Miracle-dz/UniFAR-FTUs huggingface dataset:
NEW RESULTS OF SOLAR ACTIVITY AND MAGNTIC FIELD ON THE SUN (REVIEW)

For the last decade the solar space missions (e.g. Yohkoh, Coronas, Ulysses, SOHO) make a progress in the investigations of the solar activity in Photosphere, Corona and solar wind. The Hinode and Stereo space labs continue the progress of previous missions and extend our knowledge about the solar activity, an evolution of vector magnetic field, a structure of photosphere, chromosphere and corona. Upcoming Solar Dynamics Observatory will investigate the vector magnetic field, corona and solar irradiance with a purpose to understand the nature of the solar cycle on the base of the high- resolution images. In this paper, I review the recent and most important results of the investigation of the solar activity from the interior to the corona and their relationship to the dynamo theory.
Nucleation of rotating crystals by Thiovulum majus bacteria

Thiovulum majus self-organize on glass surfaces into active two-dimensional crystals of rotating cells. Unlike classical crystals, these bacterial crystallites continuously rotate and reorganize as the power of rotating cells is dissipated by the surrounding flow. In this article, we describe the earliest stage of crystallization, the attraction of two bacteria into a hydrodynamically-bound dimer. This process occurs in three steps. First a free-swimming cell collides with the wall and becomes hydrodynamically bound to the two-dimensional surface. We present a simple model to understand how viscous forces localize cells near the chamber walls. Next, the cell diffuses over the surface for an average of 63 ± 6 s before escaping to the bulk fluid. The diffusion coefficient D eff = 7.98 ± 0.1 μ m 2 s − 1 of these 8.5 μ m diameter cells corresponds to a temperature of ( 4.16 ± 0.05 ) × 10 4 K, and thus cannot be explained by equilibrium fluctuations. Finally, two cells coalesce into a rotating dimer when the convergent flow created by each cell overwhelms their active Brownian motion. This occurs when cells diffuse to within a distance of 13.3 ± 0.2 μm of each other.
Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system.
Indirect Search for Dark Matter with the KM3NeT Neutrino Telescope

Neutrino telescopes aim to detect dark matter indirectly by observing the neutrinos produced by pair-annihilations or decays of weakly interacting massive particles (WIMPs). A signal excess of neutrinos resulting from the pair-annihilation of WIMPs can be detected in regions where large amounts of dark matter might accumulate. One possible source is the Sun, where WIMPs are expected to accumulate due to their scatterings in the dense core of the star. The dark matter halo of the Milky Way is another possible close dark matter container. The KM3NeT observatory is composed of two undersea Cherenkov neutrino telescopes (ORCA and ARCA) located in two sites in the Mediterranean Sea, offshore of France and Italy. The two detector configurations are optimised for the detection of neutrinos of different energies, which allows the search for WIMPs in a wide mass range, from the GeV to the TeV scale. In this contribution, searches for WIMP annihilations in the Galactic Centre and the Sun are presented. An unbinned likelihood method is used to discriminate the signal from the background in a 300-day livetime sample of the ARCA detector, and a 543-day sample of the ORCA detector. The limits on the velocity-averaged pair-annihilation cross section of WIMPs are computed for five different primary annihilation channels. For the ORCA analysis, the limits on the spin-dependent and spin-independent scattering cross sections are given for three annihilation channels.
Evaluation of Diagnostic Accuracy and its Standard Error using Constant Shape Weibull Mixture ROC Curve

Receiver Operating Characteristic (ROC) Curve is a widely used classification technique in Medical Diagnosis which classifies the healthy and diseased individuals on the basis of optimal cut off value of the biomarker. In this article, we have proposed Constant Shape Weibull Mixture ROC (CSWMROC) model. The properties of CSWMROC Curve are discussed and expressions for AUC, its variance and confidence interval are derived. The estimates of AUC of CSWMROC curve are obtained using Method of Moments (MOM). Numerical example is considered to support the proposed theory.
Cloning and Expression of Class I Chitinase Genes from Four Mangrove Species under Heavy Metal Stress

Chitinases are believed to act as defense proteins when plants are exposed to heavy metal stress. Typical Class I chitinase genes were cloned from Bruguiera gymnorrhiza, Rhizophora stylosa, Kandelia obovata, and Avicennia marina using the methods of reverse-transcription–polymerase chain reaction and rapid amplification of cDNA ends. All four cDNA sequences of chitinase from the mangrove plants were 1092 bp in length and consisted of an open reading frame of 831 bp, encoding 276 amino acids. However, there were differences in the sequences among the four mangrove species. Four gene proteins have a signal peptide, are located in the vacuole, and belong to the GH19 chitinase family. The sequence of chitinase was highly similar to the protein sequences of Camellia fraternal chitinases. A real-time polymerase chain reaction was used to analyze the chitinase expressions of the above four mangrove species exposed to different concentrations of heavy metal at different times. The gene expression of chitinase was higher in Bruguiera gymnorrhiza leaves than in other mangrove plant species. With an increase in heavy metal stress, the expression level of Bruguiera gymnorrhiza increased continuously. These results suggest that chitinase plays an important role in improving the heavy metal tolerance of mangrove plants.
A GRAPH REGULARIZATION BASED APPROACH FOR GENE SCORING AND GENE SET SELECTION AS APPLIED TO GLIOBLASTOMA MULTIFORME

