Miracle-dz/UniFAR-FTUs huggingface dataset:
X-ray observations of sub-mm LABOCA galaxies in the eCDFS

We explore the X-ray properties of the 126 sub-mm galaxies (SMGs) of the LABOCA survey in the CDFS and the eCDFS regions. SMGs are believed to experience massive episodes of star formation. Our goal is to examine whether star formation coexists with AGN activity, determine the fraction of highly obscured AGN, and finally to obtain an idea of the dominant power mechanism in these sources. Using Spitzer and radio arcsecond positions for the SMGs, we find 14 sources with significant X-ray detections. For most of these there are only photometric redshifts available, with their median redshift at ∼2.3. Taking only the CDFS area into account that has the deepest X-ray observations, we estimate an X-ray AGN fraction of 10 23 cm −2 ,b ut there is no unambiguous evidence of Compton-thick sources. Detailed spectral energy distribution fittings show that the bulk of total IR luminosity originates in star forming processes, although a torus component is usually present. Finally, stacking analysis of the X-ray undetected SMGs reveals a signal in the soft (0.5–2 keV) and marginally in the hard (2–5 keV) X-ray bands. The hardness ratio of the stacked signal is relatively soft (−0.40 ± 0.10) corresponding to Γ ∼ 1.6. This argues against a high fraction of Compton-thick sources among the X-ray undetected SMGs.
Comprehensive volumetric phenotyping of the neonatal brain in Down syndrome

Down syndrome (DS) is the most common genetic cause of intellectual disability with a wide spectrum of neurodevelopmental outcomes. Magnetic resonance imaging (MRI) has been used to investigate differences in whole and/or regional brain volumes in DS from infancy to adulthood. However, to date, there have been relatively few in vivo neonatal brain imaging studies in DS, despite the presence of clearly identifiable characteristics at birth. Improved understanding of early brain development in DS is needed to assess phenotypic severity and identify appropriate time windows for early intervention. In this study, we used in vivo brain MRI to conduct a comprehensive volumetric phenotyping of the neonatal brain in DS. Using a robust cross-sectional reference sample of close to 500 preterm- to term-born control neonates, we have performed normative modelling and quantified volumetric deviation from the normative mean in 25 individual infants with DS [postmenstrual age at scan, median (range) = 40.57 (32.43 – 45.57) weeks], corrected for sex, age at scan and age from birth. We found that absolute whole brain volume was significantly reduced in neonates with DS (pFDR <0.0001), as were most underlying absolute tissue volumes, except for the lentiform nuclei and the extracerebral cerebrospinal fluid (eCSF), which were not significantly different, and the lateral ventricles, which were significantly enlarged (pFDR <0.0001). Relative volumes, adjusting for underlying differences in whole brain volume, revealed a dynamic shift in brain proportions in neonates with DS. In particular, the cerebellum, as well as the cingulate, frontal, insular and occipital white matter (WM) segments were significantly reduced in proportion (pFDR <0.0001). Conversely, deep grey matter (GM) structures, such as the thalami and lentiform nuclei, as well as CSF-filled compartments, such as the eCSF and the lateral ventricles were significantly enlarged in proportion (pFDR <0.0001). We also observed proportionally reduced frontal and occipital lobar volumes, in contrast with proportionally enlarged temporal and parietal lobar volumes. Lastly, we noted age-related volumetric differences between neonates with and without a congenital heart defect (CHD), indicating that there may be a baseline brain phenotype in neonates with DS, which is further altered in the presence of CHD. In summary, we provide a comprehensive volumetric phenotyping of the neonatal brain in DS and observe many features that appear to follow a developmental continuum, as noted in older age cohorts. There are currently no paediatric longitudinal neuroimaging investigations in DS, starting from the earliest time points, which greatly impedes our understanding of the developmental continuum of neuroanatomical parameters in DS. Whilst life expectancy of individuals with DS has greatly improved over the last few decades, early interventions may be essential to help improve outcomes and quality of life. GRAPHICAL ABSTRACT
The star formation and AGN luminosity relation: predictions from a semi-analytical model

