryonic forelimbs demonstrated joint interzone formation defects and excess chondrogenesis in Gdf6 p.Tyr443Asn knock‐in mice. Further, RNA sequencing of forelimb buds revealed enhanced bone formation and upregulated bone morphogenetic protein (BMP) signaling in mice carrying the Gdf6 p.Tyr443Asn mutation. Because tightly regulated BMP signaling is critical for skeletal development and joint morphogenesis, our study shows that enhancing GDF6 activity has a significant impact on both prenatal joint development and postnatal joint maintenance. © 2023 American Society for Bone and Mineral Research (ASBMR).
The turning point of COVID‐19 severity is associated with a unique circulating neutrophil gene signature

COVID‐19 has a broad spectrum of clinical manifestations associated with the host immune response heterogeneity. Despite the advances in COVID‐19 research, it is still crucial to seek a panel of molecular markers that enable accurate stratification of COVID‐19 patients. Here, we performed a study that combined analysis of blood transcriptome, demographic data, clinical aspects and laboratory findings from 66 participants classified into different degrees of COVID‐19 severity and healthy subjects. We identified a perturbation in blood‐leukocyte transcriptional profile associated with COVID‐19 aggravation, which was mainly related to processes that disfavoured lymphocyte activation and favoured neutrophil activation. This transcriptional profile stratified patients according to COVID‐19 severity. Hence, it enabled identification of a turning point in transcriptional dynamics that distinguished disease outcomes and non‐hospitalized from hospitalized moderate patients. Central genes of this unique neutrophil signature were S100A9, ANXA3, CEACAM6, VNN1, OLFM4, IL1R2, TCN1 and CD177. Our study indicates the molecular changes that are linked with the differing clinical aspects presented by humans when suffering from COVID‐19, which involve neutrophil activation.
The relationship between noise-induced hearing loss and cognitive function

Abstract Introduction NIHL may affect some domains of cognitive function. This study was conducted to assess the relationship between NIHL and working memory, attention and response time. Materials and methods This was a cross-sectional study on 154 textile workers with exposure to noise higher than 85dBA in a textile factory. The participants were divided into two groups: with and without NIHL and some domains of cognitive function were compared between two groups. Wechsler working memory test and Stroop color-word test were used to measure working memory, selective attention and response time. Data were analyzed by SPSS (ver. 24) using student’s T test, and multiple linear regression model. Results Totally, 154 workers entered the study (77 with NIHL and 77 without NIHL). All participants were males. Working memory score and response time were higher and interference score was lower in NIHL group, although only the difference in working memory was significant. Due to the significant difference of age and work history between case and control groups, cognitive parameters were compared between two groups after adjusting for these two variables, but the significance was not changed. Conclusion This study showed that noised-exposed middle-aged males with NIHL had probably a lower working memory span than their counterparts without NIHL.
The formation of emulsions in definable fields of flow

The physical and chemical condition of emulsions of two fluids which do not mix has been the subject of many studies, but very little seems to be known about the mechanics of the stirring processes which are used in making them. The conditions which govern the breaking up of a jet of one fluid projected into another have been studied by Rayleigh and others, but most of these studies have been concerned with the effect of surface tension or dynamical forces in making a cylindrical thread unstable so that it breaks into drops. The mode of formation of the cylindrical thread has not been discussed. As a rule in experimental work it has been formed by projecting one liquid into the other under pressure through a hole. It seems that studies of this kind which neglect the disruptive effect of the viscous drag of one fluid on the other, though interesting in themselves, tell us very little about the manner in which two liquids can be stirred together to form an emulsion. When one liquid is at rest in another liquid of the same density it assumes the form of a spherical drop. Any movement of the out er fluid (apart from pure rotation or translation) will distort the drop owing to the dynamical and viscous forces which then act on its surface. Surface tension, however, will tend to keep the drop spherical. When the drop is very small, or the liquid very viscous, the stresses due to inertia will be small compared with those due to viscosity.
Genetic analysis of infectious bronchitis virus (IBV) in vaccinated poultry populations over a period of 10 years

