Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear polarization in gamma-ray burst prompt emission

Despite being hard to measure, GRB prompt γ-ray emission polarization is a valuable probe of the dominant emission mechanism and the GRB outflow’s composition and angular structure. During the prompt emission the GRB outflow is ultra-relativistic with Lorentz factors Γ ≫ 1. We describe in detail the linear polarization properties of various emission mechanisms: synchrotron radiation from different magnetic field structures (ordered: toroidal Btor or radial B∥, and random: normal to the radial direction B⊥), Compton drag, and photospheric emission. We calculate the polarization for different GRB jet angular structures (e.g. top-hat, Gaussian, power-law) and viewing angles θobs. Synchrotron with B⊥ can produce large polarizations, up to $25\%\lesssim \Pi \lesssim 45\%$, for a top-hat jet but only for lines of sight just outside (θobs − θj ∼ 1/Γ) the jet’s sharp edge at θ = θj. The same also holds for Compton drag, albeit with a slightly higher overall Π. Moreover, we demonstrate how Γ-variations during the GRB or smoother jet edges (on angular scales ≳ 0.5/Γ) would significantly reduce Π. We construct a semi-analytic model for non-dissipative photospheric emission from structured jets. Such emission can produce up to $\Pi \lesssim 15\%$ with reasonably high fluences, but this requires steep gradients in Γ(θ). A polarization of $50\%\lesssim \Pi \lesssim 65\%$ can robustly be produced only by synchrotron emission from a transverse magnetic field ordered on angles ≳ 1/Γ around our line of sight (like a global toroidal field, Btor, for 1/Γ < θobs < θj). Therefore, such a model would be strongly favored even by a single secure measurement within this range. We find that such a model would also be favored if $\Pi \gtrsim 20\%$ is measured in most GRBs within a large enough sample, by deriving the polarization distribution for our different emission and jet models.
Altered Expression of Interleukin-18 System mRNA at the Level of Endometrial Myometrial Interface in Women with Adenomyosis

Adenomyosis is a uterine pathology characterized by a deep invasion of endometrial glands and stroma, disrupting the endometrial–myometrial interface (EMI). Interleukin-18 (IL-18) system is a dominant cytokine involved in the menstrual cycle of human endometrium. IL-18 may play a defensive role against maternal immune response in the uterine cavity. The present study was designed to determine IL-18-mediated immune response at the level of EMI. We uncovered that mRNA of IL-18 system, including IL-18, IL-18 receptor (IL-18R), and its antagonist, IL-18 binding protein (IL-18BP), expressed in eutopic, ectopic endometrium, and corresponding myometrium in patients with adenomyosis. IL-18 system was demonstrated in paired tissue samples by immunochemistry and immunofluorescence study. According to RT-PCR with CT value quantification and 2−∆∆Ct method, a significant down-regulation of IL-18BP in corresponding myometrium in comparison to eutopic endometrium (p < 0.05) indicates that the IL-18 system acts as a local immune modulator at the level of EMI and regulating cytokine networks in the pathogenesis of adenomyosis. Furthermore, an increased IL-18 antagonist to agonist ratio was noted in ectopic endometrium compared with corresponding myometrium. We suggest that altered IL-18 system expression contributes to immunological dysfunction and junctional zone disturbance in women with adenomyosis.
VANDELS consortium public database

We provide access to the current VANDELS data release (DR2) through a dedicated database, accessible at the link this http URL The data release includes the spectra for all galaxies for which the scheduled integration time was completed during the first two observing seasons and the spectra for those galaxies for which the scheduled integration time was 50\% complete at the end of season two (i.e. 20/40 hours and 40/80 hours). The total number of spectra released is 1362 (586 in CDFS and 776 in UDS). Spectra are stored as multi-extension FITS files containing the 1D extracted spectrum, the 2D linearly re-sampled spectrum, the 1D sky spectrum, the 1D noise estimate and the image thumbnail of the object.
Molecular Characteristics and Pathogenicity of a Novel Recombinant Porcine Reproductive and Respiratory Syndrome Virus Strain from NADC30-, NADC34-, and JXA1-Like Strains That Emerged in China