One of the major challenges in cancer research is the problem of distinguishing driver mutations which drive neoplastic behavior and passenger mutations which have no functional purpose. The advent of high-throughput molecular assays have allowed tremendous amounts of data to be collected at fairly large sample sizes. However, it is difficult to approach the task of identifying a handful of critical genetic changes from the chaotic background alterations that is typically present in most tumor cells. This work presents a 2 stage gene scoring and gene set selection algorithm which is designed firstly to deal with missing information in a graceful manner and secondly to allow the user to leverage prior knowledge in the form of protein-interaction networks. The proposed approach is applied to the TCGA GBM dataset where it is shown that it robust to multiple forms of missing data and performs well at the task of gene prioritization and selection. Finally, the approach is used to analyze the Proneural patient cluster in GBM which shows poor response to aggressive treatment. A biologically plausible candidate pathway of 3 genes is found by our methods and is shown to be significantly associated with survival on an external validation dataset.
Optimizing Selection Criteria for the CALET Ultra-Heavy Cosmic Ray Analysis

CALET, the Calorimetric Electron Telescope, launched to the International Space Station in August 2015 and in continuous operation since, has gathered over seven years of data so far. CALET is able to measure cosmic-ray (CR) electrons, nuclei, and gamma rays and with its 27 radiation length deep Total Absorption Calorimeter (TASC), measures particle energy, allowing for the determination of spectra and secondary to primary ratios of the more abundant CR nuclei through 28 Ni, while the main charge detector (CHD) can measure Ultra-Heavy (UH) CR nuclei through 40 Zr. CALET UHCR analyses use a special high duty cycle UH trigger with an expanded geometry that does not require passage through the TASC. To effectively analyze UHCR trigger events, a number of screens and corrections have been developed for the analysis. From time-and position-dependent detector response corrections based on 14 Si and 26 Fe, to an angle-dependent geomagnetic cutoff rigidity selections and minimum deposited energy screens, a number of methods have been explored to optimize UH statistics to varying effect. In this work, we aim to show how these event selection screens and corrections have been developed, how the rigidity screens shown previously by Rauch et al. [1] compare to the newer TASC methodology shown in Zober et al. (2023) [2], and how TASC selections may be used to influence analysis on the full UH-trigger dataset.
What makes a satisfying user experience in the context of human-computer interaction?

The purpose of this research is to study the relations of user interface aesthetics, usability, and user experience in the context of human-computer interaction (HCI). This study aims to discover the key factors contributing to a satisfying user experience from the user’s perspective. We present a novel user experience model that connects perceived usability, and its subcharacteristics, into perceived user experience, and to the emotional responses it evokes. The ISO/IEC 205010:2011 standard of the International Standardization Organization will act as a framework for the constructed user experience model, combining characteristics from both Product Quality and Quality-in-Use. An empirical study including 149 participants, consisting mostly of young, Finnish university students, will be conducted, in which the respondents evaluate three European festival websites by 28 different user experience aspects per each website. A partial least squares structural equation modeling (PLS-SEM) will be used as a statistical methodology in order to discover the structural relations between usability subcharacteristics (Appropriateness Recognizability, User Interface Aesthetics, Learnability and Operability) and Satisfying User Experience in HCI.
Agreement assessment in size measurement of hepatic metastases

The purpose of the study was to investigate patient-wise agreement among multiparametric magnetic resonance (MR) imaging sequences and radiologists, respectively, in the size assessment of hepatic metastases. A total of 30 liver metastases were identified from 20 patients and three radiologists independently measured the long and short axes for all metastases in T1-weighted, T2-weighted, diffusion-weighted imaging (DWI) with b of 0 and 800 s/mm2, and the apparent diffusion coefficient (ADC) map. We calculated the patient-wise intraclass correlation coefficient (ICCs) to estimate the interobserver and intersequence agreement in measured lesion size. Interobserver ICCs were 0.92-0.98 for different MR sequences and intersequence ICCs were 0.93-0.98. In conclusion, multiparametric MR imaging is a reliable tool for hepatic metastatic lesion measurement.
Short-term Recognition of Timbre Sequences

