Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of remote field electromagnetic boundary conditions on microwave-induced plasma torches

A flexible versatile electromagnetic model constructed with the PLASIMO platform is employed to explore electromagnetic features of microwave-induced plasma torches. The bases, formed by a full-vector formulation of the Maxwell equations, provide the possibility to formulate the boundary conditions in a natural way. Together with the use of a direct matrix solver this gives a convergence speed-up of more than a factor of 100 when compared with a scalar formulation on an azimuthal magnetic field that uses an iterative solver. As a result, this electromagnetic model is ready to act in future studies as part of the self-consistent description of plasma–electromagnetic coupling. With the electromagnetic model three types of configuration were studied: the closed, semi-open and open configurations, all three based on the same simplified model plasmas. It is found that the closed configuration, acting as a cavity for which (de)tuning is extremely sensitive for the plasma conditions, is less suitable for applications in which changes in plasma compositions can be expected. The semi-open configuration can be seen as a model for the practice often used in laboratories to place microwave-induced plasma torches in a grid that aims at protecting the environment against microwave electromagnetic radiation. Calculations show that this is good practice provided the radius of this cylindrical grid is in the order of 90 mm. For the most often used configuration, the open version, we found that the power balance as expressed by the coefficients of absorption, transmission and reflection depends on the electron density of the plasma. The reason is that the plasma acts as an antenna, which converts the electromagnetic waves from the coaxial structure to that of the expansion region, and that this antenna function depends on the electron density. The influence of various other antenna elements is investigated as well.
Observations supporting hypothetical commensalism and competition between two Campylobacter jejuni strains colonizing the broiler chicken gut

Campylobacter jejuni is the most prevalent bacterial foodborne pathogen in humans. Given the wide genetic diversity of C. jejuni strains found in poultry production, a better understanding of the relationships between these strains within chickens could lead to better control of this pathogen on farms. In this study, 14-day old broiler chickens were inoculated with two C. jejuni strains (103 or 107 CFU of D2008b and 103 CFU of G2008b, alone or together) that were previously characterized in vitro and that showed an opposite potential to compete for gut colonization in broilers. Liver samples and ileal and cecal contents were collected and used to count total C. jejuni and to quantify the presence of each strain using a strain specific qPCR or PCR approach. Ileal tissue samples were also collected to analyze the relative expression level of tight junction proteins. While a 103 CFU inoculum of D2008b alone was not sufficient to induce intestinal colonization, this strain benefited from the G2008b colonization for its establishment in the gut and its extraintestinal spread. When the inoculum of D2008b was increased to 107 CFU – leading to its intestinal and hepatic colonization – a dominance of G2008b was measured in the gut and D2008b was found earlier in the liver for birds inoculated by both strains. In addition, a transcript level decrease of JAM2, CLDN5 and CLDN10 at 7 dpi and a transcript level increase of ZO1, JAM2, OCLN, CLDN10 were observed at 21 dpi for groups of birds having livers contaminated by C. jejuni. These discoveries suggest that C. jejuni would alter the intestinal barrier function probably to facilitate the hepatic dissemination. By in vitro co-culture assay, a growth arrest of D2008b was observed in the presence of G2008b after 48 h of culture. Based on these results, commensalism and competition seem to occur between both C. jejuni strains, and the dynamics of C. jejuni intestinal colonization and liver spread in broilers appear to be strain dependent. Further in vivo experimentations should be conducted to elucidate the mechanisms of commensalism and competition between strains in order to develop adequate on-farm control strategies.
Efficacy of non-invasive brain stimulation on cognitive and motor functions in multiple sclerosis: A systematic review and meta-analysis