The pathogenicity of NADC34-like PRRSV has broad variations in virulence. Importantly, NADC34-like PRRSV has undergone complex recombination with local strains since it first emerged in 2017 in China. ABSTRACT Recently, the emergence of a NADC34-like porcine reproductive and respiratory syndrome virus (PRRSV), which causes a large number of abortions in swine herds, has raised great concern in China. In this study, a PRRSV variant strain, PRRSV/CN/FJGD01/2021, evolved from recombination between NADC30-like, NADC34-like, and JXA1-like viruses was isolated in Fujian province in 2021, and its pathogenicity in piglets was examined. Animal experiments demonstrated that PRRSV/CN/FJGD01/2021 infection could induce 100% morbidity and cause higher viremia, a persistently higher fever (>40°C for 14 consecutive days), significant weight loss, and severe histopathological lung lesions compared to the NADC30-like FJZ03 strain and NADC34-like FJ0908 strain in piglets. The PRRSV/CN/FJGD01/2021 strain displayed higher pathogenicity than the FJZ03 and FJ0908 strains, but lower pathogenicity than the Chinese highly pathogenic (HP)-PRRSVs in piglets. Moreover, the Ingelvac PRRS modified live vaccine (MLV) provides incomplete cross-protection against heterologous PRRSV/CN/FJGD01/2021 in piglets. Our findings contribute to the understanding of the current epidemic situation of NADC34-like PRRSV in China. IMPORTANCE The pathogenicity of NADC34-like PRRSV has broad variations in virulence. Importantly, NADC34-like PRRSV has undergone complex recombination with local strains since it first emerged in 2017 in China. However, the pathogenicity of the recombinant NADC34-like virus was rarely experimentally evaluated in pigs. In this study, a novel PRRSV strain, PRRSV/CN/FJGD01/2021, was isolated from sows enduring a high-abortion-rate (20%) period in China in 2021. Notably, phylogenetic and recombination analyses revealed that PRRSV/CN/FJGD01/2021 is a recombinant virus from NADC30-, NADC34-, and JXA1-like isolates. PRRSV/CN/FJGD01/2021 was shown to cause higher virus load, persistent fever, significant weight loss, moderate respiratory clinical signs, and severe histopathological lung lesions in piglets. PRRSV/CN/FJGD01/2021 exhibited higher pathogenicity than NADC30-like FJZ03 and NADC34-like FJ0908, but lower than Chinese HP-PRRSVs for piglets. These data indicated that PRRSV/CN/FJGD01/2021 has intermediate virulence for piglets. Furthermore, the Ingelvac PRRS MLV could partly provide protective efficacy against PRRSV/CN/FJGD01/2021 challenge in piglets.
Long-range axonal projections of transplanted mouse embryonic stem cell-derived hypothalamic neurons into adult mouse brain

The hypothalamus is comprised of heterogenous cell populations and includes highly complex neural circuits that regulate the autonomic nerve system. Its dysfunction therefore results in severe endocrine disorders. Although recent experiments have been conducted for in vitro organogenesis of hypothalamic neurons from embryonic stem (ES) or induced pluripotent stem (iPS) cells, whether these stem cell-derived hypothalamic neurons can be useful for regenerative medicine remains unclear. We therefore performed orthotopic transplantation of mouse ES cell (mESC)-derived hypothalamic neurons into adult mouse brains. We generated electrophysiologically functional hypothalamic neurons from mESCs and transplanted them into the supraoptic nucleus of mice. Grafts extended their axons along hypothalamic nerve bundles in host brain, and some of them even projected into the posterior pituitary (PPit), which consists of distal axons of the magnocellular neurons located in hypothalamic supraoptic and paraventricular nuclei. The axonal projections to the PPit were not observed when the mESC-derived hypothalamic neurons were ectopically transplanted into the substantia nigra reticular part. These findings suggest that our stem cell-based orthotopic transplantation approach might contribute to the establishment of regenerative medicine for hypothalamic and pituitary disorders.
Applying CRISPR-Cas9 screens to dissect hematological malignancies