In a universe where active galactic nucleus (AGN) feedback regulates star formation in massive galaxies, a strong correlation between these two quantities is expected. If the gas causing star formation is also responsible for feeding the central black hole, then a positive correlation is expected. If powerful AGNs are responsible for the star formation quenching, then a negative correlation is expected. Observations so far have mainly found a mild correlation or no correlation at all [i.e. a flat relation between star formation rate (SFR) and AGN luminosity], raising questions about the whole paradigm of ‘AGN feedback’. In this paper, we report the predictions of the GALFORM GALFORM semi-analytical model, which has a very strong coupling between AGN activity and quenching of star formation. The predicted SFR–AGN luminosity correlation appears negative in the low AGN luminosity regime, where AGN feedback acts, but becomes strongly positive in the regime of the brightest AGN. Our predictions reproduce reasonably well recent observations by Rosario et al., yet there is some discrepancy in the normalization of the correlation at low luminosities and high redshifts. Though this regime could be strongly influenced by observational biases, we argue that the disagreement could be ascribed to the fact that GALFORM GALFORM neglects AGN variability effects. Interestingly, the galaxies that dominate the regime where the observations imply a weak correlation are massive early-type galaxies that are subject to AGN feedback. Nevertheless, these galaxies retain high enough molecular hydrogen contents to maintain relatively high SFRs and strong infrared emission.
C60 IN PHOTODISSOCIATION REGIONS

Recent studies have confirmed the presence of buckminsterfullerene (C60) in different interstellar and circumstellar environments. However, several aspects regarding C60 in space are not yet well understood, such as the formation and excitation processes, and the connection between C60 and other carbonaceous compounds in the interstellar medium, in particular polycyclic aromatic hydrocarbons (PAHs). In this paper, we study several photodissociation regions (PDRs) where C60 and PAHs are detected and the local physical conditions are reasonably well constrained to provide observational insights into these questions. C60 is found to emit in PDRs where the dust is cool (Td = 20–40 K) and even in PDRs with cool stars. These results exclude the possibility for C60 to be locked in grains at thermal equilibrium in these environments. We observe that PAH and C60 emission are spatially uncorrelated and that C60 is present in PDRs where the physical conditions (in terms of radiation field and hydrogen density) allow for full dehydrogenation of PAHs, with the exception of Ced 201. We also find trends indicative of an increase in C60 abundance within individual PDRs, but these trends are not universal. These results support models where the dehydrogenation of carbonaceous species is the first step toward C60 formation. However, this is not the only parameter involved and C60 formation is likely affected by shocks and PDR age.
A spiking neural network model of cortical intraregional metastability

Transient synchronization of bursting activity in neural networks, which occurs in patterns of metastable phase relationships between neurons, is a notable feature of network dynamics observed in vivo. However, the mechanisms that contribute to this dynamical complexity in neural circuits are not well understood. Local circuits in cortical regions consist of populations of neurons with diverse intrinsic oscillatory features. In this study, we numerically show that the phenomenon of transient synchronization, also referred to as metastability, emerges in an inhibitory neural population when the neurons’ intrinsic fast-spiking dynamics are appropriately modulated by slower inputs from an excitatory neural population. Using a compact model of a mesoscopic-scale network consisting of excitatory pyramidal and inhibitory fast-spiking neurons, our work demonstrates a relationship between the frequency of neural oscillations and the features of emergent metastability. In addition, a novel metric is formulated to characterize collective transitions in metastable networks. Finally, we discuss a blueprint to model the whole-brain resting-state dynamics using our scalable representation of intraregional network metastability.
Fluid extraction from the left-right organizer uncovers mechanical properties needed for symmetry breaking