Objective In this study, we aimed to investigate the effects of non-invasive brain stimulation (NIBS) on cognitive and motor functions in patients with multiple sclerosis (pwMS). Methods A literature search was performed in the Cochrane Library, Embase, PubMed, Web of Science, Medline, CNKI, and Wan fang. The time interval used for database construction was up to December 2022, and the language was not limited. The collected trials were subsequently screened, the data were extracted, the quality was evaluated, and the effect sizes were computed using STATA/MP Version 13 for outcome analysis. Standard mean difference (SMD) and 95% confidence interval (CI) were calculated for domain of interest. Results In total, 17 articles that examined 364 patients with multiple sclerosis were included in this analysis. Non-invasive brain stimulation did not improve the overall cognitive function [SMD = 0.18, 95% CI (−0.32, 0.69), P = 0.475] but helped improve motor function in patients [SMD = 0.52, 95% CI (0.19, 0.85), P = 0.002]. Moreover, this study specifically indicated that non-invasive brain stimulation improved alerting [SMD = 0.68, 95% CI (0.09, 1.26), P = 0.02], whereas non-invasive brain stimulation intervention improved motor function in patients aged <45 years [SMD = 0.67, 95% CI (0.23, 1.10), P = 0.003] and in patients with expanded disability status scale scores (EDSS) <3.5 [SMD = 0.82, 95% CI (0.22, 1.42), P = 0.007]. In particular, NIBS contributed to the improvement of spasticity in pwMS [SMD = 0.68, 95% CI (0.13, 1.23), P = 0.015]. Conclusion These results of this present study provide evidence that non-invasive brain stimulation could improve alertness in pwMS. Furthermore, NIBS may help pwMS with motor function and those who are under 45 years of age or with EDSS < 3.5 improve their motor function. For the therapeutic use of NIBS, we recommend applying transcranial magnetic stimulation as an intervention and located on the motor cortex M1 according to the subgroup analysis of motor function. These findings warrant verification. Systematic review registration https://www.crd. york.ac. uk/PROSPERO/, identifier CRD42022301012.
A study of Population MCMC for estimatingBayes Factors over nonlinear ODE models

Higher resolution biological data is now becoming available in ever greater quantities, allowing the complex behaviour of fundamental biological processes to be studied in much more detail. The area of Systems Biology is in desperate need of methods for inferring the most likely topology of the underlying genetic networks from this oftentimes noisy and poorly sampled data, to support the construction and testing of new model hypotheses. Towards that end, Bayesian methodology provides an ideal framework for tackling such challenges, and in particular offers a means of objectively comparing competing plausible models through the estimation of Bayes factors. There are, however, formidable obstacles which must be overcome to allow model inference using Bayes factors to be of practical use. Many important biological processes may be most accurately represented using nonlinear models based on systems of ordinary differential equations (ODEs), however parameter inference over these models often produces correspondingly nonlinear posterior distributions, which are very challenging to sample from, often resulting in biased marginal likelihood estimates with large variances. Such problems are commonly encountered when modelling circardian rhythms, which exhibit highly nonlinear oscillatory dynamics and play a central role in the overall functioning of most organisms. In this thesis I investigate tools for calculating Bayes factors to distinguish between ODE-based Goodwin oscillator models of varying complexity, which form the basic building blocks for describing this ubiquitous circadian behaviour. The main result in Chapter 3 of this thesis demonstrates how Population Markov Chain Monte Carlo may be employed in conjunction with thermodynamic integration methods to estimate Bayes factors which may accurately distinguish between two nonlinear oscillator models of varying complexity, given noisy experimental data generated from each of the models. In addition, it is shown how alternative methods may fail drastically in this setting, in particular harmonic mean based estimates. Suggestions are given regarding the optimal temperature schedule which should be employed for Population MCMC, and several ideas for future research extending this work are also discussed.
Infrastructure development, human development index, and CO2 emissions in China: A quantile regression approach

This study investigates the relationships between infrastructure development, human development index (HDI), and CO2 emissions in China. Infrastructure has played an essential role in achieving social and economic developmental goals in China, but environmental pollution has significantly increased in the country in the last two decades. Our analysis uses time series data from 1990 to 2021 and quantile regressions, and we find that infrastructure has positive and statistically significant relationships with HDI, CO2 emissions, and GDP in all quantiles. Recent infrastructure upgrades improve living standards and increase HDI but damage the environment, and infrastructure is the main source of CO2 emissions in the country. Therefore, the government should invest in sustainable infrastructure to mitigate CO2 emissions. The government may consider infrastructure options such as low carbon transportation, including railway infrastructure, urban metros, and light rail.
Biologically Important Areas II for cetaceans within U.S. and adjacent waters – Hawaiʻi Region

