Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermal stability of winds driven by radiation pressure in super-Eddington accretion discs

Ultraluminous X-ray sources (ULXs) are mainly powered by accretion in neutron stars or stellar-mass black holes. Accreting at rates exceeding the Eddington limit by factors of a few up to hundreds, radiation pressure is expected to inflate the accretion disc, and drive fast winds that have in fact been observed at significant fractions of the speed of light. Given the super-Eddington luminosity, the accretion disc will be thicker than in sub-Eddington accretors such as common active galactic nuclei and X-ray binaries, leading to a different spectral energy distribution and, possibly, a different thermal status of the wind. Here, we show the first attempt to calculate the photoionization balance of the winds driven by strong radiation pressure in thick discs with a focus on ULXs hosting black holes or non-magnetic neutron stars. We find that the winds are generally in thermally stable equilibrium, but long-term variations in the accretion rate and the inclination due to precession may have significant effects on the wind appearance and stability. Our model trends can explain the observed correlation between the spectral residuals around 1 keV and the ULX spectral state. We also find a possible correlation between the spectral hardness of the ULX, the wind velocity, and the ionization parameter in support of the general scenario.
Research into the corona current characteristics of polluted insulators

The contamination influences the corona performance of transmission line insulator strings very much. Not only do they change the corona-originated voltage, but also change the quantity and amplitude of the corona pulses. This paper describes experiments into the corona current at diverse contaminating condition and various voltages. The experimental results show that the corona pulses conform to statistic rules and can be used to distinguish faulty insulators from transmission line insulator strings at the definite environmental condition. A fuzzy membership function is established according to the results which can be used as one of the preconditions to detect faulty insulators.
Circumnuclear Multiphase Gas in the Circinus Galaxy. II. The Molecular and Atomic Obscuring Structures Revealed with ALMA

We used the Atacama Large Millimeter/Submillimeter Array (ALMA) to map the CO(3–2) and [C i](1–0) lines, as well as their underlying continuum emission, from the central ∼200 pc region of the Circinus galaxy that hosts the nearest type 2 Seyfert-class active galactic nucleus (AGN), with a spatial resolution of ∼6–15 pc. The lines and continuum-emitting regions consist of a circumnuclear disk (CND; 74 pc × 34 pc) and spiral arms. The distribution of the continuum emission revealed a temperature-dependent dust geometry and possibly polar dust elongation in the torus region. The molecular mass of the CND is , with a beam-averaged H2 column density of ∼5 × 1023 cm−2 toward the AGN position, which contributes significantly to the nuclear obscuration. The [C i](1–0)/CO(3–2) ratio at the AGN position is unusually high, suggesting an X-ray-dominated region-type chemistry. We decomposed the observed velocity fields into rotational and dispersion components, and revealed a multiphase dynamic nature in the r ≲ 10 pc torus region, i.e., the diffuse atomic gas is more spatially extended along the vertical direction of the disk than the dense molecular gas. Through comparisons with our model predictions based on the radiation-driven fountain scheme, we indicate that atomic outflows are the driver of the geometrical thickness of the atomic disk. This supports the validity of the radiation-driven fountain scheme in the vicinity of this AGN, which would explain the longstanding mystery of the physical origin of the AGN torus.
Methods Forum L2 GRIT A LONGITUDINAL CONFIRMATORY FACTOR ANALYSIS-CURVE OF FACTORS MODEL