Abstract Bit by bit, over the last few decades, functional genomic tools have been piecing together the molecular puzzle driving tumorigenesis in human patients. Nevertheless, our understanding of the role of several genes and regulatory elements that drive critical cancer-associated physiological processes from disease development to progression to spread is very limited, which significantly affects our ability of applying these insights in the context of improved disease management. The recent advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)–based technology and its application in cancer genomics has, however, allowed the generation of a wealth of knowledge that has helped decipher several critical questions associated with translational cancer research. Precisely, the high-throughput capability coupled with a high level of technological plasticity associated with the CRISPR-Cas9 screens have expanded our horizons from a mere struggle to appreciate cancer as a genetic disease to observing the integrated genomic/epigenomic network of numerous malignancies and correlating it with our present knowledge of drugging strategies to develop innovative approaches for next-generation precision cancer medicine. Specifically, within blood cancers, current CRISPR screens have specifically focused on improving our understanding of drug resistance mechanisms, disease biology, the development of novel therapeutic approaches, and identifying the molecular mechanisms of current therapies, with an underlying aim of improving disease outcomes. Here, we review the development of the CRISPR-Cas9 genome-editing strategy, explicitly focusing on the recent advances in the CRISPR-Cas9–based screening approaches, its current capabilities, limitations, and future applications in the context of hematological malignancies.
Internal RNA 2′O-methylation in the HIV-1 genome counteracts ISG20 nuclease-mediated antiviral effect

Abstract RNA 2′O-methylation is a ‘self’ epitranscriptomic modification allowing discrimination between host and pathogen. Indeed, human immunodeficiency virus 1 (HIV-1) induces 2′O-methylation of its genome by recruiting the cellular FTSJ3 methyltransferase, thereby impairing detection by RIG-like receptors. Here, we show that RNA 2′O-methylations interfere with the antiviral activity of interferon-stimulated gene 20-kDa protein (ISG20). Biochemical experiments showed that ISG20-mediated degradation of 2′O-methylated RNA pauses two nucleotides upstream of and at the methylated residue. Structure-function analysis indicated that this inhibition is due to steric clash between ISG20 R53 and D90 residues and the 2′O-methylated nucleotide. We confirmed that hypomethylated HIV-1 genomes produced in FTSJ3-KO cells were more prone to in vitro degradation by ISG20 than those produced in cells expressing FTSJ3. Finally, we found that reverse-transcription of hypomethylated HIV-1 was impaired in T cells by interferon-induced ISG20, demonstrating the direct antagonist effect of 2′O-methylation on ISG20-mediated antiviral activity.
Training a Deep Contextualized Language Model for International Classification of Diseases, 10th Revision Classification via Federated Learning: Model Development and Validation Study

Background The automatic coding of clinical text documents by using the International Classification of Diseases, 10th Revision (ICD-10) can be performed for statistical analyses and reimbursements. With the development of natural language processing models, new transformer architectures with attention mechanisms have outperformed previous models. Although multicenter training may increase a model’s performance and external validity, the privacy of clinical documents should be protected. We used federated learning to train a model with multicenter data, without sharing data per se. Objective This study aims to train a classification model via federated learning for ICD-10 multilabel classification. Methods Text data from discharge notes in electronic medical records were collected from the following three medical centers: Far Eastern Memorial Hospital, National Taiwan University Hospital, and Taipei Veterans General Hospital. After comparing the performance of different variants of bidirectional encoder representations from transformers (BERT), PubMedBERT was chosen for the word embeddings. With regard to preprocessing, the nonalphanumeric characters were retained because the model’s performance decreased after the removal of these characters. To explain the outputs of our model, we added a label attention mechanism to the model architecture. The model was trained with data from each of the three hospitals separately and via federated learning. The models trained via federated learning and the models trained with local data were compared on a testing set that was composed of data from the three hospitals. The micro F1 score was used to evaluate model performance across all 3 centers. Results The F1 scores of PubMedBERT, RoBERTa (Robustly Optimized BERT Pretraining Approach), ClinicalBERT, and BioBERT (BERT for Biomedical Text Mining) were 0.735, 0.692, 0.711, and 0.721, respectively. The F1 score of the model that retained nonalphanumeric characters was 0.8120, whereas the F1 score after removing these characters was 0.7875—a decrease of 0.0245 (3.11%). The F1 scores on the testing set were 0.6142, 0.4472, 0.5353, and 0.2522 for the federated learning, Far Eastern Memorial Hospital, National Taiwan University Hospital, and Taipei Veterans General Hospital models, respectively. The explainable predictions were displayed with highlighted input words via the label attention architecture. Conclusions Federated learning was used to train the ICD-10 classification model on multicenter clinical text while protecting data privacy. The model’s performance was better than that of models that were trained locally.
Discovery of a Metal-poor, Luminous Post-AGB Star that Failed the Third Dredge-up