Humans and other vertebrates define body axis left-right asymmetry in the early stages of embryo development. The mechanism behind left-right establishment is not fully understood. Symmetry breaking occurs in a dedicated organ called the left-right organizer (LRO) and involves motile cilia generating fluid-flow therein. However, it has been a matter of debate whether the process of symmetry breaking relies on a chemosensory or a mechanosensory mechanism (Shinohara et al., 2012). Novel tailored manipulations for LRO fluid extraction in living zebrafish embryos allowed us to pinpoint a physiological developmental period for breaking left-right symmetry during development. The shortest critical time-window was narrowed to one hour and characterized by a mild counterclockwise flow. The experimental challenge consisted in emptying the LRO of its fluid, abrogating simultaneously flow force and chemical determinants. Our findings revealed an unprecedented recovery capacity of the embryo to re-fil and re-circulate new LRO fluid. The embryos that later developed laterality problems were found to be those that had lower anterior angular velocity and thus less anterior-posterior heterogeneity. Next, aiming to test the presence of any secreted determinant, we replaced the extracted LRO fluid by a physiological buffer. Despite some transitory flow homogenization, laterality defects were absent unless viscosity was altered, demonstrating that symmetry breaking does not depend on the nature of the fluid content but is rather sensitive to fluid mechanics. Altogether, we conclude that the zebrafish LRO is more sensitive to fluid dynamics for symmetry breaking.
Universal monomer dynamics of a two-dimensional semi-flexible chain

We present a unified scaling theory for the dynamics of monomers for dilute solutions of semi-flexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square displacements (MSDs) of stiff chains growing like with time due to bending motions, and the Rouse-like regime where ν is the Flory exponent describing the radius R of a swollen flexible coil. We identify how the prefactors of these laws scale with the persistence length , and show that a crossover from stiff to flexible behavior occurs at a MSD of order (at a time proportional to ). A second crossover (to diffusive motion) occurs when the MSD is of order R2. Large-scale molecular-dynamics simulations of a bead-spring model with a bond bending potential (allowing to vary from 1 to 200 Lennard-Jones units) provide compelling evidence for the theory, in D = 2 dimensions where . Our results should be valuable for understanding the dynamics of DNA (and other semi-flexible biopolymers) adsorbed on substrates.
Differentially expressed tRNA-derived fragments in bovine fetuses with assisted reproduction induced congenital overgrowth syndrome

Background As couples struggle with infertility and livestock producers wish to rapidly improve genetic merit in their herd, assisted reproductive technologies (ART) have become increasingly popular in human medicine as well as the livestock industry. Utilizing ART can cause an increased risk of congenital overgrowth syndromes, such as Large Offspring Syndrome (LOS) in ruminants. A dysregulation of transcripts has been observed in bovine fetuses with LOS, which is suggested to be a cause of the phenotype. Our recent study identified variations in tRNA expression in LOS individuals, leading us to hypothesize that variations in tRNA expression can influence the availability of their processed regulatory products, tRNA-derived fragments (tRFs). Due to their resemblance in size to microRNAs, studies suggest that tRFs target mRNA transcripts and regulate gene expression. Thus, we have sequenced small RNA isolated from skeletal muscle and liver of day 105 bovine fetuses to elucidate the mechanisms contributing to LOS. Moreover, we have utilized our previously generated tRNA sequencing data to analyze the contribution of tRNA availability to tRF abundance. Results 22,289 and 7,737 unique tRFs were predicted in the liver and muscle tissue respectively. The greatest number of reads originated from 5’ tRFs in muscle and 5’ halves in liver. In addition, mitochondrial (MT) and nuclear derived tRF expression was tissue-specific with most MT-tRFs and nuclear tRFs derived from LysUUU and iMetCAU in muscle, and AsnGUU and GlyGCC in liver. Despite variation in tRF abundance within treatment groups, we identified differentially expressed (DE) tRFs across Control-AI, ART-Normal, and ART-LOS groups with the most DE tRFs between ART-Normal and ART-LOS groups. Many DE tRFs target transcripts enriched in pathways related to growth and development in the muscle and tumor development in the liver. Finally, we found positive correlation coefficients between tRNA availability and tRF expression in muscle (R=0.47) and liver (0.6). Conclusion Our results highlight the dysregulation of tRF expression and its regulatory roles in LOS. These tRFs were found to target both imprinted and non-imprinted genes in muscle as well as genes linked to tumor development in the liver. Furthermore, we found that tRNA transcription is a highly modulated event that plays a part in the biogenesis of tRFs. This study is the first to investigate the relationship between tRNA and tRF expression in combination with ART-induced LOS.
Magnetic ground state and spin fluctuations in MnGe chiral magnet as studied by muon spin rotation