Given the longitudinal nature of L2 grit, the use of conventional research methodologies with cross-sectional data to examine the validity of L2 grit scale seems inadequate. The present research was an attempt to extend the domain-speci ﬁ c phase of research on L2 grit, with the pursuit of long-term goals at its core, into a dynamic one. Thus, we adopted a longitudinal con ﬁ rmatory factor analysis-curve of factors model (LCFA-CFM) approach to trace changes in L2 learners ’ grit at different points of time in an EFL course. LCFA-CFM ensures measurement invariance over time, deals with second-order latent variables, takes into account measurement errors, and is capable of assessing interindividual differences. Withthis inmind, we, ﬁ rst, employed LCFA to test the factor invariance of L2 grit based on a bifactor CFA model over time and, second, used CFM to measure change of L2 grit during an L2 course. To do so, we collected data from 437 adult EFL learners in Iran in four time phases using the L2 grit scale and analyzed them using Mplus 7.4. The model ﬁ t was accepted and invariance of the latent factor of L2 grit was con ﬁ rmed over time. Also, the negative covariance between initial level of L2 grit and its rate of change over time (second-order latent variables) suggested a steeper increase in the construct over time for learners with lower initial scores of the construct. That is, L2 learners who started at a higher level of L2 grit experienced less change in L2 grit over time. The LCFA-CFM ensured that the factor structure of L2 grit is invariant over time and provided insights into how L2 grit changes over an L2 course. its growth level during an L2 course?
Incorporating genome-wide association study results into genomic prediction enhances the 1 predictive ability of growth and phenology traits in Norway spruce 2

: 13 Genome-wide association (GWA) has been used to detect quantitative trait loci (QTLs) in plant and animal species. 14 Genomic prediction is to predict an accumulative effect of all QTL effects by capturing the linkage disequilibrium 15 between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian 16 segregation effects, especially for an oligogenic trait. Using QTLs detected in the GWA study could improve genomic 17 prediction (GP), including informative marker selection and adding a QTL with the largest effect size as a fixed effect. 18 In this study, we performed GWA and GP studies in a population with 904 clones from 32 full-sib families planted in 19 four trials using a newly developed 50k SNP Norway spruce array. In total, GWAS identified 41 SNPs associated 20 with the budburst stage (BB) and the SNP with the largest effect size explained 5.1% of the phenotypic variation 21 (PVE). For other traits like height at tree ages six and 12, diameter at breast height, frost damage and Pilodyn 22 penetration, only 2 – 13 SNP associations were detected and the PVE of the strongest effects ranged from 1.2% to 23 2.0%. GP with approximately 100 preselected SNPs based on the smallest p -values from GWAS showed the largest 24 predictive ability (PA) for the oligogenic trait BB. But for the other polygenic traits, approximate 2000-4000 25 preselected SNPs, indicated by the smallest Akaike information criterion (AIC) to offer the best model fit, still resulted 26 in PA being similar to that of GP models using all markers. Analyses on both real-life and simulated data also showed 27 that the inclusion of a large QTL SNP in the model as a fixed effect could improve the PA and accuracy of GP provided 28 that the PVE of the QTL was ≥2.5%.
Phenotypic, molecular and functional characterisation of human in vitro-generated IL-17A+ CD8+ T-cells

IL-17A+ CD8+ T-cells, often referred to as Tc17 cells, have been identified at sites of inflammation in several immune-mediated inflammatory diseases including psoriasis and spondyloarthritis. Whilst much of our understanding of IL-17A+ CD8+ T-cells has been discerned from murine studies, human IL-17A+ CD8+ T-cells remain less-well characterised. We optimised an in vitro polarisation protocol to expand human IL-17A+ CD8+ T-cells from PBMC or bulk CD8+ T-cell populations for phenotypic and functional assessment. We show that T-cell activation in the presence of IL-1β and IL-23 significantly increased the frequencies of IL-17A+ CD8+ T-cells, which was not further enhanced by the addition of IL-6, IL-2 or anti-IFNγ mAb. In vitro-generated IL-17A+ CD8+ T-cells from healthy donors displayed a distinct type-17 profile compared with IL-17A- CD8+ T-cells, as defined by transcriptional signature (IL17A, IL17F, RORC, RORA, MAF, IL23R, CCR6, CXCR6); high surface expression of CCR6 and CD161; and polyfunctional production of IL-17A, IL-17F, IL-22, IFNγ, TNFα and GM-CSF. A significant proportion of in vitro-induced IL-17A+ CD8+ T-cells expressed TCRVα7. 2 and bound MR1 tetramers, indicative of a MAIT CD8+ T-cell population. Using an IL-17A secretion assay, we demonstrate that the in vitro-generated IL-17A+ CD8+ T-cells were biologically functional and induced pro-inflammatory IL-6 and IL-8 production by synovial fibroblasts from patients with psoriatic arthritis. Collectively, we report an in vitro culture system to expand IL-17A+ CD8+ T-cells and further characterise their phenotype, transcriptional regulation and functional relevance to human health and disease.
The VMC survey – XXV. The 3D structure of the Small Magellanic Cloud from Classical Cepheids