The goal of the current study was to explore outstanding questions in the field of timbre perception and cognition—specifically, whether memory for timbre is better in trained musicians or in nonmusicians, whether short-term timbre recognition is invariant to pitch differences, and whether timbre dissimilarity influences timbre recognition performance. Four experiments examined short-term recognition of musical timbre using a serial recognition task in which listeners indicated whether the orders of the timbres of two subsequently presented sound sequences were identical or not. Experiment 1 revealed significant effects of sequence length on recognition accuracy and an interaction of music training and pitch variability: musicians performed better for variable-pitch sequences, but did not differ from nonmusicians with constant-pitch sequences. Experiment 2 yielded a significant effect of pitch variability for musicians when pitch patterns varied between standard and comparison sequences. Experiment 3 high-lighted the impact of the timbral dissimilarity of swapped sounds and indicated a recency effect in timbre recognition. Experiment 4 confirmed the importance of the dissimilarity of the swap, but did not yield any pertinent role of timbral heterogeneity of the sequence. Further analyses confirmed the strong correlation of the timbral dissimilarity of swapped sounds with response behavior, accounting for around 90% of the variance in response choices across all four experiments. These results extend findings regarding the impact of music training and pitch variability from the literature on timbre perception to the domain of short-term memory and demonstrate the mnemonic importance of timbre similarity relations among sounds in sequences. The role of the factors of music training, pitch variability, and timbral similarity in music listening is discussed.
Kinematic and chemical analysis of PNe in NGC 3109

Abstract We present high resolution spectroscopy obtained with MIKE-Magellan and MES OAN-SPM of a number of planetary nebulae (PNe) and H ii regions, distributed along the dwarf irregular galaxy NGC 3109 and compare their kinematical behavior with the one of H i data. We aim to determine if there is a kinematical connection among these objects. We also perform a revision of the chemical composition of PNe and H ii regions in this galaxy and discuss it in comparison with stellar evolution models.
Morphological and Molecular Changes in the Cortex and Cerebellum of Immunocompetent Mice Infected with Zika Virus

Zika virus (ZIKV) disease continues to be a threat to public health, and it is estimated that millions of people have been infected and that there have been more cases of serious complications than those already reported. Despite many studies on the pathogenesis of ZIKV, several of the genes involved in the malformations associated with viral infection are still unknown. In this work, the morphological and molecular changes in the cortex and cerebellum of mice infected with ZIKV were evaluated. Neonatal BALB/c mice were inoculated with ZIKV intraperitoneally, and the respective controls were inoculated with a solution devoid of the virus. At day 10 postinoculation, the mice were euthanized to measure the expression of the markers involved in cortical and cerebellar neurodevelopment. The infected mice presented morphological changes accompanied by calcifications, as well as a decrease in most of the markers evaluated in the cortex and cerebellum. The modifications found could be predictive of astrocytosis, dendritic pathology, alterations in the regulation systems of neuronal excitation and inhibition, and premature maturation, conditions previously described in other models of ZIKV infection and microcephaly.
A Modified Constitutive Model for Isotropic Hyperelastic Polymeric Materials and Its Parameter Identification

Given the importance of hyperelastic constitutive models in the design of engineering components, researchers have been developing the improved and new constitutive models in search of a more accurate and even universal performance. Here, a modified hyperelastic constitutive model based on the Yeoh model is proposed to improve its prediction performance for multiaxial deformation of hyperelastic polymeric materials while retaining the advantages of the original Yeoh model. The modified constitutive model has one more correction term than the original model. The specific form of the correction term is a composite function based on a power function represented by the principal stretches, which is derived from the corresponding residual strain energy when the Yeoh model predicts the equibiaxial mode of deformation. In addition, a parameter identification method based on the cyclic genetic-pattern search algorithm is introduced to accurately obtain the parameters of the constitutive model. By applying the modified model to the experimental datasets of various rubber or rubber-like materials (including natural unfilled or filled rubber, silicone rubber, extremely soft hydrogel and human brain cortex tissue), it is confirmed that the modified model not only possesses a significantly improved ability to predict multiaxial deformation, but also has a wider range of material applicability. Meanwhile, the advantages of the modified model over most existing models in the literatures are also demonstrated. For example, when characterizing human brain tissue, which is difficult for most existing models in the literature, the modified model has comparable predictive accuracy with the third-order Ogden model, while maintaining convexity in the corresponding deformation domain. Moreover, the effective prediction ability of the modified model for untested equi-biaxial deformation of different materials has also been confirmed using only the data of uniaxial tension and pure shear from various datasets. The effective prediction for the untested equibiaxial deformation makes it more suitable for the practice situation where the equibiaxial deformation of certain polymeric materials is unavailable. Finally, compared with other parameter identification methods, the introduced parameter identification method significantly improves the predicted accuracy of the constitutive models; meanwhile, the uniform convergence of introduced parameter identification method is also better.
Two-dimensional derivatives obtained by oxidation of MXene for simulating the oxidative properties of natural enzymes