In this assessment we incorporated published and unpublished information to delineate and score Biologically Important Areas (BIAs) for cetaceans in the Hawaiʻi region following standardized criteria. Twenty-six cetacean species have been documented in Hawaiʻi. Eleven odontocete species have distinct small populations resident to one or more island areas: rough-toothed dolphins, pantropical spotted dolphins, common bottlenose dolphins, spinner dolphins, short-finned pilot whales, false killer whales, pygmy killer whales, melon-headed whales, Blainville’s beaked whales, Cuvier’s beaked whales, and dwarf sperm whales. Eight species of mysticetes have been documented, although their occurrence and behavior are poorly understood, with the exception of breeding humpback whales and, more recently, common minke whales. Thirty-five BIAs were delineated or revised from the initial 2015 effort: 33 for small and resident odontocete populations and two for humpback whale reproductive areas. Hierarchical BIAs reflecting core areas of use or population-specific ranges were delineated for nine species. Reproductive watch list areas were designated for common minke whales in the main Hawaiian Islands (MHI) and humpback whales in the Northwestern Hawaiian Islands (NWHI); these areas did not meet the criteria for a BIA due to limited supporting information. All but three BIAs were in the MHI, reflecting the disparities in research effort between this region and the NWHI. Spatial extents of BIA boundaries ranged from 457 km2 to 138,001 km2 (median = 8,299 km2). Scores (range: 1-3) for Data Support and Boundary Certainty were moderate to high (mean = 2.40 and 2.43, respectively), while Intensity and Importance scores were slightly lower (mean = 1.94 and 1.89, respectively). Many of the Hawaiʻi species have been extensively studied over several decades; accordingly, this region ranks among the highest in terms of Data Support relative to other regions. BIAs presented here describe known ranges of small resident populations, intensities of use, and uncertainties in important areas for cetaceans in Hawaiʻi based on the best available data, and have also revealed knowledge gaps to guide future research efforts.
An eye-tracking study on visual perception of vegetation permeability in virtual reality forest exposure

Previous studies have confirmed the significant effects of single forest stand attributes, such as forest type (FT), understory vegetation cover (UVC), and understory vegetation height (UVH) on visitors' visual perception. However, rarely study has yet clearly determined the relationship between vegetation permeability and visual perception, while the former is formed by the interaction of multiple forest stand attributes (i.e., FT, UVC, UVH). Based on a mixed factor matrix of FT (i.e., coniferous forests and broadleaf), UVC level (i.e., 10, 60, and 100%), and UVH level (0.1, 1, and 3 m), the study creates 18 immersive virtual forest videos with different stand attributes. Virtual reality eye-tracking technology and questionnaires are used to collect visual perception data from viewing virtual forest videos. The study finds that vegetation permeability which is formed by the interaction effect of canopy density (i.e., FT) and understory density (i.e., UVC, UVH), significantly affects participant's visual perception: in terms of visual physiology characteristics, pupil size is significantly negatively correlated with vegetation permeability when participants are viewing virtual reality forest; in terms of visual psychological characteristics, the understory density formed by the interaction of UVC and UVH has a significant impact on visual attractiveness and perceived safety and the impact in which understory density is significantly negatively correlated with perceived safety. Apart from these, the study finds a significant negative correlation between average pupil diameter and perceived safety when participants are viewing virtual reality forests. The findings may be beneficial for the maintenance and management of forest parks, as well as provide insights into similar studies to explore urban public green spaces.
Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat

The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02–10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.
Impulsive choice in two different rat models of ADHD—Spontaneously hypertensive and Lphn3 knockout rats

Introduction Impulsivity is a symptom of attention-deficit/hyperactivity disorder (ADHD) and variants in the Lphn3 (Adgrl3) gene (OMIM 616417) have been linked to ADHD. This project utilized a delay-discounting (DD) task to examine the impact of Lphn3 deletion in rats on impulsive choice. “Positive control” measures were also collected in spontaneously hypertensive rats (SHRs), another animal model of ADHD. Methods For Experiment I, rats were given the option to press one lever for a delayed reward of 3 food pellets or the other lever for an immediate reward of 1 pellet. Impulsive choice was measured as the tendency to discount the larger, delayed reward. We hypothesized that impulsive choice would be greater in the SHR and Lphn3 knockout (KO) rats relative to their control strains - Wistar-Kyoto (WKY) and Lphn3 wildtype (WT) rats, respectively. Results The results did not completely support the hypothesis, as only the SHRs (but not the Lphn3 KO rats) demonstrated a decrease in the percent choice for the larger reward. Because subsequent trials did not begin until the end of the delay period regardless of which lever was selected, rats were required to wait for the next trial to start even if they picked the immediate lever. Experiment II examined whether the rate of reinforcement influenced impulsive choice by using a DD task that incorporated a 1 s inter-trial interval (ITI) immediately after delivery of either the immediate (1 pellet) or delayed (3 pellet) reinforcer. The results of Experiment II found no difference in the percent choice for the larger reward between Lphn3 KO and WT rats, demonstrating reinforcement rate did not influence impulsive choice in Lphn3 KO rats. Discussion Overall, there were impulsivity differences among the ADHD models, as SHRs exhibited deficits in impulsive choice, while the Lphn3 KO rats did not.
Response of the ionosphere to the seismic trigerred acoustic waves: Electron density and electromagnetic fluctuations

