Miracle-dz/UniFAR-FTUs huggingface dataset:
The Properties of Short Gamma-Ray Burst Jets Triggered by Neutron Star Mergers

The most popular model for short gamma-ray bursts (sGRBs) involves the coalescence of binary neutron stars. Because the progenitor is actually hidden from view, we must consider under which circumstances such merging systems are capable of producing a successful sGRB. Soon after coalescence, winds are launched from the merger remnant. In this paper, we use realistic wind profiles derived from global merger simulations in order to investigate the interaction of sGRB jets with these winds using numerical simulations. We analyze the conditions for which these axisymmetric winds permit relativistic jets to break out and produce an sGRB. We find that jets with luminosities comparable to those observed in sGRBs are only successful when their half-opening angles are below ≈20°. This jet collimation mechanism leads to a simple physical interpretation of the luminosities and opening angles inferred for sGRBs. If wide, low-luminosity jets are observed, they might be indicative of a different progenitor avenue such as the merger of a neutron star with a black hole. We also use the observed durations of sGRB to place constraints on the lifetime of the wind phase, which is determined by the time it takes the jet to break out. In all cases we find that the derived limits argue against completely stable remnants for binary neutron star mergers that produce sGRBs.
X-ray emission from star-forming galaxies – I. High-mass X-ray binaries

Based on a homogeneous set of X-ray, infrared and ultraviolet observations from Chandra, Spitzer, GALEX and 2MASS archives, we study populations of high-mass X-ray binaries (HMXBs) in a sample of 29 nearby star-forming galaxies and their relation with the star formation rate (SFR). In agreement with previous results, we find that HMXBs are a good tracer of the recent star formation activity in the host galaxy and their collective luminosity and number scale with the SFR, in particular, LX � 2.6·10 39 ×SFR. However, the scaling relations still bear a rather large dispersion of rms � 0.4 dex, which we believe is of a physical origin. We present the catalog of 1057 X-ray sources detected within the D25 ellipse for galaxies of our sample and construct the average X-ray luminosity function (XLF) of HMXBs with substantially improved statistical accuracy and better control of systematic effects than achieved in previous studies. The XLF follows a power law with slope of 1.6 in the log(LX) � 35 40 luminosity range with a moderately significant evidence for a break or cut-off at LX � 10 40 erg/s. As before, we did not find any features at the Eddington limit for a neutron star or a stellar mass black hole. We discuss implications of our results for the theory of binary evolution. In particular we estimate the fraction of compact objects that once upon their lifetime experienced an X-ray active phase powered by accretion from a high mass companion and obtain a rather large number, fX � 0.2 ×(0.1 Myr/τX) (τX is the life time of the X-ray active phase). This is � 4 orders of magnitude more frequent than in LMXBs. We also derive constrains on the mass distribution of the secondary star in HMXBs.
ATM-Mediated Double-Strand Break Repair Is Required for Meiotic Genome Stability at High Temperature

In eukaryotes, the conserved kinase Ataxia Telangiectasia Mutated (ATM) negatively regulates DNA double-strand break (DSB) formation and plays a central role in DSB repair. Here, by using cytogenetic approaches, we demonstrate that ATM also plays an essential role in protecting meiotic chromosome integrity in Arabidopsis thaliana at extreme high temperature. We determined the chromosome localization patterns of DSB formation proteins SPO11-1 and DFO during prophase I, both of which were disturbed by heat stress. Evaluation of the number of RAD51, DMC1, SPO11-1 and DFO protein foci in meiocytes of Arabidopsis atm mutant clarifies that ATM does not mediate the heat-induced reduction in DSB formation. Interestingly, meiotic spread analysis showed that chromosome fragmentation level was significantly increased in atm but was lowered in the mre11 and mre11 atm mutants under high temperature, indicating that ATM-dependent meiotic chromosome integrity at high temperature relies on the functional MRE1-RAD50-NBS1 (MRN) complex. Moreover, contrary to the rad51 and mnd1 mutants, which exhibited enhanced meiotic chromosome integrity under heat stress, the rad51 atm and mnd1 atm mutants retained high levels of chromosome fragmentation at extreme high temperature. Furthermore, heat stress reduced chromosome fragmentation level in the syn1 and syn1 atm mutants. Collectively, these data suggest that ATM-mediated DSB repair is required for meiotic genome stability in plants at extreme high temperature, which possibly acts in a RAD51-independent manner and relies on functional chromosome axis.
HEATING SIGNATURES IN THE DISK COUNTERPARTS OF SOLAR SPICULES IN INTERFACE REGION IMAGING SPECTROGRAPH OBSERVATIONS