Oxidation-derived nanoparticles (CDs/TiO x ) of Ti3C2 were prepared for the first time by simple oxidation of Ti3C2. CDs/TiO x was a two-dimensional hybrid of amorphous carbon and titanium oxides with a lateral dimension of about 50 nm. H2O2 was used as the oxygenator and the reduction product was H2O, which was environmentally friendly and inexpensive. Carboxyl, carbonyl, and hydroxyl groups are formed naturally during the oxidation derivative process. The decreased size increases the specific surface area and provides the possibility for the abundant presence of functional groups. The oxidation process converts MXene from reducing to oxidizing and achieves the ability of the derivatives to mimic peroxidase. Compared with natural horseradish peroxidase, the Michaelis constant for H2O2 was ten-fold lower. A cascade catalytic reaction system of glucose oxidase with CDs/TiO x was constructed, and the generated H2O2 could be further used to catalyze the oxidation of nicotinamide adenine dinucleotide (NADH) to NAD+. With the assistance of NAD+-dependent dehydrogenase, NADH could be restored to 95% of the initial level. This assay system can detect glucose levels scientifically and accurately in the range of 0.02–10 mM and remains viable after 20 cycles.
Cross-format integration between spoken number words and Arabic digits

Spoken number words and Arabic digits are the most commonly used numerical symbols. We often transcode numerals from one to another, thus, the correspondence between them should become over-learned and automatic after years of usage. It has been shown that an integration usually exists when pairing of stimulus is over-learned, and is often reflected in the mismatch negativity (MMN). The current thesis conducted two behavioural experiments (Chapter 2) and three EEG experiments (Chapter 3 - 5) to systematically investigate the cross-modal correspondence, i.e., the integration, between spoken number words and Arabic digits in adult participants. In the behavioural experiments, a clear distance effect is shown in an audiovisual matching task. This suggests that an amodal, shared magnitude representation is activated for cross-modal numerals during a matching judgment. Moreover, the distance effect is modulated by stimulus onset asynchrony (SOA). That is, the distance effect becomes smaller with the increase of SOA. This is similar to the data pattern of a common integration effect because an integration usually shows when cross-modal stimuli are temporally close. However, a disadvantage of a behavioural task is that the RTs could be influenced by response-selection or response-execution. Hence, I then used an oddball paradigm in which no responses are required for the cross-modal numerals in my EEG experiments. The results of three EEG experiments showed that an early integration effect exists between spoken number words and Arabic digits in the mismatch negativity (MMN). This result is first to show the presence of a cross-format integration between spoken number words and Arabic digits. However, the integration effect is also modulated by distance as well as stimulus onset asynchrony (SOA), which may suggest that the cross-modal correspondence between audiovisual numerals is more complicated than other kinds of audiovisual stimuli, such as letters and speech sounds.
Investigating the VHE Gamma-ray Sources Using Deep Neural Networks

The upcoming Cherenkov Telescope Array (CTA) will dramatically improve the point-source sensitivity compared to the current Imaging Atmospheric Cherenkov Telescopes (IACTs). One of the key science projects of CTA will be a survey of the whole Galactic plane (GPS) using both southern and northern observatories, specifically focusing on the inner galactic region. We extend a deep learning-based image segmentation software pipeline (autosource-id) developed on Fermi-LAT data to detect and classify extended sources for the simulated CTA GPS. Using updated instrument response functions for CTA (Prod5), we test this pipeline on simulated gamma-ray sources lying in the inner galactic region (specifically 0 ◦ < 𝑙 < 20 ◦ , | 𝑏 | < 3 ◦ ) for energies ranging from 30 GeV to 100 TeV. Dividing the source extensions ranging from 0 . 03 ◦ to 1 ◦ in three different classes, we find that using a simple and light convolutional neural network it is possible to achieve a 97% global accuracy in separating the extended sources from the point-like sources. The neural net architecture including other data pre-processing codes is available online
VAE-based latent-space classification of RNO-G data

The Radio Neutrino Observatory in Greenland (RNO-G) is a radio-based ultra-high energy neutrino detector located at Summit Station, Greenland. It is still being constructed, with 7 stations currently operational. Neutrino detection works by measuring Askaryan radiation produced by neutrino-nucleon interactions. A neutrino candidate must be found amidst other backgrounds which are recorded at much higher rates -- including cosmic-rays and anthropogenic noise -- the origins of which are sometimes unknown. Here we describe a method to classify different noise classes using the latent space of a variational autoencoder. The latent space forms a compact representation that makes classification tractable. We analyze data from a noisy and a silent station. The method automatically detects and allows us to qualitatively separate multiple event classes, including physical wind-induced signals, for both the noisy and the quiet station.