Post-asymptotic giant branch (post-AGB) stars are known to be chemically diverse. In this paper we present the first observational evidence of a star that has failed the third dredge-up (TDU). J005252.87-722842.9 is an A-type (Teff = 8250 ± 250 K) luminous (8200 ± 700 L⊙) metal-poor ([Fe/H] = −1.18 ± 0.10) low-mass (Minitial ≈ 1.5–2.0 M⊙) post-AGB star in the Small Magellanic Cloud. Through a systematic abundance study, using high-resolution optical spectra from UVES, we found that this likely post-AGB object shows an intriguing photospheric composition with no confirmed carbon-enhancement (upper limit of [C/Fe] < 0.50) nor enrichment of s-process elements. We derived an oxygen abundance of [O/Fe] = 0.29 ± 0.1. For Fe and O, we took the effects of nonlocal thermodynamic equilibrium into account. We could not derive an upper limit for the nitrogen abundance as there are no useful nitrogen lines within our spectral coverage. The chemical pattern displayed by this object has not been observed in single or binary post-AGBs. Based on its derived stellar parameters and inferred evolutionary state, single-star nucleosynthesis models predict that this star should have undergone TDU episodes while on the AGB, and it should be carbon enriched. However, our observations are in contrast with these predictions. We identify two possible Galactic analogs that are likely to be post-AGB stars, but the lack of accurate distances (hence luminosities) to these objects does not allow us to confirm their post-AGB status. If they have low luminosities, then they are likely to be dusty post-RGB stars. The discovery of J005252.87-722842.9 reveals a new stellar evolutionary channel whereby a star evolves without any TDU episodes.
Atg9 interactions via its transmembrane domains are required for phagophore expansion during autophagy

ABSTRACT During macroautophagy/autophagy, precursor cisterna known as phagophores expand and sequester portions of the cytoplasm and/or organelles, and subsequently close resulting in double-membrane transport vesicles called autophagosomes. Autophagosomes fuse with lysosomes/vacuoles to allow the degradation and recycling of their cargoes. We previously showed that sequential binding of yeast Atg2 and Atg18 to Atg9, the only conserved transmembrane protein in autophagy, at the extremities of the phagophore mediates the establishment of membrane contact sites between the phagophore and the endoplasmic reticulum. As the Atg2-Atg18 complex transfers lipids between adjacent membranes in vitro, it has been postulated that this activity and the scramblase activity of the trimers formed by Atg9 are required for the phagophore expansion. Here, we present evidence that Atg9 indeed promotes Atg2-Atg18 complex-mediated lipid transfer in vitro, although this is not the only requirement for its function in vivo. In particular, we show that Atg9 function is dramatically compromised by a F627A mutation within the conserved interface between the transmembrane domains of the Atg9 monomers. Although Atg9F627A self-interacts and binds to the Atg2-Atg18 complex, the F627A mutation blocks the phagophore expansion and thus autophagy progression. This phenotype is conserved because the corresponding human ATG9A mutant severely impairs autophagy as well. Importantly, Atg9F627A has identical scramblase activity in vitro like Atg9, and as with the wild-type protein enhances Atg2-Atg18-mediated lipid transfer. Collectively, our data reveal that interactions of Atg9 trimers via their transmembrane segments play a key role in phagophore expansion beyond Atg9ʹs role as a lipid scramblase.Abbreviations: BafA1: bafilomycin A1; Cvt: cytoplasm-to-vacuole targeting; Cryo-EM: cryo-electron microscopy; ER: endoplasmic reticulum; GFP: green fluorescent protein; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MCS: membrane contact site; NBD-PE: N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor Ape1; PtdIns3P: phosphatidylinositol-3-phosphate; SLB: supported lipid bilayer; SUV: small unilamellar vesicle; TMD: transmembrane domain; WT: wild type
A comparison of fine particulate matter (PM2.5) in vivo exposure studies incorporating chemical analysis