SUMMARY We study the excitation of low-frequency (0.001‐10 Hz) electromagnetic and density fluctuations in the ionosphere during the passage of seismic triggered acoustic waves (AWs). The study involves the generation of ionospheric currents by AWs and subsequent perturbations of the electromagnetic fields and ion and electron density. In this study, the non-local analysis of the fluctuations is carried out in the framework of hydromagnetic theory. Our objective is to examine the spatial and frequency distributions of these fluctuations and to compare them qualitatively with the available observations. The dynamics of both electrojet and F region of ionosphere are included. Also included are the effects of the dip-angle variations of the Earth’s magnetic field. Significant anisotropy and inhomogeneities are noted in the fluctuations. The amplitudes of current and magnetic field fluctuations are found to be maximum in the F region where ion inertia is large enough to support the plasma waves and where electron number density and acoustic wave amplitudes are also large. The density fluctuations also follow similar trends. Both electromagnetic and density fluctuations are large in the latitude region where the acoustic wave vibration parallel to the Earth’s magnetic field is large. The fluctuations have the tendency to be maximum in the 0.1‐1 Hz frequency range. In this range, AWs driven currents and electromagnetic fluctuations may become of order of μAm −2 ,n V m −1 and nT, respectively in the F region.
The structure of low-frequency standing Alfvén waves in the box model of the magnetosphere with magnetic field shear

The paper is concerned with the influence of magnetic field shear on the structure of Alfvén waves standing along field lines in the one-dimensionally inhomogeneous box model of the magnetosphere, enclosed between two parallel, infinitely conducting planes (ionospheres). We consider the transverse small-scale Alfvén waves whose azimuthal component of the wave vector $k_y$ satisfies the condition $k_y l\,{\gg}\,1$, where $l$ is the distance between the ionospheres. For this model, the Alfvén resonance condition has been established. It is shown that resonance can also occur at a constant Alfvén velocity if the field-line inclination to the ionosphere is changed. On resonant magnetic shells there occurs a singularity of the wave field of the same kind as in the absence of shear. Moreover, there are found many resemblances between Alfvén-wave behavior in our one-dimensionally inhomogeneous model and in two-dimensional inhomogeneous models with plasma and magnetic field parallel inhomogeneity taken into account. Thus, the presence of shear leads to a difference of the frequencies of poloidal and toroidal oscillations of field lines, and to the dependence of the wave's frequency on the transversal components of wave vector. Then, in the sheared magnetic field with highly conductive boundaries the source excites multiple standing Alfvén harmonics at different locations. In general, the localization regions of different longitudinal harmonics overlap. However, in the small but finite shear limit, a total wave field represents a set of mutually isolated transparent regions corresponding to different harmonic numbers. In each of these regions the waves are found to be travelling across the magnetic shells, and the transparent region is limited in the coordinate $x$ by two turning points, at one of which the mode is poloidally polarized, and the other point it is toroidally polarized (it is at this latter point where Alfvén resonance occurs). Furthermore, the phase velocity of the wave is directed toward the poloidal point, and the group velocity is directed at the toroidal point.
Molecular subtypes predict the preferential site of distant metastasis in advanced breast cancer: a nationwide retrospective study

Objective This study aimed to explore possible associations between molecular subtypes and site of distant metastasis in advanced breast cancer (ABC). Methods 3577 ABC patients were selected from 21 hospitals of seven geographic regions in China from 2012-2014. A questionnaire was designed to collect medical information regarding demographic characteristics, risk factors, molecular subtype, recurrence/metastasis information, and disease-free survival (DFS). The cancers were classified into Luminal A, Luminal B, HER2-enriched and Triple Negative subtypes. Chi-square test and multivariate Cox proportional hazard models were performed to explore the associations between molecular subtypes and distant metastasis sites. Results A total of 2393 cases with molecular subtypes information were finally examined. Patients with Luminal A (51.1%) and Luminal B (44.7%) were most prone to bone metastasis, whereas liver metastasis was more frequently observed in HER2-enriched ABC patients (29.1%). The cumulative recurrence and metastasis rates of ABC patients at 36 months of DFS were the most significant within molecular types, of which Triple Negative was the highest (82.7%), while that of Luminal A was the lowest (58.4%). In the adjusted Cox regression analysis, Luminal B, HER2-enriched and Triple Negative subtypes increased the risk of visceral metastasis by 23%, 46% and 87% respectively. In addition, Triple Negative patients had a higher probability of brain metastasis (HR 3.07, 95% CI: 1.04-9.07). Conclusion Molecular subtypes can predict the preferential sites of distant metastasis, emphasizing that these associations were of great help in choices for surveillance, developing appropriate screening and cancer management strategies for follow-up and personalized therapy in ABC patients.