The "VISTA near-infrared YJKs survey of the Magellanic System" (VMC) is collecting deep Ks-band time-series photometry of pulsating stars hosted by the two Magellanic Clouds and their connecting Bridge. Here we present YJKs light curves for a sample of 717 Small Magellanic Cloud (SMC) Classical Cepheids (CCs). These data, complemented with our previous results and V magnitude from literature, allowed us to construct a variety of period-luminosity and period-Wesenheit relationships, valid for Fundamental, First and Second Overtone pulsators. These relations provide accurate individual distances to CCs in the SMC over an area of more than 40 sq. deg. Adopting literature relations, we estimated ages and metallicities for the majority of the investigated pulsators, finding that: i) the age distribution is bimodal, with two peaks at 120+-10 and 220+-10 Myr; ii) the more metal-rich CCs appear to be located closer to the centre of the galaxy. Our results show that the three-dimensional distribution of the CCs in the SMC, is not planar but heavily elongated for more than 25-30 kpc approximately in the east/north-east towards south-west direction. The young and old CCs in the SMC show a different geometric distribution. Our data support the current theoretical scenario predicting a close encounter or a direct collision between the Clouds some 200 Myr ago and confirm the presence of a Counter-Bridge predicted by some models. The high precision three-dimensional distribution of young stars presented in this paper provides a new testbed for future models exploring the formation and evolution of the Magellanic System.
Efficient SARS-CoV-2 detection utilizing chitin-immobilized nanobodies synthesized in Ustilago maydis

The COVID-19 pandemic has greatly impacted the global economy and health care systems, illustrating the urgent need for timely and inexpensive responses to a pandemic threat in the form of vaccines and antigen tests. The causative agent of COVID-19 is SARS-CoV-2. The spike protein on the virus surface interacts with the human angiotensin-converting enzyme (ACE2) via the so-called receptor binding domain (RBD), facilitating virus entry. The RBD thus represents a prime target for vaccines, therapeutic antibodies, and antigen test systems. Currently, antigen testing is mostly conducted by qualitative flow chromatography or via quantitative ELISA-type assays. The latter mostly utilize materials like protein-adhesive polymers and gold or latex particles. Here we present an alternative ELISA approach using inexpensive materials and permitting quick detection based on components produced in the microbial model Ustilago maydis. In this fungus, heterologous proteins like biopharmaceuticals can be exported by fusion to unconventionally secreted chitinase Cts1. As a unique feature, the carrier chitinase binds to chitin allowing its additional use as a purification or immobilization tag. In this study, we produced different mono- and bivalent SARS-CoV-2 nanobodies directed against the viral RBD as Cts1 fusions and screened their RBD binding affinity in vitro and in vivo. Functional nanobody-Cts1 fusions were immobilized on chitin forming an RBD tethering surface. This provides a solid base for future development of an inexpensive antigen test utilizing unconventionally secreted nanobodies as RBD trap and a matching ubiquitous and biogenic surface for immobilization.
A programmable reaction-diffusion system for spatiotemporal cell signaling circuit design