We have studied by muon spin resonance $(\ensuremath{\mu}\mathrm{SR})$ the helical ground state and fluctuating chiral phase recently observed in the MnGe chiral magnet. At low temperature, the muon polarization shows double-period oscillations at short-time scales. Their analysis, akin to that recently developed for MnSi [A. Amato et al., Phys. Rev. B 89, 184425 (2014)], provides an estimation of the field distribution induced by the Mn helical order at the muon site. The refined muon position agrees nicely with ab initio calculations. With increasing temperature, an inhomogeneous fluctuating chiral phase sets in, characterized by two well-separated frequency ranges which coexist in the sample. Rapid and slow fluctuations, respectively, associated with short-range and long-range ordered helices, coexist in a large temperature range below ${T}_{\mathrm{N}}=170$ K. We discuss the results with respect to MnSi, taking the short helical period, metastable quenched state, and peculiar band structure of MnGe into account.
Metabolic plasticity of T-cell therapies: multi-omic profiling of interacting human tumor-infiltrating lymphocytes and autologous tumor adoptive cell therapy

Adoptive cell therapy (ACT) based on ex vivo expanded autologous tumor-infiltrating lymphocytes (TILs) can mediate durable antitumor responses even in heavily pretreated patients. However, only a subset of patients responds to ACT; efforts to identify correlates of response have focused on profiling the tumor or the TIL but rarely in an interactive environment. Interactive profiling can provide unique insights into the clinical performance of TILs since the fate, function, and metabolism of TILs are influenced by autologous tumor-derived factors. Here, we performed a suite of cell-sparing assays dubbed holistic analysis of the bioactivity of interacting T cells and autologous tumor cells (HABITAT). HABITAT profiling of TILs used for human ACT and their autologous tumor cells included function-based single-cell profiling by timelapse imaging microscopy in nanowell grids (TIMING); multi-omics using RNA-sequencing and proteomics; metabolite inference using genome-scale metabolic modeling, and pulse-chase assays based on confocal microscopy to profile the uptake and fate of fatty acids (FA). Phenotypically, the ACT TILs from both responders (Rs) and nonresponders (NRs) were comprised of predominantly effector memory T cells (TEM cells) and did not express a high frequency of programmed death ligand-1 (PD-L1) and showed no differences in TCR diversity. Our results demonstrate that while tumor cells from both Rs and NRs are efficient at uptaking FAs, R TILs are significantly more efficient at utilizing FA through fatty acid oxidation (FAO) than NR TILs under nutrient starvation conditions. While it is likely that lipid and FA uptake is an inherent adaptation of TIL populations to lipid-rich environments, performing FAO sustains the survival of TILs and allows them to sustain antitumor cytolytic activity. We propose that metabolic plasticity enabling FAO is a desirable attribute of human TILs for ACT leading to clinical responses.
Predictive coding in ASD: reduced adaptability of priors to 1 environmental changes

1 2 Individuals with autism spectrum disorder (ASD) have been widely reported to show 3 atypicalities in predictive coding, though there remains a controversy regarding what causes 4 such atypical processing. Suggestions range from overestimation of volatility to rigidity in the 5 reaction to environmental changes. Here, we tested two accounts directly using duration 6 reproduction of volatile and non-volatile interval sequences, which were generated from the 7 same set of intervals (i.e., the same ensemble prior). We found that both individuals with ASD 8 and matched controls were able to adjust the weight of the ensemble prior for the reproduction 9 according to the volatility of the sequence. However, the ASD group, as compared to the 10 control group, relied generally less on the prior while also exhibiting marked carry-over of the 11 weight of the prior when environmental volatility changes. Of note, though, four extremes 12 among the 32 ASD individuals showed a reproduction pattern on the opposite end of the 13 spectrum: heavy reliance on the prior in the volatile environment. Overall, our findings suggest 14 that it is not the learning of the prior per se that is compromised in ASD. Rather, a less adaptive 15 response to a change of the volatility regimen or to a volatile environment causes a highly 16 inflexible weighting of prediction errors and the prior. 17
Cortical thickness, gray matter volume and cognitive performance: a cross-sectional study of the moderating effects of age on their inter-relationships