We use coordinated observations with the Interface Region Imaging Spectrograph (IRIS) and the Swedish 1 m Solar Telescope to identify the disk counterpart of type II spicules in upper-chromospheric and transition region (TR) diagnostics. These disk counterparts were earlier identified through short-lived asymmetries in chromospheric spectral lines: rapid blue- or red-shifted excursions (RBEs or RREs). We find clear signatures of RBEs and RREs in Mg ii h & k, often with excursions of the central h3 and k3 absorption features in concert with asymmetries in co-temporal and co-spatial Hα spectral profiles. We find spectral signatures for RBEs and RREs in C ii 1335 and 1336 Å and Si iv 1394 and 1403 Å spectral lines and interpret this as a sign that type II spicules are heated to at least TR temperatures, supporting other recent work. These C ii and Si iv spectral signals are weaker for a smaller network region than for more extended network regions in our data. A number of bright features around extended network regions observed in IRIS slit-jaw imagery SJI 1330 and 1400, recently identified as network jets, can be clearly connected to Hα RBEs and/or RREs in our coordinated data. We speculate that at least part of the diffuse halo around network regions in the IRIS SJI 1330 and 1400 images can be attributed to type II spicules with insufficient opacity in the C ii and Si iv lines to stand out as single features in these passbands.
Microbiota-dependent histone butyrylation in the mammalian intestine

Posttranslational modifications (PTMs) on histone proteins are a key source of regulation on chromatin through impacting genome organization and important cellular processes, including gene expression. These PTMs often arise from small metabolites and are thus impacted by cellular metabolism and environmental cues. One such class of metabolically regulated PTMs are histone acylations, which include histone acetylation, along with butyrylation, crotonylation, and propionylation. We asked whether histone acylations of intestinal epithelial cells (IECs) are regulated through the availability of short chain fatty acids (SCFAs), which are generated by the commensal microbiota in the intestinal lumen. We identified IECs from the cecum and distal mouse intestine as sites of high levels of histone acylations, including histone butyrylation and propionylation. We identified specific sites of butyrylation and propionylation on lysine 9 and 27 on histone H3. We demonstrate that these acylations are regulated by the microbiota, whereas histone butyrylation is additionally regulated by the metabolite tributyrin. Furthermore, we identify tributyrin-regulated gene programs that correlate with histone butyrylation and demonstrate that histone butyrylation (H3K27bu) is associated with active gene regulatory elements and levels of gene expression. Together, our observations demonstrate a physiological setting in which previously uncharacterized histone acylations are dynamically regulated and associated with gene expression.
The hard X-ray luminosity function of high-redshift (3 < z ≲ 5) active galactic nuclei

We present the hard-band ($2-10\,\mathrm{keV}$) X-ray luminosity function (HXLF) of $0.5-2\,\mathrm{keV}$ band selected AGN at high redshift. We have assembled a sample of 141 AGN at $3 10^{44}\mathrm{erg\,s^{-1}}}$) obscured AGN fraction from $z=0$ to $z>3$.
The BeMoBIL Pipeline for automated analyses of multimodal mobile brain and body imaging data