Cells self-organize molecules in space and time to generate complex behaviors, but we lack synthetic strategies for engineering spatiotemporal signaling. We present a programmable reaction-diffusion platform for designing protein oscillations, patterns, and circuits in mammalian cells using two bacterial proteins, MinD and MinE (MinDE). MinDE circuits act like “single-cell radios”, emitting frequency-barcoded fluorescence signals that can be spectrally isolated and analyzed using digital signal processing tools. We define how to genetically program these signals and modulate their dynamics using engineerable protein-protein interactions. By connecting MinDE to endogenous cellular pathways, we built circuits that broadcast frequency-barcoded single-cell kinase activity or that synthetically pattern actin polymerization. Our work establishes a new paradigm for probing and engineering cellular activities at length and timescales critical for biological function.
Age-dependent dysregulation of locus coeruleus firing in a transgenic rat model of Alzheimer's disease

Accumulation of hyperphosphorylated tau in the locus coeruleus (LC) is a ubiquitous feature of prodromal Alzheimer’s disease (AD), and LC neurons degenerate as AD progresses. Tau-mediated LC dysfunction may contribute to early neuropsychiatric symptoms, while loss of LC integrity is associated with conversion to cognitive impairment. Hyperphosphorylated tau alters firing rates in other brain regions, but its effects on LC neurons have not been described. The purpose of this study was to characterize changes in firing properties of LC neurons when they are the only cells containing hyperphosphorylated tau, as well as later in disease when β-amyloid (Aβ) and tau pathology is abundant in the forebrain. Single unit LC activity was recorded from anesthetized wild-type (WT) and TgF344-AD rats, which carry the APP/PS1 transgene. Similar to human AD, these rats develop hyperphosphorylated tau in the LC (at 6 months) prior to Aβ or tau pathology in forebrain regions (at 12-15 months). At baseline, LC neurons from TgF344-AD rats were hypoactive at both ages compared to WT littermates, but showed elevated spontaneous bursting properties, particularly in younger animals. Differences in footshock-evoked LC firing depended on age, with 6-month TgF344-AD rats demonstrating aspects of hyperactivity, and aged transgenic rats showing hypoactivity relative to WT. Tau-induced alterations in LC firing rates may contribute to the pathophysiology of AD, with early hyperactivity associated with prodromal symptoms, followed by hypoactivity contributing to cognitive impairment. These results support further investigation into disease stage-dependent noradrenergic interventions for AD. Highlights Recorded locus coeruleus (LC) neurons in a rat model of Alzheimer’s disease (AD) TgF344-AD rats develop early endogenous LC tau pathology akin to human AD 6- and 15-month TgF344-AD rats had reduced tonic LC firing LC neurons from 6-month TgF344-AD rats were hyperactive in response to footshock LC neuron dysfunction may contribute to AD symptoms
Pseudomonas aeruginosa mechanosensing controls cell polarity during twitching by activating two antagonistic response regulators

The opportunistic pathogen Pseudomonas aeruginosa adapts to solid surfaces to enhance virulence and infect its host. Type IV pili (T4P), long and thin filaments that power surface-specific twitching motility, allow single cells to mechanosense surfaces. For example, cells sense T4P attachment to control the direction of twitching motility. In this process, they establish a local positive feedback that polarizes T4P distribution to the sensing pole. A complex chemotaxis-like system called Chp mediates this response. The signalling mechanism allowing for transduction of this spatially-resolved signal is however unresolved. Here we demonstrate that the two Chp response regulators PilG and PilH enable dynamic cell polarization by coupling their antagonistic functions on T4P extension. By precisely quantifying the localization of fluorescent protein fusions, we show that PilG polarizes in response to mechanosensing through phosphorylation by the histidine kinase ChpA. We find that PilH is not inherently required for reversals. However, PilH activation is necessary to break the local positive feedback established by PilG so that forward-twitching cells can reverse. To spatially resolve mechanical signals, Chp thus locally transduces signals with a main output response regulator, PilG. To respond to signal changes, Chp uses its second regulator PilH to break the local feedback. By identifying the molecular functions of two response regulators that dynamically control cell polarization, our work provides a rationale for the diversity of architectures often found in non-canonical chemotaxis systems.
Auditory prediction hierarchy in the human hippocampus and amygdala