In a sample comprising younger, middle-aged and older cognitively healthy adults (N = 375), we examined associations between mean cortical thickness, gray matter volume (GMV) and performance in four cognitive domains - memory, speed, fluency and crystallized intelligence. In almost all cases, the associations were moderated significantly by age, with the strongest associations in the older age group. An exception to this pattern was identified in a younger adult sub-group aged less than 23 yrs, when a negative association between cognitive performance and cortical thickness was identified. Other than for speed, all associations between structural metrics and performance in specific cognitive domains were fully mediated by mean cognitive ability. Cortical thickness and GMV explained unique fractions of the variance in mean cognitive ability, speed and fluency. In no case, however, did the amount of variance jointly explained by the two metrics exceed 7% of the total variance. These findings suggest that cortical thickness and GMV are distinct correlates of domain-general cognitive ability, that the strength and, for cortical thickness, the direction of these associations is moderated by age, and that these structural metrics offer only limited insights into the determinants of individual differences in cognitive performance across the adult lifespan.
HG-Meta: Graph Meta-learning over Heterogeneous Graphs

Prevailing supervised graph neural networks suﬀer from potential performance degradation in the label sparsity case. Though increasing attention has been paid to graph few-shot learning methods for learning eﬀective graph embed-dings under the scarcity of labeled data, most existing works study homogeneous graphs while ignoring the ubiquitous-ness of heterogeneous graphs (HG), where multi-typed nodes are interconnected by multi-typed edges. To this end, we propose to tackle few-shot learning on HG and develop a novel model for H eterogeneous G raph Meta -learning (a.k.a. HG-Meta ). Regarding the graph heterogeneity, HG-Meta ﬁrstly builds a graph encoder to aggregate heterogeneous neighbors information from multiple semantic contexts (generated by meta-paths). Secondly, to train the graph encoder with meta-learning in a few-shot scenario, HG-Meta tackles meta-task diﬀerences produced from meta-task sampling procedure on HG with a task feature scaling module and a degree based task attention module. To further alleviate low-data problem, HG-Meta leverages unlabelled information in HG with auxiliary self-supervised learning task along-side the meta-optimization process to facilitate node embedding. Extensive experiments on two HG datasets demonstrate that HG-Meta outperforms state-of-the-art methods for multiple few-shot node classiﬁcation tasks.
Mass estimation in the outer non-equilibrium region of galaxy clusters

We discuss a new criterion to estimate the mass in the outer, non-equilibrium region of galaxy clusters, where the galaxy dynamics are dominated by an overall infall motion towards the cluster centre. In the framework of the spherical infall model, the local mean velocity of the infalling galaxies at every radius provides information about the integrated matter overdensity 8. Thus, a well-defined value of the overdensity δ t is expected at the turnaround radius r t , that is the radius where the Hubble flow balances the infall motion. Within this scenario, we analysed the kinematical properties of a large catalogue of simulated clusters, using both dark matter particles and member galaxies as tracer of the infall motion. We also compared the simulation with analytical calculation performed in the spherical infall approximation, to analyse the dependence of the results on cosmology in spatially flat Universe. If we normalize cluster mass profiles by means of the turnaround mass M t (i.e. the mass within r t ), they are consistent with an exponential profile in the whole non-equilibrium region (0.5 ≤ r/r t ≤ 2). Turnaround radii are proportional to virialization radii (r t ≃3.5r v ), while turnaround masses are proportional to virialization masses, that is M t ≃ 1.7M v , where M v is the mass within r v . Actually, the mass evaluated within the turnaround radius is a more exhaustive evaluation of the total mass of the cluster. These results can be applied to the analysis of observed clusters.