Advancements in hardware technology and analysis methods allow more and more mobility in electroencephalography (EEG) experiments. Mobile Brain/Body Imaging (MoBI) studies may record various types of data such as motion or eye tracking in addition to neural activity. Although there are options available to analyze EEG data in a standardized way, they do not fully cover complex multimodal data from mobile experiments. We thus propose the BeMoBIL Pipeline, an easy-to-use pipeline in MATLAB that supports the time-synchronized handling of multimodal data. It is based on EEGLAB and fieldtrip and consists of automated functions for EEG preprocessing and subsequent source separation. It also provides functions for motion data processing and extraction of event markers from different data modalities, including the extraction of eye-movement and gait-related events from EEG using independent component analysis. The pipeline introduces a new robust method for region-of-interest-based group-level clustering of independent EEG components. Finally, the BeMoBIL Pipeline provides analytical visualizations at various processing steps, keeping the analysis transparent and allowing for quality checks of the resulting outcomes. All parameters and steps are documented within the data structure and can be fully replicated using the same scripts. This pipeline makes the processing and analysis of (mobile) EEG and body data more reliable and independent of the prior experience of the individual researchers, thus facilitating the use of EEG in general and MoBI in particular. It is an open-source project available for download at https://github.com/BeMoBIL/bemobil-pipeline which allows for community-driven adaptations in the future.
Long-term polarimetric observations of OH127.8+0.0

OH 1612- and 1667-MHz masers from the well known object OH127.8+0.0 were monitored in full-polarization mode over a period of 6.5years and mapped with MERLIN at one epoch. The OH variability pattern of the star is typical of extremely longperiod AGB stars. The distance determined from the 1612-MHz light curve and a new measurement of the angular radius is 3.87±0.28kpc. At both frequencies, the flux of polarized emission tightly follows the total flux variations while, the degrees of circular and linear polarization are constant within measurement accuracy. There is net polarization at both lines. The magnetic field strength estimated from a likely Zeeman pair is 0.6mG at the distance of 5400au from the star.At the near and far sides of the envelope, the polarization vectors are well aligned implying a regular structure of the magnetic field. The polarization characteristics of the OH maser emission suggest a radial magnetic field which is frozen in the stellar wind.
Brain‐wide associations between white matter and age highlight the role of fornix microstructure in brain ageing

Unveiling the details of white matter (WM) maturation throughout ageing is a fundamental question for understanding the ageing brain. In an extensive comparison of brain age predictions and age- associations of WM features from different diffusion approaches, we analysed UK Biobank diffusion Magnetic Resonance Imaging (dMRI) data across midlife and older age (N = 35,749, 44.6 to 82.8 years of age). Conventional and advanced dMRI approaches were consistent in predicting brain age. WM-age associations indicate a steady microstructure degeneration with increasing age from midlife to older ages. Brain age was estimated best when combining diffusion approaches, showing different aspects of WM contributing to brain age. Fornix was found as the central region for brain age predictions across diffusion approaches in complement to forceps minor as another important region. These regions exhibited a general pattern of positive associations with age for intra axonal water fractions, axial, radial diffusivities and negative relationships with age for mean diffusivities, fractional anisotropy, kurtosis. We encourage the application of multiple dMRI approaches for detailed insights into WM, and the further investigation of fornix and forceps as potential biomarkers of brain age and ageing.
Accelerated signal propagation speed in human neocortical microcircuits

Human-specific cognitive abilities depend on information processing in the cerebral cortex, where neurons are significantly larger and sparser compared to rodents. We found that, in synaptically-connected layer 2/3 pyramidal cells (L2/3 PCs), soma-to-soma signal propagation delay is similar in humans and rodents. Thus, to compensate for the increase in neurons’ size, membrane potential changes must propagate faster in human axons and/or dendrites. Dual somato-dendritic and somato-axonal patch recordings show that action potentials (APs) propagation speed is similar in human and rat axons, but the forward propagation of the EPSPs and the back-propagating APs are ∼ 26 and 47% faster in human dendrites respectively. Faithful biophysical models of human and rat L2/3 PCs, combined with pharmacological manipulations of membrane properties, showed both the larger diameter of the apical dendrite and the larger conductance load imposed by the basal tree in human, combined with differences in cable properties, underlie the accelerated signal propagation in human cortical circuits.
Neural correlates of extinction in a rat model of appetitive Pavlovian conditioning