ABSTRACT The complex, variable mixtures present in fine particulate matter (PM2.5) have been well established, and associations between chemical constituents and human health are expanding. In the past decade, there has been an increase in PM2.5 toxicology studies that include chemical analysis of samples. This investigation is a crucial component for identifying the causal constituents for observed adverse health effects following exposure to PM2.5. In this review, investigations of PM2.5 that used both in vivo models were explored and chemical analysis with a focus on respiratory, cardiovascular, central nervous system, reproductive, and developmental toxicity was examined to determine if chemical constituents were considered in the interpretation of the toxicity findings. Comparisons between model systems, PM2.5 characteristics, endpoints, and results were made. A vast majority of studies observed adverse effects in vivo following exposure to PM2.5. While limited, investigations that explored connections between chemical components and measured endpoints noted significant associations between biological measurements and a variety of PM2.5 constituents including elements, ions, and organic/elemental carbon, indicating the need for such analysis. Current limitations in available data, including relatively scarce statistical comparisons between collected toxicity and chemical datasets, are provided. Future progress in this field in combination with epidemiologic research examining chemical composition may support regulatory standards of PM2.5 to protect human health. Graphical Abstract
Using nonequilibrium thermodynamics to optimize the cooling of a dilute atomic gas

Optimizing thermodynamic processes far from equilibrium is a challenge. We report the experimental optimization of cooling and thermalization of a gas of few noninteracting Cesium atoms confined in a nonharmonic optical dipole trap. To this end, we combine degenerate Raman sideband cooling and nonequilibrium thermodynamics. We determine the axial phase-space distribution of the atoms after each Raman cooling pulse by tracing the evolution of the gas with position-resolved fluorescence imaging. We further minimize the entropy production to a target thermal state to specify the optimal spacing between a sequence of pulses, thus achieving optimal thermalization. We finally study the dynamics of the cooling process by measuring the statistical distance between each cooling step. Our results provide a method to systematically optimize the cooling of nonharmonically trapped dilute gases and illustrate the power of nonequilibrium thermodynamics.
Action growth for black holes in modified gravity

The general form of the action growth for a large class of static black hole solutions in modified gravity which includes $F(R)$-gravity models is computed. The cases of black hole solutions with non vanishing Ricci curvature are also considered, generalizing the results previously found and valid only for constant curvature black holes. An argument is put forward to provide a physical interpretation of the results.
Weak magnetic fields of intermediate-mass stars ?

Department of Physics, Royal Military College of Canada, PO Box 17000, Station Forces, Kingston, Ontario, CanadaThe dates of receipt and acceptance should be inserted laterWe present the result of a highly sensitive spectropolarimetric study dedicated to intermediate mass stars. We report thedetection of sub-gauss surface magnetic ﬁelds on the normal, rapidly-rotating A-type star Vega and on the moderately-rotating Am star Sirius A. These magnetic detections constitute the ﬁrst evidence that tepid stars that do not belong tothe class of Ap/Bp stars can also host magnetized photospheres, suggesting that a signiﬁcant fraction of stars in thismass regime are magnetic. We present here the observational clues gathered so far to progress towards understanding thephysical processes at the origin of this newly identiﬁed Vega-like magnetism.