ABSTRACT Infectious bronchitis virus (IBV) is an avian pathogen from the Coronavirus family causing major health issues in poultry flocks worldwide. Because of its negative impact on health, performance, and bird welfare, commercial poultry are routinely vaccinated by administering live attenuated virus. However, field strains are capable of rapid adaptation and may evade vaccine-induced immunity. We set out to describe dynamics within and between lineages and assess potential escape from vaccine-induced immunity. We investigated a large nucleotide sequence database of over 1700 partial sequences of the S1 spike protein gene collected from clinical samples of Dutch chickens submitted to the laboratory of Royal GD between 2011 and 2020. Relative frequencies of the two major lineages GI-13 (793B) and GI-19 (QX) did not change in the investigated period, but we found a succession of distinct GI-19 sublineages. Analysis of dN/dS ratio over all sequences demonstrated episodic diversifying selection acting on multiple sites, some of which overlap predicted N-glycosylation motifs. We assessed several measures that would indicate divergence from vaccine strains, both in the overall database and in the two major lineages. However, the frequency of vaccine-homologous lineages did not decrease, no increase in genetic variation with time was detected, and the sequences did not grow more divergent from vaccine sequences in the examined time window. Concluding, our results show sublineage turnover within the GI-19 lineage and we demonstrate episodic diversifying selection acting on the partial sequence, but we cannot confirm nor rule out escape from vaccine-induced immunity. RESEARCH HIGHLIGHTS Succession of GI-19 IBV variants in broiler populations. IBV lineages overrepresented in either broiler, or layer production chickens. Ongoing episodic selection at the IBV S1 spike protein gene sequence. Several positively selected codons coincident with N-glycosylation motifs.
Benchmark solution for unsteady state CFD problems

Unsteady convective dominated flows are Very common in engineering and science. There is a need to develop an accurate numerical scheme to predict unsteady flaw and heat transfer to understand the physics of instability and the flow evolution process. No numerical scheme is free from errors. It is essential to reduce the numerical errors to some extent, so that the prediction results are dependable. This article suggests two platform problems to test the accuracy of a time marching numerical scheme. One problem is buoyancy driven flow in a differentially heated cavity. This problem has importance in melting and solidification processes. The other problem is the forced flow in an oscillatory lid driven cavity. These problems are chosen because they have well-defined geometry, boundary, and initial conditions, yet the flow exhibits complexity and skewness with the grid line. High-order schemes are used to generate benchmark solutions for the mentioned problems. It is believed that Ike predicted results are .
Comparative Assessment of Indoor Positioning Technologies, Techniques, and Algorithms

Indoor positioning systems (IPS) are used to locate the position of objects in indoor environments. Due to its many real-world applications, IPS has garnered interest from both academia and industry. Each IPS is made up of three major components: sensor technology, position-finding technique, and operating algorithm. The goal of this paper is to examine and independently compare different types of components with the aim to understand and make useful suggestions for improvement. This paper also presents the past and current trends in IPS and predict the future trends in approaches to the design and implementation of IPS.
Thermosensitive and biodegradable PCL-based hydrogels: potential scaffolds for cartilage tissue engineering

Abstract Due to a lack of sufficient blood supply and unique physicochemical properties, the treatment of injured cartilage is laborious and needs an efficient strategy. Unfortunately, most of the current therapeutic approaches are, but not completely, unable to restore the function of injured cartilage. Tissue engineering-based modalities are an alternative option to reconstruct the injured tissue. Considering the unique structure and consistency of cartilage tissue (osteochondral junction), it is mandatory to apply distinct biomaterials with unique properties slightly different from scaffolds used for soft tissues. PCL is extensively used for the fabrication of fine therapeutic scaffolds to accelerate the restorative process. Thermosensitive PCL hydrogels with distinct chemical compositions have paved the way for sophisticated cartilage regeneration. This review aimed to collect recent findings regarding the application of PCL in hydrogels blended with natural, synthetic materials in the context of cartilage healing.
Slower Calcium Handling Balances Faster Cross-Bridge Cycling in Human MYBPC3 HCM