Extinction is a fundamental form of inhibitory learning that is important for adapting to changing environmental contingencies. While numerous studies have investigated the neural correlates of extinction using Pavlovian fear conditioning and appetitive operant reward-seeking procedures, less is known about the neural circuitry mediating the extinction of appetitive Pavlovian conditioned responding. Here, we aimed to generate an extensive brain activation map of extinction learning in a rat model of appetitive Pavlovian conditioning. Male Long-Evans rats were trained to associate a conditioned stimulus (CS; 20 s white noise) with the delivery of a 10% sucrose unconditioned stimulus (US; 0.3 ml/CS) to a fluid port. Control groups also received CS presentations, but sucrose was delivered either during the inter-trial interval or in the home-cage. After conditioning, 1 or 6 extinction sessions were conducted in which the CS was presented but sucrose was withheld. We performed Fos immunohistochemistry and network connectivity analyses on a set of cortical, striatal, thalamic, and amygdalar brain regions. Neural activity in the prelimbic cortex, ventral orbitofrontal cortex, nucleus accumbens core, and paraventricular nucleus of the thalamus was greater during recall relative to extinction. Conversely, prolonged extinction following 6 sessions induced increased neural activity in the infralimbic cortex, medial orbitofrontal cortex, and nucleus accumbens shell compared to home-cage controls. All these structures were similarly recruited during recall on the first extinction session. These findings provide novel evidence for the contribution of brain areas and neural networks that are differentially involved in the recall versus extinction of appetitive Pavlovian conditioned responding.
Heterogeneous distribution of sex ratio distorters in natural populations of the isopod Armadillidium vulgare

In the isopod Armadillidium vulgare, many females produce progenies with female-biased sex ratios, due to two feminizing sex ratio distorters (SRD): Wolbachia endosymbionts and the f element. We investigated the distribution and population dynamics of these SRD and mitochondrial DNA variation in 16 populations from Europe and Japan. Confirming and extending results from the 1990’s, we found that the SRD are present at variable frequencies in populations, and that the f element is overall more frequent than Wolbachia. The two SRD never co-occur at high frequency in any population, suggesting an apparent mutual exclusion. We also detected Wolbachia or the f element in some males, which likely reflects insufficient titer to induce feminization or presence of masculinizing alleles. Our results are consistent with a single integration event of a Wolbachia genome in the A. vulgare genome at the origin of the f element, which contradicts an earlier hypothesis of frequent losses and gains. We identified strong linkage between Wolbachia strains and mitochondrial haplotypes, but no association between the f element and mitochondrial background. Our results open new perspectives on SRD evolutionary dynamics in A. vulgare, the evolution of genetic conflicts and their impact on the variability of sex determination systems.
Machine learning for discovery: deciphering RNA splicing logic

Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the-art neural networks are limited by their uninterpretability: despite their excellent accuracy, they cannot describe how they arrived at their predictions. Here, using an “interpretable-by-design” approach, we present a neural network model that provides insights into RNA splicing, a fundamental process in the transfer of genomic information into functional biochemical products. Although we designed our model to emphasize interpretability, its predictive accuracy is on par with state-of-the-art models. To demonstrate the model’s interpretability, we introduce a visualization that, for any given exon, allows us to trace and quantify the entire decision process from input sequence to output splicing prediction. Importantly, the model revealed novel components of the splicing logic, which we experimentally validated. This study highlights how interpretable machine learning can advance scientific discovery.
Loss of ZNF251 stimulates NHEJ resulting in PARP inhibitor resistance in BRCA1 mutated cancer cells