Our brains can extract structure from the environment and form predictions given past sensory experience. Predictive circuits have been identified in wide-spread cortical regions. However, the contribution of subcortical areas, such as the hippocampus and amygdala in the formation of predictions remains under-explored. Here, we hypothesized that the hippocampus would be sensitive to predictability in sound sequences, while the amygdala would be sensitive to unexpected violations of auditory rules. We presented epileptic patients undergoing presurgical monitoring with standard and deviant sounds, in a predictable or unpredictable context. Onsets of auditory responses and unpredictable deviance effects were detected at earlier latencies in the temporal cortex compared to the amygdala and hippocampus. Deviance effects in 1-20 Hz local field potentials were detected in the lateral temporal cortex, irrespective of predictability. The amygdala showed stronger deviance responses in the unpredictable context. Additionally, low frequency deviance responses in the hippocampus (1-8 Hz) were observed in the predictable but not in the unpredictable context. Our results reveal a distributed cortical-subcortical network underlying the generation of auditory predictions, comprising temporal cortex and the hippocampus and amygdala, and suggest that the neural basis of sensory predictions and prediction error signals needs to be extended to subcortical regions.
Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia

Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes and stable-isotope probing incubations from the water column and subseafloor of the Benguela Upwelling System. Taxonomic assemblages and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity towards mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification prevails over canonical denitrification when Namibian coastal waters are ventilated during austral winter.
A semi-analytical perspective on massive galaxies at z ∼ 0.55

DS, FP, ADMD, SRT, GF, and AAK want to thank the support of the Spanish Ministry grant AYA2014-60641-C2-1-P managed by the Instituto de Astrofisica de Andalucia (IAA-CSIC). WC and AK are supported by the Ministerio de Economia y Competitividad and the Fondo Europeo de Desarrollo Regional (MINECO/FEDER, UE) in Spain through grant AYA2015-63810-P. WC further acknowledges the supported by the European Research Council under grant number 670193. AK is also supported by the Spanish Red Consolider Multi-Dark FPA2017-90566-REDC. He further thanks Lance Jyo for dreamwalking. ADMD thanks Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) for financial support. DS fellowship is funded by the Spanish Ministry of Economy and Competitiveness (MINECO) under the 2014 Severo Ochoa Predoctoral Training Programme.
Inference of Phylogenetic Networks from Sequence Data using Composite Likelihood

While phylogenies have been essential in understanding how species evolve, they do not adequately describe some evolutionary processes. For instance, hybridization, a common phenomenon where interbreeding between two species leads to formation of a new species, must be depicted by a phylogenetic network, a structure that modifies a phylogeny by allowing two branches to merge into one, resulting in reticulation. However, existing methods for estimating networks are computationally expensive as the dataset size and/or topological complexity increase. The lack of methods for scalable inference hampers phylogenetic networks from being widely used in practice, despite accumulating evidence that hybridization occurs frequently in nature. Here, we propose a novel method, PhyNEST (Phylogenetic Network Estimation using SiTe patterns), that estimates phylogenetic networks directly from sequence data. PhyNEST achieves computational efficiency by using composite likelihood as well as accuracy by using the full genomic data to incorporate all sources of variability, rather than first summarizing the data by estimating a set of gene trees, as is required by most of the existing methods. To efficiently search network space, we implement both hill-climbing and simulated annealing algorithms. Simulation studies show that PhyNEST can accurately estimate parameters given the true network topology and that it has comparable accuracy to two popular methods that use composite likelihood and a set of gene trees as input, implemented in SNaQ and PhyloNet. For datasets with a large number of loci, PhyNEST is more efficient than SNaQ and PhyloNet when considering the time required for gene tree estimation. We applied PhyNEST to reconstruct the evolutionary relationships among Heliconius butterflies and Papionini primates, characterized by hybrid speciation and widespread introgression, respectively. PhyNEST is implemented in an open-source Julia package and publicly available at https://github.com/sungsik-kong/PhyNEST.jl.