Background: The pathogenesis of MYBPC3-associated hypertrophic cardiomyopathy (HCM) is still unresolved. In our HCM patient cohort, a large and well-characterized population carrying the MYBPC3:c772G>A variant (p.Glu258Lys, E258K) provides the unique opportunity to study the basic mechanisms of MYBPC3-HCM with a comprehensive translational approach. Methods: We collected clinical and genetic data from 93 HCM patients carrying the MYBPC3:c772G>A variant. Functional perturbations were investigated using different biophysical techniques in left ventricular samples from 4 patients who underwent myectomy for refractory outflow obstruction, compared with samples from non-failing non-hypertrophic surgical patients and healthy donors. Human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes and engineered heart tissues (EHTs) were also investigated. Results: Haplotype analysis revealed MYBPC3:c772G>A as a founder mutation in Tuscany. In ventricular myocardium, the mutation leads to reduced cMyBP-C (cardiac myosin binding protein-C) expression, supporting haploinsufficiency as the main primary disease mechanism. Mechanical studies in single myofibrils and permeabilized muscle strips highlighted faster cross-bridge cycling, and higher energy cost of tension generation. A novel approach based on tissue clearing and advanced optical microscopy supported the idea that the sarcomere energetics dysfunction is intrinsically related with the reduction in cMyBP-C. Studies in single cardiomyocytes (native and hiPSC-derived), intact trabeculae and hiPSC-EHTs revealed prolonged action potentials, slower Ca2+ transients and preserved twitch duration, suggesting that the slower excitation-contraction coupling counterbalanced the faster sarcomere kinetics. This conclusion was strengthened by in silico simulations. Conclusions: HCM-related MYBPC3:c772G>A mutation invariably impairs sarcomere energetics and cross-bridge cycling. Compensatory electrophysiological changes (eg, reduced potassium channel expression) appear to preserve twitch contraction parameters, but may expose patients to greater arrhythmic propensity and disease progression. Therapeutic approaches correcting the primary sarcomeric defects may prevent secondary cardiomyocyte remodeling.
A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images

Abstract Motivation Mass Spectrometry Imaging (MSI) analyzes complex biological samples such as tissues. It simultaneously characterizes the ions present in the tissue in the form of mass spectra, and the spatial distribution of the ions across the tissue in the form of ion images. Unsupervised clustering of ion images facilitates the interpretation in the spectral domain, by identifying groups of ions with similar spatial distributions. Unfortunately, many current methods for clustering ion images ignore the spatial features of the images, and are therefore unable to learn these features for clustering purposes. Alternative methods extract spatial features using deep neural networks pre-trained on natural image tasks; however, this is often inadequate since ion images are substantially noisier than natural images. Results We contribute a deep clustering approach for ion images that accounts for both spatial contextual features and noise. In evaluations on a simulated dataset and on four experimental datasets of different tissue types, the proposed method grouped ions from the same source into a same cluster more frequently than existing methods. We further demonstrated that using ion image clustering as a pre-processing step facilitated the interpretation of a subsequent spatial segmentation as compared to using either all the ions or one ion at a time. As a result, the proposed approach facilitated the interpretability of MSI data in both the spectral domain and the spatial domain. Availabilityand implementation The data and code are available at https://github.com/DanGuo1223/mzClustering. Supplementary information Supplementary data are available at Bioinformatics online.
Curve Skeletons of Planar Domains

AbstractCurve skeletons are 1D entities that capture the essential topology and geometry of a shape in a simple and very compact form, and have found a multitude of applications in engineering and science. The concept itself is ill-defined, which is why the many existing definitions are ad-hoc and employ heuristic algorithms revolving around the (unique) medial axis. We propose a framework for computing curve skeletons for arbitrary planar domains that relies on a modified medial axis, and is based on R-functions that can be thought of as continuous forms of the Boolean logic functions. Furthermore, we propose one particular definition of such a curve skeleton that preserves the homotopy of the domain, is stable in the presence of noise and is well-suited to downstream applications. The framework can be implemented in any commercial geometric kernel for planar domains, and has attractive computational properties. Furthermore, the mathematical concepts are extendable to medial surfaces and curve skeletons .