The poly (ADP-ribose) polymerases (PARPs) inhibitors are an exciting new class of agents that have shown efficacy in treating various cancers, especially those harboring BRCA1/2 mutations. The cancer associated BRCA1/2 mutations disrupt DNA double strand break (DSB) repair by homologous recombination (HR). PARP inhibitors (PARPi) have been applied to trigger synthetic lethality in BRCA1/2 -mutated cancer cells by promoting the accumulation of toxic DSBs. Unfortunately, PARPi resistance is common and develops through multiple mechanisms. Restoring HR and/or stabilizing replication forks are two major mechanisms of PARPi resistance in BRCA1/2 -mutated cells. To further understand the mechanisms of drug resistance to PARPi, we took an unbiased approach with a CRISPR-pooled genome-wide library to screen new genes whose loss-of-function confers resistance to PARPi olaparib. We identified ZNF251, a transcription factor, and found that its loss-of-function led to the PARPi resistance in multiple BRCA1 -mutated breast and ovarian cancer lines. Elevated activities of both HR and nonhomologous end joining (NHEJ) repair were detected in cancer cells harboring BRCA1 mutation and ZNF251 deletion ( BRCA1 mut+ ZNF251 del) and were associated with enhanced expression of RAD51 and Ku70/Ku80, respectively. Furthermore, we showed that a DNA-PKcs inhibitor restored sensitivity of BRCA1 mut+ ZNF251 del cells to PARPi ex vivo and in vivo . Taken together, our study discovered a novel gene ZNF251 whose loss-of-function conferred resistance to PARPi in BRCA1 -mutated breast and ovarian cancers and identified DNA repair pathway responsible for this effect.
Phosphatidylserine controls synaptic targeting and membrane stability of ASIC1a

Phospholipid-protein interaction is highly specialized at the membranous nanodomains and critical for membrane receptor signaling. Calcium-permeable acid-sensing ion channel isoform 1a (ASIC1a) is a major neuronal proton sensor that contributes to synaptic plasticity. The functional outcome of ASIC1a is dependent on its surface targeting in synaptic subdomains; however, the lipid environment for ASIC1a and its role in channel targeting remain poorly understood. Here, we report that anionic phosphatidylserine (PS) is enriched in dendritic spines during neurodevelopment and it directly binds to ASIC1a through an electrostatic interaction with a di-arginine motif at ASIC1a C-terminus. PS regulates the membrane targeting and function of ASIC1a, which are both strongly suppressed by inhibition of PS synthesis. In cortical neuron dendrites, both PS and ASIC1a are predominately localized to peri-synaptic sites of spine heads, surrounding instead of overlapping with postsynaptic markers, PSD-95 and GluN1. Uncoupling the interaction between PS and ASIC1a by changing the charges to neutral or acidic at the di-arginine PS-binding motif, or applying a membrane penetrating competing peptide, caused mistargeting of ASIC1a at the synaptic sites, an overall increase in internalization and/or cytoplasmic accumulation of ASIC1a, and a decrease in its channel function. Together, our results provide novel insights on lipid microenvironment that governs ASIC1a expression and function at the membrane surface, especially peri-synaptic regions of dendritic spines, through an electrostatic interaction with anionic phospholipids.
Poor attentional control as a sex-specific biomarker to assess vulnerability to nicotine addiction in mice

Every day thousands of people smoke a first cigarette, exposing themselves to the risk of becoming addicts. But this risk is not equal from individual to individual, inviting the hypothesis of potential biomarkers for predicting baseline vulnerability to addiction. One property of nicotine is to increase attentional capacities. However, the role of this pro-cognitive nicotinic effect in initiation of habitual smoking is unknown. Here, we investigated whether the differential effects of nicotine on cognitive performance in mice were predictive of sensitivity to nicotine reward and, if so, whether this characteristic was sex dependent. Naïve populations of male and female mice were first assessed for their attentional performances in the attentional cued-Fixed-Consecutive-Number task (FCNcue) in baseline conditions and after nicotine injections (0.15 and 0.30 mg/kg). Next, all mice underwent nicotine-induced conditioned place preference (CPP) in order to evaluate inter-individual differences in nicotine (0.30 mg/kg) reward sensitivity. Our results showed that innately impulsive males, but not females, benefited from the pro-cognitive effect of nicotine and were also subsequently more sensitive to nicotine reward, indicating increased vulnerability to developing nicotine addiction. Females displayed a completely different behavioural pattern, whereby nicotine reward sensitivity was independent of baseline attentional performances. These results suggest that the pro-cognitive effect of nicotine plays a key role in the development of nicotine addiction in males but not females. Moreover, they signal that the cognitive processes and neurobiology underpinning innate impulsivity may differ significantly between males and females.